BIOL 1000 A01 Fall 2015 Foundations of Life Course Outline Appendix

Appendix 12. BIOL 1000 A01 Fall 2015 Foundations of Life Course Outline

Lecturer: Dr. K. Blaschuk Office: 421D- Biological Sciences Building Office Hours: Monday, Wednesday, and Friday from 2:30 p.m. to 3:30 p.m. E-mail: [email protected]

Objective and description of course: To introduce students to major topics currently studied in the field of Biology. Topics introduced will include basic chemistry as it relates to life, cell biology, metabolism, reproduction, genetics and evolution.

Important dates: September 11, 2015- First Biology class October 7, 2015- Biology Mid-term #1 October 12, 2015- Thanksgiving (no classes) November 6, 2015- Mid-term #2 November 11, 2015- Remembrance Day (no classes) November 18, 2015- Last day for voluntary withdrawal from course without academic penalty. December 9, 2015- Last Biology class December 11- 23, 2015- Fall term final examination period

Course organization: a) Lectures Lectures are designed to clarify and explain essential concepts. Lectures will deal with information found primarily in the course textbook. You will be responsible for all material presented in class, in the Power Point slides, and in the textbook reading assignments. Power Point lectures will be posted on JUMP but you should be aware that these are outlines only, and that the actual lectures will be more detailed. You are strongly advised to take good notes during class. You are also strongly advised to attend lectures.

Since we cannot possibly cover all the information found in the text, the lectures will be on selected topics. Further, though every effort to cover all the topics listed in this outline will be made, not all the topics listed in the outline may be covered. A brief lecture outline and assigned text page references are found below.

Lectures are held every Monday, Wednesday, and Friday from 10:30 a.m. to 11:20 a.m. in 204 Armes.

b) Textbook The course text is Campbell Biology: Concepts and connections, by Reece J. B. et al., First Canadian edition, Pearson Canada Inc. (2015).

The textbook is required.

All of the section numbers given in the lecture outline refer to this text. The readings given contain much more information than we will cover in the lectures, but the readings will enrich your knowledge about the subjects that we will cover in class. You will also note that we are covering only a portion of the textbook. We will study Units One and Two in detail and Unit Three in less detail. Though lectures do not extend beyond Chapter 15, material from later chapters may be included to supplement lectures.

c) Course Grading i. Tests and Examinations The emphasis will be on material covered in lectures, but the text readings are also important. You will be responsible for any material discussed in class (including any material presented on PowerPoint slides and any material I present, whether spoken or written on the board/over-head) and any material that is part of your assigned readings.

Mid-term #1 will examine lecture and reading material covered up to the end of CH 5: Cellular function.

Mid-term #2 will examine lecture and reading material covered from CH 6: How Cells Harvest Chemical Energy to the end of CH 9: Patterns of Inheritance.

The final examination is cumulative and will cover all course material with emphasis on material not previously tested.

All examinations will be Multiple Choice in style. Please also note that you will need an HB pencil to fill in the answer sheet.

Students will be asked for identification when writing a test or examination. No cell phones, computers or other unauthorized materials are allowed during examinations. Any student found guilty of contributing to or cheating in examinations will be subject to serious academic penalty. Please see: http://umanitoba.ca/faculties/science/student/webdisciplinedocuments.html,for further information.

Please also note, that if you miss a test or the final exam, you will be required to provide documentation that is valid and verifiable and that supports the reason you were absent, in order to write a make-up test or deferred final exam. An example of such documentation is a physician’s note.

ii. Schedule of Tests and Exams

Mid-term #1 October 7 (Wednesday), 2015; in class 25% Mid-term #2 November 6 (Friday), 2015; in class 25% Final exam TBA, 2.0 hours 50%

iii. Marking Scheme: Department of Biological Sciences, University of Manitoba guidelines.

A+ 90 – 100 A 80 – 89 B+ 74 - 79 B 68 - 73 C+ 62 – 67 C 56 – 61 D 50 – 55 F 0 – 49

2 d) Voluntary withdrawal

Please note that the last date for voluntary withdrawal for courses at the University of Manitoba without academic penalty is November 18, 2015. Marks obtained from the mid-term examinations will be returned to students before the voluntary withdrawal date. If you do experience difficulty with this course, please do come and see me before withdrawing and I will do all we can to help you.

Summary of lectures and reading assignments:

Topic Chapters Reading Assignment Introduction Exploring biology CH 1 Themes in biology 1.1-1.4 (read 1.2 and 1.4 for enjoyment) Evolution, the core theme of biology 1.5-1.7 The process of science 1.8-1.9 Biology and everyday life 1.10-1.11 (read for enjoyment) The Living Cell The essential chemistry of life CH 2 Elements, atoms, and compounds 2.1-2.3 Chemical bonds 2.5-2.9 Water’s life supporting properties 2.10 (read for fun) 2.11-2.15 2.16-2.17 (read for fun) The compounds of cells CH 3 Introduction to organic compounds 3.1-3.3 Carbohydrates 3.4-3.5, 3.7 Lipids 3.8-3.10 Proteins 3.11-3.12 Nucleic acids 3.14-3.15 3.16 (read for interest) Cellular structure CH 4 Introduction Introduction to the cell 4.1-4.4 The nucleus and ribosomes 4.5-4.6 The endomembrane system 4.7-4.10, 4.12 Energy-converting organelles 4.13-4.15 (the latter for interest) The cytoskeleton and cell surfaces 4.16, 4.19-4.22 Cellular function CH 5 Introduction Membrane structure and function 5.1-5.8 Energy and the cell 5.9-5.11 How enzymes function 5.12-5.14, 5.16 (read 5.15 for the truth about raw food diets) How cells harvest chemical energy CH 6 Cellular respiration 6.1-6.3, 6.5 Stages of cellular respiration 6.6-6.12 Fermentation 6.13 Connections 6.15-6.17 Photosynthesis CH 7 An overview 7.1-7.5 The light reactions 7.6-7.9

3 The Calvin cycle 7.10 Reviewed 7.12-7.14 Cellular Reproduction and Genetics The cellular basis of reproduction and CH 8 inheritance Cell division and reproduction 8.1-8.2 The eukaryotic cell cycle and mitosis 8.3-8.9 Meiosis and crossing over 8.12-8.18 Alterations of chromosome number and structure 8.19-8.24 Patterns of inheritance CH 9 Introduction (read for interest) Mendel’s laws 9.1-9.8 Variations 9.10-9.15 The chromosomal basis of inheritance 9.16-9.19 Sex chromosomes and sex-linked genes 9.20-9.23 (read 9.21 for fun) Molecular genetics CH 10 The structure of the genetic material 10.2-10.3 DNA replication 10.4-10.5 The flow of genetic information 10.6-10.19 Gene expression CH 11 Control of gene expression 11.1-11.10 Cloning of plants and animals 11.12-11.14 The genetic basis of cancer 11.15-11.18 DNA technology and genomics CH 12 Gene cloning 12.1-12.2, 12.4-12.5 Genetically modified organisms 12.6-12.10 DNA profiling 12.11-12.15 Genomics 12.17-12.18, 12.20-12.21 Concepts of evolution Evolution: in the beginning CH 13 Darwin’s theory of evolution 13.1-13.7 Early Earth and the origin of life 13.8-13.10 Major events in the history of life 13.11-13.13 Mechanisms of evolution CH 14 The evolution of populations 14.1-14.2 Mechanisms of microevolution 14.5-14.8, 14.10 Speciation and phylogeny CH 15 Introduction (for interest) Defining species 15.1-15.3 Mechanisms of speciation 15.4- 15.8, 15.10-15.11

ENJOY!!!

4 BIOLOGY 1010 BIOLOGY: BIOLOGICAL DIVERSITY AND INTERACTIONS A01 – FALL 2015

COURSE DESCRIPTION: This course is designed as an introduction to several important concepts in the field of biology. Topics introduced to the student include evolution, diversity of living organisms, the form and function of both plants and animals, and basic ecological principles. The main objective of this course is to give students a broad look at these unifying concepts of modern biology. Students who take Biology 1010 come with a broad range of academic and personal interests. Some students in this course will have had some biology classes before whereas others will not. The intent of instruction in this course is to build a basic understanding for ALL students, regardless of their background. This course cannot be used for credit in any Majors or Honours program in Biological Sciences.

WHEN AND WHERE: Section A01 MWF 10:30 – 11:20 AM 208 Armes

ATTENDANCE: Punctual attendance to lecture is expected. If you are going to be late, please use the back door.

INSTRUCTOR: DR. KEVIN SCOTT W473 Duff Roblin Email: [email protected]

E-MAIL POLICY: The easiest mechanism to contact me is through email. If and when you decide to email me, please make sure you do the following: • Check this Syllabus first. If you are asking about course or exam information, chances are the answers are already in the syllabus. • Use a proper salutation. “Hey prof” is not appropriate but “Hello Kevin” is. • Always include your name. If I don’t know who you are, I will not respond. • Use full, properly structured sentences and do not use textese. • Use your University email account. • I do not respond to emails on weekends or for 24 hours prior to an exam.

I will not answer questions about lecture material via email. It is best to make an appointment to discuss any concepts in person.

– 1 – REQUIRED MATERIALS: Campbell Biology: Concepts & Connections (Canadian Edition) By: Reese, Taylor, Simon, Dickey, and Scott Pearson Publishing Company Inc. Available at the U. of M. Bookstore

MasteringBiology Student Access code. A code comes packaged with the purchase of a new textbook. Alternatively, you can purchase an access code with a credit card directly from the Pearson website.

EVALUATION: Your final grade will be based on two examinations, and online quizzes as follows: MasteringBiology Quizzes Portion of course grade ------10% Mid-term Examination based on Lectures 1 – 18 45 multiple-choice questions – 90 minutes Portion of course grade ------35% 6:00 – 7:30PM – Monday, 2 November 2015 Exam Rooms – TBA Final Examination based on Lectures 1 – 36 60 multiple-choice questions – 120 minutes 10 questions on lectures 1–18 50 questions on lectures 9–36 Portion of course grade ------55% Scheduled and seated by the Registrar’s Office.

Your mark at the end of the course will be out of 100%. The final grade will be assigned by converting your final cumulative percent score (rounded to the closest percent) into a letter grade according to the following breakdown:

90% or higher … A+ 80-89%………… A 76-79%………… B+ 70-75%………… B 60-69%………… C+ 55-59%………… C 50-54%………… D 49% or lower ….. F

– 2 – MASTERINBIOLOGY ASSESSMENT On MasteringBiology you will see a total of 11 assignments based on the lecture material. These assignments are formative and not for credit and therefore not required. However, the assignments are designed to help guide you through the material and keep you on track. Completion of these assignments will help you achieve a better grade in Biology 1010. Online assignments are a good way to test your own knowledge and understanding. You will also have 10 quizzes to complete on MasteringBiology over the term. These quizzes are mandatory and summative and will account for 10% of your final grade. Quizzes will become available ON the date indicated in the schedule below for 24 hours. Within this 24- hour window (12:00 AM – 11:59 PM), you must login to MasteringBiology and complete the quiz. Failure to do so before midnight will result in a grade of zero for that quiz. Do not begin a quiz too close to the deadline (i.e., 11:52 PM), as you may not have enough time to complete it. No extensions or make-up possibilities will be given for any quiz. Your best 8 (of 10) quizzes will be averaged and used to calculate your mark out of the possible 10% of your final grade.

MASTERINGBIOLOGY SCHEDULE Assignment 1 23 September Quiz 1 24 September Assignment 2 30 September Quiz 2 01 October Assignment 3 07 October Quiz 3 08 October Assignment 4 14 October Quiz 4 15 October Assignment 5 21 October Quiz 5 22 October Assignment 6 04 November Quiz 6 05 November Assignment 7 11 November Quiz 7 12 November Assignment 8 18 November Quiz 8 19 November Assignment 9 25 November Quiz 9 26 November Assignment 10 02 December Quiz 10 03 December Assignment 11 09 December

SETTING UP MASTERINGBIOLOGY Register for online assignments and quizzes on MasteringBiology.com (MB). All required information for your registration to MB and the proper use of this system is given in detail in your Student Access Kit for MasteringBiology. 1. Make sure your computer meets the system requirements (see your MB Student Access Kit and http://www.masteringhelp.com/system_requirements.htm). Although MB can be used with Internet Explorer or Safari, using the most current Firefox seems to generate fewer problems. 2. Go to http://www.masteringbiology.com/ site. 3. If you are a first-time user, click on “New Students” and follow the instructions. If you have used MB before, simply login to the system using your previous Login Name and Password. 4. To enroll in the course, enter your 7-digit University of Manitoba student number (usually starting with a 7) as your “Student ID” and enter the correct “Course ID” below:

UMBIOLOGY1010F15A01

You must enter your 7-digit U of M student number correctly for your scores to count. Please double check. 5. If you experience technical difficulties with the MasteringBiology online assignment system contact MasteringBiology at this URL: http://www.masteringbiology.com/site/support/faq- students.html.

– 3 – LECTURE OUTLINE & TEXTBOOK REFERENCES: During the course you will encounter topics, which the textbook covers in greater detail than the lectures, while in other areas the lecturer may expand upon the textbook. Although classes do not strictly adhere to the order of the text, I do consider it essential reading. Students who expand upon each topic by reading will understand and perform better on examinations. Modules in parentheses are topics covered in Biology 1000 and are very useful review. They include background information essential to the understanding of the concepts discussed in class. Very little time will be devoted to these modules in class, however, you are expected to understand this information. Topic Modules Introduction Introduction to science 1.8–1.9 What is biology 1.1–1.2 Themes in biology 1.3–1.7 Evolution Natural selection 13.2, 13.4–13.6, 14.6–14.8 Speciation 15.1–15.3, 15.8 Evolutionary history 13.11, 14.12–14.13, 14.16 Phylogeny 15.12–15.14 Diversity of Living Things Acellular “Life” 16.1–16.3, 16.13–16.14 Prokaryotes (4.3–4.4), 17.1–17.5 Protists (4.15), 18.1, 18.3, 18.5–18.9 Plants 19.1–19.4, 19.6, 19.8–19.11, 19.13 Fungi (8.14), 18.10–18.16 Animals 20.1–20.16, 21.1–21.6, 21.8–21.11 Plant Form & Function Plant structure 22.2–22.6 Plant reproduction 22.10–22.14 Plant growth and development 22.7–22.8 Plant tissue needs (6.12, 7.12), 23.1–23.7 Plant control systems & behaviour 24.2–24.7, 24.10, 24.14 Animal Form & Function Animal structure 25.1–25.8, 25.10 Animal reproduction 30.1–30.2, 30.11, (8.13) Animal growth and development 30.3–30.6 Animal tissue needs 26.1–26.4, 26.13 27.1–27.4, 27.7, 27.9, 27.12, 28.1–28.2, 28.15 Animal control systems 29.1–29.2, 29.4, 29.8 31.1–31.3, 31.7–31.11 25.13–25.19 Animal behaviour 36.1–36.7, 36.9–36.11, 36.13–36.15 Ecology Populations 35.1, 37.1–37.5 Species Interactions 38.3–38.8, 39.1–39.2, 39.4–39.7, 39.10–39.12, 38.7–38.8, 38.10 Ecosystems 40.1, 40.3–40.7

– 4 –

FREQUENTLY ASKED QUESTIONS: I missed a MasteringBiology quiz, what can I do? In short, nothing. There will be no make up quizzes on MasteringBiology. To this end, only the best 8 of 10 quiz marks will be used in the calculation of your final mark. The quiz you just missed will be one of the two that isn’t counted.

Should I read the textbook for the exam? Absolutely! The exam will be based largely on the lecture material. However, reading the text offers an alternative explanation for the concepts you are expected to know. It also includes other examples to illustrate concepts. As such, reading the indicated modules will undoubtedly help you succeed in Biology 1010.

If I have a conflict with the midterm, what happens? In summer session, there is very little chance that you will have a valid conflict with the scheduled midterm date. If, however, you feel you do, see us as soon as possible. If the exam conflicts with your work schedule, we expect you to reschedule your shift to sit the exam. If this is impossible, we require a letter from your employer on company header explaining that your shift cannot be changed. Bring this to documentation to the main Biological Sciences office in 212 Biological Science Building.

If I miss the midterm, what happens? If you have valid documentation the value of the midterm will be prorated to the final exam. If you do not have appropriate documentation, a mark of zero will be given for the midterm.

If I miss the final, what can I do? The only thing you can do in this situation is contacting your home faculty. They are the only body that can grant a deferred exam. Be ready to present your valid documentation to them.

– 5 – BIOL 1020 FALL 2015

BIOLOGY 1: PRINCIPLES AND THEMES

COURSE SYLLABUS

INSTRUCTORS DR. JOY STACEY COURSE INSTRUCTOR 471 Duff Roblin Phone: 204 474-6380 Email: [email protected]

MR. MICHAEL SHAW LAB INSTRUCTOR & COURSE INSTRUCTOR 208 Buller Bldg. Phone: 204 474-9732 Email: [email protected]

COURSE The objective of this course is to give students a broad and comprehensive background OBJECTIVE in modern biology and thus to prepare them for entry into biology-oriented programs in the Faculty of Science and in other Faculties and Schools.

COURSE A laboratory-based course in unifying principles of biology including cell biology, DESCRIPTION bioenergetics, cell division, genetics and evolution. This course is intended for major and honours students in the biological sciences as well as those in other faculties (Agriculture, Kinesiology, Environmental Sciences etc.) requiring a comprehensive lab based introduction to the Biological Sciences.

Course site : http://umanitoba.ca/d2l COURSE WEBSITES MasteringBiology Code : MBBIOLOGY1020F2015

Course Twitter : @UofManBiology

Lab site: http://umanitoba.ca/science/biological_sciences/BIOL1020/1020.html

LECTURE Section Location Time and Day SLOTS AND A01 205 Armes 8:30 AM (MWF) LOCATIONS A02 204 Armes 9:30 AM (MWF) A03 201 Armes 9:30 AM (MWF) A04 100 St. Paul’s 10:30 AM (MWF) A05 201 Armes 10:30 AM (MWF) A06 205 Armes 11:30 AM (MWF) A07 208 Armes 12:30 PM (MWF) A08 204 Armes 12:30 PM (MWF) A09 205 Armes 1:30 PM (MWF) A10 201 Armes 1:30 PM (MWF) A11 204 Armes 2:30 PM (MWF) A12 204 Armes 3:30 PM (MWF)

2 Mon. Tues. Wed. Thurs. Fri. LABORATORY 8:30 AM - 11:00 AM B07-12 B19-24 B31-36 B43-48 SLOTS & 2:30 PM - 5:00 PM B01-06 B13-18 B25-30 B37-42 B49-54 LOCATIONS 7:00 PM - 9:30 PM B55-60

Your first lab session will take place during the week of September 21-25. To find your lab seat follow these instructions: 1. Be sure you know your lab section number (B01 - B60) 2. Use the chart above to find your lab day and time.

e.g. B37-42 is THURS. @ 2:30 - 5:00 PM

At the scheduled time, go to the assigned room on the main floor of the Buller Bldg (211A, 211B, 212A, 212B, 215 or 216 Buller--The room number is on your registration printout). Your assigned seat will be posted on the assigned room door. Your teaching assistant will introduce him/herself to you and commence the first lab session.

LABS BEGIN DURING THE WEEK OF SEPT. 21-25. THERE ARE NO LABS UNTIL THEN!!

TEXTBOOK Required text: Campbell Biology (Canadian Edition) with & MasteringBiology.com access. LAB MANUAL Pearson Canada, Toronto Required Lab Manual: BIOLOGY 1020 Lab Manual, Fall 2015 edition MASTERING BIOLOGY Register for online assignments and quizzes on MasteringBiology.com (MB): All required information for your registration to MB and the proper use of this system is given in detail in your Student Access Kit of MasteringBiology.

1. Make sure your computer meets the system requirements (see your MB Student Access Kit and http://www.masteringhelp.com/system_requirements.htm). Using the most ciurrent Firefox seems to generate fewer problems. 2. Go to http://www.masteringbiology.com/ site. 3. If you are a first-time user, click on “New Students” and follow the instructions. If you have used MB before, simply login to the system using your previous Login Name and Password. 4. To enroll in the course, enter your 7-digit University of Manitoba student number as your “Student ID” and enter the correct “Course ID” below:

MBBIOLOGY1020F2015

You must enter your 7 digit U of M student number correctly for your scores to count. Please double check.

5. If you experience technical difficulties with the MasteringBiology online assignment system contact MasteringBiology at this URL: http://www.masteringbiology.com/site/support/faq-students.html. Make sure to have your MasteringBiology Student Access Kit or your login name/password handy. 6. If you have troubles with the assignment content make an appointment with the appropriate instructor for help. 3 VIDEOS All of the sections are taught by video. The video format is used to ensure a uniform presentation to all students in a very large class. Instructors can put more effort into lecture production when they don’t have to repeat the same lecture to numerous sections. This gives them the time to visit the labs to chat with students informally and answer questions about the course. It also gives students greater access to the lectures and greater flexibility in viewing them. If a lecture is missed, or if you which to watch a DVD it can be viewed individually in library. A problem with the video format is the lack of immediate student feedback or questions. You will have to jot down your questions and ask them later, either in the Instructor’s office, or when you next see him/her in the laboratory.

Although the Coordinator does check the lecture rooms for problems, the lectures are largely unsupervised. You must be quiet in class so that all students can benefit from the lecture. Students found to be disruptive will be warned once and then ejected from the room. Once ejected, a student will not be allowed to continue in the course without a letter from the Dean or Director of his/hers Faculty of School.

ATTENDANCE LECTURES: Punctual attendance is expected. Attend only in the section to which you have been assigned. LABORATORIES: Attendance at laboratories is mandatory. Attendance will be taken by the laboratory TA during each laboratory 2 hours into the class time. Students must be in attendance for a minimum of 2 hours. Students who miss more than 2 out of 8 labs, without a documented reason, during the regular session shall receive a grade of F for BIOL 1020 Biology 1.

STUDENT The final grade in BIOL 1020 will be based on the following: EVALUATION 1. Mastering Biology Quizzes Portion of course grade (best 8 out of 10) ------10%

2. In Laboratory Assignments 1 assignment, worth 1%, to be completed in each lab. Portion of course grade ------8%

3. Mid Term Examination I 30 Multiple Choice Questions - 4 based on Laboratories 1 – 2 -26 based on Lectures1 - 10 Scheduled by the Department (October 13, 2015- 6:00-7:00 pm) Portion of course grade ------12 %

4. Mid Term Examination II 40 Multiple Choice Questions -6 based on Laboratories 3- 5 -30 based on Lectures 11 - 23 Scheduled by the Department (November 10, 2015 – 6:00 -7:00 pm) Portion of course grade ------20 %

5. Final Examination – 2 Hours 96 Multiple Choice Questions -22 based on Laboratories 1 - 8 -74 based on Lectures 1 - 36 Scheduled by the Registrar’s Office in the December Examination period. Portion of course grade ------50 % Calculators and other electronics are not allowed during examinations!

4 On MasteringBiology you will see a total of 5 assignments based on Dr. Stacey’s material and 5 assignments based on Mr. Shaw’s material. These assignments are not for credit and therefore not required. However, the assignments are designed to help guide you through the material and keep you on track. Completion of these assignments will help you achieve a better grade in Biology 1020. Online assignments are a good way to test your own knowledge and understanding.

You will also have 10 quizzes to complete on MasteringBiology over the term (5 based on Dr. Stacey’s material and 5 based on Mr. Shaw’s material). These quizzes are mandatory and will account for 10% of your final grade. Quizzes will become available ON the date indicated in the schedule below for 24 hours. Within this 24 hour window you must login to MasteringBiology and complete the quiz. Failure to do so before midnight will result in a grade of zero for that quiz. Do not begin a quiz too MASTERING close to the deadline (Monday at midnight), as you may not have enough time to BIOLOGY complete it. No extensions or make-up possibilities will be given for any quiz. Your QUIZ DATES best 8 (of 10) quizzes will be averaged and used to calculate your mark out of the possible 10% of your final grade.

Quiz 1 September 28, 2015 Quiz 2 October 05, 2015 Quiz 3 October 13, 2015 *Tuesday Quiz 4 October 19, 2015 Quiz 5 October 26, 2015 Quiz 6 November 9, 2015 Quiz 7 November 16, 2015 Quiz 8 November 23, 2015 Quiz 9 November 30, 2015 Quiz10 December 7, 2015

GRADING Grades are assigned at the end of the year by converting your cumulative percentage SCHEME mark into a letter grade, using the following table:

90 + - A+ 80 - 89 - A

76 - 79 - B+

70 - 75 - B 60 - 69 - C+ 50 - 59 - C 46 - 49 - D 0 - 45 - F

Very slight modifications of this scheme are sometimes made to compensate for a class average that may be judged to be too low or too high.

LABORATORY Each exam has a laboratory section which contributes to the total exam mark but which MARKS will also be tabulated separately. You must achieve a "D" standard in the lab (15 correct out of 32 lab questions from the exams only for the year) to pass the course. If you score 14 or less out of the 32 lab marks you will receive a grade of F, regardless of your marks for the lecture questions.

IN Diring each of the 8 labs you will complete a single sheet assignment and hand it in to LABORATORY your lab TA. This assignment MUST be your own work and based on the results and ASSIGNMENTS observations in the lab. Outside information (such as the internest) is not allowed. If you miss a lab you must do a make up lab that same week to recive this mark.

EXAM If you are caught in a dishonest act during the course of an examination you will be IRREGULAR- reported to University authorities. Penalties may be imposed at the discretion of the ITIES relevant authorities.

The day after each of the three exams in the course, the answers will be posted in the POSTING OF first floor hallway of the Buller Bldg. As soon as the tests are marked, your mark will ANSWERS AND appear next to your student number at the same location. Take note of both your total MARKS mark and your lab mark and let us know (at 212B Biological Sciences Building) immediately if you think there has been a marking error.

LIBRARY Several copies of each video lecture will be made available in the Sciences and DVD’s Technology Library (Machray Hall) immediately after each lecture has been shown in the lecture sections. Please view missed lectures as soon as possible as the tapes are in high demand closer to exam time.

FACULTY Day Sections (video lectures) will be divided among Faculty as follows: Lecture 0 In person Introduction by Faculty Lectures 1 - 17 Dr. Joy Stacey, Department of Biological Sciences Lectures 18 -36 Mr. Michael Shaw, Department of Biological Sciences Labs 1 - 8 Mr. Michael Shaw, Department of Biological Sciences

QUESTION In addition to normal office hours and laboratory visits you can meet with the Biology PERIOD instructors during question period. There are three question periods throughout the term, one immediately prior to each exam, in which you can discuss questions of an academic nature with your Biology instructors.

Fall term session will be held in 208 Armes (4:30 - 6:30 pm) on the following dates: Dr. Joy Stacey - October 08, 2015 Dr. Joy Stacey and Mr. Michael Shaw— November 05, 2015 Mr. Michael Shaw - December 8, 2015

Administrative help: Academic help: HOW TO GET To: -change section -Consult your textbook for explanations. HELP -registration or exam problems -Go to your instructor's office to get help. -report problems in lecture hall (You might want to e-mail or phone first to make -etc. sure the instructor is available). Go to the Biological Sciences office in -Try to form study groups with friends or 212B Biological Sciences Building your laboratory partners Phone: 474-9245 -Remember that the T.A. is always there for you too! Please make sure you do the following prior to emailing a course instructor: • Check this Syllabus first. If you are asking about course or exam information, chances are the answers are already in the syllabus.

EMAIL POLICY • Use a proper salutation. “Hey prof” is not appropriate. • Always include your name. If we don’t know who you are, we will not respond to you. • Use full, properly structured sentences and do not use textese. • Use your University email account. Your U of M account is free and you can have it forwarded to any other email address. As per university policy we will only respond to email from a University of Manitoba account

We will not answer questions about lectures that require complex answers via email. Please make an appointment!

Should I read the textbook for the exam? FREQUENTLY Absolutely! The exam will be based on the lecture material. However, reading the text ASKED offers an alternative explanation for the concepts we expect you to know. Reading QUESTIONS: through the indicated modules will undoubtedly help you.

If I have a conflict with the midterm, what happens? If you have a regularly schedule course activity on the evening of one of the exams take your class schedule to the main Biological Sciences office in 212 Biological Science Building and we will schedule an early write exam. If the exam conflicts with your work schedule, we expect you to reschedule your shift to sit the exam. If this is impossible, we require a letter from your employer on company header explaining that your shift cannot be changed. Bring this to documentation to the main Biological Sciences office in 212 Biological Science Building

If I am sick for the final, what can I do? The only thing you can do in this situation is to contact your home faculty. They are the only body that can grant a deferred exam.

TIMETABLE

M T W Th F Lecture No. Laboratories M W F September 07 08 09 10 11 0 No Laboratory 14 15 16 17 18 1 2, 3 No Laboratory 21 22 23 24 25 4, 5, 6 1. An Introduction to the Laboratory Sept/Oct 28 29 30 01 02 7, 8, 9 2. Biological Molecules 05 06 07 08 09 10, 11, 12 3. Cells 12 13 14 15 16 ---, 13, 14 No Laboratory 19 20 21 22 23 15, 16, 17 4. Cellular Energetics 1 26 27 28 29 30 18, 19, 20 5. Cell Energetics II November 02 03 04 05 06 21, 22, 23 No Laboratory 09 10 11 12 13 24, --, 25 No Laboratory 16 17 18 19 20 26 , 27, 28 6. Mitosis & Meiosis 23 24 25 26 27 29, 30, 31 7. Genetics Nov/Dec 30 01 02 03 04 32, 33, 34 8. Population Genetics 07 08 09 10 11 35, 36 No Laboratory

October 13 and November 10 are the dates of the BIOL 1020 midterm exams. See page 3 of this syllabus for more information.

LECTURE OUTLINE & TEXTBOOK REFERENCES FOR

Dr. Joy Stacey: 1 to 17

Please note that the textbook covers some material in more detail than will be covered in lecture and that some topics are not covered in the textbook. You are responsible for lecture material. Some figures from the text have been modified for use in lecture and may not appear as in the textbook.

Textbook Lecture sections 1. Introduction to biology 1.1-1.3 2. Water as a vehicle for life 3.1-3.3 3. Organic chemistry 4.1-4.3, 5.1 4. Biological macromolecules: carbohydrates and lipids 5.1-5.3 5. Biological macromolecules: proteins and nucleic acids 5.4-5.5 6.Cell structure 1: Prokaryotic cells, Hypotheses regarding 4.1, 6.1-6.3 formation of the first cells, eukaryotic cell structure: nucleus, 25.1, 25.3 ribosomes 8 Textbook Lecture sections 7.Cell structure 2: Eukaryotic endomembrane system, 6.4-6.5, 25.3 mitochondria, chloroplasts, endosymbiotic theory 8. Cell structure 3: Cytoskeleton, extracellular elements, cell 6.1 , 6.6,6.7 fractionation 9. Membrane structure and function 1: fluid mosaic model, fatty 7.1-7.3 acid composition, protein types and intro. to passive transport 10. Membrane structure and function 2: Osmosis, bulk transport, 7.3-7.5 active transport 11. Introduction to metabolism 8.1-8.4 12. Enzyme function, Introduction to cellular respiration 8.4-8.5, 9.1-9.2 13. Cellular respiration 1: glycolysis and the citric acid cycle 9.2-9.3 14. Cellular respiration 2: oxidative phosphorylation and 9.4-9.5 fermentation 15. Fermentation continued, Photosynthesis 1: light reactions 9.5-9.6, 10.1-10.2 16. Photosynthesis 2: Calvin cycle and alternative modes of 10.2-10.4 carbon fixation 17. Cell communication and cell signaling 11.1-11.4

Mr. Michael Shaw Lectures: 18 to 36

You are responsible for lecture material. Note that some lecture material does not appear in the textbook and that the textbook covers some material in more detail than will be covered in lecture. Some figures from the text have been modified for use in lecture and may not appear as in the textbook.

Lecture Textbook Sections Lecture Textbook Sections 18 12.1, 12.2 28 16.1, 16.2 19 12.2 29 16.2,16.3, 17.1 20 12.3, 13.1, 13.2 30 17.1, 17.2 21 13.2, 13.3 31 17.2, 17.3, 17.4 22 13.3, 13.4 32 17.4, 17.5 23 14.1 33 22.1, 22.2 24 14.1, 14.3 34 22.3 25 14.3 35 23.1, 23.2, 23.3 23.4 26 15.1, 15.2, 15.3 36 23.4 27 15.3, 15.4

Faculty of Science Statement on Academic Dishonesty

Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another student, plagiarism, and examination impersonation.

Note: cell phones, pagers or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations.

Penalties that may apply, as provided for under the University of Manitoba's Student Discipline By-Law, range from a grade of zero for the assignment or examination, failure in the course, to expulsion from the University. The Student Discipline By-Law may be accessed at: http://umanitoba.ca/admin/governance/governing_documents/students/student_discipline. html

All Faculty members (and their teaching assistants) have been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department.

BIOL 1030 A01 –A12 WINTER 2016 BIOLOGY 2: BIOLOGICAL DIVERSITY, FUNCTION & INTERACTION COURSE SYLLABUS

INSTRUCTORS DR KEVIN SCOTT First Half Lectures W473 Duff Roblin. Phone: 474-8413 Email: [email protected]

DR CARLA ZELMER Second Half Lectures 219 Buller Bldg. Phone: 480-1454 Email: [email protected]

MR MICHAEL SHAW Laboratory Instructor 208 Buller Bldg. Phone: 474-9732 Email: [email protected]

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COURSE The objective of this course is to give students a broad and comprehensive background in modern OBJECTIVE biology and thus to prepare them for entry into biology-oriented programs in the Faculty of Science and in other Faculties and Schools.

COURSE A laboratory-based course introducing biological diversity including prokaryotes, protists, fungi, plants DESCRIPTION and animals; the form and function of plants and animals and basic concepts of ecology. This course is intended for major and honours students in the biological sciences.

COURSE Course site: www.umanitoba.ca/d2l WEBSITES MasteringBiology Code : MBBIOLOGY1030W2016

Course Twitter : @UofManBiology

Lab site: http://umanitoba.ca/science/biological_sciences/BIOL1030/1030.html

LECTURE Section Location Time and Day SLOTS AND A01 204 Armes 8:30 AM (MWF) LOCATIONS A02 204 Armes 9:30 AM (MWF) A03 118 St. John’s 9:30 AM (MWF) A04 100 St. Paul’s 10:30 AM (MWF) A05 205 Armes 10:30 AM (MWF) A06 201 Armes 11:30 AM (MWF) A07 205 Armes 12:30 PM (MWF) A08 208 Armes 12:30 PM (MWF) A09 205 Armes 1:30 PM (MWF) A10 208 Armes 1:30 PM (MWF) A12 208 Armes 3:30 PM (MWF)

2 MASTERING BIOLOGY Sections A01 – A12 use MBBIOLOGY1030W2016 COURSE CODE

LABORATORY Mon. Tues. Wed. Thurs. Fri. SLOTS & 8:30 AM - 11:00 AM B07-12 B19-24 B31-36 B43-48 LOCATIONS 2:30 PM - 5:00 PM B01-06 B13-18 B25-30 B37-42 B49-54 7:00 PM - 9:30 PM B55-60

Your first lab session will take place during the week of January 11-15. To find your lab seat follow these instructions: 1. Be sure you know your lab section number (B01 - B60) 2. Use the chart above to find your lab day and time. e.g. B37-42 is THURS. @ 2:30 - 5:00 PM

TEXTBOOK Required text: Campbell Biology (Canadian Edition) by Reese et al. with MasteringBiology access. & Pearson Publishing Company Inc. LAB MANUAL Required Lab Manual: BIOLOGY 1030 Lab Manual, Winter 2016 edition Dissection kits, available in the bookstore, are also required.

Register for online assignments and quizzes (MasteringBiology, MB): MASTERING All required information for your registration to MB and the proper use of this system is given in detail in BIOLOGY your Student Access Kit of MasteringBiology.

If you purchased Mastering Biology (MB) for Biology 1020 in Fall of 2015, you DO NOT need to REPURCHASE it. Your code is good for 12 months from the time you first registered it. Log in and add the new course. If you do not have MasteringBiology.com access follow the instructions below.

1. Make sure your computer meets the system requirements (see your MB Student Access Kit and http://www.masteringhelp.com/system_requirements.htm). Although MB can be used with Internet Explorer or Safari, using the most current Firefox seems to generate fewer problems. 2. Go to http://www.masteringbiology.com/. 3. If you are a first-time user, click on “New Students” and follow the instructions. If you have used MB before, simply login to the system using your previous Login Name and Password. 4. To enroll in your course, enter your 7-digit University of Manitoba student number as your “Student ID” and enter the correct “Course ID” from the 2 choices below. 5. Sections A01 – A12 use MBBIOLOGY1030W2016

6. Additional instructions may be given to you during class or on the D2L BIOL 1030 site. 7. If you experience technical difficulties with the MasteringBiology online assignment system contact MasteringBiology at this URL: http://www.masteringbiology.com/site/support/faq-students.html. Make sure to have your MasteringBiology Student Access Kit or your login name/password handy. 8. If you have troubles with the assignment content make an appointment with the appropriate instructor (K. Scott or C. Zelmer) for help.

3 All of the sections are taught by video. The video format is used to ensure a uniform presentation to all students in a very large class. Instructors can put more effort into lecture production when they don’t VIDEO TAPES have to repeat the same lecture to numerous sections. This gives them the time to visit the labs to chat with students informally and answer questions about the course. It also gives students greater access to the lectures and greater flexibility in viewing them. If a lecture is missed, or if you which to watch a DVD it can be viewed individually in library. A problem with the video format is the lack of immediate student feedback or questions. You will have to jot down your questions and ask them later, either in the Instructor’s office, or when you next see him/her in the laboratory.

ATTENDANCE LECTURES: Punctual attendance is expected. Attend only in the section to which you have been assigned. LABORATORIES: Attendance at laboratories is mandatory. Attendance will be taken by the laboratory TA during each laboratory 2 hours into the class time. Students must be in attendance for a minimum of 2 hours. Students who miss more than 2 out of 10- labs during the regular session shall receive a grade of F for BIOL 1030 Biology 2.

STUDENT The final grade in BIOL 1030 will be based on 10 MasteringBiology quizzes, 10 in Laboratory EVALUATION assignments and two multiple choice examinations as follows:

1. MasteringBiology Quizzes Portion of course grade (best 8 out of 10) ------10%

2. In Laboratory Assignments 1 assignment, worth 1%, to be completed in each lab. Portion of course grade ------10%

3. Mid Term Examination – 1.5 Hours 70 Multiple Choice Questions - 15 based on Laboratories 1 – 5 - 55 based on Lectures 1 – 18 Scheduled by the Department (March 1, 2016 from 6:00 – 7:30 pm) Portion of course grade ------35%

4. Final Examination – 2 Hours 100 Multiple Choice Questions - 5 based on Laboratories 1 – 5 - 20 based on Laboratories 6 – 10 - 10 based on Lectures 1 – 18 - 65 based on Lectures 19 – 36 Scheduled by the Registrar’s Office in the April Examination period. Final examination will be 2 hours. Portion of course grade ------45 %

Calculators are not allowed during examinations!

4 GRADING Grades are assigned at the end of the year by converting your cumulative percentage mark into a letter SCHEME grade, using the following table:

90 + - A+ 80 - 89 - A

76 - 79 - B+

70 - 75 - B

+ 60 - 69 - C 50 - 59 - C 46 - 49 - D 0 - 45 - F

Very slight modifications of this scheme are sometimes made to compensate for a class average that may be judged to be too low or too high.

LABORATORY Each exam has a laboratory section which contributes to the total exam mark but which will also be MARKS tabulated separately. You must achieve a "D" standard in the lab (18 correct out of 40 lab questions for the year) to pass the course. If you score 17 or less out of the 40 lab marks you will receive a grade of F, regardless of your marks for the lecture questions.

MASTERING On MasteringBiology you will see a total of 5 assignments based on Dr. Scott’s material and 5 BIOLOGY assignments based on Dr. Zelmer’s material. These assignments are not for credit and therefore not MARKS required. However, the assignments are designed to help guide you through the material and keep you on track. Completion of these assignments will help you achieve a better grade in Biology 1030. Online assignments are a good way to test your own knowledge and understanding.

You will also have 10 quizzes to complete on MasteringBiology over the term (5 based on Dr. Scott’s material and 5 based on Dr. Zelmer’s material). These quizzes are mandatory and will account for 10% of your final grade. Quizzes will become available ON the date indicated in the schedule below for 24 hours. Within this 24 hour window you must login to MasteringBiology and complete the quiz. Failure to do so before midnight will result in a grade of zero for that quiz. Do not begin a quiz too close to the deadline (Monday at midnight), as you may not have enough time to complete it. No extensions or make-up possibilities will be given for any quiz. Your best 8 (of 10) quizzes will be averaged and used to calculate your mark out of the possible 10% of your final grade.

MASTERING Quiz # Date Material Covered BIOLOGY QUIZ 1 Monday January 18 Assignment 1 & Animal Diversity SCHEDULE 2 Monday January 25 Assignment 2 & Animal RDF&F

3 Monday February 1 Assignment 3 & Meeting Animal Needs 4 Monday February 8 Assignment 4 & Control Systems (Nervous) 5 Monday February 22 Assignment 5 & Endocrine sys & Behaviour 6 Monday March 7 Assignment 6 & Lectures 19-21 7 Monday March 14 Assignment 7 & Lectures 22-25 8 Monday March 21 Assignment 8 & Lectures 26-29 9 Monday March 28 Assignment 9 & Lectures 30-32 10 Monday April 4 Assignment 10 & Lectures 33-35

5 IN During each of the 10 labs, you will complete a single sheet assignment and hand it in to your lab TA. LABORATORY This assignment MUST be your own work and based on the results and observations in the lab. Outside ASSIGNMENTS information (such as the internet) is not allowed. If you miss a lab you must do a make up lab that same week to receive this mark.

EXAM If you are caught in a dishonest act during the course of an examination you will be reported to IRREGULAR- University authorities and will be given "0" for the test in question. Further penalties may be imposed at ITIES the discretion of the relevant authorities.

POSTING OF The day after each of the two exams in the course the answers will be posted in the first floor hallway of ANSWERS AND the Buller Bldg. As soon as the tests are marked, your mark will appear next to your student number at MARKS the same location. Take note of both your total mark and your lab mark and let us know immediately if you think there has been a marking error.

LIBRARY Several copies of each video lecture will be made available in the Sciences and Technology Library DVD’s (Machray Hall) immediately after each lecture has been shown in the lecture sections. Please view missed lectures as soon as possible as the tapes are in high demand closer to exam time.

QUESTION In addition to scheduled appointments, office hours and laboratory visits you can meet with your PERIOD instructors during a question period. There are two question periods throughout the year, one immediately prior to each exam, in which you can discuss questions of an academic nature with your Biology instructors.

Winter term question period sessions will be held in 208 Armes on the following dates and times:

Dr. K. Scott—Thursday, February 25, 2016 from 4:30 to 6:30 pm Dr. Zelmer– Thursday, April 07, 2016 from 4:30 to 5:30 pm

HOW TO GET Administrative help: Academic help: HELP To: -change section -Consult your textbook for explanations -registration or exam problems -Go to your instructor's office to get help. -report problems in lecture hall (You might want to phone or email first to make -etc. sure the instructor is available). Go to the Biological Science Office -Try to form study groups with friends or in the Biological Sciences Bldg. rm. 212 your laboratory partners Phone: 474-9245. -Remember that the T.A. is always there for you too!

EMAIL POLICY Note: Instructors emails are for making appointments only. The instructor is always willing to answer any of your questions, but they prefer to do this by phone or in person. Please make sure you do the following prior to emailing a course instructor:

• Check this Syllabus first. If you are asking about course or exam information, chances are the answers are already in the syllabus. • Use a proper salutation. “Hey prof” is not appropriate. • Always include your name. If we don’t know who you are, we will not respond to you. • Use full, properly structured sentences and do not use textese. • Use your University email account. The university will only use students’ U of M email accounts when communicating electronically. Visit umanitoba.ca/studentemail for more information.

We will not answer questions about lectures that require complex answers via email. It is best to

make an appointment

6 Should I read the textbook for the exam? Absolutely! While the exam will be based largely on the lecture material, reading the text offers an alternative explanation for the concepts we expect you to know. This will undoubtedly help you in your understanding of these concepts. Reading through the indicated modules will undoubtedly help you. FREQUENTLY ASKED QUESTIONS: If I have a conflict with the midterm, what happens? If you have a regularly schedule course activity on the evening of one of the exams take your class schedule to the main Biological Sciences office in 212 Biological Science Building and we will schedule a nearly write exam. If the exam conflicts with your work schedule, we expect you to reschedule your shift to sit the exam. If this is impossible, we require a letter from your employer on company header explaining that your shift cannot be changed. Bring this to documentation to the main Biological Sciences office in 212 Biological Science Building

If I miss the midterm, what happens? If you have valid documentation the value of the midterm will be prorated to the final exam. There will be no deferred midterm. If you do not have appropriate documentation, a mark of zero will be given for the midterm.

If I am sick for the final, what can I do? The only thing you can do in this situation is to contact your home faculty. They are the only body that can grant a deferred exam.

TIMETABLE M T W R F Lecture No. M W F January 4 5 6 7 8 1, 2 No Laboratory 11 12 13 14 15 3, 4, 5 1. Animal Diversity I 18 19 20 21 22 6, 7, 8 2. Animal Diversity II 25 26 27 28 29 9, 10, 11 3. Animal Form And Function I February 1 2 3 4 5 12, 13, 14 4. Animal Form And Function II 8 9 10 11 12 15, 16, 17 5. Animal Form And Function III 15 16 17 18 19 Study Week No Laboratory 22 23 24 25 26 18, 19, 20 No Laboratory Feb/March 29 1 2 3 4 21, 22, 23 6. Diversity of the Microorganisms March 7 8 9 10 11 24, 25, 26 7. Plant Diversity I 14 15 16 17 18 27, 28, 29 8. Plant Diversity II 21 22 23 24 25 30, 31 9. No Laboratory Mar/April 28 29 30 31 1 32,9. 33, 34 9. Plant form and Function I April 4 5 6 7 8 35, 36 10. Plant form and Function I

7 Lecture Outline & Textbook References For Campbell Biology – Canadian Edition

Dr. Kevin Scott’s Lectures (1–18)

Topic Concepts Figures Used Animal Diversity Lecture 1 26.1–3, 28.1 26.6,10-11, 34.43, 28.3,5,7,19 Lecture 2 32.1–4, 33.1-2 13.6, 32.2–4,7–8,11, 33.4–7 Lecture 3 33.5, 34.1–7 49.2, 32.5, 33.40, 34.2–5,9–10,13,15–16, 21–23,25–26 Lecture 4 33.3 32.13, 33.14–17,19,21,24,9–12 Lecture 5 33.4 33.26,31–34,37,39 Animal Reproduction, Development, Form & Function Lecture 6 46.1,3 46.2–3,5–6,12, 12.7, 13.8 Lecture 7 46.3, 47.1 47.3–4,6–7 Lecture 8 47.2, 40.1 47.9–11,14, 40.5 Lecture 9 40.1 40.5 Meeting Animal Needs Lecture 9.5 41.1 41.3–4 Lecture 10 41.2–4 40.4, 41.5–8,11–12,15–16 Lecture 11 41. 4, 42.5 41.17, 42.21–22,24, 33.4 Lecture 12 42.6–7, 44.2–4 41.23,25–26, 44.8,10–15 42.2–3 Lecture 13 42.3 40.4, 42.4 Animal Control Systems Lecture 13.5 49.1, 48.1–2, 50.5 49.2–3, 48.3–6, 50.26 Lecture 14 48.3 48.10–13 Lecture 15 48.4, 50.6 48.15,17–18, 50.30,26–29,34 Lecture 16 45.1 45.2,4–6,9,11 Lecture 17 45.1–3 45.10,12–13,15–18 Animal Behaviour Lecture 17.5 51.1 51.3,5 Lecture 18 51.2–3 51.7–9,12,1519–20

Dr. Carla Zelmer’s Lectures (19–36)

This is a general outline only. Please check UM Learn closer to the time of these lectures for more information.

Lectures Topics Concepts 19-21 Microorganisms, prokaryotes, fungi, algae 6.1, 27.1, 27.3-5, 28.1-3, 28.5, 28.7, 31.1-2, 31.4-5 22-24 Intro to land plants, bryophytes, seedless vascular 29.1-3 plants 25-26 Seed plants, Angiosperms, Gymnosperms 30.1-4 27-31 Plant form and function 35.1-5, 36.4, 38.1-2 32-34 Transport in vascular plants, plant nutrition and 36.1-5, 37.2-3, 39.2 hormones 35-36 Introduction to ecology 54.1-2, 55.1, 55.3-4

Faculty of Science Statement on 8 Academic Dishonesty

Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another student, plagiarism, and examination personation.

Note: cell phones, pagers or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations.

Suggested penalties assessed by the Faculty of Science for acts of academic dishonesty are available on the Faculty of Science web-page: http://umanitoba.ca/faculties/science/

All Faculty members (and their teaching assistants) have been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department.

REGISTRATION RESTRICTIONS

PLEASE ENSURE THAT YOU THE STUDENT ARE ENTITLED TO BE REGISTERED IN THIS COURSE:

THIS MEANS THAT YOU THE STUDENT HAVE:

-the appropriate prerequisites, as noted by the calendar description, or have permission from the instructor to waive these prerequisites

-not previously taken, or are concurrently registered in this course and another that has been identified as “not to be held with”

The registration system may have allowed the student to register but it is up to the student to ensure that they have met all the requirements.

Consequences may be the student being withdrawn from the course part way through the term, or the course not used in the degree program. There will be no fee adjustment. This is not appealable.

BIOL 1410 ANATOMY OF THE HUMAN BODY (3CH) SEPT 2015 This course is designed to meet the needs of those preparing for health-oriented careers as well as those wanting to know about the structure of the human body. The course provides an introduction to cellular, histological and gross anatomy.

Required Texts: (Available at the U. of M. Bookstore) 1. Human Anatomy and Physiology 10th edition (or Custom Edition for U of M) by Elaine N. Marieb & K. Hoehn 2. BIOL 1410 Laboratory Guide - Dept. of Biol. Sci., U. of Manitoba. Instructors: Office hours: TBA - Appointments suggested. Dr. J. McLeese Biological Sciences Building, 421B Dr. P. Messing Biological Sciences Building, 421C Dr. K. Campbell Duff Roblin Building, W465 Lab Coordinator: Office hours will be posted. Ms. K. Lester Biological Sciences Building, 221A

Study Recommendation 1. See attached study guide. 2. Lecture exams are based primarily on class notes and diagrams discussed. Lecture notes will be posted on UM Learn, but they are incomplete and attending the lectures is strongly recommended. It will increase your likelihood of success. 3. Sample exam questions are available on UM Learn. 4. Exams can only be deferred for reasons of illness or on compassionate grounds - both of which require documentation. 5 Labs: Read the laboratory guide before each lab. Attendance should be for the entire 2 hours and you must go to your registered slot. Roll call is taken.

Schedule of Lectures and Laboratories: Lectures: Rooms associated with your lecture slots. Please attend the lecture slot in which you are registered. Laboratories: Biological Sciences Building 211 (even numbered slots) or 223 (odd numbered slots). You will find your name on a list on the door of your lab room when you go to your first lab. Labs will be run on the following weeks, with the date given as the Monday of that week (go to your lab on the day of your registered lab slot of each listed week): Lab 1 - Sept 28th; Lab 2 - Oct 5th; Lab 3 - Oct 12th; Lab 4 - Oct 19th; Lab 5 - Oct 26th; Lab 6 - Nov 16th; Lab 7 - Nov 23rd; Lab 8 - Nov 30th

EXAMINATION DATES: Lecture Midterm 1: Saturday Oct. 10th 9:00 am - 10:00 am - 15% To the end of tissues/membranes: 30 multiple choice questions. Lecture Midterm 2: Saturday Nov. 7th 9:00 am - 10:00 am - 20% To the end of the lymphatic system: 35 multiple choice questions (5 on material covered on midterm 1) Lab: Week of November 2nd to 6th during your lab slots in your lab room. (Labs 1 to 5 inclusive: ID exam- identification of specimens and structures on slides, models) - 20% Final: Date and time to be posted by Student Records. ALL questions multiple choice. Lecture (10 questions from midterm material, 55 from new material) and Lab (Labs 6, 7 and 8 only; 20 questions) - 45%

BIOL 1410 Anatomy of the Human Body

Suggested reference pages from Human Anatomy of Physiology, 10th ed. by Elaine N. Marieb are given in bold and from the Custom ed. in brackets. Note: 1. Lecture exams are based mainly on information discussed in lectures, so you should focus your studying on the class lecture notes. 2. The reference pages given below, which can be used for understanding the lecture notes or for the diagrams, should be read bearing in mind that the pages contain more information than was covered in lecture. These are not required readings. pp 2-4; 11-19; (2-4; 11-20) definitions, levels of organization, anatomical position, directional terms p 25; (25) atomic structure pp 32-33 (32 -33) ionic and covalent bonds pp 38-39; (38-39) inorganic compounds pp 39-40 (39-40) acids, bases, pH pp 41-49; 52-55; (42-50; 53-56) organic compounds pp 62-66; 83-96; (62-65; 81-96) the cell pp 96-98; 100-101; 1036-1039; 1107-1109; (96-99; 100 - 101; 1027-1030; 1096- 1098) cell cycle; mitosis and meiosis pp 1075-1085; (1065-1074) early development pp 1107-1112; (1096-1101) heredity pp 66-68; (66-67) cell junctions pp 115-143; (116-142) histology pp 150-162; 487-488; (150-162; 485-487) integumentary system pp 199-227; (200-226) axial skeleton pp 227-245; (227-243) appendicular skeleton pp 173-175; 177-183; (174; 177-183) bone tissue pp 251-269; (249-267) joints/articulations pp 321-383; (319-381) skeletal muscles pp 279-288; (278-285) muscle tissue pp 664-678; (659-672) heart anatomy pp 728-731; 732-733; 742-743; 1090-1091; (722-725; 727; 736-737; 1079-1081) blood vessels pp 699-705; (693-699) blood vessel anatomy pp 635-639; 644-649; 650; (631-635; 640-644; 645-646) blood pp 758-767; (752-759) lymphatic system pp 807-822; (801-816) respiratory system pp 857-871; 873-875; 881-887; 888-891; 894-897; 736; 738-739; 748-749; (850-863; 864-867; 874-881; 882-883; 887-890; 730; 732-733; 742-743) digestive pp 961-970; 988-990; (954-963; 979-982) urinary system pp 1026-1034; 1036-1042; 1044- 1050; 1052; (1018-1033; 1035-1047) male and female reproductive systems pp 596-597; 603-607; 611-612; 615-617; 620-621; 622-623; 624-627; (591-593; 598-601; 606-607; 610-612; 615-616 618; 620-621) endocrine system pp 389-397; 409-411; (386-395; 407-409) nervous tissue pp 432-454; 460-463; 732-733; 466-476; (430-452; 458-462; 726-727; 464-473) nervous system pp 485-488; 492- 511; (483-487; 490- 509) nerves pp 528-537; (524-533) autonomic nervous system pp 549-550; 552-557; 574-579; (545-546; 548-552; 570-575) special senses

Note: 1. The University of Manitoba takes academic integrity seriously. Go to http://umanitoba.ca/faculties/science/undergrad/resources/webdisciplinedocuments .html to learn about regulations, processes and penalties regarding cheating, plagiarism and other forms of academic dishonesty.

2. Any exam preparation seminars given for BIOL 1410 are not affiliated with the course nor are they sanctioned by the Department of Biological Sciences or by the course instructors. .

BIOL1410 Anatomy of the Human Body OUTLINE (Approximate number of lecture hours in each topic are given in brackets) A. Definitions 1. Anatomy: subdivisions, methods of study 2. Levels of organization: cell to organism

B. Chemicals in living matter (2 hr) 1. Atoms; ions 2. Inorganic compounds: water, acids, bases; pH 3. Organic compounds: carbohydrates, lipids, proteins, nucleic acids

C. The cell (4 hr) 1. Microanatomy of the cell: cell (plasma) membrane, cytoplasm, organelles 2. Cell cycle: interphase (G1, G0, S, G2); cell division (mitosis, meiosis, cytokinesis) 3. Early stages of development; zygote to embryo to fetus 4. Inheritance: definitions, chromosomes, Punnett square, probabilities, sex-linked inheritance

D. Tissues (2 hr) 1. Cell junctions 2. Epithelium: general features, specific types 3. Connective tissues: general features, specific types 4. Muscular tissue: general features, specific types 5. Nervous tissue: general features, specific types 6. Membranes: serous, mucous, synovial, cutaneous

E. Integumentary System (1.5 hr) 1. Skin: general features, dermis, epidermis 2. Subcutaneous layer 3. Epidermal derivative - hair, nail, glands 4. Cutaneous sense receptors

F. Skeletal and Muscular Systems (5 hr) 1. Axial skeleton: skull, vertebral column, sternum, ribs 2. Appendicular skeleton: pectoral girdle, pelvic girdle, limbs 3. Components of a long bone 4. Microanatomy of skeletal tissue: bone, cartilage 5. Articulations: classification; structure of a synovial joint 6. Muscle - bone relationship: how movement is produced 7. Naming of muscles; origin, insertion; action of muscles 8. Microanatomy of skeletal muscle tissue

G. Circulatory System (3 hr) 1. Circulatory routes: adult overall plan: pulmonary and systemic circulations 2. Fetal circulation 3. Heart: gross and microanatomy 4. Microanatomy of blood vessels 5. Microanatomy of blood; hemopoiesis

H. Circulatory System: Lymphatic (1 hr) 1. Organization 2. Circulation 3. Organs and tissues

I. Respiratory System (2 hr) 1. Upper: nasal cavity to pharynx: gross and microanatomy 2. Lower: larynx to lungs: gross and microanatomy 3. Blood supply and innervation 3. Muscles used for breathing

J. Digestive System (3 hr) 1. Organization, abdominal regions and quadrants 2. Peritoneum 3. Histology and modifications of the digestive system 4. Gross anatomy of organs 5. Innervation and blood supply

K. Urinary System (2 hr) 1. Organization 2. Gross and microanatomy of: kidney, ureters, urinary bladder, urethra 3. Innervation and blood supply

L. Reproductive Systems (2.5 hr) 1. Gross anatomy of male system; microanatomy of testis 2. Gross anatomy of female system; microanatomy of ovary and uterus 3. Gamete formation; spermatogenesis, oogenesis

M. Endocrine System (1.5 hr) 1. Organization 2. Classes of hormones 3. Endocrine glands, endocrine tissue, hormones

N. Nervous System (7 hr) 1. Organization: CNS, PNS, receptors, effectors 2. Microanatomy of nervous tissue: neurons, neuroglia 3. Meninges, cerebrospinal fluid, blood-brain barrier and blood supply (arterial circle) 4. Central nervous system: brain, spinal cord (gross and microanatomy) 5. Peripheral nervous system: sense receptors, afferent division (sensory pathways); efferent division (motor pathways - somatic and autonomic), microanatomy of nerves 6. Special sense organs: eye and ear

STUDYING ANATOMY: BIOL 1410 and PHYSIOLOGY: BIOL 1412

1. ORGANIZE YOUR TIME..... Enter into a daily minder or facsimile: i) when assignments are due ii) exam dates iii) times set every day for studying each subject (starting from the first day of lecture). 2. During lectures...listen to what is being said, then write notes. Write figure numbers and use the figures from the text as you study. 3. Studying i) reading the notes and text doesn’t necessarily mean that you are “studying” ii) after lecture every day--highlight the major topics in your notes. This breaks up a sea of words into more easily digestible sections! iii) read the information in each highlighted section. Use diagrams in the text as needed. Then ask yourself “what do I need to know about this?” iv) write this on scrap paper in an abbreviated form without looking at the notes. Then go back and read the notes to see if you made any mistakes or left any information out. v) you had heard the information in lecture that day, you have now read it three times that evening as you study. That’s four times in your memory! vi) try to understand the big picture of the topic– e.g. For Anatomy: What is mitosis? Then tackle the details e.g. what are the phases of mitosis? What occurs in each of these phases? For Physiology: What is the resting membrane potential? What factors produce that potential? Ask yourself these questions out loud as you study. Studying this way provides understanding which is important for anatomy and crucial for Physiology. vii) For labs, keep reviewing the material during lab and during the term. 4. Writing Exams i) Be rested, have a meal containing carbohydrates. ii) Read each question carefully and completely. Read the stem of the question while covering the rest of the question with the computer sheet. Circle key words and draw simple diagrams at the side of the paper if applicable. Think about what the question is asking then slowly expose each answer. iii) Don’t second guess the question. Questions test knowledge and the ability to integrate the information . iv) Do not change answers, do the question carefully and right the first time. v) Do the questions you know first, then go back to those that you were not sure about. vi) If you don’t do well on the midterm exam, reevaluate where you might have gone wrong. Did you leave studying for the last week before exams? Did you spend enough time studying the correct way? Did you read the questions too quickly? Was anxiety a significant problem? (Seek Help). Were you sleep deprived? Hungry? (Brain cells need glucose).

Help is available from the Academic Learning Centre and from the Instructors (by appointment).

NOTE: The lectures and all material delivered or provided in BIOL 1410 and BIOL 1412 are subject to copyright owned by the Instructors teaching these courses. It is prohibited to record or publish any material provided, by any means, in any format, in whole or in part without express written permission from the Instructors. Physiology of the Human Body BIOL 1412: A05 Winter 2016: 3 credit hours COURSE SYLLABUS

INSTRUCTOR: Diana Mlinar, M.Sc. 493 Helen Glass Center email: [email protected]

TIME/LOCATION: Monday/Wednesday/Friday 9:30-10:20 a.m. Room 316 Machray Hall

OFFICE HOURS: By appointment only

COURSE OBJECTVE AND DESCRIPTION:

The objective of this course is to introduce concepts of physiology and physiological mechanisms that regulate homeostasis. This course is designed to provide the physiology background necessary for students wishing to pursue a career in a health-related field.

TEXTBOOK:

- Human Anatomy and Physiology Custom Edition for the U. of M. (or 8th ed.) by Elaine N. Marieb and Katja Hoehn - BIOL 1412 Laboratory Guide - Department of Biological Sciences, University of Manitoba

EVALUATION:

The course evaluation will include two mid-term exams and a final exam. Mid-term #2 and the final exam will cover material from both the lecture and the laboratory. The dates and values of these examinations are as follows: Lecture Mid-term #1: Friday February 5, 2016 9:30am, 50 minutes…...... 15% Lecture Mid-term #2: Wednesday March 9, 2016 9:30am, 50 minutes…...... 25% Final Exam: TBD, 2.0 hours………….…..….……………………………..….....60%

OTHER IMPORTANT DATES: Week of January 18th, 2016: Tutoring Begins Week of February 15th, 2016: No classes-Reading Week Friday March 18th, 2016: Last Day for Voluntary Withdrawl Friday March 25th, 2016: No classes- Good Friday Friday April 8th, 2016: Last Day of Classes

Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another student, plagiarism, and examination impersonation.

Note: cell phones, pagers or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests and examinations.

Penalties that may apply, as provided for under the University of Manitoba’s Student Discipline By-Law, range from a grade of zero for the assignment or examination, failure in the course, to expulsion from the University. The Student Discipline By-Law may be accessed at: http://umanitoba.ca/admin/governance/policies/section_1200/1202.shtml Suggested penalties assessed by the Faculty of Science for acts of academic dishonesty are available on the Faculty of Science web-page: http://umanitoba.ca/faculties/science

All Faculty members (and their teaching assistants) have been instructed to be vigilant and report all acts of academic dishonesty to the Head of the Department.

REGISTRATION RESTRICTIONS

PLEASE ENSURE THAT YOU THE STUDENT ARE ENTITLED TO BE REGISTERED IN THIS COURSE:

THIS MEANS THAT YOU THE STUDENT HAVE: -the appropriate prerequisites, as noted by the calendar description, or have permission from the instructor to waive these prerequisites -not previously taken, or are concurrently registered in this course and another that has been identified as “not to be held with” The registration system may have allowed the student to register but it is up to the student to ensure that they have met all the requirements. Consequences may be the student being withdrawn from the course part way through the term, or the course not used in the degree program. There will be no fee adjustment. This is not appealable.

DEFERRED EXAMS: Deferred exams will not be administered. Failure to write a mid-term exam will result in the weight of the mid-term being added to the weight of the final exam. Students may not transfer the weight of two missed mid-term exams to the weight of the final exam. The weight of the missed mid-term exam will only be transferred to the weight of the final exam in the presence of a valid medical certificate or on compassionate grounds when accompanied by a note from clergy or another creditable source. Failure to provide necessary documentation will result in a grade of 0 for the missed exam.

ATTENDANCE:

Attendance of both the lecture and the tutoring sessions are mandatory. It is imperative that you attend the both the lecture and the tutoring sessions in order to maximize your understanding of the material and the resources available to you. Attendance will be taken and forwarded to the Access program councellor. Up to 10% of the final grade will be deducted if attendance is poor and supporting documentation is not provided.

TUTORING:

Students registered in this section are entitled to additional tutoring periods each week. The tutoring times will be determined during the first week of classes.

TOPICS AND LECTURE OUTLINE:

Topic Introduction to Physiology and Homeostasis Cell Membrane Physiology Nervous System Physiology *End Material Mid-term #1

Endrocrine System Physiology Protein Synthesis and Glycolysis Skeletal System Physiology Skeletal Muscle Physiology **End Material Mid-term #2

Cardiovascular and Lymphatic System Physiology Respiratory System Physiology The Digestive System Physiology The Urinary System Physiology

BIOL 2200- The Invertebrates- 2015

Lecture: 11:30 am - 12:20 pm MWF BULLER 306

LECTURE INSTRUCTOR: Dr. Brenda Hann ([email protected]) W463 Duff Roblin. Meetings by appointment. LAB INSTRUCTOR: Dr. Joy Stacey ([email protected]) W471 Duff Roblin. Meetings by appointment.

Textbook: Pechenik, J. A. 2015. Biology of the Invertebrates. 7th ed., McGraw-Hill Co, Inc. Earlier editions of the textbook will be useful for most content. However, some material (especially taxonomy and phylogeny) has changed from earlier editions. It is the responsibility of the student to find the appropriate chapters/sections in older textbooks.

Laboratory Manual: BIOL 2200: The Invertebrates, Course Information and Laboratory Manual (2015 edition) Note: most other editions of the lab manual will not be appropriate for this offering of the course as the organization and content has changed significantly.

COURSE CONTENT/TEXTBOOK READINGS: Lectures will cover textbook material with some additional subjects. Reading the textbook chapters is essential but you will be examined on material presented in lecture.

ATTENDANCE: Lecture and lab attendance is essential. The provided supplementary lab material does not necessarily cover all material presented in lab and does not replace attendance. Important announcements regarding exams and assignments may be given in class or lab. Last date for voluntary withdrawal is November 18.

COMMUNICATION/APPOINTMENT POLICIES: • Use your University email account. • Always include your name and the name of this course. We will not respond to an unsigned email. • We do not answer questions about lectures that require complex answers via email, especially in the 24 hours leading up to the exam. • When requesting an appointment, it is efficient to suggest multiple days and times to expedite scheduling a time. We do not take appointments for the day of an exam.

Faculty of Science Policies Academic Dishonesty: http://umanitoba.ca/faculties/science/undergrad/resources/webdisciplinedocuments.html EVALUATION: The contribution of lecture and lab exams, and assignments to the final grade is in the table below. L ecture exams may include multiple choice and short/long answer questions.

Students with appropriate documentation may write a deferred midterm lab exam only if it can be completed the day after the scheduled exam. If this is not possible, students with appropriate documentation ( http://umanitoba.ca/student/records/finals/682.html) will write a cumulative lab exam worth 25% of the final grade during the final examination period. Deferred lab exams may not be the same format as the regular lab exam. The details of the Laboratory assignment will be provided in separate documents on UMLearn.

Item Mark allocation Midterm Laboratory Exam 10 (Labs 1-4) Final Laboratory Exam 15 (Labs 5- 9) Laboratory assignment 5 Midterm Lecture Exam 25 Final Lecture Exam 45

Total 100

LABORATORY AND EXAM SCHEDULE

Date Event Description Sept.16-18 Lab Introduction (mandatory) Sept. 23-25 Lab 1: PROTOZOA Sept. 30- Oct. 2 Lab 2:RADIATE PHYLA: Porifera, Cnidaria (assignment specimen distribution) Oct. 7-9 Lab 3: PLATYHELMINTHES

Oct. 14-16 Lab 4: ANNELIDA, BRYOZOA, BRACHIOPODA Oct. 21 Open lab session 9 am- 5pm (tentative) Oct. 22 EXAM Laboratory midterm exam 2:30, 4:00, 5:30, 7pm Oct. 26 LECTURE EXAM Schultz Lecture Theatre, 5:30-7:00pm (1 hour exam) Oct. 28-30 Lab 5: MOLLUSCA Nov. 4-6 Lab 6:NEMATODA, ONYCHOPHORA Nov. 12-13 Lab* - Note that the B01 lab slot 7: ARTHROPODA 1: Trilobites & Crustaceans will meet on Thursday, November 12, 7-10pm for this week only.

Nov. 16 LAB ASSIGNMENT: due in Late assignments will be penalized 15% laboratory D2L drop box per day and will not be accepted after 4 before 5pm. days late. Nov. 18-20 Lab 8: ARTHROPODA 2: Chelicerates, Terrestrial Mandibulates Nov. 25-27 Lab 9: ECHINODERMATA Dec. 2 Open lab session 9am – 5 pm (tentative) Dec. 3 EXAM Laboratory final exam 2:30, 4:00, 5:30 or 7:00 pm

BIOL 2210: THE CHORDATES Tentative Schedule 2016 Associated Readings for Lecture Topics are from the 8th or 9th Edition of “Vertebrate Life” Associated Readings from the Lab Manual Should be Completed before the Lab

M W F Labs (T, W, Th) Jan 6 Jan 8 Lab 1 (Jan 6, 7) Introduction Vertebrate Relationships and Early chordates and external Course Introduction Basic Structure morphology of fish Diversity and Classification of Origin of the Chordates The Tues (B01) laboratory slot will Vertebrates (Chapter 1) Vertebrate Characteristics and meet Thurs, Jan 7, 6:30–9 pm for this Relationships week only (Chapter 2) Jan 11 Jan 13 Jan 15 Lab 2 (Jan 12, 13, 14) Early Vertebrates Primary Literature Searches: Extant Jawless Fishes: Hagfishes Fish anatomy 1 (skeleton) Early Jawless Vertebrates, Ms. Vickie Albrecht (Biological and Lampreys Agnatha (Chapter 3) Sciences Librarian) (Chapter 3)

Jan 18 Jan 20 Jan 22 Lab 3 (Jan 19, 20, 21) Origin of Jaws, Early Introduction to Non-Amniotic Cartilaginous Fishes, Fish anatomy 2 (musculature and Gnathostomes Vertebrates (Fishes and Chondrichthyes viscera) (Chapter 3) Amphibians) Early Chondrichthyans Living in Water (Chapter 5) (Chapter 4) Jan 25 Jan 27 Jan 29 Lab 4 (Jan 26, 27, 28) Extant Chondrichthyans – Bony Fishes (“Osteichthyes”) Ray-Finned Fishes, Actinopterygii Amphibians: external morphology and Sharks, Skates, Rays, Ratfishes Lobe-Finned Fishes, (Chapter 6) anatomy 1 (Chapter 5) Sarcopterygii (Chapter 6)

Feb 1 Feb 3 Feb 5 Lab 5 (Feb 2, 3, 4) Teleost Adaptations (Chapter 6) Living on Land Midterm 1 Amphibian anatomy 2 (musculature and (Chapter 8) 207 Buller or 315 Buller viscera) Feb 8 Feb 10 Feb 12 LAB MIDTERM (Feb 11) Origin and Radiation of Tetrapods Amphibians Biology of Amphibians 2:30, 4:00, 5:30, or 7:00 pm Early Tetrapods Extant Amphibians, (Chapter 10) (Chapter 9) Characteristics and Diversity Open Lab Review Feb 9 (11 am–7 pm) (Chapter 10) M W F Labs (T, W, Th) Feb 15 Feb 17 Feb 19

------MID-TERM BREAK ------MID-TERM BREAK ------MID-TERM BREAK ------MID-TERM BREAK ------

Feb 22 Feb 24 Feb 26 Lab 6 (Feb 23, 24, 25) Biology of Amphibians, Cont’d Introduction to Amniotic Turtles Reptile diversity and anatomy 1 (Chapter 10) Vertebrates: Structure and Function (skeleton) Essay Topic Approval Synapsids vs. Sauropsids (Chapter 12) (Chapter 11) Feb 29 Mar 2 Mar 4 Lab 7 (Mar 1, 2, 3) Turtle Ecology and Behaviour Introduction to Lepidosaurs Radiation of Squamates (Lizards Reptile anatomy 2 (viscera and (Chapter 12) (Tuatara, Lizards, Snakes) and Snakes) musculature) and birds (Chapter 13) (Chapter 13) Mar 7 Mar 9 Mar 11 Lab 8 (Mar 8, 9, 10) Ecology and Behaviour of Biology of Squamates, Cont’d Midterm 2 Mammalian diversity and anatomy 1 Squamates (Chapters 13, 14) 207 Buller or 315 Buller (skeleton) (Chapter 13) Mar 14 Mar 16 Mar 18 Lab 9a (Mar 15, 16, 17) Introduction to Archosaurs Dinosaurs (Chapter 16) Dinosaurs, Cont’d (Chapter 16) Mammal anatomy 2 (musculature) (Chapter 16) Extant Archosaurs (Chapter 16) Essay Due (12:30 pm) Mar 21 Mar 23 Mar 25 Lab 9b (Mar 22, 23, 24) Evolution of Birds and Flight Bird Flight, Cont’d (Chapter 16) Good Friday (no classes) Mammalian anatomy 2 (musculature) (Chapter 16)

Mar 28 Mar 30 Apr 1 Lab 10 (Mar 20, 30, 31) Biology of Birds (Chapter 16) Synapsida: The Mammals Mammalian Characteristics and Mammalian anatomy 3 (viscera) Origin of Synapsids Diversity Non-Mammalian Synapsids and Mammalian Features the First Mammals (Chapter 20) (Chapter 18) Apr 4 Apr 6 Apr 8 LAB FINAL (Apr 7) Major Lineages of Mammals Mammalian Reproduction Biology of Mammals (Chapter 22) 2:30, 4:00, 5:30, or 7:00 pm (Chapter 20) Reproduction of Eutherians Course Wrap-up (Chapter 21) Open Lab Review Apr 5 (11 am–7 pm)

COURSE SYLLABUS Non-Flowering Plants—BIOL 2240 Lecture section A01, Term 2-Regular Session 2015/16 Instructor: Mrs. Karen Sereda, M.Sc. 421A Biological Sciences phone: 474-9130 email: [email protected] Office Hours: Mondays 3-4 pm, Tuesdays and Thursdays 10-11 am OR by appointment

Textbook: Evert, RF & Eichhorn SE. 2013. Raven Biology of Plants, 8th ed. W. H. Freeman and Company, New York.

Lectures: Tuesdays and Thursdays 8:30—9:45 am in 315 Buller

Laboratories: Wednesdays 2:30 – 5:30 pm OR 6-9 pm in 314 Buller

Course description: This course is an introduction to the major groups of non-vascular plants specifically treating the morphology, anatomy, ecology and evolution of mosses, liverworts, hornworts, ferns and other spore-bearing vascular plants, gymnosperms and angiosperms.

Laboratory attendance is compulsory (see attached schedule). No student is allowed to miss more than two laboratory periods without a medical certificate or the consent of the instructor. There is no lab manual for the course. Lab directions will be provided as *pdf files in UM Learn. Students are responsible for downloading and printing their own lab handouts! Please bring blank (unlined) paper, a pencil and an eraser to each laboratory period.

Laboratories begin January 20, 2016

Faculty of Science Statement on Academic Dishonesty The Faculty of Science and The University of Manitoba regard acts of academic dishonesty in quizzes, tests, examinations, laboratory reports of assignments as serious offences and may assess a variety of penalties depending on the nature of the offence. Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another student, plagiarism, and examination impersonation. Note: cell phones, pagers or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations. Penalties that may apply, as provided for under the University of Manitoba’s Student Discipline By-Law, range from a grade of zero for the assignment or examination, failure in the course, to expulsion from the University. Suggested penalties assessed by the Faculty of Science for acts of academic dishonesty are available on the Faculty of Science web-page: http://umanitoba.ca/faculties/science/ All Faculty members (and their teaching assistants) have been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department. Academic dishonesty will not be tolerated. All cases of academic dishonesty will be reported to the Head, Department of Biological Sciences and/or the Dean, Faculty of Science.

Last date for voluntary withdrawal is Friday, March 18, 2016

- 1 -

Evaluation: 1. Midterm lecture exam. Tuesday, March 1, 2016 from 8:30 - 9:45 am, location TBA, worth 15% of the final grade. Format will be a mixture of multiple choice and written answers varying from fill-in-the-blanks to several paragraphs. Material tested will be based on lectures, although laboratory exercises are designed to reinforce lecture material.

2. Laboratory assignments. Drawings will be done in all lab periods, and some drawings will be marked for all laboratories. These will be handed in at the end of the laboratory period; each will be worth an equal amount, for a total of 15% of the final grade.

3. Laboratory station exam. Date and time TBA, held in 314 Buller. It will be scheduled by the university during the final exam period (Apr 11-25), and is worth 30% of the final grade. Exam format will be a series of 30 stations with questions based on materials observed in labs, such as microscope slides, preserved and/or fresh specimens.

4. Final exam. Date, time and location TBA, and will be scheduled by the university during the final exam period (Apr 11-25). The final exam will be worth 40% of the final grade. Exam format will be similar to the midterm lecture exam. Material tested will be based primarily on that lecture material covered after the midterm cut-off.

Other Important Information  Attendance at lectures and labs is mandatory. You are responsible for all material covered in lecture and lab, assigned readings, and any announcements made in class.  Selected course materials will be posted on UMLearn. Posted lecture notes are not 100% complete, as students are expected to attend classes.  Missed lab work and exams will be assigned a grade of zero (0) unless documentation (note from a counselor or physician) is provided.

Lecture Outline 1. Introduction 2. Evolutionary processes 3. Systematics: the science of biodiversity 4. Bryophyta (mosses) 5. Marchantiophyta (liverworts) 6. Anthocerophyta (hornworts) 7. Organization of the vascular plant body 8. Lycopodiophyta (club mosses, spike mosses, quillworts) 9. Monilophyta (whisk ferns, grape ferns, marattioid ferns, horsetails, ferns) 10. Evolution of seed and pollen 11. Gymnosperms: Coniferophyta (conifers), Ginkgophyta (maidenhair tree), Cycadophyta (cycads), and Gnetophyta (gnetophytes) 12. Introduction to the Anthophyta (flowering plants)

Note: Chapters in the textbook cover slightly differing topics than will be discussed in lecture. Some topics are not covered in the textbook, but will be discussed in lecture. Material tested is based on that presented in lecture, whether verbal or written. Anything covered in lecture is testable! See the attached reading list for pages in the Biology of Plants.

- 2 -

READING LIST

Raven, P. H., R. F. Evert, and S. E. Eichhorn. 2005. Biology of Plants, 7th edition. W. H. Freeman and Company, New York. Evert, R. F. and S. E. Eichhorn. 2013. Raven Biology of Plants, 8th edition. W. H. Freeman and Company, New York.

7th edition 8th edition

Chptr. 11. The Process of Evolution, pgs. Chptr. 11. The Process of Evolution, pgs. 198-203 & 207-217. Not responsible for 209 -214 & 218-231. Not responsible for section “The Behavior of Genes in section “The Behavior of Genes in Populations: The Hardy-Weinberg Law”. Populations: The Hardy-Weinberg Law”

Chptr. 12. Systematics the Science of Chptr. 12. Systematics the Science of Biodiversity, pgs. 219-237. For the section Biodiversity, pgs. 234-255. For the section “The Eukaryotic Kingdoms” focus on “The Protists and Eukaryotic Kingdoms” Kingdom Plantae. focus on Kingdom Plantae.

Chptr. 15. Green Algae, pgs. 327-330, 335- Chptr. 15. Green Algae, pgs. 345-347, 353- 340. 358.

Chptr. 16. Bryophytes, pgs. 345-367. Chptr. 16. Bryophytes, pgs. 366-390.

Chptr. 17. Seedless Vascular Plants, pgs. Chptr. 17. Seedless Vascular Plants, pgs. 368-407. 391-429.

Chptr. 18. Gymnosperms, pgs. 408-433. Chptr. 18. Gymnosperms, pgs. 430-456.

Chptr. 19. Introduction to the Angiosperms, Chptr. 19. Introduction to the Angiosperms, pgs. 434-451. pgs. 457-476.

Chptr. 20. Evolution of the Angiosperms, Chptr. 20. Evolution of the Angiosperms, pgs. 452-458. pgs. 477-485, 492-494.

Chptr. 23. Vascular tissue, pgs. 516-523. Chptr. 23. Vascular tissue, pgs. 544-553. Periderm, pgs. 525-526. Periderm, pg. 555.

Chptr. 26. Secondary growth, pgs. 581-591. Chptr. 26. Secondary growth, pgs. 615-626.

Lab Schedule: Jan 20 Lab1-Microscope/Bryophyta I Jan 27 Lab 2-Bryophyta II Feb 3 Lab 3-Marchantiophyta (liverworts) / Anthocerophyta (hornworts) Mar 2 Lab 4-Lycopodiophyta I (club mosses, spike mosses) Mar 9 Lab 5-Lycopodiophyta II (quillworts) / Monilophyta I (whisk ferns, horsetails) Mar 16 Lab 6-Monilophyta II (grape ferns, ferns) Mar 30 Lab 7-Coniferophyta (conifers) Apr 6 Lab 8-Cycadophyta (cycads) / Ginkgophyta (maidenhair tree) / Gnetophyta

- 3 - BIOL 2242 The Flowering Plants Fall Term 2015 3 credit hours

A study of the structure and function of the flowering plants. Lecture topics are supplemented by laboratory exercises that focus on the anatomy and morphology of roots, stems, leaves, and reproductive organs. Adaptations of plants to their natural environment are stressed.

Instructor: Dr. Isobel Waters. Office: 318 Buller. Office Hours: Mon, Wed and Fri 11:30- 12:30; or by appointment. Phone: 474-8739. E-mail: [email protected]

Required Textbook: Evert, R.F. and S.E. Eichorn. 2012. Raven Biology of Plants. New York, Worth Publishers, Inc. (8th edition). If you are using an earlier edition, you are responsible for differences in pagination. The textbook is essential for both the lecture and lab material. Lectures: Slot 8, 1:30-2:20 Mon, Wed, Fri. 306 Buller. Laboratories: Slots 25, 27 and 29. Wed, Thurs and Fri 2:30-5:30. 314 Buller. The lab manual will be available in the bookstore. Labs begin on September 23-25. Attendance at lectures and labs is compulsory. You are responsible for material covered in lectures, labs, assigned readings, and any announcements made in class. Course materials such as Powerpoint files, etc. will be posted in D2L.

Examinations/Assignments: ` 1. Midterm lecture exam. Tues 27 Oct 2015. 6:30-8:30 PM. Location TBA. 20% of final grade. Format will be a mixture of multiple choice plus written answers varying from fill-in- blanks to several paragraphs. Material tested will be based on lectures, although lab exercises are designed to reinforce lecture material. A sample midterm will be provided. 2. Laboratory assignments. Laboratory drawings will be handed in each week. On two occasions to be announced, these will be worth 2.5 marks for a total of 5% of final grade. These drawings must be handed in during the lab period. 3. Laboratory station exam. December exam period (TBA) 75 mins. 25% of final grade. Format will be a series of 25 stations with questions based on lab material, plus 5 rest stations. Questions will be based on microscopes and/or photographic images. 4. Final lecture examination. December exam period (TBA). 3 hours. 50% of final grade. Format will be similar to the midterm exam. The majority of material tested will be from after the midterm, but there will be some exceptions. Details will be provided in class. Missed exams or lab work will be assigned a grade of 0 unless documentation acceptable to the Faculty of Science is provided. Final voluntary withdrawal date is 18 November, 2015.

Statement on Academic Dishonesty The Faculty of Science and The University of Manitoba regard acts of academic dishonesty in quizzes, tests, examinations, laboratory reports or assignments as serious offences and may assess a variety of penalties depending on the nature of the offence.All Faculty members and teaching assistantshave been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department. Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another individual, using answers provided by tutors, plagiarism, and examination personation. Note: cell phones, pagers, PDAs, M P3 units or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations. Penalties that may apply, as provided for under the University of Manitoba's Student Discipline ByLaw, range from a grade of 0 for the assignment or examination, failure in the course, to expulsion from the University. The Student Discipline By Law may be accessed at: http://umanitoba.ca/admin/governance/governing_documents/stud ents/868.ht Suggested minimum penalties assessed by Faculty of Science for acts of academic dishonesty are available on the Faculty of Science webpage: http://umanitoba.ca/faculties/scien ce/resources/Discipline__Penalties_Table_Jul09.pdf

BIOL 2242 The Flowering Plants: Lecture Topic Outline 2015

NOTE: Specific page numbers are provided only in those chapters where a small section of a chapter is used; otherwise, the entire chapter is pertinent. Additional material not found in the text will be covered in lectures. Condensed notes of Powerpoint presentations will be posted on D2L. Copyrighted images from the textbook and other sources are not provided on-line.

I. Introduction: Food for thought (Ch 1; overview; Ch 19, pp. 457-460) - why study plants? - key features of Phylum Anthophyta II. Starting out: Structure and development of the young plant body (Ch.22; pp. 530-536) - importance of the seed for survival and dispersal - parts of the seed and seedling - patterns of germination - basic plant growth form types (Ch. 26; pp. 614-615) III. Building blocks: Plant cells (Chs. 2,3,4 (parts only) and Ch 23) - production of cells by meristems - a "typical" plant cell - properties and functions of subcellular components - structure of the cell wall and implications for function - membrane properties and transport mechanisms - secondary metabolites (Ch 2; pp. 30-35) - specialized plant tissue and cell types - ground, dermal and vascular tissue systems IV. Establishing a foundation: Structure and development of roots (Ch. 24) - basic root system types - zonation patterns in the growing primary root - anatomy of the primary root of monocots and eudicots - symbiotic associations of roots V. Reaching out: Structure and development of stems (Ch. 25) - development of the shoot apical meristem - anatomy of the primary stem of monocots and eudicots - variations in stem morphology VI. Solar collectors: Leaf structure and development (Ch. 25) - leaf morphology and anatomy - leaf development from initiation to abscission - environmental adaptations of leaves VII. Getting bigger: Secondary tissue development (Ch. 26 and Ch. 24, pp. 569-571) - vascular and cork cambial development in stems and roots - types of secondary tissue and their cellular composition - categories and properties of wood VIII. Making more: Plant reproduction (Ch 19) - asexual vs sexual reproduction - parts of the flower and variations in floral structure - angiosperm life cycle - micro and mega sporo- and gametogenesis - pollination and double fertilization - fruit and seed development

BIOL2260 Biology of fungi and lichens

BIOL2260: Biology of Fungi and Lichens Information for students

INSTRUCTOR INFORMATION Dr. Tom Booth Dr. Michele Piercey-Normore 404 Biological Sciences Building, Ph: 474-6588 507/508 Buller Building, Ph: 474-9610 [email protected] [email protected]

COURSE INFORMATION Lecture: Tue and Thurs 10:00–11:15; 207 Buller Lab: Monday & Tuesday 2:30–5:25; 305 Biological Sciences Building

Evaluation: Midterm #1 October 13 (Tue), 2015 15% Midterm #2 November 17 (Tue), 2015 15% Labs see lab for due dates 20% Final exam TBA 50%

Note: 5% per day will be removed for late reports. Exams will be based on lecture and lab material. Therefore attendance in class and labs will be necessary to be successful in this course. Grading: 90- 100=A+; 80-89=A; 74-79=B+; 68-73=B; 62-67=C+; 56-61=C; 50-55=D; 0-49=F.

RECOMMENDED TEXT: Webster, J. and Webster, R. W. S. 2007. Introduction to Fungi. Cambridge University Press, Cambridge, U. K.

GENERAL INFORMATION Voluntary withdrawal deadline: 18 November 2015

STATEMENT ON ACADEMIC DISHONESTY (http://umanitoba.ca/faculties/science/undergrad/resources/webdisciplinedocuments.html)

The Faculty of Science and The University of Manitoba regard acts of academic dishonesty in quizzes, tests, examinations, laboratory reports or assignments as serious offences and may assess a variety of penalties depending on the nature of the offence. Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another individual, using answers provided by tutors, plagiarism, and examination personation. Note: cell phones, pagers, PDAs, MP3 units or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations. Penalties that may apply, as provided for under the University of Manitoba's Student Discipline By-Law, range from a grade of zero for the assignment or examination, failure in the course, to expulsion from the University. The Student Discipline By-Law may be accessed at: http://umanitoba.ca/admin/governance/governing_documents/students/868.htm Suggested minimum penalties assessed by the Faculty of Science for acts of academic dishonesty are available on the Faculty of Science webpage: http://umanitoba.ca/faculties/science/resources/Acad_Dishon_TABLE_RevCSS_AdminC_Jul2012_WEB. pdf All Faculty members (and their teaching assistants) have been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department.

1 BIOL2260 Biology of fungi and lichens

LECTURE OUTLINE

PART I: Basidiomycota Instructor: Dr. T. Booth

General topic and location in text Topics to be covered ~ Week Lab book & Day Dates 1. Collecting Macrofungi & Lichens Fungi as unique organisms; how fungi grow & gain 1 (9/10) (1.1; 1.2-1.4; 1.4.3-1.4.4; 1.5; 18.1; nutrients; fungi as hunters & gathers; some fungal 18.7.5) propagules & taxonomy & antiquity of fungi

2. Identifying Macrofungi & Lichens General fruiting body types (ascocarps & 2 (9/15) 9/14&15 (1.3.5-1-1.3.6; 8.1; 8.7; 16.1-16.2.1; basidiocarps); lichen thallus types; general structure of 16.3-16.3.4; 19.1-19.25) ascocarps & basidiocarps.

3. Introduction to Basidiomycota Basidium morphology & development: basidiospore 2 (9/17) (18.2-18.74; 18.10-18.12; 19.3- development, discharge & numbers per basidiocarp; 19.3.2) spore germination and development of hyphae & mycelia; & the importance of Homobasidiomycetes 4. Euagaric Clade Agaricaceae, Clavariaceae, Coprinaceae 3 (9/22) 9/21&22 (19.4-19.4.14) (Psathyrellaceae), Amanitaceae, Pluteaceae, Pleurotaceae, Schizophyllaceae, Bolbitiaceae, Hygrophoraceae, Mycenaceae, Trichoiomataceae, Strophariaceae, & Cortinariaceae 5. Boletoids & Polyporoid Clades Paxillaceae, Boletaceae, Gomphidiaceae, Suillaceae, 3 (9/24) (19.5-19.5..4; 19.6) Coniophoraceae; Polyporaceae, Fomitopsidaceae, Ganodermataceae, & Phanerochaetaceae 6. Russuloid & other Cades Russulaceae, Bondarzewiaceae, Stereaceae; 4 (9/29) 9/28&29 (19.7-19.7.4; 19.8; 19.9-19.9.1; Bankeraceae (Hydnellum) & Thelephoraceae in 19.10-19.10.3; 19.11-19.11.1) Thelephorids: Hymenochaetaceae in Hymenochaetoids; Cantharellaceae & Clavulinaceae in Cantharelloids; & Clavariaceae & Gomphidiaceae in Gomphoid-Phalloids 7. Gastomycetes Gasteromycete evolution & phylogeny; Euagarics: 4 (10/1) (20.1-20.5.3) Boletoids; & Gomphoid-Phalloids

8. Heterobasidiomycetes Ceratobasidiales; Dacrymycetales; Auriculariales; & 5 (10/6) 10/5&6 (21.1-21.5.1) Tremellales

9. Rusts Uredinales 5 (10/8) (22.1- 22.7)

10. Smuts Utilaginales; Microbotryales; & Exobasidiales 6 (10/15) (23.1-23.4.1)

11. Basidiomycete yeasts Morphology, life-cycles & phylogeny; 7 (10/20) (24.1-24.4.1) Heterobasidiomycete yeasts; Urediniomycete yeasts; & Ustilaginomycete yeasts 12. Nematophagous & Aquatic Nematophagous fungi, aquatic hyphomycetes; & 7 (10/22) Basidiopmycota & Ascomycota aeroaquatic fungi (25.1-25.3.2)

PART 2: Ascomycota Instructor: Dr. M. Piercey-Normore

General topic and location Topics to be covered Approx. Lab in text book time period Ascomycota (Ch 8; p 226-249) Introduction to ascomycetes; lifestyles; life cycles (sexual Week 1 and asexual); development of ascus, spores, and ascocarp; apical apparatus and dispersal; simplified classification. 2 BIOL2260 Biology of fungi and lichens

Archiascomycetes (Ch 9 p Introduction and Taphrina. 250-253)

10. Hemiascomycetes (Ch 10, Ascomycete yeasts: Introduction; Saccharomyces; Week 2 p 261-276)

Plectomycetes (Ch 11) Introduction; Onygenales; Eurotiales

11. Hymenoascomycetes: Introduction Pyrenomycetes (Ch 12) Sordariales (Sordaria, Podospora, Neurospora, Chaetomium) Xylariales (Xylaria, Hypoxilon) Hypocreales (Hypocrea, Nectria, Fusarium) Claviceptales (Claviceps, Epichloe) Ophiostomatales (Ophiostoma) Diaporthales (Diaporthe) 12. Hymenoascomycetes: Introduction Week 3 Erysiphales (Ch 13) Powdery mildews: Erysiphe, Microsphaera, Phyllactinia

Hymenoascomycetes: Introduction; Pezizales (Pyronema, Peziza, Helvella, Tuber, Pezizales (operculate Morchella) discomycetes) (Ch 14)

13. Hymenoascomycetes: Introduction; Helotiales (Sclerotinia, Rhytisma, Week 4 Helotiales (inoperculate Geoglossaceae, Leotiaceae, Helotiaceae) discomycetes) (Ch 15)

14. Lichenized fungi Introduction; morphology, reproduction, lichen thallus, Week 5- (Hymenoascomycetes, Lecanora, Xanthoria, Peltigera, Cladonia. 6 Lecanorales) (Ch 16)

15. Loculoascomycetes (Ch Pleosporales: Pleospora, Alternaria, Venturia Week 7 17) Dothideales: Mycosphaerella, Dibotryon (Apiosporina)

Deuteromycetes Black mold Stachybotrys chartarum

3 BIOL2260 Biology of fungi and lichens

LABORATORY OUTLINE

Lab 1: Processing basidiocarps for identification (September 14th & 15th

Lab 2: Homobasidiomyceytes: Agaricales, Gasteromycetes and Aphyllophorales (September 21st & 22nd)

Lab 3: Heterobasidiomycetes: jelly fungi & related forms (September 28th & 29th)

Lab 4: Basidiomycetes: smuts and rusts (October 5th & 6th)

Lab 5: Archiascomycetes, Plectomycetes, Pyrenomycetes (October 19, 20)

Lab 6: Erisiphales, Pezizales, Helotiales, Loculoascomycetes (October 26 and 27)

Lab 7: Lecanorales: Lecanora, Cladonia (November 2 and 3)

Lab 8: Lecanorales: Xanthoria, Peltigera (November 9 and 10)

4 Biology of Algae (BIOL2262) January – April 2016

Description This course is a survey of the major algal groups. We will discuss algal taxonomy and classification, systematics, cellular morphology, genetics and reproduction, physiology, and ecology. Labs will deal with identification of major algal groups, culturing of live algae, and the use of algae for environmental reconstruction.

Instructor Dr. Gordon Goldsborough Office: 314 Biological Sciences Building Phone: 204-474-7469 (voice mail after four rings) Email: [email protected] (this is the best way to reach me) Office hours: whenever my door is open

Lectures Mondays, Wednesdays, Fridays; 11:30 AM to 12:20 PM 301 Biological Sciences Building

Labs Tuesdays 2:30 to 5:15 PM / Tuesdays 6:00 to 8:45 PM / Fridays 2:30 to 5:15 PM 314 Buller Building TA: Paige Kowal (Tuesday afternoon / evening)

Website UMLearn (http://umanitoba.desire2learn.com) has copies of the syllabus, lecture slides, assignments, marks, course news, and miscellaneous information

Marks lab project 10 marks lab exam (2 hours) 20 marks midterm test (1 hour) 20 marks final exam (3 hours) 50 marks

Grades 90 - 100 ...... A+ 70 - 75 ...... B 50 - 59 ...... D 80 - 89 ...... A 66 - 69 ...... C+ < 50 ...... F 76 - 79 ...... B+ 60 - 65 ...... C

Text Phycology (4th edition) by Robert E. Lee, 2008 Cambridge University Press, ISBN 9780521682770 Optional but highly recommended – on 24-hour Reserve at Science Library

Exams The midterm test (week of 22 February) and final exam will consist of multiple-choice, definition-type short answers, diagrams, concise paragraphs and, as time permits, short essay questions. The questions will be drawn from material presented in lectures. A separate exam at the end of the course will test material presented in labs.

Bad stuff Please become acquainted with the Faculty of Science Policy on Academic Dishonesty (http://umanitoba.ca/science/undergrad/resources/webdisciplinedocuments.html). Acts of academic dishonesty include, but are not limited to, bringing unauthorized materials into a test or exam, copying from another person, examination impersonation, and plagiarism. The copying of another student’s work, submission of the same material for two or more courses, and the use of unaltered and unattributed text from print and Internet sources are all examples of plagiarism, which will not be tolerated. LECTURE OUTLINE 1. Introduction to the study of algae 2. Survey of the major algal groups and their features o Morphology: pigmentation, storage products, cell coverings, motility o Nutrition o Reproduction: lifecycles o Environmental requirements a) Cyanobacteria b) Diatoms c) Chrysophytes d) Brown algae e) Miscellaneous chromophytes f) Dinoflagellates g) Cryptomonads h) Euglenids i) Red algae j) Green algae 3. Ecology: algae, human affairs and the environment

LAB SCHEDULE

Date Lab 19, 22 January Microscope calibration and cell biovolume determination 26, 29 January Cyanobacteria 2, 5 February Chromophyta – diatoms, part 1 9, 12 February Lab project introduction – algal culturing 15-19 February Mid-term break: No lab 23, 26 February Chromophyta – chrysophytes/synurids, brown algae 1, 4 March Batch culture calculations – no new lab material presented 8, 11 March Dinoflagellates, euglenids, red algae 15, 18 March Chromophyta – diatoms, part 2 22, 25 March Green algae, part 1 29 March, 1 April Green algae, part 2 Week of 4 April Lab exam

Introduction to Toxicology BIOL 2380 / ENVR2180 / AGRI 2190 Winter 2015

Description A survey of general principles underlying the effects of toxic substances on biological systems, including consideration of the history, scope and applications of toxicology, toxicant exposure, the mechanisms of toxic action, and some major types of toxicants.

Instructor Dr. Jake Stout Department of Biological Sciences Office: 505C Buller Building Phone: 204-474-8493 (I rarely check my voicemail though!) Email: [email protected] Office hours: Tuesday and Thursday, 11 AM to noon (or by appointment via email)

Lectures Tuesday and Thursday, 8:30 to 9:45 AM. Fletcher Argue 200.

Website All course material (lecture slides, etc.) will be available on D2L.

Marks Option 1 Option 2 Option 3 Midterm 1 25% Midterm 35% Final 90% Midterm 2 25% Quizzes 10% Quizzes 10% Quizzes 10% Final exam 55% Final exam 40%

Exams a. The midterm exams will be non-cumulative. All midterms questions will be multiple choice. These exams will be 50 minutes long and will be held in class (see schedule for times). b. There will be NO deferred (aka ‘makeup’) midterm exams. . If you miss either midterm 1 or 2, you automatically qualify for grading options 2 or 3. If you miss both midterm s 1 and 2, then you qualify only for grading option 3. No doctor’s note/explanation is required if you miss tests 1 or 2. You are adults and can choose your best option, and I don’t want to congest our doctors’ offices with people seeking sick notes. c. The final exam will consist of short-answer and multiple choice questions. A heavier weighting will be placed upon the final 1/3rd of the course. d. You must write the final exam to pass the course. e. If you miss the final exam, you will require a doctor’s not or you must provide other documentation to the Faculty of Science office (i.e. don’t give it to me!) in order to qualify to write the final exam at a later date. e. Your final grade will be the BEST combination of the above ‘options’.

Textbook A Small Dose of Toxicology. Free!! Available at: http://www.toxipedia.org/display/dose/A+Small+Dose+of+Toxicology An English copy of the text is uploaded onto UManLearn. Readings will be assigned, and the online-quizzes will be based upon the readings. More details to follow in lecture.

Grades 90 - 100 A+ 70 - 75 B 50 - 59 D 80 - 89 A 66 - 69 C+ < 50 F 76 - 79 B+ 60 - 65 C

Course timetable

This is version 2.0 of the course, and lecture topics may shift around a bit!

Lecture Date Topic 0 Jan 7 Intro 1 Jan 12 Detection of toxins 2 Jan 14 Dose response curves & bioassays 3 Jan 19 Factors affecting toxicity 4 Jan 21 Absorption & toxicokenetics 5 Jan 26 Metabolic conversion and elimination of toxicons 6 Jan 28 Cellular and tissue targets of toxicity Feb 2 Midterm 1 7 Feb 4 Metals 8 Feb 9 Food toxicology 9 Feb 11 No class Feb 16 Winter break Feb 18 Winter break 10 Feb 23 Particulates and air pollution 11 Feb 25 Solvents and hydrocarbons 12 Mar 1 Persistent environmental contaminants 13 Mar 3 Pesticides 14 Mar 8 Radiation 15 Mar 10 Plant and animal toxins Mar 15 Midterm 2 16 Mar 17 Environmental risk assessment 17 Mar 22 Bioaccumulation and biomagnification 18 Mar 24 Environmental chemistry 19 Mar 29 Guest lecture 20 Mar 31 Guest lecture 21 Apr 5 Guest lecture 22 Apr 7 Review Faculty of Science Statement on Academic Dishonesty

Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another student, plagiarism, and examination impersonation.

Note: cell phones, pagers or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations.

Suggested penalties assessed by the Faculty of Science for acts of academic dishonesty are available on the Faculty of Science web-page: http://umanitoba.ca/faculties/science/

All Faculty members (and their teaching assistants) have been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department.

Jake’s statement on academic dishonesty

Although you’re sitting in a giant lecture hall feeling like a single student amongst thousands, when you get further along in any career you’ll generally get hired based upon your REPUTATION. Cheating and other forms of dishonesty shows that your character may not be the best. Also, you may need at some point a professor to write you a letter of reference… academic dishonesty doth not lead to glowing reviews. So don’t do it, m’kay?

REGISTRATION RESTRICTIONS

PLEASE ENSURE THAT YOU THE STUDENT ARE ENTITLED TO BE REGISTERED IN THIS COURSE:

THIS MEANS THAT YOU THE STUDENT HAVE:

-the appropriate prerequisites, as noted by the calendar description, or have permission from the instructor to waive these prerequisites

-not previously taken, or are concurrently registered in this course and another that has been identified as “not to be held with”

The registration system may have allowed the student to register but it is up to the student to ensure that they have met all the requirements.

Consequences may be the student being withdrawn from the course part way through the term, or the course not used in the degree program. There will be no fee adjustment. This is not appealable.

COURSE OUTLINE Biol 2410: Human Physiology I Fall 2015 Credit: 3 hours Lectures: 3 per week, (9:30 am 10:20 AM), 200 Fletcher Argue Laboratories: None

BIOL 2410 - Human Physiology 1 (AURORA)

BIOL 2410 - Human Physiology 1 (Formerly ZOOL 2530, 022.253) The mechanisms of action of the body's major control systems (nervous and endocrine) and of the muscular and reproductive systems are examined. Not to be held with BIOL 2411 (ZOOL 2531) or BIOL 3460 (ZOOL 3530, 022.353). Prerequisite: a “C” or better in one of BIOL 1030, BIOL 1031, the former 071.125, or BIOL 1412 (ZOOL 1330, 022.133); or a “C+” or better in both BIOL 1000 (or equivalent - BIOL 1001, 071.100) and BIOL 1010 (or equivalent - BIOL 1011, 071.101). -0.000 TO 3.000 Credit hours

Instructors: • Dr W Mark Fry (coordinator) – W469 Duff Roblin, 474-7498, – email [email protected] – http://umanitoba.ca/science/biological_sciences/people/fry/ – https://www.obesityresearch.ca/ • Dr Gary Anderson – W475 Duff Roblin, 474-7496 – Email [email protected] – http://umanitoba.ca/science/biological_sciences/people/ganderson/

Office hours for Dr. Fry and Dr. Anderson Our offices are always open for students, however, to ensure we have time to see you please e-mail for an appointment time.

Course Content: BIOL 2410 aims to introduce the principles of homeostasis and the nervous and endocrine mechanisms that monitor or regulate the internal environment. Muscular and reproductive function are also covered. BIOL 2420, Human Physiology II is the sister course to BIOL 2410, offered in the winter term and summer session, covers the remaining effector organ systems and immune defense. Structure is described to the extent required to understand function. The distribution and subject matter of the lectures are given below.

Date of Midterm Exam: Oct 27, 6-7:30 PM, location to be announced

EMAIL POLICY Use your UofM email account. As per UofM policy (Sept 2013) we cannot reply to email from other accounts (i.e. gmail, Hotmail…) Use Human Physiology 2410 in the subject line Use a proper salutation. “Hey Prof!” is not appropriate Always include your name and student number. If we do not know who you are, we cannot reply to you. Use full, grammatical sentences. Please do not use textese.

We will not answer questions about lectures via email. It is best to make an appointment. If we can provide an answer to a question on course material by e-mail then you, as a student, should be capable of finding that answer in the textbook or within the notes for the class. By doing so your learning experience is enriched. Therefore, we do not, and will not, answer by e-mail any questions on course material, so please e-mail us to set up an appointment. We will be happy to discuss any aspect of the course material in person.

How to get academic help Consult your textbook and/or Mastering A&P Go to instructor’s office to get help (it’s advisable to make an appointment first) Try to form a study group with classmates

Other Supplementary Texts (not required) (greater depth and detail – available Science Library, or Bookstore): "Review of Medical Physiology" (any recent edition), W.F. Ganong, Lange Publ. "Physiology", (any recent edition) R.M. Berne and M.N. Levy, Mosby Publ.

Lectures The organization and content of the lectures are often but not always based on the textbook. Wherever possible, lecturers will use terminology and illustrations consistent with Silverthorn’s. Examinations will be based on material presented in assignments, lectures and notes, as well as required readings from the text or posted on JUMP.

Date of Midterm Exam: Oct 27, 6-7:30 PM, location to be announced

Mastering A&P (Mastering anatomy and physiology) Register for online assignments and quizzes (see attached sheet) All required information for your registration and the proper use of this system is given in detail in your Student Access Kit of Mastering A&P.

1. Make sure your computer meets the system requirements (see your Mastering A&P Student Access Kit and http://www.masteringaandp.com/site/support/system- requirements.html. Any current common browser (Firefox, Google Chrome, Internet Explorer and Safari) may be used, however fewer problems have been reported with Firefox. 2. Go to http://www.masteringaandp.com/ To enroll in the course, enter your 7-didgit university of Manitoba student number as your student ID and enter the correct Course ID below

UMANHPHYS12015

3. If you experience technical difficulties with the Mastering A&P assignment system, contact Mastering A&P at this URL http://www.masteringaandp.com/site/support/faq- students.html. Make sure to have your Mastering A&P Student Access Kit or Username/password handy. 4. If you have troubles with the content, please make an appointment with your instructor.

Grading Grading in 2410 is based on two multiple choice examinations and ten Mastering A&P quizzes as follows: • Mastering A&P quizzes – Portion of course grade (best 8 scores) ------10% • Midterm Exam* – 35 multiple choice questions, 1.5 hours – Portion of course grade ------35% • Final Exam – 55 multiple choice questions, 2 hours – Portion of course grade ------55%

* venues and seating for the midterm will be announced in class

Mastering A&P Quiz dates There will be ten Mastering A&P quizzes, usually on a Monday, during the term on the following dates. You must log into the Mastering A&P system during the 24 hours that the quiz will be available in order to complete the quiz for marks. For example, the quiz for Sept 22 will be available to complete from 12:01 AM until 11:59 PM Sept 22, 2014. It will be available for viewing until the exam period is finished.

When calculating your score on the quiz we will use the best 8 scores. Each quiz and your score will be available for review the day after the quiz date. A missed quiz cannot be made up.

Letter grade system Grades are assigned at the end of the year by converting your cumulative percentage mark into a letter grade, using the following table: 90-100 A+ 80-89 A 74-79 B+ 68-73 B 62-67 C+ 56-61 C 50-55 D 0-49 F A note on rounding: to calculate your final letter grade, marks are rounded according to standard methods where for example, 89.49 is rounded to 89% and receives an A; 89.50 is rounded to 90%, and receives an A+. As instructors for the course we do reserve the right to make slight modifications to the above marking scheme depending on the performance of the class as a whole.

Honesty Any form of academic dishonesty will carry severe penalties. For further details see the 2012- 2013 Undergraduate Calendar, and the statement from Faculty of Science. http://umanitoba.ca/faculties/science/resources/Science_StatementOnAcademicDishonestyJul09. pdf

Missing an AandP quiz We cannot provide makeup quizzes for the Mastering AandP section of the course for any reason. If you miss a quiz for any reason, we will take the best 8/9 marks. If you miss two quizzes, we will take the 8 remaining marks. If you miss three quizzes, we will use the seven quiz marks and a 0/10 for the eighth.

Missing the Midterm Absence from an exam will result in loss of credit unless compelling grounds for absence are documented or satisfactorily explained; if absence is acceptable, a deferred exam will be arranged at a time suitable to student and examiner.

The J.C. Rauch Memorial Prize of $200 is awarded to the student completing 2420 with the highest overall average in 2410 and 2420, both taken in regular session.

TOPICAL OUTLINE OF LECTURES (content and order subject to minor changes)

INTRODUCTION (1 lecture - WMF) Chapter 1 & 2 Course organization. What is Physiology? What is homeostasis?

MOLECULES OF LIFE (2 lectures-WMF) Chapter 2, 3 Water, salts and solutes. Measuring solute concentrations Biomolecules (Fatty acids, Glycerides, Phospholipids & Sphingoloipds, Steroids, Eicosanoids

MEMBRANE DYNAMICS. (2 lectures WMF) Chapter 5 Transport of materials across cell membranes: Diffusion protein mediated transport and vesicular transport. Transport across cells. Active and passive transport Concentration of water and solutes: osmosis, measuring solute concentrations, consequences of altering solute concentrations. Introduction to resting membrane potential.

COMMUNICATION (2 lectures - WMF) Chapter 6 Communication between cells Local, cell to cell, autocrine and long distance signaling Communication inside cells Membrane receptors, g-proteins Second messenger signaling pathways Physiological Control pathways

NERVOUS SYSTEM (12 lectures - WMF) Cells of the nervous system Chapter 8 Electrical signaling within the nervous system The Nernst equation Ion channels The GHK equation Graded potentials Action potentials The role of axons and myelin Synaptic communication Electrical vs chemical neurotransmisstion: neurotransmitters Synaptic integration The neuromuscular junction Long term potentiation Organization of the nervous system Chapter 9 Organization reflected in development Connective tissue of the CNS Blood brain barrier Brain function, regional anatomy: spinal cord, brain.

Sensory physiology Chapter 10 Properties of sensory systems Somatic senses Chemoreception Vision Hearing and equilibrium The autonomic nervous system Chapter 11 Sympathetic and parasympathetic NS ANS pathways and transmitters Pharmacological treatments and toxins

MUSCLE (6 lectures – WMF) Skeletal muscle Chapter 12 Muscle fibre anatomy Sliding filaments Excitation contraction coupling Fibre types Use of energy in skeletal muscle Generation of tension Control of skeletal muscle: reflexes, voluntary and rhythmic control Chapter 13 Neural Reflexes Autonomic reflexes Skeletal muscle reflexes Muscle spindles Golgi tendon organs Stretch reflexes Central pattern generators Smooth muscle Chapter 12 Types of smooth muscle Anatomy of smooth muscle Mechanism of contraction Slow waves and pacemaking Cardiac muscle Chapter 14 Types of cardiac muscle cells Excitation contraction coupling Cardiac action potentials Pacemaking, and electrical conduction

ENDOCRINE SYSTEMS (7 lectures - GA) What are hormones? Chapter 7 Review of homeostasis from a hormonal perspective Transport in the blood Chemical classification Binding proteins Receptor activation The “Master gland” Chapter 7 Hypothalamic pituitary axis Adenohypophysial and neurohypophysial hormones The endocrinology of growth Chapter 23 Somatomedins Bone and somatic growth Thyroid and Pineal glands Chapter 23 Metabolism Rhythm The adrenal gland Chapters 11 & 23 Adrenal medulla and cortex Steroidogenesis “Stress” hormones Pancreatic hormones Chapters 7 & 23 Glucagon vs Insulin Calcium regulation Bone remodeling Hypercalcaemic and hypocalcaemic hormones

REPRODUCTION (6 lectures - GA) Chapter 26 Sex determination Genetic basis Meiosis and spermatogenesis Male reproductive system Testes Accessory glands Female reproductive system Ovaries and uterus Menstrual cycle Sex hormones Androgens Estrogens Birth control Procreation Male erection and ejaculation Fertilization and meiotic events in the oocyte Pregnancy and parturition Embryonic development Placenta Hormones Lactation

Dear Student: In this course you will be using MasteringAandP™, an online tutorial, homework and evaluation program that accompanies your textbook.

What You Need:  A valid email address (Use your UofM address)  A student access code (Comes in the Student Access Kit that may have been packaged with your new textbook or is available separately in your school’s bookstore. Otherwise, you can purchase access online at www.masteringaandp.com.)  The ZIP code for your school: ___R3T 2N2______

Course ID: ______UMANHPHYS12015______

Register  Go to www.masteringaandp.com and click New Students under Register.  Click Continue under Step 1.  License Agreement and Privacy Policy: Click I Accept to indicate that you have read and agree to the license agreement and privacy policy.  Select the appropriate option under “Do you have a Pearson Education account?” and supply the requested information. Upon completion, the Confirmation & Summary page confirms your registration. This information will also be emailed to you for your records. You can either click Log In Now or return to www.masteringaandp.com later.

Enroll in Your Instructor’s Course and/or Access the Self-Study Area Upon first login, you’ll be prompted to do one or more of the following:  Join your online course by entering your instructor’s MasteringAandP Course ID (above).  Enter a Student ID.   Congratulations! You have completed registration and have enrolled in your instructor’s MasteringAandP course. To access your course from now on, simply go to www.masteringaandp.com, enter your Login Name and Password, and click Log In. If your instructor has created assignments, you can access them in the Assignments Due Soon area or by clicking View All in this area. Otherwise, click on Study Area to access self-study material.

Support Access Customer Support at www.masteringaandp.com/support, where you will find:  System Requirements  Answers to Frequently Asked Questions  Additional contact information for Customer Support, including Live Chat

Frequently asked questions

Q: Do I have to buy the required textbook and Mastering A&P package. A: You must purchase the Mastering A&P login new from the bookstore or online in order to gain access to the website. The code is packaged with the textbook and also sold separately. The textbook is required to fully participate in the Mastering A&P assignments. In addition, much of the material covered in class is based on material in the textbook. You can purchase the textbook new or used. While most of the material in the 6th edition of the textbook is similar if not identical to the 7th edition, some of the organization has changed. We will be referencing ONLY the 7th edition in class.

Q: I’ve missed the midterm. What do I do now? A: It’s your responsibility to contact Dr Fry or Dr Anderson. Absence must be documented, by providing the appropriate notification (eg: medical note). Please note that we verify authenticity of your documentation. There will be one opportunity to write the deferred midterm: Nov 3, 6pm.

Q: I’ve missed a Mastering A & P quiz. What do I do now? A: There are 10 quizzes, we will take the best 8 marks. You do not need to document a missed Mastering A&P quiz , however there will be no makeups or adjusted marks.

Q: Why don’t you answer questions about course material by email? A: The most important reason we do not answer questions about course material by email is that if we can answer it in an email, then the student can look it up in the text or their notes. Complex explanations are better suited to one-on-one conversations.

Q: What’s covered on the exam? A: If we covered it class, if it was covered on a posted handout, if it was covered in a required reading, if it was in one of the Mastering A and P assignments or if it was in one of the Mastering A and P assignments quizzes, the material may be on the midterm or final exam. The final is cumulative.

Q: Do we need calculators for the exam? A: No. Do not bring a calculator to the exam (see below). Any calculations you have to do will be simple arithmetic.

Q: What can I bring to the exam? A: All you need is a pencil and eraser. Electronic devices are prohibited, and having such a device in your possession during the exam may result in academic penalties as described in the university calendar.

Please see University regulations covering what is permitted at your seat during a final exam.

COURSE OUTLINE (2014–2015 2nd Term)

BIOL 2420 HUMAN PHYSIOLOGY II

LECTURES: 3 per week, MWF 9:30 am, 200 Fletcher Argue Building

INSTRUCTORS: Dr. K. L. Campbell (Course coordinator) W465 Duff Roblin Bldg; Tel: 474-6397; Email: [email protected]

Dr. W.G. Anderson W475 Duff Roblin Bldg; Tel: 474-7496; Email: [email protected]

Dr. D. Weihrauch W467 Duff Roblin Bldg; Tel: 474-6310; Email: [email protected]

IMPORTANT NOTE: Email is only to be used for general enquiries or to book appointments. Questions regarding material covered in class will not be answered via email. Please turn off cell phones while in class; texting, browsing, and photography are strictly prohibited.

SUGGESTED TEXT: Silverthorn, D.U. 2013. "Human Physiology: An Integrated Approach with MasteringA&P®", 6th Ed., Benjamin Cummings.

COURSE CONTENT: The functions of the human body’s homeostatic effector organ systems (cardiovascular, respiratory, renal, digestive) and of the immune system are examined. Structure is described to the extent required to understand function.

The organization and content of the lectures are not based on any one textbook, but, wherever possible, lecturers use terminology and illustrations consistent with Silverthorn's. The text is intended to be used as a reference for detailed information (as in figures and tables) and as a general aid to understanding. The lecture outline below gives references to lecture-related material in Silverthorn. A pdf copy of notes accompanying the lectures will be available on D2L. Note: these ‘skeleton notes’ are solely intended to facilitate in-class note taking, and are not a substitute for attending class as examinations will be based on oral and written material presented during the lectures, together with the ten Mastering A&P tutorials. Specific passages in the text or material posted on D2L that are designated in class as required reading may also be evaluated on exams.

GRADING is solely based on the Mastering A&P quizzes and two multiple-choice examinations:

1. Mastering A&P quizzes (best 8 out of 10) 10% 2. Mid-term exam (February 23rd, 2015*; 6:00 pm) 1.5hrs, 36 questions 36% 3. Final exam (April 13-27th, 2015 on whole term) 2hrs, 54 questions 54%

*Seating: 100 Fletcher Argue (Addison to Jubenvill); 200 Fletcher Argue (Kaegi to Zhao); midterm exam covers the cardiovascular and respiratory systems ONLY (lectures 1 to 17). Venue for the final exam will be announced in class and on D2L.

To facilitate learning of key course concepts, we will be using the Mastering A&P® (Mastering anatomy and physiology) online tutorial and assessment system. Please see the last page of this document for assistance with registering for online assignments and quizzes. If you have troubles

1 with the A&P material, please make an appointment with your instructor. SYNOPSIS: The course BIOL 2420, together with BIOL 2410, is designed to provide students with a basic understanding of how the human body functions and regulates itself. Lectures cover anatomy and function of the cardiovascular, respiratory, renal, digestive, and immune systems.

CARDIOVASCULAR SYSTEM: (11 lectures – KLC), Chapters 14, 15 and 16

BASIC COMPONENTS AND CIRCUITRY OF THE CARDIOVASCULAR SYSTEM. Blood. Pathway of blood flow. Functional anatomy of the heart. Origin of the heart beat: pacemaker cells and electrical pathways in the heart. Cardiac muscle action potentials: review of properties, underlying ion transport events, and relevance to heart function. THE ELECTROCARDIOGRAM (ECG): electrical basis, description of wave form, and diagnostic value of the ECG. THE CARDIAC CYCLE: stages and accompanying volume/pressure changes. CARDIAC OUTPUT: control of heart rate and stroke volume; Frank-Starling Law of the Heart; afterload. ARTERIAL SYSTEM: vessel anatomy and concept of compliance; functions of arteries; determinants of systolic, diastolic, and pulse pressure; regulation of tissue blood flow. BASIC HEMODYNAMICS: concepts of flow, pressure, and resistance; autoregulation; non-metabolic chemical mediators. SYSTEMIC REGULATION: total peripheral resistance, neural and hormonal control of MAP. CAPILLARIES: organization and structure of vessels; transcapillary exchange mechanisms; the Starling forces and fluid balance. THE LYMPHATIC SYSTEM: vessel anatomy; edema. THE VENOUS SYSTEM: vessel anatomy; functions of veins; determinants of venous return. CONTROL OF MEAN ARTERIAL PRESSURE: short-term regulation; long-term regulation; hypertension.

RESPIRATORY SYSTEM: (6 lectures – KLC), Chapters 17 and 18

THE OXYGEN PATHWAY: an overview. Organization and functional anatomy of the lungs; conducting and respiratory zones. Lung volumes and capacities. MECHANICS OF BREATHING: pressure changes accompanying the respiratory cycle; role of breathing muscles in establishing pressure gradients. Factors governing airway resistance and lung compliance in health and in disease. LUNG VOLUMES: determinants of minute and alveolar ventilation. PROPERTIES OF GASES: partial pressures of gases in lungs and blood; gas exchange between lungs and blood; ventilation/perfusion matching. OXYGEN TRANSPORT IN BLOOD: structure and function of hemoglobin; characteristics of the oxygen-hemoglobin equilibrium curve; P50; effects of pH, temperature, anions and organophosphates on blood-O2 affinity; nitric oxide; fetal hemoglobin; carbon monoxide. CARBON DIOXIDE TRANSPORT IN BLOOD: modes of carriage. CONTROL OF BREATHING: peripheral and central chemoreflex pathways.

RENAL SYSTEM: (6 lectures – WGA), Chapters 19 and 20

BASIC ANATOMY OF THE URINARY SYSTEM. Functions of the kidney. THE NEPHRON: cortical and juxtamedullary nephrons. Basic processes of nephrons. GLOMERULAR FILTRATION: forces driving/resisting filtration. Regulation of filtration; intrinsic and extrinsic control. Structure and function of the juxtaglomerular apparatus. TUBULAR REABSORPTION: active reabsorption. Renin-angiotensin-aldosterone system. Roles of Na+ reabsorption. Glucose reabsorption and the concept of tubular maximum. Passive reabsorption; Cl-, water and urea. Control of vasopressin secretion. TUBULAR SECRETION: regulation of K+ and water balance. The countercurrent multiplier system; urea trapping; production of hypo- and hyperosmotic urine. ROLE OF KIDNEYS IN ACID-BASE BALANCE: renal mechanisms of bicarbonate reabsorption and

2 acid secretion; urinary buffers. DIGESTION AND NUTRIENT METABOLISM: (7 lectures – DW), Chapters 21 and 22

Metabolism, nutrients and vitamins. Function of the digestive system. Basic anatomy and histology of the alimentary tract. GENERAL PRINCIPLES OF GASTROINTESTINAL MOTILITY AND SECRETION; neural and hormonal regulation. DIGESTION: salivary glands; deglutition (swallowing); peristalsis. STOMACH ANATOMY: gastric motility; gastric secretions. Accessory organs (liver, gallbladder, pancreas) and their involvement in the digestion of food. Control of gastric functions. SMALL INTESTINE: secretions; digestive enzymes. Control of cellular secretions; hormones. Digestion and absorption in the small intestine; carbohydrates; proteins, lipids; vitamins, minerals and water. Small intestine motility; segmentation; migrating motility complex. ANATOMY AND FUNCTION OF THE LARGE INTESTINE. Control of large intestine motility. Defecation reflex. Hepatic portal system. MAJOR METABOLIC PATHWAYS OF ABSORPTIVE METABOLIC STATE; fate of absorbed carbohydrates, lipids and amino acids. POST-ABSORPTIVE STATE; gluconeogenesis; glucose sparing. Control of plasma glucose concentration; effects of insulin and glucagon. GASTROINTESTINAL PATHOPHYSIOLOGY; cholera, giardiasis, amoebiasis.

IMMUNE SYSTEM: (7 lectures – DW), Chapter 24

NONSPECIFIC IMMUNE MECHANISMS: barriers, complement system, phagocytosis, inflammation (local and systemic effects), natural killer cells. SPECIFIC IMMUNE RESPONSES: Roles and origins of lymphocytes. Antibody-mediated specific immunity – antibody release, antibody structure, genetic basis of antigen-specificity and variation. Immune memory and self tolerance. Role of helper T cells in humoral immunity; antibody-mediated mechanisms of immune defence; TH1 & TH2 cytokines. Cytotoxic T cell-mediated specific immunity: TC cell activation and actions, role of helper T cells. IMMUNE RESPONSES: Viral clearance; Immune evasion.

The J.C. Rauch Memorial Prize of $200 is awarded annually to the student(s) with the highest overall average grade in BIOL 2410 and BIOL 2420 combined, both taken in regular sessions of the same academic year.

3 ANSWERS TO FREQUENTLY ASKED QUESTIONS:

Q: Do I have to buy the required textbook and Mastering A&P package? A: You must purchase the Mastering A&P kit new from the bookstore in order to gain access to the website. It is packaged with the textbook and is also sold separately. The textbook is required to fully participate in the Mastering A&P assignments. In addition, much of the material covered in class is based on material in the textbook. You can purchase the textbook new or used. While much of the material in the 5th edition of the textbook is similar to the 6th edition, some of the organization has changed. We will be referencing the 6th edition in class.

Q: I’ve missed the midterm. What do I do now? A: It’s your responsibility to contact Dr. Campbell ASAP. Absence must be documented, by providing the appropriate notification (e.g. medical note) to qualify to write the make-up exam. Please note that we verify authenticity of your documentation. A failure to write the mid-term exam will result in a score of 0/36; there is no option of a “100% final”.

Q: I’ve missed a Mastering A&P quiz. What do I do now? A: There are 10 quizzes, though your mark on this section of the course only uses the 8 highest marks. You do not need to document a missed Mastering A&P quiz, however there will be no make-ups or adjusted marks in the case of a missed quiz.

Q: Why don’t you answer questions about course material by email? A: We are often unable to gauge what you do or do not know based on an email question, nor are we certain that you will understand our answer. Complex explanations are best suited to one-on-one conversations, and we are happy to answer any questions you may have in person.

Q: What’s covered on the exam? A: ALL MATERIAL covered in class (including referenced figures in the text book), provided in handouts, covered in the Mastering A&P assignments, and quizzes is examinable for both the midterm and final exam. Please note that the final exam is cumulative, while the mid-term exam only covers the cardiovascular and respiratory systems.

Q: Do we need calculators for the exam? A: No. Do not bring a calculator to the exam (see below).

Q: What can I bring to the exam? A: All you need is a pencil and eraser. ALL electronic devices (including cell phones) are strictly prohibited during the exam, and having such a device in your possession during the exam may result in academic penalties as described in the university calendar.

Note: We advise you not to bring extra materials such as backpacks to the exam room as there have been instances at the University where backpacks and personal laptop computers have been stolen from exam rooms.

4 MASTERING A&P QUIZ DATES

There will be ten Mastering A&P quizzes during the term on the following dates. You must log into the Mastering A&P system during the 24 hours that the quiz will be available in order to complete the quiz for marks. When calculating your score on the quiz we will use the best 8 of the 10. Each quiz – and your score – will be available for review the day after the quiz date.

Quiz 1 Cardiovascular System Wednesday, January 21st, 2015 Quiz 2 Cardiovascular System Wednesday, January 28th, 2015 Quiz 3 Cardiovascular System Wednesday, February 4th, 2015 Quiz 4 Respiratory System Wednesday, February 11th, 2015 Quiz 5 Renal System Wednesday, March 4th, 2015 Quiz 6 Renal System Wednesday, March 11th, 2015 Quiz 7 Digestive System Wednesday, March 18th, 2015 Quiz 8 Digestive System Wednesday, March 25th, 2015 Quiz 9 Immune System Wednesday, April 1st, 2015 Quiz 10 Immune System Wednesday, April 8th, 2015

LETTER GRADE SYSTEM Grades are assigned at the end of the year by converting your cumulative percentage mark into a letter grade. Typical departmental grade boundaries are as follows.

90-100 A+ 80-89 A 74-79 B+ 68-73 B 62-67 C+ 56-61 C 50-55 D 0-49 F

MISSING EXAMS If you are unable to attend the midterm exam due to a course or exam conflict, please contact the course coordinator prior to the exam. Absence from the midterm exam will result in a score of zero unless compelling grounds for absence are documented (e.g. Doctor’s note); in this case, a deferred exam will be arranged at a time suitable to student and examiner. If you miss the final exam, you must contact your faculty office. Failure to write the final exam will result in course mark of “F”.

ACADEMIC DISHONESTY: Penalties will be imposed for any evidence of “academic dishonesty”, including plagiarism, cheating and fraud following the University of Manitoba Student Discipline Bylaw: (http://umanitoba.ca/admin/governance/governing_documents/students/student_discipline.html).

Other important University Policies can be found at: http://crscalprod1.cc.umanitoba.ca/Catalog/ViewCatalog.aspx?pageid=viewcatalog&catalogid=240& chapterid=2130&loaduseredits=False

The Faculty of Science Statement on Academic Dishonesty (and other important policies) can be found at: http://umanitoba.ca/faculties/science/undergrad/resources/webdisciplinedocuments.html

Dear Student: In this course you will be using MasteringA&P® an online tutorial, homework and evaluation program that accompanies your textbook.

What You Need:  A valid email address  A student access code (Comes in the Student Access Kit that may have been packaged with your new textbook or is available separately in your school’s bookstore. Otherwise, you can purchase access online at www.masteringaandp.com.)  The ZIP code for your school: ___R3T 2N2______

 A Course ID: ______BIOL2420HUMANPHYSW15______

Enroll in Your Instructor’s Course and/or Access the Self-Study Area Upon first login, you’ll be prompted to do one or more of the following:  Join your online course by entering your instructor’s MasteringA&P Course ID (above).  Enter a Student ID. Your instructor may request that you enter a special Student ID for this course. If so, be sure to enter this information EXACTLY as instructed.

Congratulations! You have completed registration and have enrolled in your instructor’s MasteringA&P course. To access your course from now on, simply go to www.masteringaandp.com, enter your Login Name and Password, and click Log In. If your instructor has created assignments, you can access them in the Assignments Due Soon area or by clicking View All in this area. Otherwise, click on Study Area to access self-study material.

6 BIOL 2500 – GENETICS 1

Instructor: Dr. Dana Schroeder (520 Buller Bldg) [email protected] Lab (Tutorial) Instructor: Sean Asselin [email protected]

Required Readings: 1. Textbook: Genetic Analysis: An Integrated Approach 1st Ed (Sanders & Bowman, 2012) 2. 2015-2016 BIOL 2500 Lab Manual

BIOL 2500 Genetics 1 - Principles of heredity in plants and animals. The concepts of dominance and genetic interaction, sex and inheritance, linkage, chromosomal variations, quantitative and population genetics, and the genetic code will be covered. Since the ability to solve genetic problems is essential to success in this course, the lab component will consist exclusively of tutorials and quizzes.

Course grades will be based on tutorial quizzes and two examinations. Missed work will be assigned 0 marks, unless appropriate documentation (note from counsellor, physician, or clergy) is provided within 48 hours of the scheduled exam.

Laboratory (tutorial) component (20%) (Two quizzes, 10% each) Quiz 1 – October 6 (B01) October 8 (B02) Quiz 2 - November 17 (B01) November 19 (B02)

Mid-Term Exam (30%) Thursday October 22 (during class)

Final Exam (50%) Scheduled by student records during the December examination period

Course Outline

I. Introduction - mitosis, meiosis (Chapter 3) II. Mendelian Genetics – monohybrid crosses, dihybrid crosses, Chi-squared statistics, probability (Chapter 2) III. Chromosomal Basis of Inheritance, Sex Linkage, and Sex Determination (Chapter 3) IV. Extensions of Mendelian Genetic Analysis – modified dominance, lethal alleles, epistasis (Chapter 4) V. Gene Mapping in Eukaryotes (Chapter 5) VI. Chromosomal Mutations – alteration in chromosome number and structure (Chapter 13) VII. Population Genetics (Chapter 22) VIII. Quantitative Genetics (Chapter 21) IX. DNA & DNA Replication (Chapter 7) X. The Genetic Code (Chapter 8, 9) XI. DNA Cloning and Manipulation (Chapter 10, 16)

Faculty of Science Statement on Academic Dishonesty

Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another student, plagiarism, and examination impersonation.

Note: cell phones, pagers or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations.

Suggested penalties assessed by the Faculty of Science for acts of academic dishonesty are available on the Faculty of Science web-page: http://umanitoba.ca/faculties/science/

All Faculty members (and their teaching assistants) have been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department.

REGISTRATION RESTRICTIONS

PLEASE ENSURE THAT YOU THE STUDENT ARE ENTITLED TO BE REGISTERED IN THIS COURSE:

THIS MEANS THAT YOU THE STUDENT HAVE:

-the appropriate prerequisites, as noted by the calendar description, or have permission from the instructor to waive these prerequisites

-not previously taken, or are concurrently registered in this course and another that has been identified as “not to be held with”

The registration system may have allowed the student to register but it is up to the student to ensure that they have met all the requirements.

Consequences may be the student being withdrawn from the course part way through the term, or the course not used in the degree program. There will be no fee adjustment. This is not appealable.

CELL BIOLOGY BIOL 2520 - WINTER 2016 SYLLABUS

COURSE CONTENT: A survey of cell biology. Focus is on an integrative examination of the structure and function of subcellular compartments, organelles, and key molecules. The course attempts to explain how the cell functions and how it interacts with other cells and its environment.

INSTRUCTOR: Dr. Jake Stout Office: Buller Bldg, Room 505C Email: [email protected] Office Hours: 1:30-2:30 Wednesday and Thursday, or by appointment (arranged by email)

WEB Site: Lecture notes will usually be available from the internet (UMLearn) the evening before each lecture. Print and bring these notes to class to facilitate note-taking.

LECTURES: 9:30-10:20 Mon, Wed, Fri. Armes 200

TEXT: Cell and Molecular Biology – Concepts and Experiments 7th edition, by Gerald Karp. (6th edition is also acceptable). The syllabus indicates the suggested readings. These readings are intended to help you understand the material covered in class. If you do not understand the lecture material, please read the textbook for clarification. You are not expected to know the material in the textbook beyond what is covered in class, but knowing more than what is covered in lectures is always useful!

GRADING: Three options for grading are provided – whichever grade is highest will be used to determine your final grade.

Option 1: All tests are used to calculate your grade Midterm 1 (approximately first 10 to 12 lectures) 25% Midterm 2 (next 10 to 12 lectures) 25% Final exam 40% Assignment 10%

Option 2: If midterm 1 or midterm 2 is missed, then your grade is calculated as follows: Midterm 1 or 2 40% Final exam 50% Assignment 10% [Note, if you write both tests 1 and 2, you are not eligible for this option]

Option 3: If both midterm 1 and 2 are missed, then your grade is calculated as follows: Final exam 90% Assignment 10%

TESTS/EXAMS: a. There will be two non-cumulative midterm tests, which will be entirely multiple choice questions. The first two tests will be 50 minutes long and will be held in the classroom during the normal class schedule. The final exam, which will be held in a large exam hall, will be comprised of two parts – one part will cover material specific to the last third of the lectures, and the other part will be comprised of questions that cover content from the entire course. b. You must write the final exam to pass the course. c. There will be no make-up exams for tests 1 and 2. If you miss either test 1 or 2, you automatically qualify for grading options 2 or 3. If you miss tests 1 and 2, then you qualify only for grading option 3. d. No doctor’s note/explanation is required if you miss tests 1 or 2. You are adults and can choose your best option, and I don’t want to congest our doctors’ offices with people seeking sick notes. e. If you miss the final exam, you will require a doctor’s note or you must provide other documentation to the Faculty of Science office (i.e. don’t give it to me) in order to qualify to write the final exam.

ASSIGNMENT There is a small written assignment in this course based upon how to research, interpret, organize, and properly reference scientific literature. A secondary purpose of the assignment is to assess your writing skills to identify weakness that may be a problem in upper-year courses. Thus, the written component of the assignment will not be graded on the scientific content of the material presented, but rather on the quality, organization, and structure of the writing itself. Details on the assignment will be presented in lecture 12.

BIOLOGICAL SCIENCES GRADING STANDARDS:

90 + - A+ 80 - 89 - A 74 - 79 - B+ 68 - 73 - B 62 - 67 - C+ 56 - 61 - C 50 - 55 - D 0 - 49 - F

CLASS ATTENDANCE: It is important that you attend class. In the process of developing an understanding of cells, every lecture is a building block for the next; missing even one lecture will weaken your understanding for the rest of the semester.

LECTURE SCHEDULE WINTER 2016

Lecture Date Topic Chapter Recommended reading 7th ed. 6th ed. 0 Jan 6 Course Intro 1 Jan 8 Introduction to cells 1 1-13 1-12 2 Jan 10 Macromolecules 2 40-60 39-59 3 Jan 13 Cell cycle 14 573-581 561-569 4 Jan 15 Mitosis and cytokinesis 14 581-603 569-591 5 Jan 18 Nucleus structure 12 488-493 476-481 6 Jan 20 DNA packaging 12 493-501 481-489 7 Jan 22 Chromosome structure 12 501-512 489-499 8 Jan 25 Transcription 12 512-532 503-521 9 Jan 27 mRNA 11 435-455 428-448 10 Jan 29 tRNA and rRNA 11 135-455 428-448 11 Feb 1 Translation 11 468-477 461-468 Feb 3 Non-coding RNAs 11 455-461 448-455 12 Feb 5 Literature and assignment 13 Feb 8 Midterm I 14 Feb 10 Endomembrane system 8 270-288 264-283 15 Feb 12 ER proteins and lipids 8 290-300 284-294 Feb 15-19 Winter break 16 Feb 22 Golgi and vesicular traffic 8 300-303 294-297 17 Feb 24 Lysosomes and endosomes 8 303-315 297-309 18 Feb 26 Plasma membrane 4 121-140 118-136 19 Feb 29 Membrane transport I 4 147-156 143-151 20 Mar 2 Membrane transport II 4 156-163 151-158 21 Mar 4 Cell signaling I 15 618-625 606-612 Mar 7 Cell signaling II 15 634-636 622-622 22 Mar 9 Cell signalling III 15 636-655 623-640 23 Mar 11 Midterm II 24 Mar 14 Cell energetics I 5 198-206 191-201 25 Mar 16 Cell energetics II 6 211-232 206-227 26 Mar 18 Cytoskeleton I 9 324-353 318-346 27 Mar 21 Cytoskeleton II 9 354-364 347-358 28 Mar 23 Cytoskeleton III 9 356-364 347-358 29 Mar 25 Cell interactions I 7 235-269 230-263 30 Mar 28 Cell interactions II 7 235-269 230-263 31 Mar 30 Good Friday 32 Apr 1 Cancer I 15 656-660 642-646 33 Apr 4 Cancer II 15 656-660 642-646 34 Apr 6 Cancer III 15 656-660 642-646 35 Apr 8 Review

Faculty of Science Statement on Academic Dishonesty

Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another student, plagiarism, and examination impersonation.

Note: cell phones, pagers or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations.

Suggested penalties assessed by the Faculty of Science for acts of academic dishonesty are available on the Faculty of Science web-page: http://umanitoba.ca/faculties/science/

All Faculty members (and their teaching assistants) have been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department.

Jake’s statement on academic dishonesty

Although you’re sitting in a giant lecture hall feeling like a single student amongst thousands, when you get further along in any career you’ll generally get hired based upon your REPUTATION. Cheating is a real jerk move, and shows that your character may not be the best. Also, you may need at some point a professor to write you a letter of reference… academic dishonesty doth not lead to glowing reviews. So don’t do it, m’kay?

REGISTRATION RESTRICTIONS

PLEASE ENSURE THAT YOU THE STUDENT ARE ENTITLED TO BE REGISTERED IN THIS COURSE:

THIS MEANS THAT YOU THE STUDENT HAVE:

-the appropriate prerequisites, as noted by the calendar description, or have permission from the instructor to waive these prerequisites

-not previously taken, or are concurrently registered in this course and another that has been identified as “not to be held with”

The registration system may have allowed the student to register but it is up to the student to ensure that they have met all the requirements.

Consequences may be the student being withdrawn from the course part way through the term, or the course not used in the degree program. There will be no fee adjustment. This is not appealable.

1 BIOL 3100 Skills in the Biological Sciences Syllabus 2015

Tuesdays & Thursdays 10:00 - 11:15am – 401 Biological Sciences Building. Fridays 2:30-5:15 pm – 401 Biological Sciences Building.

Instructor: Dr. Jane Waterman Office: 424 Biological Sciences Bldg Phone: 204-272-1678 Email: [email protected] Office hours: By appointment

Course Rationale and Objectives: This course is a pre-requisite for students in the Honours program in the Biological Sciences and recommended for students in the 4-year Major program in Biological Sciences who are contemplating post-graduate work. The course is designed to introduce students to the concepts and skills necessary to succeed in a biology-based career, including:

1. Communication skills, including scientific writing and oral presentation skills, and critical thinking. 2. Knowledge of different types of biological research, which will help students realize their research interests and find potential advisors for their Honours project; and 3. Exposure to a variety of Biology-based career paths.

The content and format of this course differs from other courses offered by the Department of Biological Sciences in that guests who specialize in the topic under consideration present the majority of lectures. Students contribute to the course through regular attendance at lectures and seminars and through participation in discussions. Perhaps more so than in other courses, student participation contributes significantly to everyone’s learning experience, and is critical to the success of the course.

Using the techniques introduced in class, students will undertake readings and assignments in both oral and written communication. These assignments will pertain to a biological topic of the student’s choice, in consultation with a Biological Sciences faculty advisor will provide hands-on experience with technical aspects of obtaining, processing, and presenting scientific material to audiences ranging from the general public to professional scientists.

Upon completion of this course, the student should be able to: 1. In consultation with a faculty advisor, formulate a research topic 2. Search the literature, both written and electronic, to find information on a given research topic and write a focused interpretive literature review. 3. Deliver a 15-minute oral presentation (Powerpoint) on a research proposal developed from your literature review topic. 4. Present your research proposal in poster format.

Required Text: Writing Papers in the Biological Sciences (5th edition) 2012. Victoria E. McMillan. Bedford/St. Martins Boston New York.

2 Department of Biological Sciences Faculty by Research Area:

umanitoba.ca/faculties/science/departments/bio_sciences/people/researchers.html

Class information: You will be submitting your course assignments using email. Because of the time-sensitive nature of the work, I will only accept late assignments for two days after they are due (10% deducted per day late). After 2 days I will not accept the assignments. My policy for missed assignments: You must inform me, IN WRITING, ASAP if you will be or have missed a class where an assignment is due or where participation is required. If you have a valid reason to miss class, then you will be allowed to make up the work. However if you wait to let me know you will not be allowed to make up assignments unless you have a doctor’s note. ALL papers must be typed, unless it is an in-class assignment.

Course Evaluation: Component Mark Literature Review Draft 20 Literature Review Final 25 Oral Presentation of Research Proposal 20 Research Proposal Poster 25 Class Participation 10  Peer-review of oral presentations – 3%  Peer-review of poster presentations – 3%  Review of seminars, in-class assignments – 4% 100

Grades (A-F) will be assigned as 90+ A+ 80-89 A 76-79 B+ 70-75 B 66-69 C+ 60-65 C 50-59 D 0-49 F

Assignment Deadlines: Due Date Assignment Sept 29 Topic & Faculty advisor due Oct 8 Literature Review outline Oct 23 Literature Review Draft Nov 12 Literature Review Final Nov 17-26th Oral presentations Dec 3 Research Proposal Poster due to advisor Dec 4 Poster Presentation 201BSB 3 The University of Manitoba’s Faculty of Science Statement on Academic Dishonesty The Faculty of Science and the University of Manitoba regard acts of academic dishonesty in quizzes, tests, examinations, laboratory reports or assignments as serious offences and may assess a variety of penalties depending on the nature of the offence. Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another student, plagiarism, and examination impersonation. Note: cell phones, pagers, or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations. Penalties that may apply, as provided for under the University of Manitoba’s Student Discipline By- Law, range from a grade of zero for the assignment or examination, failure in the course, to expulsion from the University. The Student Discipline By-Law may be accessed at: http://umanitoba.ca/admin.governance/policies/section_1200/1202.shtml Suggested penalties assessed by the Faculty of Science for acts of Academic Dishonesty are available on the Faculty of Science web page: http://umanitoba.ca/faculties/science/student/webdisiplinedocuments.html

Good references or websites:

Writing advice WEB sites: www.writing.utoronto.ca www.writingcenter.uconn.edu/s_biology.php

How do distinguish scholarly from non-scholarly articles: http://www.lib.ncsu.edu/guides/spmaterials

Writing a rationale & literature review: http://users.aber.ac.uk/dgc/Modules/dissertation.html#B

Cahill Jr J.F., Lyons D., Karst J. 2011. Finding the “Pitch” in Ecological Writing. Bull. Ecol. Soc. Amer. 92: 196-205. http://www.esajournals.org/doi/abs/10.1890/0012-9623-92.2.196

Scientific writing: The Structure, Format, Content, and Style of a Journal-Style Scientific Paper- http://abacus.bates.edu/~ganderso/biology/resources/writing/HTWsections.html

Sterling E., DeJong MR. Scientific writing. http://www.afrc.uamont.edu/whited/Sterling%20and%20DeJong%202009.pdf

Magnusson W.E. 1996. How to write backwards. Bull. Ecol. Soc. Amer. 77: 88.

Marek P. The basics of scientific writing in APA style. http://www.macmillanhighered.com/Catalog/uploadedFiles/Content/Worth/Custom_Solutions/Psycholo gy_ForeWords/Marek_Ch04_APAstyle_Color.pdf

Carraway LN. 2006. Improve scientific writing and avoid perishing. Am. Midl. Nat. 155: 383-394. Has a nice list of superfluous or misused words in scientific writing. Biol3100: Skills in Biological Sciences Tues/Thurs 10‐11:15 Friday 2:30‐5:15

Schedule McMillan Date Topic Readings 10‐Sep‐15 Introduction to BIOL 3100: Overview & writing a lit review 104‐123 11‐Sep‐15 Rationale, hypotheses & predictions; My research talk 210‐217 15‐Sep‐15 Faculty research presentations ‐ Plants 17‐Sep‐15 Facult research presentations 18‐Sep‐15 Facult research presentations 22‐Sep‐15 Facult research presentations 24‐Sep‐15 Facult research presentations 25‐Sep‐15 Literature searches via library resources 5‐21 29‐Sep‐15 Reading scientific papers General research area/topic & choice of Faculty advisor due 21‐26 1‐Oct‐15 Writing a Review Paper; documenting the paper (citations) 124‐142 2‐Oct‐15 Literature searches 6‐Oct‐15 Drafting and Revising; (Re)writing in Science: 144‐171 8‐Oct‐15 (Re)writing in Science: Lit review outline due 9‐Oct‐15 References, Reference Software and tricks in WORD 13‐Oct‐15 Preparing the draft 172‐181 15‐Oct‐15 Oral/powerpoint presentations; 191‐201 16‐Oct‐15 Planning a biological investigation 20‐Oct‐15 Awards, Scholarships, NSERC FOS VP URA: 22‐Oct‐15 Developing proposal ideas 23‐Oct‐15 Seminar attendance? Lit review draft due 27‐Oct‐15 Resume: Career Services 29‐Oct‐15 Job interviews: Career Services 30‐Oct‐15 Poster presentations: McMillan 201‐209; Dr. G, Goldsborough 3‐Nov‐15 Work on Literature Review; Talk to advisors about proposals; no class 5‐Nov‐15 Oral Presentation Rubric Development; 6‐Nov‐15 Seminar attendance ‐ Crackerjack? 10‐Nov‐15 Preparation for Student Presentations/Posters 12‐Nov‐15 Preparation for Student Presentations/Posters; Final Lit Review due 13‐Nov‐15 Preparation for Student Presentations/Posters 17‐Nov‐15 Student presentations 18‐Nov‐15 Last date for voluntary withdrawal from Fall Term 2015 courses without academic penalty 19‐Nov‐15 Student presentations 20‐Nov‐15 Student presentations 24‐Nov‐15 Student presentations 26‐Nov‐15 Student presentations 27‐Nov‐15 Work on posters 1‐Dec‐15 Posters to CADlab printer 3‐Dec‐15 Proposal Posters PDF Due to Advisors 4‐Dec‐15 Poster Presentations for Biological Sciences Faculty & Students. 201 BSB 1 BIOL 3242 VASCULAR FLORA OF MANITOBA

Welcome to the Vascular Flora of Manitoba Course!

During the term you will become familiar with many of the plant families found in the province and learn how to identify plants to species using various technical keys and manuals. As part of your course work you will need to make a plant collection. This project is worth 20% of your final grade. In order to provide yourself with a variety of wild plants, it is best to start your collection in the summer. If you are unable to make a collection during the summer there should be enough time for you to do this in early September.

Your plant collection must consist of twenty (20) specimens identified to species. It should include at least 10 different families and should include at least one sedge (Cyperaceae), one grass (Gramineae or Poaceae), and one composite (Compositae or Asteraceae). The plant collection should be handed in with each specimen in a folded sheet of newspaper with a herbarium data label (unattached) with each specimen. Details on how to make a plant collection are summarized below.

The collection will be marked using the following criteria: accuracy of identification, information content of the labels, taxonomic diversity, quality of specimens.

Equipment

1. Commercial plant press frame or two pieces of 18" X 12" X 3/8" plywood.

2. 20 cardboard corrugates (ventilators) 12" X 18". These may be obtained from the Department of Biological Sciences General Office.

3. Folded sheets of newspapers.

4. Two webbed press straps, ca. 6' long and 1-1/4" wide, fitted with cinch buckles. These may be obtained from most hardware or outdoor stores.

5. Field book for notes.

6. Plastic bags.

7. Pruning shears or sharp knife.

8. Digging tool - trowel, weeding tool, stout knife, etc.

2 Collecting Specimens

Only plants that are growing naturally (not planted or cultivated) may be collected. By law, no collecting is allowed in provincial or national parks. In addition, collecting on private property should be avoided unless you have permission from the landowner.

A specimen should be complete and consist of flower and/or fruit, stem, leaves, and roots. Woody plants are obviously too large to collect as a whole plant. Specimens should consist of a twig with at least some parts that are more than one year old.

When in the field, place specimens in a plastic bag with some damp moss or paper towel. Do not leave plants in the sun. If you visit many localities during the course of a day, make sure that you know where each specimen came from. It is often easiest to use a series of plastic bags with each bag holding specimens from a single location. By writing the name of each location on a piece of scrap paper, which you place inside each bag, you will be able to sort your specimens more easily at the end of the day. For each site you visit, make sure that you write notes about your geographic location and the habitat from where your plants were collected.

Location information should include a detailed description that would allow someone to find your location on a road map (e.g., Hwy. 240, 3.6 km north of its jct. with Hwy. 2) as well as your latitude and longitude if you have a GPS unit. If you do not have a GPS unit, latitude and longitude can be determined after the fact using Google Maps. It is critical that you read the separate handout entitled “Georeferencing Your Plant Collections” before you start collecting plants for this assignment.

Habitat data should include information on associated vegetation. This is usually a short description such as “Mature Acer negundo/Fraxinus pennsylvanica forest” or if you are unsure of what the associated species might be you could describe this same habitat as a “Mature deciduous forest”. Information on soil substrate/moisture should also be recorded (e.g., moist, organic soil).

Collection Data and Organizing Your Plant Specimens

Once you have returned home from your day of collecting, it is time to properly record and organize location and habitat data and press each of your specimens in a plant press. The easiest way to start this process is to organize your bags chronologically based on the sites that you visited during the day. For each site record the following information in a notebook:

• Date.

• Geographic location (from the notes you recorded in the field).

• Habitat data (from the notes you recorded in the field).

After this information is recorded you will need to assign a collection number to each specimen that you will be pressing. Reach into your first bag and randomly pull out a specimen and write its collection number in your book. Number your collections chronologically starting at 1. This same number will appear on the newspaper in which you press your specimen (see figures following page). Beside each collection number you can place a tentative name if you like, along with information about the specimen that will not be available when it is dry - e.g., flower color and patterning, size of plant (if you cannot collect the whole plant), habit-branching pattern, bark characteristics of trees, etc.

Repeat this process for each location you visit making sure that you start your collection numbering with the next available number (do not go back to 1 again). Collection numbers must be unique. If they are not, your collection data and specimens will become hopelessly confused. An example of a collection book entry can be found on the next page.

A typical collection book entry might look like this:

June 26, 2014

Manitoba, Roadside rest area on N side of Hwy. 2, 3 km E of the junctions of Hwy. 2 and 242 (south) in Treherne, 49.6408333˚, -98.6441667˚, Map datum WGS 84.

Shaded edge of Quercus macrocarpa dominated forest, dry sandy soil.

1. Grass-like plant – has bright red bases 2. Yellow flower ?? 3. ?? 4. Lilium philadelphicum

June 27, 2014

Manitoba, Souris Wildlife Management Area, E side of Hwy. 346 on N side of the Souris River, 49.4630556˚, -99.8727778˚, Map datum WGS 84.

Steep slope above river with scattered Quercus macrocarpa and graminoid understory, dry soil over shale bedrock.

5. Astragalus ?? – purple flowers 6. Elaeagnus commutata

Pressing Plant Specimens

Before pressing, write the plant’s collection number on the upper corner of a folded piece of newspaper. This will ensure that you can cross-reference your collection information with your specimen (see figure below). A single specimen should be placed in a single fold of newspaper. Plants too large to fit in the folded newspaper may be bent in a "V", "N", or "M" figure. When putting a specimen in the press it is important to arrange it properly so that the upper and lower surfaces of the leaves are flat (not folded or crumpled) and that reproductive structures are visible. Specimens with thick stems or twigs are greatly improved if crumpled newspaper is placed over the specimen so that the thinner portions (leaves and flowers) are held flat. Otherwise, the thick portions will hold the cardboard up in those areas and the leaves and flowers near them will become distorted and wrinkled on drying.

To load the press, place one of the press frames over the two straps. The straps should be well separated and the buckles should be at the edge of the frame. Place one sheet of corrugated cardboard on the frame, then one specimen (in its newspaper), a corrugate, a specimen, etc. Finish with a corrugate and the second press frame. Bring the free ends of the straps over the press and through the buckles. Pull on the straps to tighten. It often helps to stand on the press to give added weight while you are tightening the straps. 4 It is critical that you dry your plants as quickly as possible. The quicker the drying time the greater the chances that your plant will retain its natural color and will not rot. Place your press in a well-ventilated location with the corrugated cardboards facing in the direction of airflow. The use of a space heater or an electric fan will greatly speed drying time. It will take your specimens at least two days to dry. It is important to periodically check the straps on your press to make sure that they remain tightened throughout the drying process. Do not place your press in the basement or in any area where it will not receive adequate heat or ventilation.

To determine if your specimens are dry, touch each plant with the bases of your fingers. If your specimens feel cool or damp to the touch return them to the press for further drying. Once dry, the specimens in their papers may be removed from the press and stored in a dry place (not a damp basement or garage).

Identification

During the time that you are collecting do not be too concerned about identification, except trying to ensure that you are collecting different species that are likely to be from different families. Preliminary identification can be achieved using popular guides such as Newcomb's Wildflower Guide, but you will need to confirm your identification in the lab using the keys in the course lab manual as well as the reference works listed below. I will be discussing the steps required to identify your plants in more detail during lecture. Copies of the reference works will be available in the lab; some are also available in the library.

Labels

Properly identified specimens that you are handing in for this assignment must be accompanied by a label. Labels for each specimen must provide the following information:

• Technical name, including the author. • Geographic location. Start with a general area e.g., Manitoba, Canada; then a detailed description so that the position can be approximately pinpointed on a road map (e.g., Hwy. 59, 3 km south of Victoria Beach); finally a longitude and latitude for the location (e.g., 49.0158333, -95.2625). For more information on determining your geographic location, see the handout entitled “Georeferencing Your Plant Collections”. • Habitat data. • Date you collected your specimen. • Collector(s) (this includes your name plus the names of people who were with you at the time of collection). • Collection number.

A typical label might look like this:

PLANTS OF MANITOBA, CANADA

Carex projecta Mack.

S side of Buffalo Point Road, 10.6 km E of its jct. with Hwy 12, 49.0158333˚, -95.2625˚ [Datum WGS84, determined using Google Maps].

Deciduous woods with herbaceous understory dominated by grass and sedge species, wet, organic soil.

B. A. Ford 156 and E. C. Punter

July 19, 2014

5 Helpful Publications

BARKLEY, T. M. ed. 1991. Flora of the Great Plains. University of Kansas Press, Lawrence, Kansas.

GLEASON, H. A. and A. CRONQUIST. 1991. Manual of vascular plants of Northeastern United States and Adjacent Canada. The New York Botanical Garden, Bronx, New York.

JOHNSON, D., L. KERSHAW, A. MACKINNON and J. POJAR. 1995. Plants of the Western Boreal Forest and Aspen Parkland. Lone Pine Publishing, Edmonton, Alberta.

NEWCOMB, L. 1977. Newcomb's wildflower guide. Little, Brown and Company (Canada) Limited, Toronto.

PETERSON, R. T. and M. MCKENNY. 1968. A field guide to wildflowers of Northeastern and North- central North America. Houghton Mifflin Company, Boston.

VANCE, F. R., J. R. JOWSEY and J. S. MCLEAN. 1991. Wildflowers across the Prairies. Western Producer Prairie Books, Saskatoon, Saskatchewan.

SCOGGAN, H. J. 1957. Flora of Manitoba. National Museum of Canada, Bulletin 140 (pdf version available on memory stick in lab).

SOPER, J. H. and M. L. HEIMBURGER. 1982. Shrubs of Ontario. Royal Ontario Museum, Life Sciences Miscellaneous Publication (pdf version available on memory stick in lab).

On-Line Resources

FLORA OF NORTH AMERICA (http://floranorthamerica.org) - An ongoing project documenting all species of plants north of the Mexican border. Great keys, maps and illustrations.

FLORA OF MICHIGAN (http://www.michiganflora.net) - One of the best state floras ever produced is now available on-line. The keys work very well for the vascular flora of southeastern Manitoba.

Other Important Points

• Plants must be collected by you - no swapping of specimens. • Label preparation and identifications must be done independently. • Plants collected in conjunction with another course are not permitted. • Your collection must be of plants that were not planted or cultivated. Be aware that all conifers in the city of Winnipeg have been planted. • Once you have completed your collection, bring your specimens into the University. I will quickly go through your plants to make sure that your specimens can be identified (i.e., have the requisite features such as flowers, fruits, etc. that might be necessary for identification) and that you have the required family diversity to complete the assignment. • Collect more specimens than you need to complete the assignment. You may find that some of your specimens lack the necessary structures for identification or that a number of your specimens are from a single family (e.g., Asteraceae).

Questions?

If you have any questions regarding your plant collection feel free to contact Dr. Bruce Ford, Room 433 Buller. Telephone: 474-6994. Email: [email protected]. 1 BIOL 3242 VASCULAR FLORA OF MANITOBA

GEOREFERENCING YOUR PLANT COLLECTIONS

Perhaps the most important piece of data on your collection label is your locality information. Someone can always re-identify your specimen if you make a mistake, but no one can know exactly where you collected your sample.

When you are in the field collecting plants, it is important that you keep notes on where you obtained your specimens. Be aware of street names, highway numbers, trail names, distances from major highway/street intersections, distances walked along trails from trailheads, etc. All locality citations on a label start with the province and country (Manitoba, Canada), followed by a detailed description that would allow someone to find your location on a road map (e.g., Hwy. 240, 3.6 km north of its jct. with Hwy. 2). Finally, you will need to provide a latitude and longitude coordinate for your location. This detailed information can be determined using any of the following:

Using a GPS Unit

GPS units are devices that receive locational data from a network of 24 satellites that were placed into orbit by the U.S. Department of Defense. While GPS units provide the quickest and most precise way of recording your location, inaccuracies can occur if you do not pay attention two important features – datum and coordinate grid systems.

The datum is a mathematical model describing the earth’s surface that takes into account the distortion that is created when depicting a spherical world on a flat map. Hundreds of datums have been developed. However, in GPS units the most commonly used setting is WGS84 (World Geodetic System of 1984). Other commonly used datums are NAD27 (1927 North American Datum) and NAD83 (1983 North American Datum). The latter is almost identical to WGS84. GPS coordinates should always be accompanied by the datum. In this way the datums from coordinates and maps can be easily matched. Coordinates can also be converted if necessary to match the projection of a specific map using the online tools described below (whatcom.wsu.edu/4-h/mapping/GPSGlossaryMJC.doc).

In a GPS unit, you can use a number of different coordinate grid systems to identify your location (= latitude and longitude). The settings most often used are: ddd°mm’ss.s” (degrees, minutes, seconds), ddd°mm.mmm’ (degrees, decimal minutes), and ddd.ddddd° (decimal degrees). By convention, latitude always precedes longitude in any grid system (e.g., 49.81334249˚, -97.12841034˚). Note that the map datum for recently produced topographic maps is NAD83. Older maps use NAD27 (most Manitoban maps use NAD27). When set to the correct datum, a GPS receiver allows you to easily and accurately pinpoint your location on these maps (whatcom.wsu.edu/4-h/mapping/GPSGlossaryMJC. doc). Note that coordinates can be converted between NAD83 and NAD27 using the online tools described below.

2 For the purposes of this course I would like you to record your location as decimal degrees. When determining your coordinates, remember that your collections are from the Northern and Western Hemispheres. North latitudinal values are always positive, while west longitudinal numbers are negative (e.g., 49.81334249˚, -97.12841034˚). The failure to pay attention to this detail has a dramatic consequence on the accuracy of your labels. For example, 49.81334249˚, -97.12841034˚ is a location on the University of Manitoba campus. This same set of coordinates, all in a positive form (49.81334249˚, 97.12841034˚), is from the border between Mongolia and Russia! Note that Northern and Western Hemispheres are sometimes designated using “N” and “W” (e.g., 49.81334249˚N, 97.12841034˚W). However, please denote hemispheres using positive and negative values, as described above, for locations given on your labels.

Using Google Maps

If you do not have a GPS unit, you can use your detailed field notes to find your position using Google Maps. Always indicate on your label that you have used Google Maps to determine your location and that the datum setting is WGS84.

To determine your location using Google Maps do the following:

1. Go to www.google.ca/maps. Note that the functions listed below are not available using the Lite mode of Google Maps (Lite mode is indicated by a lightning bolt in the bottom right hand corner).

2. In the search box type in a phrase describing your location (e.g., Winnipeg, Manitoba; University of Manitoba; etc.). If you are not sure what to type, use the zoom function to find your location. By clicking on the box in the bottom left hand corner of the screen, “Earth” vs. “Map” views of your location are available. The “Earth” view is particularly useful if you are trying to determine your location in relation to specific buildings or forested vs. open habitats.

3. Click the location where you collected your plant. A gray coloured “Show My Location” icon will appear on the map. The name of your location, and its coordinates in decimal degrees, will appear in the upper left hand corner of the screen. If you right click on the location icon (for Macs use the control button), a number of other options are available. “Measure distance” is a particularly useful tool if you are trying to describe a location that is a certain distance from a known point such as an intersection (e.g., Hwy. 240, 3.6 km north of its junction with Hwy. 2). After selecting the distance measurement tool, simply click a known reference point, such as a highway intersection. A line connecting your collection location and your reference point, along with the distance between these two points, will appear on the map. You can grab the ends of this line to make further adjustments to your measurement.

3 Using iTouchMap iTouchMap is a handy website for accessing Google Maps and to easily obtain coordinates. Always indicate on your label that you have used iTouchMap to determine your location and that the datum setting is WGS84. To determine your location do the following:

1. Go to the iTouchMap website (http://itouchmap.com/latlong.html).

2. Click on the map and move the red marker to the correct point or enter the location (e.g., Winnipeg, Manitoba; University of Manitoba; etc.) in the “Address Field. Use the zoom button on the map and/or move the red marker to improve your mapping accuracy. Your location will be displayed in decimal degrees and degrees minutes seconds in the boxes entitled “Get the Latitude and Longitude of a Point”.

Converting Coordinates Using The FCC Website

The Federal Communications Commission (FCC) website is useful for converting a set of coordinates between degrees minutes seconds, and decimal degrees. To convert a set of coordinates do the following:

1. Go to the FCC website (http://transition.fcc.gov/mb/audio/bickel/DDDMMSS-decimal.html).

2. Enter your latitude and longitude numbers into the boxes, and click “Convert to Decimal” or “Convert to Degrees Minutes Seconds”, depending on which conversion is required. The conversion appears in the yellow fields.

Converting Map Datums Using the NADCON Computations Website

Another useful georeferencing tool for converting between NAD27 to NAD83, or vs. versa, can be found on the NADCON (North American Datum Conversion) website.

1. Go to the website (www.ngs.noaa.gov/cgi-bin/nadcon.prl).

2. Under “Compute datum shift for a specific location”, select the direction of conversion (i.e., NAD27 to NAD83 or vs. versa).

3. Enter in your latitude and longitude values. Note that latitude and longitude must both be positive but will be interpreted as north latitude and west longitude.

4. Click “Compute Datum Shift for a Single Location”. A converted set of coordinates will appear in a new window.

INTRODUCTORY PARASITOLOGY BIOL 3270 Winter 2016

Course learning objectives: At the conclusion of this lecture and laboratory, you should be able to 1) explain the basic biology of parasites within most of the major animal groups, 2) identify a select set of parasites using distinguishing morphological features 3) describe the associations between parasites and hosts and their outcomes such as host pathology, 4) summarize and assess the efficacy of the current treatments/solutions to animal parasitism. Most examples will focus on parasites that affect humans. Throughout the lectures basic concepts of parasitology will be emphasized, including ecological, physiological, immunological and biochemical perspectives.

Instructor: Dr. Jillian Detwiler, Rm. 208B Buller E-Mail: [email protected] – I will make every attempt to respond within 24 hours of receiving your email Monday – Friday. Phone: 474-8689 Office Hours: By appointment. I find this method works best because everyone has different schedules. Feel free to drop by my office any time from 9 - 4:30 pm without prior notice, although emailing/calling to set a time may work best in case I am already committed to another activity/student at that time.

Teaching Assistant for lab: Chenhua Li, E-Mail: [email protected]

Required Text and Equipment: 1) Roberts, L. S. and John Janovy, Jr. Foundations of Parasitology, 9th Ed. I will not always provide you all the information in the lecture needed for exams (see 9 attributes of parasites below). Use your book to fill in the gaps. If you don’t want to purchase the newest edition of the book, older editions will have most of the required information so you can borrow from someone who took the course before you, or buy a used edition. 2) Readings presented in lecture (posted on D2L). While the book provides an excellent overview of what we know about parasites, I will supplement this with papers that present individual studies. This will introduce you to Parasitology research and give you a better idea of how to write your manuscript (outlined in laboratory activities). These readings will be sources of exam and quiz questions. 3) Dissecting Kit. Includes forceps, scissors, needle probe, and a fine, natural bristle paint brush. As fine a pair of forceps as possible is best. 4) Laboratory coat. This is recommended as some laboratories will expose you to animal tissues, blood, and chemicals. If you do not have one, there are some available in the lab that you can check out for the semester and leave in lab for the duration of the course.

Lecture MWF 10:30-11:20 am, BSB 301. Powerpoints and additional readings will be posted on D2L following the lecture. They will look exactly as you see them in class. Lecture attendance is not mandatory, but I do keep track of your attendance. I encourage you to take advantage of the small class size and ask questions that help clarify the material, but also about your interests pertaining to the material. In addition, I encourage you to share your own thoughts or experiences that relate to the course. Active participation will help you engage with the material much better than taking the passive approach of sitting back and simply listening to my

1 lectures. I encourage everyone in the course to summon your courage and respond to my questions. Everyone will be required to come to the front board for group activities.

In addition to the material presented in lecture, for selected species you will be responsible for describing 9 attributes (Morphology, Taxonomy, Life Cycle, Geographic Distributions, Symptoms, Pathology, Diagnosis, Epidemiology, Drug of Choice). Dr. Detwiler will define these attributes in Lecture 2 and make clear what the selected species are.

Tentative Lecture Topics 1) Introduction to Parasitology and its Significance in World Affairs 2) Principles & Definitions in Parasitology 9 topics to know for selected parasites 3) Amoebas: Structure by ontogenetic stage; life history 4) Amebiasis: Course of infection, gross and histopathology, treatment and prognosis 5) Epidemiology of intestinal protozoans 6) Differential diagnosis of amoebe of people; serodiagnosis and fluorescent antibody techniques 7) Flagellate structure and ontogeny 8) Intestinal flagellates of people 9) Hemoflagellates of people 10) Kala-azar: course of infection, gross and histopathology, treatment and prognosis 11) Cutaneous and mucocutaneous leishmaniasis: clinical manifestations and treatment 12) Trypanosomiasis and human affairs 13) African trypanosomiasis: course of infection, pathology, and treatment 14) Antigenic variation and immunization strategies; current research on trypanosome control 15) American trypanosomiasis: Chagas’ disease 16) Plasmodium life history and course of infection 17) Malaria: pathology, symptoms, treatment, and prognosis 18) Malaria and human affairs including role in evolution of humans 19) Current research on malaria control: monoclonal antibody production and recombinant DNA 20) Coccidiosis: economic impact in animals and role as human pathogens 21) Toxoplasmosis: epidemiology and course of infection 22) Epidemiological models: mathematical models and malaria, ecological models and control 23) Paragonimiasis 24) Liver flukes: life history, epidemiology, and pathology 25) Schistosomiasis: course of infection, gross and histopathology, treatment and prognosis 26) Schistosomiasis and human affairs 27) Pseudophyllidea of humans: Dibothriocephalus and sparganosis 28) Cyclophyllidea of man: taeniasis and echinococciasis 29) Larval tapeworms and human disease 30) Enterobiasis: clinical manifestations, treatment and prognosis, parasitism and human institutions 31) Trichinosis: course of infection, treatment, and biopsies in diagnosis 32) Humans and epidemiology of Trichinella spiralis; moral implications of control 33) Trichuriasis and Ascariasis: the diseases 36) Hookworm disease 37) Filariasis and oncocerciasis: course of infection, gross pathology, treatment and control

2 Laboratories: R 2:30-5:25 pm, Duff Roblin W240 Through first-hand experience, the lab introduces students to the tools used to study parasites. You will examine host-parasite interactions by completing necropsies, preserving and identifying parasites, completing a tapeworm life cycle using beetle and rats, and exploring the diversity of parasites with specimens in demonstrations and your assigned slide box.

You should take organized notes during the laboratory especially for the demonstration and slide box material because they relate to lecture and lab exams. I also encourage you to draw the parasites you see, or take some pictures so that you can study outside of class.

Each student will write a manuscript based on the data we collect from the beetle and rat infections with Hymenolepis diminuta. The format will follow the most recent instructions to authors from the Journal of Parasitology.

Note: When making permanent slides of parasites, students will be required to come in outside of the normal lab time (see Laboratory 6) because the exercise requires chemical changes over the course of a day.

Tentative Laboratory Schedule: - subject to minor changes, check D2L regularly before lab January 07 Laboratory 1 A. Introduction to the laboratory: Overview of the goals of the lab Laboratory safety and rules B. Writing activity related to the ethics of using animals in research and teaching* -Before coming to lab, read the paper by Gauthier & Griffin, 2005. Bring a paper or electronic copy to lab for the writing activity.

January 14 Laboratory 2 A. Frog necropsy - recovery and fixation of parasites - Bring a pencil and the necropsy sheet you designed in Lab 1. If you forget it, you will not be able to start the necropsy until you present your necropsy sheet. At several points in the necropsy, you will require a signature from myself or the TA before you move on. Completed necropsy sheets will be turned in at the end of lab.* B. Isolation and starvation of beetles. C. Slide box – the protozoans D. Demonstrations – the protozoans

January 21 Laboratory 3 A. Turn in data analysis from frog necropsies. See laboratory 2 for details. B. Dr. Terry Galloway demonstrates how to wash birds to obtain ectoparasites. C. Isolation of Hymenolepis diminuta proglottids and beetle exposures. D. Examine fecal pellet of tapeworm infected rat. E. Start going through slide box – the protozoans.

January 28 Laboratory 4 A. Bird and mammal necropsy - recovery and fixation of parasites B. Trophic Transmission: Make a prediction about parasite species diversity C. Find a peer-reviewed paper in a parasitology journal that will help you identify the parasites from the animals we necropsied.

3 D. Slide box (if you have time)

February 04 Laboratory 5 A. Turn in PDF of paper that describes parasites from one of the animals we necropsied in Lab 4. B. Beetle necropsy and cysticercoid count. C. Enter data into computer and turn in datasheet before leaving class. D. Review slide box material E. Use class data to create a frequency histogram of cysticercoid infection in beetles and calculate overdispersion (k). Make your frequency histograms in excel so that you can use them for your manuscript. Turn in at Lab 6 on Feb. 12.

February 11 Laboratory 6 A. Turn in frequency histogram using parasite data from beetles. B. Staining and mounting of parasites acquired from previous labs

February 15-19 Study week - no laboratories. Laboratory available on request – make arrangements by February 12.

February 25 Midterm Laboratory Examination – slide box to end of protozoa, demonstrations, and lab activities to date.

March 03 Laboratory 7 A. Necropsy of rats infected in Lab 5 - Parasite distribution.

March 10 Laboratory 8 A. Organization of Hymenolepis diminuta data in tables and lab report Taxonomy and Diagnostics. Overview of morphology and the use of keys. B. Slide box C. Demonstrations D. Turn in hypotheses and predictions associated with the beetle and rat data.

March 17 Laboratory 9 A. Slide box B. Identification of parasite slides C. Demonstrations D. Turn in a draft of your figures and tables to be included in your results section of the manuscript.

March 24 Laboratory 10 A. Slide boxes B. Identification of parasite slides C. Demonstrations

March 31 A. Final Laboratory Examination B. Hand in prepared slides with write-up (can turn in earlier). C. Hand in manuscript (word document file) on Monday April 4 by 5 pm.

4 Grades: Your final grade will be based on the percentages shown below. One grade is deducted for each day an assignment is late (e.g. A+ to A). For in class assignments and laboratories, there are no make-ups, so if you are not present, no points will be earned.

Lecture Midterm Exam Monday February 22 (in class) 15% Final Exam (TBA) 30%

Laboratory Weekly quiz/assignment (denoted by * above) 5% Midterm (February 25) (in laboratory) 10% Final (March 31) 20% Parasite slides (2 different parasites, each with write-up) 5% Manuscript based on laboratory activities with H. diminuta 15%

Academic Honesty: There is no tolerance for plagiarism and cheating. Consequences include a grade of zero for the assignment/quiz/exam, failure in the course, or expulsion from the University. Assume that all work for the course is individual-based unless told otherwise.

BIOLOGY 3300: Evolutionary Biology Winter 2016 Time and Location: Lecture: M, W, F 12:30-1:20 pm, 401 Biological Science Building Lab: W 2:30-5:25 pm, Tutorial/Discussions: 418 Machray Hall Computer Labs: 115 Machray Hall

Recommended Text: Herron, J.C. and S. Freeman. 2014. Evolutionary Analysis, 5th ed. Pearson Prentice, Upper Saddle River, NJ. (on reserve in Science Library) Additional required readings for class discussions will be provided in class.

Instructor: Dr. Jeffrey Marcus Email: [email protected] Office: 600 Buller Building (really!)

Office Hours: Office hours by appointment only. Email the instructor with a request for a meeting and indicate several days and times when you are available. The instructor will email you back with an appointment time. Make sure you include your full name in the email. Please note that same-day appointments may not always be available.

Course Website: The slides and supporting materials will be posted to the course website on Desire to Learn (D2L) after each lecture.

Course Description and Objectives: Evolution is the ultimate cause of all biological diversity. This course introduces major questions and research methods in evolutionary biology. Topics include evolutionary genetics, adaptation, speciation, and the reconstruction of evolutionary history. By the end of this course you should: 1. understand how evolution occurs within populations, how species are formed, and major events in the history of life; 2. be familiar with the approaches used to study evolution; 3. have honed your critical thinking skills through evaluating relevant literature.

Learning & Teaching Philosophy: I hope you will approach the course with enthusiasm and curiosity. I expect you to be ready to explore new ideas, ask for clarification when needed, and participate in class discussions. I will do my best to create a comfortable atmosphere, present the material in an organized manner, and be open to questions and constructive feedback. It is essential that you read assigned readings in advance, so that class discussions can be used to solidify your understanding of the material. I also expect you to complete assignments by the deadline. If you cannot meet a deadline, please discuss it with me as soon as possible. Work that is handed in late without sufficient documentation will be docked 10% per day.

Course Grading: Midterm Exam (Feb. 24) 14 % Lab Quizzes and Discussions 12 % Population Genetics Assignment 15 % Molecular Phylogenetics Assignment 22 % Final Exam 37 %

Should major disruptions to university activities occur (e.g., as a result of a pandemic or zombie apocalypse), the course content, grading scheme, and other provisions of this document may be adjusted as the circumstances warrant. Note: Make-up exams will only be given in cases of serious illness (medical certificate required), a death in the immediate family (written verification from a

physician or a religious authority required) or a compulsory religious observance (written verification from a religious authority required).

Grades will be assigned using the following scale: Percentage Grade 90 -100 A+ 80 - 89 A 75-79 B+ 70-74 B 65-69 C+ 55-64 C 50-54 D 0-49 F

Lecture Topics (subject to change):

1. History of evolutionary theory (Chapters 2 & 3) a. Evidence for evolution, natural selection, evolutionary synthesis Discussion 1: Evolutionary exploration 2. Mendelian genetics in populations (Chapters 5-7) a. Genetic variation & Hardy-Weinberg…again! b. Selection, non-random mating, drift, & migration Computer assignment: population genetics simulation 3. Quantitative Genetics: traits controlled by multiple genes (Chapter 9) a. Genetic variation & selection response b. Genetics of adaptation Discussion 2: Selection & evolution in contemporary populations 4. Adaptation (Chapters 8, 10, 11, 13) a. Comparative method b. Diversity in reproductive systems and life histories Discussion 3: Evolution of sex / reproductive evolution 5. Speciation (Chapter 16) a. Species concepts b. Mechanisms of speciation c. Genetics of speciation Discussion 4: Speciation & hybridization 6. Phylogenetic systematics (Chapters 4, 15) a. Principles of systematics b. Reconstructing evolutionary trees c. Molecular systematics and evolution Computer assignment: molecular phylogenetic assignment 7. Patterns of species diversity in time and space (Chapter 18) a. The fossil record b. Punctuated equilibrium and mass extinctions Discussion 5a: Mass extinctions 8. Human evolution (Chapters 20, 14) a. Relationships among the great apes & Origin of Homo sapiens b. Evolution and human health Discussion 5b: Human evolution

IMPORTANT DATES: Jan 6 NO LAB Jan 131 418 Machray Discussion 1 Evolutionary Exploration2 Jan 20 115 Machray Computer Labs Population Genetics Exercise4 Jan 27 115 Machray Computer Labs Population Genetics Exercise, Cont’d Feb 31 418 Machray Discussion 2 Contemporary Evolution & Selection2,3 Feb 5 before class Population Genetics Assignment due Feb 101 418 Machray Discussion 3 Reproductive Strategies2,3 Feb 17 Reading week NO LAB Feb 24 NO LAB, Midterm Exam in Lecture Mar 21 418 Machray Discussion 4 Speciation & Hybridization2,3 Mar 9 115 Machray Computer Labs Phylogenetic Exercise4 Mar 16 115 Machray Computer Labs Phylogenetic Exercise, Cont’d Mar 23 before 5 pm NO LAB, Phylogenetics Assignment due Mar 30 before class Phylogenetics Peer Reviews due Mar 301 418 Machray Discussion 5 Mass Extinctions, Human Evolution2,3 Apr 6 NO LAB Apr 8 before class Phylogenetics Assignment Revision due

Jan 19, 2016: Deadline for late registration / withdrawal with no record on transcript Mar 18, 2016: Last Date for voluntary withdrawal

1 for Discussions 1–5, students attend 2:30–3:45 p.m. or 3:45–5:00 p.m. slots (as assigned by instructor); for computer labs all students should arrive at 2:30 for the entire time slot 2:30–5:20 p.m. 2 pre-lab quiz at beginning of lab; class discussion during lab 3 student-led discussion of article(s) during lab; leaders e-mail discussion questions and statement of relevance to instructor by 6:00 p.m. on the day before their lab ([email protected]) 4 preliminary computer assignment due at the end of lab.

LAB DISCUSSIONS (12%): Group A: 2:30 p.m.–3:45 p.m., Group B: 3:45 p.m.–5:00 p.m. (as assigned) We will discuss literature relevant to the lectures (up to three articles per lab, depending on their length). It is essential that everybody read the articles in advance. These discussions will help reinforce material introduced in the lecture, and allow students to explore these topics in small groups. For Discussions 1 through 5, there will be a short “quiz” during the first five minutes of the discussion time. This will require you to answer one to two questions about the reading. In total the quiz marks will be 5% (1% per quiz). For Discussions 1–5, the class will be divided into small groups (3–5 students) to discuss general questions about the reading. After discussion within the groups, we will briefly discuss the papers as a class. The first discussion will be led by the instructor. The remaining discussions will be led by one student per group (leaders will sign up in advance); each student is expected to lead one group discussion during the semester. You will give a brief verbal summary of each paper to your group, come up with general questions about the reading for discussion, and help students tie the discussion material to topics presented during lectures. Student leaders will e-mail the relevant instructor their discussion questions and a brief statement outlining how the topic relates to lecture material (3–5 sentences); discussion questions should also be distributed to group members during the lab discussion. Your mark will be based on your ability to lead your discussion (3%). Students will also be graded on their participation in the discussions led by others (1% per discussion = 4%).

POPULATION GENETICS ASSIGNMENT (15%): One way to gain an understanding of population genetic predictions is to simulate the effects of mutation, selection, migration and drift on allele frequencies. Lab exercises are based on the simulation program, AlleleA1, written by Jon Herron. This program is free and is available in campus computer labs, or you can download it onto your own computer. You will be required to complete a short assignment during the first week’s lab (3%) and submit a written interpretation of results from more detailed questions (12%). These labs will be held in the Machray Hall computer labs.

PHYLOGENETICS ASSIGNMENT (22%): To gain an appreciation for the advantages and challenges of using DNA sequence data to reconstruct the evolutionary history of various taxa, we will spend two lab periods doing a computer-based molecular phylogenetic exercise. This will involve gathering sequence data from a web-based database, aligning and analyzing the data using programs that you can also download onto your home computer, and inferring evolutionary relationships among organisms from the gene trees you generate. These labs will be held in the Machray Hall computer labs. You will be required to complete a short assignment during the first phylogenetics lab (3%) and write a report for this assignment in the form of a journal article (10%). You will also provide constructive criticisms of two other students’ phylogenetics assignments in the form of Peer Reviews (2 X 3%= 6%). Note that your mark will not be determined by the peer reviewers, but the quality of your own peer reviews will be evaluated and marked. You will then edit your own phylogenetics assignment in response to the comments of the instructor and the student peer reviewers and submit a revision (3%). MIDTERM EXAM (14%, Wednesday, Feb. 24, 12:30-1:20 pm, 301 Biological Science Building): Sample questions will be provided at least a week before the test.

FINAL EXAM (37%, during scheduled exam period): The final exam will be comprehensive, and will consist of short answer and paragraph questions.

Disability Policy: The University of Manitoba Accessibility for Students with Disabilities Policy states “Students requesting accommodations are responsible to initiate contact with the Disability Services (DS) office and make the nature of their disability and/or their needs known in a timely fashion. Where possible, students are requested to declare their needs to DS staff before or at the time they register for, or are admitted into, a program.” and “The University will use reasonable efforts to offer reasonable accommodations in the delivery of academic programs and services to students with disabilities.” Please DO NOT request accommodations directly from the instructor without a letter of accommodation from Disability Services office.

Academic Integrity: Plagiarism and Cheating: Plagiarism or any other form of cheating in examinations, term tests or academic work is subject to serious academic penalty (e.g. suspension or expulsion from the faculty or university). Cheating in examinations or tests may take the form of copying from another student or bringing unauthorized materials into the exam room (e.g., crib notes, pagers or cell phones). Note: cell phones, pagers, PDAs, MP3 units or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations. Exam cheating can also include exam impersonation. (Please see Section 4.2.8 on Exam Personation). A student found guilty of contributing to cheating in examinations or term assignments is also subject to serious academic penalty. To plagiarize is to take ideas or words of another person and pass them off as one's own. In short, it is stealing something intangible rather than an object. Plagiarism applies to any written work, in traditional or electronic format, as well as orally or verbally presented work. Obviously it is not necessary to state the source of well-known or easily verifiable facts, but students are expected to appropriately acknowledge the sources of ideas and expressions they use in their written work, whether quoted directly or paraphrased. This applies to diagrams, statistical tables and the like, as well as to written material, and materials or information from Internet sources. To provide adequate and correct documentation is not only an indication of academic honesty but is also a courtesy that enables the reader to consult these sources with ease. Failure to provide

appropriate citations constitutes plagiarism. It will also be considered plagiarism and/or cheating if a student submits a term paper written in whole or in part by someone other than him/herself, or copies the answer or answers of another student in any test, examination, or take-home assignment. Working with other students on assignments, laboratory work, take-home tests, or on-line tests, when working together is not specifically allowed by the instructor can constitute Inappropriate Collaboration and may be subject to penalty under the Student Discipline By-Law. An assignment that is prepared and submitted for one course should not be used for a different course. This is called "duplicate submission" and represents a form of cheating because course requirements must be fulfilled through original work for each course.

Examinations: Personations A student who arranges for another individual to undertake or write any nature of examination for and on his/her behalf, as well as the individual who undertakes or writes the examination, will be subject to discipline under the university's Student Discipline Bylaw, which could lead to suspension or expulsion from the university. In addition, the Canadian Criminal Code treats the personation of a candidate at a competitive or qualifying examination held at a university as an offence punishable by summary conviction. Section 362 of the code provides: Personation at Examination Every one who falsely, with intent to gain advantage for him/herself or some other person, personates a candidate at a competitive or qualifying examination held under the authority of law or in connection with a university, college or school or who knowingly avails him/herself of the results of such personation is guilty of an offence punishable on summary conviction. 1953- 54,c.51, s.347. Both the personator and the individual who avails him/herself of the personation could be found guilty. Summary conviction could result in a fine being levied or up to two years of imprisonment. When in doubt about any practice, ask your professor or instructor. The Student Advocacy Office, 519 University Centre, 474-7423, is a resource available to students dealing with Academic Integrity matters. *************************************************************************************** IMPORTANT NOTES: 1. Reminder: deadline for late registration/withdrawal with no record on transcript is January 19, 2016. 2. Reminder: deadline for voluntary withdrawal is March 18, 2016. 3. Exam questions may come from the parts of the textbook indicated in this outline and from material presented during class. Questions that require detailed recall will derive primarily from lecture material. Designated readings and material covered in class will supply all of the information tested on the exams. 4. The lecture materials available on the web are incomplete. You will be responsible for additional material that will be presented during class. If you miss class for any reason, it is your responsibility to obtain the slides from the lecture you missed from the web site and the additional information presented in class from a classmate. The instructor will not provide lecture notes beyond what is available online.

Agreement Form

All students who wish to remain enrolled in BIOL 3300 are required to sign and return this form to the instructor by the third class meeting. By submitting your name on the form you are agreeing to the following statement:

"I have read the BIOL 3300 course syllabus and understand and accept its contents. I also understand that all work in this course must be my own, in my own words, and all required assignments, projects, and tests must be completed to receive a passing grade for this course. I understand that facilitating academic dishonesty such as plagiarism by another student is an academic offense for both students and both students will be penalized for such behavior. I stipulate that I have reviewed the following websites: http://umanitoba.ca/faculties/science/undergrad/resources/webdisciplinedocuments.html http://www.umanitoba.ca/student/resource/student_advocacy/cheating_plagiarism_fraud.html and understand what constitutes academic dishonesty. I further agree that is it my responsibility to withdraw or make other changes in my enrollment status, according to the policies and deadlines outlined in the University Catalog and/or Academic Calendar."

______Signature ______Print your Name ______Date ______Semester Taken

BIOL 3312 Community Ecology Fall Term 2015 3 Credit Hours

This course investigates the structure and function of terrestrial communities. Emphasis is placed on observing community patterns in space and time, as well as understanding the biotic and abiotic processes that contribute to these patterns. Lectures are supplemented by a field trip that exposes students to major boreal terrestrial communities in Manitoba.

Instructor: Dr. Isobel Waters Office: 318 Buller. Phone: 474-8739. Office Hours: Mon, Wed and Fri 11:30-12:30, or by appt. E-mail: [email protected]

Required Text: Smith, R., T. Smith, and I. Waters. Elements of Ecology: Canadian edition. Toronto: Pearson.

Lecture Slot: 10:30-11:20 Mon, Wed, Fri. 315 124 Machray Hall. You are responsible for material covered in lectures, assigned readings, and any announcements made in class. Course materials such as Powerpoint files, etc. will be posted in D2L.

Laboratory Slot: Field trips will be held on Saturday Sept. 12 (B01) and Sept. 19 (B02) in Whiteshell Provincial Park. Bus transportation is provided. We leave at 6:45 on Saturday morning from the parking lot behind the Biology building and return to the university at about 7:30 pm. Details regarding the trip will be provided in class. Attendance is compulsory.

Evaluation: Mid-term examination (in class) Fri 23 October 2014 20% Field trip report Due date TBA 25% Final examination (3 hours) Scheduled by Student Records 55% Examinations will consist of written answers ranging from short notes to essay length. A sample mid-term from a previous year will be posted. Examinations can be deferred only on medical and compassionate grounds recognized by the Faculty of Science. A passing grade will only be awarded if the student has passed both the field trip and lecture (midterm/final exam) portions of the course. The deadline for voluntary withdrawal is 18 November, 2015.

Statement on Academic Dishonesty The Faculty of Science and The University of Manitoba regard acts of academic dishonesty in quizzes, tests, examinations, laboratory reports or assignments as serious offences and may assess a variety of penalties depending on the nature of the offence.All Faculty members and teaching assistants have been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department. Acts of academic dishonesty include but are not limited to bringing unauthorized materials into a test or exam, copying from another individual, using answers provided by tutors, plagiarism, and examination personation. Note: cell phones, pagers, PDAs, MP3 units or electronic translators are explicitly listed as unauthorized material s, and must not be present during tests or examinations. Penalties that may apply, as provided for under the University of Manitoba's Student Discipline ByLaw, range from a grade of zero for the assignment or examination, failure in the course, to expulsion from the University. The Stude nt Discipline ByLaw may be accessed at: http://umanitoba.ca/admin/governance/governing_d ocuments/students/868.ht Suggested minimum penalties assessed by the Faculty of Science for a cts of academic dishonesty are available on the Faculty of Science webpage: http://umanitoba.c a/faculties/science/resources/Discipline__Penalties_Table_Jul09.pdf

BIOL 3312 Lecture Outline (summary only; not all portions of all chapters covered)

Topic 1: Introduction (Chs 1 & 16) Defining communities and subsets Contrasting views of community Objectives of community ecology Topic 2: Studying the Community (Chs 1 & 16) Patterns and processes Types of interactions Experimentation in ecology Topic 3: Classifying Communities (Chs 16 & 23) Abiotic, taxonomic, and statistical criteria Topic 4. Community Structure: Patterns in Space (Chs 16, 18, & 23) Biological structure Physical structure General model Topic 5. Community Succession: Patterns in Time (Chs17, 8 & 18) Definitions, types, and ways of documenting succession Principles and mechanisms of succession Changing attributes of ecosystems and species Topic 6. Productivity & Decomposition: Energy Dynamics of Communities (Chs 6, 16, 20, & 21) Primary productivity and factors affecting Secondary productivity and efficiency ratios Trophic structure Decomposition, mineralization, and factors affecting Topic 7: Niche Packing and Community Structure (Chs 16 & 13) Niche concept and related terms Determining niche Importance of niche for community structure Topic 8i. Community Processes I. Competition (Chs 13 & 16) Types and mechanisms Tests and models of competition Impacts on community Topic 8ii. Community Processes II. Predation (Chs 14 & 16) Types of predation and interactions with competition Impacts on community Evolutionary impacts Topic 8iii. Community Processes III. Other Interactions (Chs 15 & 16) Types of mutualisms and impacts on community Types and impacts of indirect interactions Topic 9. Factors Influencing Community Interactions (Ch 16) (Topics as time permits) Topic 10. Patterns and Consequences of Species Richness (Chs 16, 18 & 27) Global trends and factors affecting Island biogeography Significance of diversity for stability & productivity

Condensed PowerPoint notes will be posted on D2L (excluding copyrighted images from the text). Students are responsible for material discussed in class that is not present on the PowerPoint notes, as well as specified reading assignments from the textbook. Boreal Ecology - BIOL 3318 Winter 2016 11:30 am - 12:45 pm, Tues/Thurs 306 Buller

Instructor: Dr. James Roth office: BSB 418 phone: 204-272-1677 email: [email protected] office hours: by appointment

Teaching Assistant: Dawn Wood, BSB 421F, [email protected]

Course Description: The objective of this course is to examine the ecology of northern ecosystems, including the physical environment, species interactions, and conservation issues. We will assume a familiarity with basic ecological concepts learned in Ecology (BIOL 2300 or 2390), which is a prerequisite for this course.

Textbook: There will be no required textbook to purchase for this course, but assigned readings will be available for you to download.

Evaluation: The final grade will be based on three examinations (75%, or 25% each), and five written reading reports (25%, or 5% each). Exam questions will be based primarily on lecture material and information introduced in the readings, and will emphasize critical thinking and synthesis. Exams are not cumulative and will each be worth 25% of the course grade; the first exam will be February 4, the second will be March 15, and the last exam will be held during the final examination period (April 11-25).

Reading Reports: For several of the assigned readings you will write a report on the material you read. These reading reports are designed to help you to synthesize and interpret the assignment and help us determine how well you have understood the material. Specific instructions on what to include in these reports, and the due dates, will be posted online.

Course material will be posted in UM Learn. These materials will include lecture notes, required and recommended readings, and information on the reading reports. To access this material you must be registered in this course. To log on to UM Learn follow the link on the University of Manitoba homepage, or go to: https://universityofmanitoba.desire2learn.com/ Lecture notes will not necessarily be complete. The purpose of the notes is to facilitate keeping up with the presentation of class material; notes are not a substitute for class attendance. Notes will normally be posted shortly before class.

IMPORTANT NOTE: Each student is responsible, for the purposes of examinations, for all material presented in the course. Plagiarism and cheating are serious offenses. For details on the consequences of committing such offenses, please refer to the “General Calendar of the University of Manitoba.”

1 Grades (A-F) will be assigned as 90+ A+ 80-89 A 76-79 B+ 70-75 B 66-69 C+ 60-65 C 50-59 D < 50 F

Lecture Topics will include the following.

What is Boreal? Geological History & Physical Environment Climate, cryosphere, permafrost. Biological Habitats & Ecosystems Forest, tundra, wetlands Disturbance Environmental Adaptations Migration Ecological Interactions Predation and food webs Plant-animal interactions Population cycles Patterns of species diversity Invasive species

The last day for voluntary withdrawal from the course is March 18, 2016.

2 BIOL 3340 (Section A01) – PRIMITIVE FUNGI & THEIR ALLIES

Winter 2016 (3 credit hours)

SYLLUBUS & COURSE OUTLINE

INSTRUCTORS: Dr. Tom Booth 404 Biological Sciences Bldg. e-mail: [email protected] OFFICE HOURS: Please arrange appointments with the instructor. CLASSROOMS: Lecture section A01 in 315 Buller. TIME SLOTS: 10:00 – 11:15 a.m. (Lecture) Tu–Th

COURSE DESCRIPTION: Studies on the biology of primitive fungi & slime moulds focusing on the evolution of ancestral fungi, relevant Chromista & slime molds within the wider context of evolution of derived fungi & ancient groups basal to fungi and animals. The course also encompasses their cogent life histories, development, structure, taxonomy, & fundamental biochemistry. General methods for environmental collection, isolation & study of these organisms will be presented in lectures. This course is aimed to provide introductory information on a group of fungi & fungal-like organisms, which are increasingly being utilized as experimental systems by a wide range of biologists, biochemists, physicists & mathematical scientists.

ATTENDANCE: It is important for a student to attend all classes. Examinations will be based on the material posted on UM Learn & presented in lectures.

UNIVERSITY OF MANITOBA POLICIES: Plagiarism and Cheating: “To plagiarize is to take ideas or words of another person & pass them off as one’s own. In short, it is stealing something intangible rather than an object. It will also be considered plagiarism and/or cheating if a student copies the answer or answers of fellow students in any take-home assignment, test, or examination. Plagiarism or any other form of cheating in assignments, tests, or examinations (e.g. crib notes) is subject to serious academic penalty (e.g. suspension or expulsion from the faculty or the university). A student found guilty of contributing to cheating in assignments, tests, or examinations will also be subject to serious academic penalty.”

FACULTY OF SCIENCE STATEMENT ON ACADEMIC DISHONESTY: The Faculty of Science and The University of Manitoba regard acts of academic dishonesty in quizzes, tests, examinations, laboratory reports or assignments as serious offences & may assess a variety of penalties depending on the nature of the offence. Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another student, plagiarism, & examination impersonation. Cell phones, pagers or electronic translators are explicitly listed as unauthorized materials, & must not be present during tests or examinations. Penalties that may apply, as provided for under the University of Manitoba's Student Discipline By-Law, range from a grade of zero for the assignment or examination, failure in the course, to expulsion from the University. The Student Discipline By-Law is at: http://umanitoba.ca/admin/governance/policies/section_1200/1202.shtml. Suggested penalties assessed by the Faculty of Science for acts of academic dishonesty are available on the Faculty of Science web-page: http://umanitoba.ca/faculties/science/

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EVALUATIONS AND EXAMINATIONS: The final grade in BIOL 3340 A01 will be based on two examinations: 1. Midterm Examination I – Tuesday, February 2nd, 2016 Time: ...... 10:00 TO 11:15 AM Location: ...... 315 Buller Portion of the final grade: ...... 25% 2. Midterm Examination II – Tuesday, March 1st, 2016 Time: ...... 10:00 TO 11:15 AM Location: ...... 315 Buller Portion of the final grade: ...... 25% 3. Final Examination – Scheduled by the Registrar’s Office for April 2016 Final Examination Period* Time: ...... TBA (Announced by the University) Location: ...... TBA (Announced by the University) Portion of the final grade: ...... 50% *Make every effort to write the Final Examination on the date & time scheduled by the University. It is stressed that you must write the final on the date, time & location announced by the University. Do not plan other events until you are appraised of said date, time & location.

MIDTERM BREAK: February 15th through 19th (including two weekends & Louis Riel Day)

VOLUNTARY WITHDRAWAL DATE: Friday, March 18th, 2016

END OF CLASSES: Thursday April 9th, 2016

EXAMINATION PERIOD: April 11 through April 25th, 2016

LECTURE OUTLINE: Although the Instructor will try to adhere to this lecture outline, it may not be strictly followed, due to the natural fluctuations in the time that it takes to deliver lectures. Certain topics may be omitted as the course progresses, but no topics will be added to the basic outline. The general sequence of presented topics follows.

SEQUENCE OF GENERAL LECTURE TOPICS: I. Taxonomy and evolution of lower true fungi (Eumycota) & “fungal” Straminipila & Protozoa II. General aspects of the spores of lower fungi & their allies III. Introduction to the body plans (thalli) of lower fungi & their allies IV. Hyphae: growth, wall synthesis, the cytoskeleton, secretion & membrane traffic, nutrient uptake, branching, & aggregates V. Major groups of the Zygomycota & Glomeromycota (Eumycota) & their evolution VI. Chytridiomycota (Eumycota) VII. Hyphochytridiomycota (Stramenopila/Heterokonta/Chromista) VIII. Labyrinthulomycota … The “track moulds” (Stramenopila/Heterokonta/Chromista) IX. Oomycota … The “fish moulds” (Stramenopila/Heterokonta/Chromista) X. Heterolobosea … Acrasids … The “acrasid cellular slime moulds” XI. Mycetozoa … Protostelids … The “protoplasmodial slime moulds” XII. Mycetozoa … Dictyostelids … The “cellular slime moulds” XIII. Mycetozoa … Myxomycetes (Myxogastria) … The “true slime moulds” XIV. Cercozoa … Plasmidiophorids … The “endoparasitic slime moulds”

LIMNOLOGY—BIOL 3370

Limnology is the study of freshwaters. Limnology is a multidisciplinary science that incorporates elements of environmental chemistry, biogeochemistry, earth science, physics, and ecology. The course is structured to illustrate the linkages among these disciplines. The first part of the course emphasizes the origin of lakes, and their physical and chemical properties. It sets the framework for understanding biological processes within lakes. The next portion of the course focuses on biological interactions among organisms that live suspended in water--the plankton. Finally, the course closes with an integrative consideration of ecosystem interactions, and the historical development of lakes.

The course emphasizes the significant contributions of Canadian limnologists. Limnology is a field-based science that has made important contributions to our understanding of human impacts on the environment (e.g. acid precipitation, eutrophication, global climate change, contaminants and toxins).

INSTRUCTOR: Dr. B.J. Hann, 463 Duff Roblin, Department of Biological Sciences 474-7450 (office with voice mail); 474-9245 (Biological Sciences General Office to leave message) e-mail: [email protected] COMMUNICATION/APPOINTMENT POLICIES: • Use your University email account. • Always include your name and the name of this course. We will not respond to an unsigned email. • I do not answer questions about lectures that require complex answers via email, especially in the 24 hours leading up to the exam. • When requesting an appointment, it is efficient to suggest multiple days and times to expedite scheduling a time. We do not take appointments for the day of an exam.

UNIVERSITY EMAIL POLICY: The University has a new email policy. If you are a student at the UofM you must send all emails from your UofM email account. All official notices from the University will be sent to your UofM email account and be aware that certain University electronic communications may be time-critical. Students are responsible for checking their University email account on a regular basis in order to stay current with University communications.

For assistance with your university email or to activate your email account, please contact the IST Help and Solutions Centre:

https://webtools.cc.umanitoba.ca/webmail/horde/imp/alt-login/custom_login.php

Remember to include your full name, student number and faculty in all correspondence.

For more information visit: http://umanitoba.ca/registrar/e-mail_policy

TEXTBOOK (recommended only): Wetzel, R.G. 2001. Limnology: Lake and River Ecosystems (3rd edition)

Supplemental materials (as pdfs or links to articles) will be posted on UMLearn.

LECTURES: Tues. & Thurs. 11:30 am, BSB 401

LABS: Monday or Tuesday, W332 Duff Roblin Building, 2:30-5:30 pm

Schedule for lectures and labs will be posted on UMLearn including DUE DATES for lab reports. Last date for voluntary withdrawal is November 18.

MIDTERM LECTURE EXAM: 29 October--This exam will cover all material in the course to this date, to be written in the lecture slot (75 minutes) in class.

FINAL LECTURE EXAM: Comprehensive written exam (3 hours) including all material in the course. Date, time, and place set by Student Records Office.

MARKS: Midterm exam 20% Lab reports 35% (5 lab reports) Lab 1: 15 Lab 2: 15 Lab 3: 30 Lab 4: 15 Lab 5: 15 Final exam 45% COURSE OBJECTIVES:

1. to provide a comprehensive, synthetic, and contemporary view of the principles of limnology, the study of inland waters; this includes consideration of physical (light, waves), chemical (nutrients), and biological (biota) limnology. 2. to increase your understanding of the structure and function of aquatic ecosystems (e.g. food webs, energy flow) with a focus on Lake Winnipeg. 3. to develop skills and understanding of current limnological issues and broaden your perception of aquatic environmental problems (e.g. eutrophication, invasive species). 4. to learn to collect data accurately in a lab or field setting, and manipulate data to produce scientific tables, figures and graphs. 5. to interpret data in order to assemble a scientific/limnological report, including introduction, methods and materials, results, discussion sections.

Late Penalty: Assignments received late (i.e. past the due date) will be assessed a late penalty of 1 mark/day (including weekends and holidays). Assignments received more than 4 days after the due date will not be marked unless the delay is explained adequately.

Academic Integrity: http://umanitoba.ca/student/resource/student_advocacy/cheating_plagiarism_fraud.shtml

Students have an obligation to act in a fair and reasonable manner toward their peers, the faculty, staff, administration, and the physical property of the University. Any student found guilty of plagiarism, cheating, or academic fraud shall receive a zero grade on the assignment, and further academic penalty may be assessed.

Academic Honesty Declaration (copy on UMLearn): Submit with first lab report and applicable to all lab reports.

The student discipline by-law provides guidance to those individuals charged with administering disciplinary actions as well as outlining the protection to students through their right of appeal. http://umanitoba.ca/admin/governance/governing_documents/students/discipline

Week Lecture Topic Laboratory (see Lab Handout/Readings (see UMLearn) Report UMLearn) Due Dates 1 Introduction Properties of water 2 Properties of water NO LAB Schindler & Donahue Origins of lakes 2006 3 Lakes of the world How to write a lab Lab report format and Lake morphometry report: 21-22 Sept. requirements

4 Light in lakes Lake morphometry Lab 1: Temperature, heat, and 28-29 Sept. 8 Oct. stratification 5 Stratification and lake Temperature Lab 2: types, Heat budgets profiles: depth and 22 Oct. Meromictic lakes & seasonal variation paleolimnology Physical & chemical profiles (oxygen, pH, conductivity, light): 5-6 Oct. 6 Climate change NO LAB: Waves, seiches Thanksgiving Dissolved oxygen profiles 7 Dissolved oxygen Smol (e-lecture) or Winterkill Gregory-Eaves (e- Conductivity DIC/DOC lecture) 8 Nutrients in lakes: P, N Temperate Lake Lab 3: Midterm exam: 29 Oct Models: 26-27 Oct. 12 Nov. 9 P management in lakes: Is Lake Winnipeg Schindler et al. 2008 Lake Washington, Lake “Canada’s Sickest Carpenter 2005 Winnipeg Lake”? Fat Lake Leavitt et al. 2006 video: 2-3 Nov. 10 Lake biota and Nutrients Lab 4: Thornton & Laurin 2005 zooplankton assignment: 9-10 26 Nov Nov 11 Zooplankton communities Zooplankton lab: 16- Cyclomorphosis, DVM 17 Nov. Size efficiency hypothesis 12 Food webs: benthic- Trophic Cascade Lab 5: pelagic coupling problem assignment: 3 Dec 23-24 Nov. 13 Trophic cascades: NO LAB resources(bottom up) vs predation (top down) control of food webs 14 Trophic cascades

COURSE OUTLINE (2015-2016 Fall Term)

BIOL 3470 Environmental Physiology of Animals I

Credit: 3 hours

Lectures: 3 per week, Section A01, MWF 1:30–2:20 pm, 401 Biological Sciences Building

Laboratories: W270 Duff Roblin Building, Sections B01 and B02

Instructors: Dr. K. L. Campbell (Course coordinator) W465 Duff Roblin Bldg; Tel: 474-6397; email: [email protected]

Dr. W. G. Anderson W475 Duff Roblin Bldg; Tel: 474-7496; email: [email protected]

Dr. K. G-E. Scott (Laboratory instructor) W473 Duff Roblin Bldg; Tel: 474-8413; email: [email protected]

Suggested Text: “Animal Physiology”. Hill, Wyse and Anderson, 2012, 3rd Ed., Sinauer Associates [2nd (2008) Edition is also acceptable].

The suggested text is intended to be used as an aid to understanding the concepts and principles presented in class. Examinations on the lecture portion of the course will be based on material presented or handed out in class, unless specific figures and passages in the textbook (or posted online) are designated by the instructor as required reading.

Grading is based on the following assignments and short- and long-answer examinations:

A. Lecture component of course:

1. Mid-term exam – TBA (late October); 6:00 pm; Room TBA; 1 hr) 20% 2. Final exam – December 11-23, 2015 (covers entire term; 3 hr) 50%

B. Laboratory component of course: (labs begin September 16th/17th, 2015)

1. Written reports (as per lab manual) 25% 2. Final lab exam (December 8, 2015; 5:30–6:30 pm; Room TBA; 1 hr) 5%

Important Note: Scores of ≥50% in both the lecture and laboratory components are required to obtain a passing grade (D or better) in this course. Attendance in labs is mandatory (assignments will not be accepted from labs with unexcused absences). For more information on lab requirements, please see below.

Synopsis: This course is intended to acquaint students with some of the major environmental challenges encountered by animals in nature, and stresses the diversity of physiological solutions to these problems in aquatic and terrestrial organisms, and their evolutionary origins. The sequence of lectures is designed to first introduce students to the physical problems confronting animals in nature, and the evolutionary time frame of biochemical and physiological adaptive responses to environmental perturbations. Laboratories explore related subjects in various animal model systems.

Thermal Adaptations and Energy Metabolism: (13 lectures) Principle of homeostasis. Negative feedback. Terminology. Thermal environments of organisms. Ectothermy: temperature dependence of metabolic rate. Adaptive strategies for survival to extreme cold: “freeze-avoidance” and “freeze-tolerance” strategies; metabolic compensation to temperature; biochemical basis. Metabolic implications of body size; introduction to allometry and scaling. Endothermy: “advantages” of ectothermy/endothermy. Relationship of metabolic rate to ambient temperature; temperature regulation; tactics for conserving body heat; shivering and non-shivering modes of heat production; daily and seasonal torpor; origin of mammalian hibernation. Regional Endothermy in Ectotherms: non-shivering thermogenesis in fishes; insect endothermy.

Gas Exchange: (13 lectures) Internal vs. external respiration. Concept of partial pressures; physical properties of gases; solubility; diffusion; air and water as gas exchange media. Aquatic respiration: simple diffusion, gill-breathers, countercurrent gas exchange, teleost water pump, ram ventilation, insect “gas gill” and plastron. Aerial respiration: insect tracheal system; microscopic and macroscopic ventilation; discontinuous gas exchange. Evolution and diversity of vertebrate lungs. Tidal versus crosscurrent gas exchange. Evolution of the bird lung. Evolution, diversity and function of respiratory pigments (hemocyanins, hemerythrins, globins); oxygen equilibrium curves; P50; factors affecting blood O2 affinity; allosteric modulation; CO2 transport; effects of temperature; hemoglobin multiplicity; maternal/fetal gas exchange. Adaptations of hemoglobin- and myoglobin-less Antarctic icefish. Adaptations to seasonal oxygen shortages: facultative anaerobiosis in freshwater turtles.

Circulation: (6 lectures) Hearts as pumps, principles of pressure, flow and resistance. Invertebrates: open circulatory systems. Vertebrates: circulation in fish, circulation in amphibians and reptiles, circulation in birds and mammals.

Buoyancy and Diving: (5 lectures) Strategies to approach neutral buoyancy; rigid-walled gas floats; osmotic pump; local osmosis; soft-walled gas floats; external bubbles, physostome and physoclist swimbladders; Root effect; swimbladder countercurrent multiplier. Physiology of diving in air breathing vertebrates. Balancing the conflicting demands of exercise and oxygen rationing while submerged: aerobic dive limit (ADL); strategies to maximize ADL; strategies to minimize oxygen utilization.

Laboratories: Experiments include examining: 1) the effect of temperature on the metabolic rate of ectotherms and endotherms; 2) the effect of exercise on the metabolic rate and cardio-respiratory function of humans; 3) gas exchange in amphibians; 4) control of the crustacean heart rate; and 5) the human dive response. Labs will occur over two weeks with a prelude discussion one week followed by the experimental protocols and data collection the next. Labs will be reported in written form.

Important information regarding laboratories:

A passing grade (50% or better) for the lab component is required to pass the course. Regardless of performance in the lecture component, a mark of 49% or less will result in an overall grade of F.

Attendance in the labs is mandatory and will be taken by the TA at the end of each lab. Two or more unexcused absences throughout the term will result in a failing grade for the lab and the course. Assignments will not be accepted from labs with unexcused absences.

All assignments are due at 2:30 pm exactly on the date given by the lab instructor (e.g. an assignment submitted at 2:35 pm will be considered late). The penalty for late assignments is 20% for up to 24 hours late, 50% for up to 48 hours late. Assignments will not be accepted more than 48 hours late (100% penalty).

Any questions regarding the marking of lab assignments must be submitted to Dr. Scott along with a written explanation no later than 10 days after the date your assignment was returned. In your statement you must include specific references from Appendix 1 of the manual on scientific writing, as well as any relevant literature supporting your argument. Upon receipt of your statement, Dr. Scott will re-evaluate the entire section based upon your argument. There is no guarantee your mark will change, however, it could change in either direction.

A final lab exam will be held on December 8th from 5:30–6:30 pm. The types of questions you can expect on this exam include data interpretation and discussion type questions based on all five experiments (5 marks each).

Academic Dishonesty: With respect to written reports and all examinations, penalties will be imposed for any evidence of “academic dishonesty”, including plagiarism, cheating and fraud following the University of Manitoba Student Discipline Bylaw: (http://umanitoba.ca/admin/governance/governing_documents/students/student_discipline.html).

The Faculty of Science Statement on Academic Dishonesty (and other important policies) can be found at http://umanitoba.ca/faculties/science/undergrad/resources/webdisciplinedocuments.html

Please review these. COURSE OUTLINE (2016 Winter Term)

Biol. 3472 ENVIRONMENTAL PHYSIOLOGY OF ANIMALS 2

CREDIT: 3 hours

LECTURES: 3 per week (MWF 1:30-2:20 PM), 315 Buller Building

LABORATORIES: Wednesday or Thursdays (2:30-5:25PM), W270 Duff Roblin INSTRUCTORS: Dr. D. Weihrauch (Course coordinator) W467 Duff Roblin; Tel: 474-6310; email: [email protected] Dr. M. Fry W469 Duff Roblin; Tel: 474-7498; email: [email protected]

Ms. Lauren Shute (Laboratory instructor) W472 Duff Roblin; email: [email protected]

SUGGESTED TEXT: “Animal Physiology”. Hill, Wyse and Anderson, 2012, 3rd Ed., Sinauer Associates 1st (2004) Edition is also acceptable. Primary Literature!!

OPTIONAL SUPPLEMENTARY TEXT (greater depth and detail): “Environmental Physiology of Animals”, 2nd edition. Wilmer, Stone and Johnson, Blackwell Publishing, 2005.

These texts are intended to be used as an aid to understanding the concepts and principles presented in class. Examinations on the lecture portion of the course will be based on material presented or handed out in class, unless specific figures and passages in the textbook (or posted online) are designated by the instructor as required reading. Be advised that most material for osmoregulation, nitrogen balance and acid-base regulation is not covered in text books!!!

GRADING is based on the following assignments and short- and long-answer examinations:

A. LECTURE COMPONENT OF COURSE: 1a. Mid-term exam - covering material taught by Mark Fry 15% 1b. In class assignments - covering material taught by Mark Fry 5% 1c. In class quizzes – covering material taught by Dirk Weihrauch 6% 2. Final exam – to be announced (covers entire term; 3 hr) 44% B. LABORATORY COMPONENT OF COURSE: (labs begin 6–7 (W–R) January, 2016, see below) 1. Written reports and a final lab exam (see below or manual) 30%

IMPORTANT NOTE: Scores of ≥50% in both the lecture and laboratory components are required to obtain a passing grade (D or better) in this course. Attendance in labs is mandatory (assignments will not be accepted from labs with unexcused absences).

SYNOPSIS: This course is intended to acquaint students with some of the major environmental challenges encountered by animals, and stresses the diversity of physiological solutions to these problems in aquatic and terrestrial organisms. The sequence of lectures is designed to first introduce students to the physical problems confronting animals in nature, and the time frame of adaptive responses to environmental perturbations. This will be followed by discussion of selected topics:

NEURO-PHYSIOLOGOY: (12 lectures – MF) In depth analysis of the basis of resting membrane potential, action potentials, and synaptic transmission; evolution of ion channels and nervous systems; electric organs.

COMPARATIVE OSMOREGULATION: (DW) Osmoregulatory strategies employed by invertebrates and vertebrates in terrestrial, semi-aquatic, freshwater and marine environments. Renal & extra-renal mechanisms regarding the control of solute and volume balance of the internal milieu. Adaptive responses by animals to environmental extremes. Cellular volume regulation. Ways of how to investigate osmoregulatory mechanisms.

NITROGEN BALANCE: (DW) Nitrogen cycle. Nitrogen balance in invertebrates and vertebrates. Metabolic end products. Nitrogen conversion and excretion. Invertebrate nitrogen handling. Vertebrate nitrogen handling – ammonio, urico, and ureotelism. Methods to investigate transepithelial nitrogen transport. Nitrogen as a useful end product, where in nature and why?

ACID-BASE BALANCE: (DW) Introduction to the concept of acid base balance; principle effectors of acid base balance; role of CO2 in acid base balance; ammonia and pH regulation. Effects of global change (increased ocean pCO2 levels)

IN CLASS ASSIGNMENTS (MARK FRY SECTION ONLY): There will be three in class assignments, two worth 2% and one worth 1%, for an overall contribution of 5% to your final mark. Because of the nature of these, there will be no opportunity to make up one if you miss it: i.e. there are no make-ups and all three will be counted.

IN CLASS QUIZZES (DIRK WEIHRAUCH SECTION ONLY):

There will be three in class quizzes, worth 2% each, for an overall contribution of 6% to your final mark. As above, because of the nature of these, there will be no opportunity to make up one if you miss it.

LABORATORIES: The 30% of your grade based upon the laboratory is determined by 5 laboratory exercises, specifically by the lab assignments/report required for each, and a pre-lab quizzes based on these exercises and on the principles they illustrate. Passing the lab is mandatory in order to pass the course. i.e. if you fail the lab component (<50%), you fail the course regardless of your performance in the lecture component.

Attendance in the labs is mandatory and will be taken by the TA at the end of the lab. Two or more unexcused absences throughout the term will result in a failing grade for the lab and the course. Assignments will not be accepted from labs with unexcused absences.

Assessment in the lab will be based on written assignments and an exam as follows: 3 written assignments focused on components of a manuscript (5% each) 15% 1 full lab report (manuscript format) 10% Final lab exam (April 6th from 6:00–7:00 PM, room TBA) 5% Total lab mark 30% Late assignments BIOL3472: Assignments are due at 2:30 PM on the date given by the lab instructor. An assignment submitted after 2:30 PM will be considered late. The penalty for late assignments is 20% for up to 24 hours late, 50% for up to 48 hours late. Assignments will not be accepted more than 48 hours late (100% penalty). For appeals of lab assignment marking: Any questions regarding the marking of lab assignments must be submitted to Ms. Shute along with a written explanation no later than 10 days after the date your assignment was returned to you. In your statement you must include specific references from the appendix of the manual on scientific writing as well as any literature supporting your argument. Upon receipt of your statement, Ms. Shute will reevaluate the entire assignment based upon your argument. Your grade may change in either direction. An introductory lab will be held separately for each individual lab section during the scheduled lab periods on January 6th (B02) and 7th (B01), in Room W270 Duff Roblin. Full details on requirements for the lab component, including the schedule of lab exercises, due dates for reports, and the date of the lab exam, will be provided in the manual or in the orientation lecture. Any questions regarding the labs should be directed to the lab instructor.

Experiments examining the compound action potential of frog sciatic nerves, the neuroendocrine control of colour change in fish melanocytes, the iono- and osmoregulatory abilities of freshwater crustaceans, ammonia transport across the crab gill, and acid-base balance in crustaceans will be performed and reported in formal written form.

NOTE: With respect to written reports, penalties will be imposed for late assignments or for any evidence of “academic dishonesty”, including plagiarism and cheating (see Section 7 of the 2009-10 Undergraduate Calendar or at http://webapps.cc.umanitoba.ca/calendar10/regulations/). Other important University Policies can be found in the Undergraduate Calendar or at http://webapps.cc.umanitoba.ca/calendar10/policies/. The Faculty of Science Statement on Academic Dishonesty (and other important policies) can be found at http://umanitoba.ca/faculties/science/student/webdisciplinedocuments.html – Please review these.

Faculty of Science Statement on Academic Dishonesty

Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another student, plagiarism, and examination impersonation.

Note: cell phones, pagers or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations.

Suggested penalties assessed by the Faculty of Science for acts of academic dishonesty are available on the Faculty of Science web-page: http://umanitoba.ca/faculties/science/

All Faculty members (and their teaching assistants) have been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department.

REGISTRATION RESTRICTIONS

PLEASE ENSURE THAT YOU THE STUDENT ARE ENTITLED TO BE REGISTERED IN THIS COURSE:

THIS MEANS THAT YOU THE STUDENT HAVE:

-the appropriate prerequisites, as noted by the calendar description, or have permission from the instructor to waive these prerequisites

-not previously taken, or are concurrently registered in this course and another that has been identified as “not to be held with”

The registration system may have allowed the student to register but it is up to the student to ensure that they have met all the requirements.

Consequences may be the student being withdrawn from the course part way through the term, or the course not used in the degree program. There will be no fee adjustment. This is not appealable.

BIOL 3500 – GENETICS 2

Instructor: Dr. Dan Gietz (Duff Roblin W369)

BIOL 3500 is a continuation of BIOL 2500, exploring in greater detail mapping of genes and linkage analysis along with more detailed analysis of DNA structure and function.

Course grades will be based on lab work and two examinations.

Laboratory component------30% Midterm Examination------20% Final Examination------50% (covers lab and lecture material)

Missed work or exams will be assigned 0 marks, unless documentable (notes from counsellor, physician, or clergy) reasons can be provided.

The lab component starts Sept. 16th, 2015 and will be held in room 305 Biological Sciences Building (BSB) 2:30 to 5:20 pm. every Wednesday. Marks for the lab component (30%) are based on one major report (10%) and several minor reports (2-3% each). Minor reports are often due during the lab period so it is recommended that students review lab material before class. See BIOL 3500 Lab Manual for full details.

The Midterm examination will be held during the lab period of Oct. 21nd, 2015. Results of this examination will be available before the deadline for voluntary withdrawal from the course.

The Final examination will cover lab and lecture material and be scheduled by student records during the December examination period.

Final Grade assignment will be based on the standard for the Department of Biological Sciences as follows:

Marking Scheme

A+ 90 - 100 A 80 - 89 B+ 74 - 79 B 68 - 73 C+ 62 - 67 C 56 - 61 D 50 - 55 F 0 - 49

Biol 3500 - Page 1 of 2 Students should be aware of the following items: a) Last date for voluntary withdrawal: November 18th, 2015. c) Students are directed to the Faculty of Science Academic Dishonesty website http://umanitoba.ca/science/undergrad/resources/webdisciplinedocuments.html for regulations in regard to cheating, plagiarism and examination impersonation.

Required Readings:

1. Textbook: Genetic Analysis: An Integrated Approach 1st Edition Mark F. Saunders and John Bowman (2012).

The Previous Textbook Used in Biol 2500 Winter 2013 iGenetics: A Molecular Approach 3rd Ed, Peter J. Russell (2010). Excerpts from iGenetics (2006) PJ Russell Can Be Used as a Reference Textbook for this course but Students will be Responsible for Finding the Corresponding Reading Material within this Textbook.

2. Lab Manual for BIOL 3500

NOTE: Due to the rapid pace of new developments in the field of Genetics a certain amount of material will be extracted from the current literature (i.e. scientific journals). Relevant articles will be put on reserve in the Science library and/or posted on D2L.

Biol 3500 - Page 2 of 2

Lecture Schedule and Required Reading: Subject to Change at Instructors Discretion

Material Covered for First Mid-term Genetic Analysis: An Integrated Approach 1st Edition Mark F. Saunders and John Bowman (2012).

Lecture (Date) Topic Required Reading 1. Sept. 11, 2015 Introduction Chromosome Structure & Chapter 7 [7.4:240-248] 2. Sept. 14, 2015 Replication Continuous and Discontinuous Strand Replication, RNA Primer Removal Chromosome Structure & and Okazaki Fragment Ligation, Simultaneous Synthesis of Leading and 3. Sept. 16, 2015 Lagging Strands, DNA Proofreading, Eukaryotic DNA Polymerases, Replication Telomeres, Telomeres Aging and Cancer 4. Sept. 18, 2015 Chromosome Structure & Replication Chapter 11 [11.1, 11.2 & 11.3: 361-368; 370-372] Bacterial Chromosome Compaction, Eukaryotic Chromosomes Are Organized as Chromatin, Chromatin Composition, Higher Order Chromatin Structure, Nucleosome Distribution and Synthesis during Replication, Chromatin Remodeling; Heterochromatin and Euchromatin, Centromere Structure, Centromeric Heterochromatin

Chapter 15 [15.2:502-508; 509-512] Chromatin Remodeling Regulates Eukaryotic Transcription, Open and Covered Promoters, Chromatin Remodeling by Nucleosome Modification, Chemical Modification of Chromatin; Epigenetic Heritability, Genomic Imprinting and Silencing by Nucleotide Methylation

Chapter 13 [13.1:428-429] Uniparental Disomy

Chapter 11 [11.4:373-377] Chromatin Structure Influences Gene Transcription, Chromosome Territory during Interphase, Dynamic Chromatin Structure, PEV Mutations, Chromatin-Remodeling Proteins, Inactivation of Mammalian Female X Chromosomes

5. Sept. 21, 2015 Regulation of Gene Expression Chapter 15 [15.1:495-502] Cis-Acting Regulatory Sequences Bind Trans-Acting Regulatory Proteins 6. Sept. 23, 2015 Regulation of Gene Expression to Control Eukaryotic Transcription, Structural Motifs of DNA-Binding 7. Sept. 25, 2015 Regulation of Gene Expression Proteins, Transcriptional Regulatory Interactions, Enhancer-Sequence Conservation, Yeast Upstream Activator Sequences, Locus Control Regions, Repressor Proteins and Silencer Sequences, Transcription Regulation by Enhancers and Silencers, Insulator Sequences, Enhancer Mutations

Chapter 8 [8.3 & 8.4:270-276; 278-287] Eukaryotic Polymerases, Consensus Sequences for RNA Polymerase II Transcription, Promoter Recognition, Detecting Promoter Consensus Elements, Enhancers and Silencers, Transcription Factors and Signal Transduction; Post-Translatiional Processing Modifies RNA Molecules, Capping 5’ mRNA, Polyadenylation of Pre-mRNA, Pre-mRNA Intron Splicing, Splicing Signal Sequences, Coupling of Pre-mRNA Processing Steps, Alternative Transcripts of Single Genes

Chapter 9 [9.1, 9.2 & 9.3:299-310] Ribosomes Are Translation Machines, Bacterial and Eukaryotic Ribosome Structures, The Three-Dimensional Structure of the Ribosome, Translation Initiation, Bacterial Translational Initiation, Polypeptide Elongation, Translation Termination, Translation Complex

Biol 3500 - Page 1 of 3 Regulation of Gene Expression Chapter 15 [15.3:512-517] Cont. RNA-Mediated Mechanisms Control Gene Expression, Gene Silencing by Double-Stranded RNA, Chromatin Modification by RNAi, The Evolution of RNAi

8. Sept. 28, 2015 Allelism and Complementation Chapter 4 [4.1, 4.2, 4.3 & 4.4:106-118; 119-122; 122- 9. Sept. 30, 2015 Allelism and Complementation 133; 133-135] The Molecular Basis of Dominance, Effects of Mutation, Incomplete Dominance, Codominance, Lethal Mutations, Sex-Limited Traits, Sex- Influenced Traits, Delayed Age of Onset; Incomplete Penetrance, Variable Expressivity, Gene-Environment Interactions, Pleiotropic Genes; Gene Interaction Modifies Mendelian Ratios, Gene Interaction in Pathways, The One Gene-One Enzyme Hypothesis, Genetic Dissection to Investigate Gene Action, Epistasis and Its Results; Complementation Analysis Distinguishes Mutations in the Same Gene from Mutations in Different Genes

10. Oct. 2, 2015 Review of Two and Three Point Chapter 5 [5.1, 5.2 & 5.3:144-150] Crosses Linked Genes Do Not Sort Independently Introduction, Indications of Genetic Linkage, The Discovery of Genetic Linkage, Detecting Autosomal Genetic Linkage through a Test-Cross Analysis; The First Genetic Linkage Map, Map Units, Chi-Square Analysis of Genetic Linkage Data; Three-Point Test-Cross Analysis Maps Genes, Finding the Relative Order of Genes by Three-Point Mapping, Construction a Three-Point Recombination Map

11. Oct. 5, 2015 Tetrad Analysis Chapter 5 [5.7 170-174] Genetic Linkage in Haploid Eukaryotes Is Identified by Tetrad Analysis, 12. Oct. 7, 2015 Tetrad Analysis Analysis of Unordered Tetrads, Ordered Ascus Analysis

Recombination & Mapping Chapter 5 [5.4:159-165] 13. Oct. 9, 2015 Functions Recombination Results from Crossing Over, Cytological Evidence of Recombination, Limits of Recombination along Chromosomes, 14. Oct. 12, 2015 NO Lecture Recombination within Genes, Biological Factors Affecting Accuracy of Recombination & Mapping Genetic Maps, Correction of Map Distances 15. Oct. 14, 2015 Functions Chapter 12 [12.7 & 12.8:410-415] Meiotic Recombination Is Controlled by Programmed Double-Strand Breaks, The Holliday Model, The Double-Stranded Break Model of Recombination & Mapping Meiotic Recombination, Holliday Junction Resolution; Gene Conversion 16. Oct. 16, 2015 Functions Is Directed Mismatch Repair in Heteroduplex DNA

Chapter 5 [5.8:174-176] Mitotic Crossover Produces Distinctive Phenotypes Oct. 19, 2015 No Lecture 17. Oct. 21, 2015 Molecular Markers Chapter 7 [7.5:248-253] Molecular Genetic Analytical Methods Make Use of DNA in Replication Process, The Polymerase Chain Reaction, Separation of PCR Products, Dideoxynucleotide DNA Sequencing

Chapter 10 [10.2:335-348] Genetic Variation Can Be Detected by Examining DNA RNA and 18. Oct. 23, 2015 Molecular Markers Proteins, Gel Electrophoresis, Identification of DNA Sequence Variation, Molecular Probes, Electrophoretic Analysis of Sickle Cell Disease

Chapter 16 [16.2 & 16.5:531-540; 550-555] Specific DNA Sequences Are Recognized Using Recombinant DNA Technology, Restriction Enzymes, Molecular Cloning; Positional Cloning

19. Oct. 26, 2015 Review Midterm in During Lab – No Oct. 28, 2015 Class

Biol 3500 - Page 2 of 3

Lecture Schedule and Required Reading: Subject to Change at Instructors Discretion

Material Covered for Mid-term to Final Exam Genetic Analysis: An Integrated Approach 1st Edition Mark F. Saunders and John Bowman (2012).

Lecture (Date) Topic Required Reading 20. Oct. 30, 2015 Cytoplasmic Inheritance 19.1:642-646 21. Nov. 2, 2015 Cytoplasmic Inheritance Cytoplasmic Inheritance Transmits Genes Carried on Organelle Chromosomes, The Discovery of Cytoplasmic 22. Nov. 4, 2015 Cytoplasmic Inheritance Inheritance, Homoplasmy and Heteroplasmy, Genome Replication in Organelles, Variable Segregation of Organelle Genomes 19.2:646-656 Modes of Cytoplasmic Inheritance Depends on the Organism, Mitochondrial Inheritance in Mammals, Mating Type and Chloroplast Segregation in Chlamydomonas, Biparental Inheritance in Saccharomyces cerevisea 19.3:656-659 Mitochondrial Genome Structure and Gene Content, Mitochondrial Transcription and Translation 23. Nov. 6, 2015 Mutation and DNA Repair 12.1:384-386 24. Nov. 9, 2015 Mutation and DNA Repair Mutations Are Rare and Occur at Random, Mutation Frequency, The Fluctuation Test 25. Nov. 11, 2015 Thanksgiving Holiday 12.2: 386-392 26. Nov. 13, 2015 Mutation and DNA Repair Gene Mutations Modify DNA Sequence, Base-Pair 27. Nov. 16, 2015 Mutation and DNA Repair Substitution Mutations, Frameshift Mutations, Regulatory Mutations, Forward Mutations and Reversion 12.3:392-395 Gene Mutations May Arise from Spontaneous Events, DNA Replication Errors, Spontaneous Nucleotide Base Changes, DNA Nucleotide Lesions 12.4:395-402 Mutations May Be Induced by Chemicals or Ionizing Radiation, Chemical Mutagens, Radiation-Induced DNA Damage, The Ames Test 12.5:402-407 Repair Systems Correct Some DNA Damage, Direct Repair of DNA Damage, Nucleotide Excision and Replacement, DNA Recombination Repair, DNA Damage Signaling Systems, DNA Damage Repair Disorders 12.6:407-410 Proteins Control Translesion DNA Synthesis and the Repair of Double Stranded Breaks, Translesion DNA Synthesis, Double-Strand Break Repair

Biol 3500 - Page 1 of 4

Lecture (Date) Topic Required Reading 28. Nov. 18, 2015 Transposable Elements 13.5:444-445 29. Nov. 20, 2015 Transposable Elements Transposable Genetic Elements Move Throughout the Genome, The Discovery of Transpostion, Characteristics of Transposable Genetic Elements 13.6:445-449 Transposition Modifies Bacterial Genomes, Insertion Sequences, Transposons, Transpostion Mechanisms 13.7:449-451 Transpostion Modifies Eukaryotic Genomes, Drosophila P elements, Retrotransposons 16.5:550 Using Transposons to Clone Genes 16.1:523-530 Forward Genetic Screens Identify Genes by Their Mutant 32. Nov. 23, 2015 Forward Genetic Screens Phenotype, Designing a Genetic Screen, Analysis of Mutagenesis, Identifying Interacting and Redundant Genes Molecular Biology and 16.2:531-540 30. Nov. 25, 2015 Genomics Specific DNA Sequences Are Recognized Using 31. Nov. 27, 2015 Molecular Biology and Recombinant RNA Technology, Restriction Enzymes, Genomics Molecular Cloning 16.3:542-543 DNA Sequencing Technologies Have Revolutionized Biology, Sequencing Long DNA molecules, New Sequencing Technologies: Next Generation and Third Generation 16.5:550-555 Positional Cloning 17.1:563-569, 571-578 Introducing Foreign Genes into Genomes Creates Transgenic Organisms, Transgenes in Escherichia coli, Production of Human Insulin in E. coli, Changing the Sequence of DNA Molecules, Transformation of Plant Genomes by Agrobacterium, Transgenic Animals 18.1:603-606 33. Nov. 30, 2015 Modern Genomics Structural genomics Provides a Catalogue of Genes in a Genome, The Clone-by-Clone Sequencing Approach, Whole Genome Shotgun Sequencing 18.2:614-620 Evolutionary Genomic Traces History of Genomes, Interspecific Genome Comparisons: Gene Content 18.3:627-630 Transcriptomics

Biol 3500 - Page 2 of 4

Lecture (Date) Topic Required Reading 34. Dec. 2, 2015 Developmental Genetics 20.1:675-677 35. Dec. 4, 2015 Developmental Genetics Development is the Building of a Multicellular Organism, Cell Differentiation, Pattern Formation 36. Dec. 7, 2015 Developmental Genetics 20.3:692-693 Cellular Interactions Specify Cell Fate, Inductive Signalling Between Cells, Lateral Inhibition, Cell Death During Development 20.2:677-680 Drosophila Development Is a Paradigm for Animal Development, The Developmental Toolkit of Drosophila, Maternal Effects on Pattern Formation, Coordinate Gene Patterning of the Anterior-Posterior Axis, Domains of Gap Gene Expression, Regulation of Pair-Rule Genes, Specification of Parasegments by Hox Genes, Downstream Targets of Hox Genes, Hox Genes in Metazoans, Stabilization of Cellular Memory by Chromatin Architecture 37. Dec. 9, 2015 Review Dec 11-23, Final Exam Location TBA 2015

Biol 3500 - Page 3 of 4 BIOL 3600: Biological Diversity and Sustainability (3 CH) Winter 2016 J. Detwiler

Course learning objectives: Students should be able to (1) explain the significance of anthropogenic drivers of change on biological diversity, (2) critically examine the resulting impacts on ecosystem structure, function and capacity to provide essential goods and services for human well-being, and (3) evaluate current sustainability practices and suggest future alternatives.

Questions? Contact Dr. Jillian Detwiler, 208B Buller, [email protected], Office Phone: 204- 474-8689. I do not set specific office hours because in my experience few people can make the time I designate. Thus, if you would like to meet with me, please email to set an appointment.

I will post the key to the midterm exam outside of 208 Buller. If you have concerns about your grade, you must submit a professionally written email to me that states the question(s) you are concerned with, your original answer, and a justification for why you think you deserve more points. In addition, you will need to return your exam to me. I will respond to your email with a thoughtful response, and then set an in person appointment if it is necessary to further discuss the matter. I adopted this strategy because I think it helps you think more about the course material and how to respond to short and long answer questions.

Class time: Tuesday, Thursday 11:30-12:45 in Buller 527. Most weeks, the format will lean towards lecture punctuated by short student-student or small group discussions. You will also do some short in class writing assignments, some of which are geared towards “doing” best writing practices, as opposed to just “knowing” what they are (Griffin, 1998). In addition, you will share your ideas with your peers, and review each other’s essays. This is a large class, yet I am striving for an intellectually stimulating environment bolstered by active participation. I will do my best to make class time thought provoking and I expect the same effort from you. Be present and learn!

Limit your technology use during class: Focus on learning instead of distracting yourself and peers with texting, vibrating cellphones, websites not related to class, etc. Class participation points will be deducted if distracting use of technology is noted.

Lecture Notes: PDFs of the lectures will be posted on UM LEARN following that day’s lecture.

Textbook and Reading Materials: There is no required textbook, but there will be required reading in the form of articles posted on UM LEARN/downloadable via the Library. Material from these articles will appear on exams.

Written Responses to questions on UM LEARN (submitted via Dropbox): This is an effort to ensure that you read the assigned materials and are prepared for in class discussion. In addition, these responses help you practice your writing and develop your own thinking on particular ideas related to the course. When you submit on Dropbox, be sure to submit a word file that has your student number in the title as well as information as to what the assignment relates to. For example, for the first assignment #####_Griffin. These responses are part of your participation grade.

In Class Discussions: To get full credit for these discussions, you must have the article with you (electronic or paper copy). The instructor will circulate and confirm your participation or responses to questions will be turned in at the end of class to confirm your participation.

Essay (2000-3000 words): Written communication is an essential life skill that will be further developed by 1 required essay. In addition, you will improve your editorial skills by providing feedback on other student essays and your ability to understand, interpret, and cite scientific literature. Find specific guidelines and grading rubrics for the essays in UM LEARN.

Tentative Lecture Schedule (will be updated regularly as semester progresses. CHECK UM LEARN before each class)

Date Topic In class Readings activities Jan 7 Syllabus Time Read Griffin, 1998 about student writing strategies. Capsule Write responses to questions posted on UM LEARN and submit a .doc file Part I in DropBox. Name your file with your student number and Griffin. Ex: Detwiler_Griffin. Submit by start of class on Jan 12. Jan 12 State of the Research ideas for your essay. Search either Planet: http://news.mongabay.com/, click on Daily Environmental News link or Problems & http://conservationmagazine.org/ for ideas related to essay topic. Consequences Submit a file that summarizes 3 articles which you read. Each summary should be 3-5 sentences in length. Name your file with your student number and _EssayResearch. Submit by start of class on Jan 14. Jan 14 State of the Discuss Read Herndon & Butler, 2010 for Jan. 19. Submit by start of class on Jan Planet: responses 19. Response to Griffin questions. Start Biodiversity Discuss research ideas with classmates. Jan 19 Finish Bring your Biodiversity marked up copy of Herndon & Butler to class. Discuss responses to questions.

Jan 21 Valuing Read this article that gives tips about peer review. Biodiversity http://sciencecareers.sciencemag.org/career_magazine/previous_issues/ articles/2001_04_20/nodoi.5045631236818121057. Jan 26 Extinctions Jan 28 Bioindicators & Bring Submit first draft of essay in a word doc file via DropBox by start of class. Exotic Invasive paper copy Name file with student number and _Essay1. Ex) #####_Essay1 Species lecture of 1st draft Essay #1 to class, in class peer review of essay Turn in both at end of class (45 minutes). Feb 2 Arctic Pick-up Ecosystems peer Guest Lecturer reviews Dr. Dave Yurkowski Feb 4 Tropical Ecosystems: Bird diversity in Belize and bird- friendly coffee farming Guest Lecture Dr. Emily McKinnon Feb 9 Read Pauly, 1995 to understand shifting baseline syndrome. Respond to Overexploitation questions posted on UM LEARN via Dropbox. Submit by the start of class on Feb 11.

Feb Midterm (Buller Exam 11 527 &?) covers material through Feb 11. Feb 16, 18 MIDTERM BREAK Feb Perils of Small 23 Populations Feb Overharvesting Read Phelps et al., 2011 for March 1 in class discussion. Respond to 25 and recovery of questions posted on UM LEARN via Dropbox. Submit by the start of class small on March 1. populations Guest Lecturer Dr. Colin Garroway

March Fragmentation Bring Keep answers to questions about ARC –re-watch video to study for exam 1 Phelps et and answer all questions posted in class. Discussion of al., 2011 to Phelps et al., class. http://www.humansandnature.org/to-build-or-not-to-build-a-road---- 2011 Discuss how-do-we-honor-the-landscape--question-1.php Dr. Nina-Marie Lister, and Ryerson University Video about respond to ARC competition article. March Habitat Revised Essay #1 and “Response to Reviewers” document due (send via 3 Destruction Dropbox by start of class).

March Finish Habitat Midwest Greenhouse Gas Reduction Accord http://www.c2es.org/us- 8 Destruction. states-regions/regional-climate-initiatives/mggra

The Nature Conservancy’s World Risk Report. Focus on being able to describe trends associated with human risks shown in the maps on pages 2 & 3. March Start 10 Conservation/ Planning and Unprotected Areas March Finish Planning 15 & Planning and Unprotected Areas. Start Biotic Response to Climate Change March Conservation 17 planning with TEK Guest Lecturer Elly Bonny March Finish Biotic 22 Response to Climate Change. Start Policy Responses to Biodiversity Loss and Ecosystem Degradation

March Finish Policy Read Favaro et al 2014. Respond to questions posted on UM Learn via 24 Responses to Dropbox. Submit by the start of class on March 29. Biodiversity Loss and Ecosystem Degradation. March Sustainability & Discussion 29 Resilience of Favaro et al 2014 March Conservation 31 Successes April Sustainability SEEQs 2 successes: CEO perspectives April Reflection & Time 7 Review of goals Capsule & for course Short Evaluation

UM Learn: This site will contain the syllabus, lecture notes, readings, and supplementary materials. You will need to consult it frequently!

Grading Policy: Your final grade will be based on the percentages shown below. Zero points will be awarded for that day if first essay is not brought to class. One grade is deducted for each day the final essay is late (e.g. A+ to A). For in class assignments, there are no make-ups so if you are not present no points will be earned. Each student starts with a freebie, meaning that the lowest participation grade will be dropped from the final grade. If you have a pre-approved excuse, please discuss make-up options with Dr. Detwiler.

Essay 30% Research Essay #1 1st draft of Essay 1 20% of final essay grade In class peer review of 1st 5% of final essay grade draft Revised Essay 1 75% of final essay grade Mid Term 30% In class participation In class writing assignments, participating in 10% discussions, responses submitted to Dropbox Final exam Comprehensive review of lecture topics/readings 30%

Academic Honesty: There is no tolerance for plagiarism and cheating. For the essay, we will be using iThenticate software to help detect instances of plagiarism. Consequences include a grade of zero for the essay or exam, failure in the course, or expulsion from the University. Assume that all work for the course is individual-based unless told otherwise.

BIOL 4100 - HONOURS THESIS COURSE OUTLINE 2015-2016

CREDIT: 6 hours (both terms)

PREREQUISITE: Fourth Year Honours status in Biological Sciences

COORDINATORS: Members of the Honours Thesis Committee (HTC): Dr. Jason Treberg, 474-8122, [email protected] (chair 2015-2016) Dr. Dirk Weihrauch, 474-6310, [email protected] Dr. Anne Worley, 474-9541, [email protected] Dr. Sylvie Renault, 474-6914, [email protected] Dr. Jay Kormish, 474-7810, [email protected] Dr. Jillian Detwiler, 474-8689, [email protected] Dr. Jane Waterman, 272-1678, [email protected]

CLASS MEETINGS AND DEADLINES:

There are no regular lectures or labs, but the following general meetings of the class are scheduled:

→ symposium for the oral examination of all theses. Date: TBA (the symposium is typically between the last day of classes and the start of the winter-term final exam period, which is April 10-11 this year, and may take place on a weekend)

Once set by the HTC the thesis symposium dates are immutable - no extensions will be given.

In addition, each student must meet with his or her advisory committee (see below for description):

1. By 22 May 2015 (for summer research projects) or before 18 September 2015 (for regular session projects) to present the research proposal orally for discussion and approval by the advisory committee. Although not mandatory, it is generally in the student’s best interest to have the proposal meeting completed before commencing research; however, if this is not possible you should contact the HTC Chair by email in advance of the deadline. Contact the HTC Chair as soon as possible if you, or your advisor, have questions or will have difficulty meeting these deadlines. Copies of the proposal document must be submitted, one to each member of the advisory committee, at least one week prior to the proposal meeting. These copies may be electronic (e.g., Word documents) or printed, depending on the preference of committee members. An electronic copy MUST also be provided to the HTC Chair on this same date.

2. Before the 15 of January 2016 (end of the 2nd week of January 2016) to present orally a progress report for discussion and review (see below). A copy of the written progress report must be submitted to each advisory committee member by 15 December 2015, with an electronic copy sent to the HTC Chair.

A first draft of the thesis document should be given to your advisor(s) by 4 March 2016 or earlier, and a revised version should be submitted to all members of the advisory committee by 29 March 2016 for grading. A final corrected copy of the thesis for the Department's archives is due in the Biological Sciences General Office on 29 April 2016. A failing grade will be assigned if the revised thesis is not submitted by this date.

COURSE CONTENT AND PROCEDURES: The course is designed to give Honours students experience in scientific research, from the inception and planning stages through experimental execution, data analysis, written reporting and oral communication.

Advisor. Each student will be responsible for finding an advisor from among the Biological Sciences faculty who is willing and able to supervise the research project and provide facilities/resources for it. If a non-department advisor is desired, the student must first consult with the course chair to seek approval of that advisor. If an advisor is selected from outside the Department of Biological Sciences, a co-advisor from within the department will be appointed. Note: Each co-advisor has equal stature on the committee, and together they count as a single vote.

Advisory Committee. An advisory committee consisting of the advisor (and co-advisor if required), one HTC member, and one additional committee member will then be set up for each student, to give advice and assess progress. Note: the student and/or the student’s Advisor must identify and contact the additional committee member well in advance (by 15 April or 15 Aug.) of the proposal meeting. It is the responsibility of the student to provide the Advisor’s and committee member’s name and contact information to the HTC chair. The HTC member of the advisory committee will be assigned by the HTC chair.

The experimental part of the project may be carried out during the fall term of the fourth (or fifth) year or during the preceding summer. Students may also use data gathered during summer employment outside the Department, provided that both the employer and the student's thesis advisor(s) agree in writing beforehand to the student's use of these data. Non-experimental projects involving either the original compilation and analysis of existing data or the theoretical exploration of a problem (e.g. model development) may also be acceptable. Please contact the Chair of the HTC for permission.

Information. In the spring term (February), the Honours Thesis Committee will hold an information meeting with students interesting in taking the Honours Thesis course in the following academic year. This orientation will provide information on course requirements and procedures, and will help students to contact possible advisors, if they have not already done so.

Research proposal and review. In consultation with the advisor(s), each student will prepare a written research proposal, ideally before starting a project, and will distribute this proposal to the advisory committee. At the subsequent proposal review meeting, the student will present the proposal orally (see Guidelines below) to the advisory committee, who will discuss it and possibly suggest modifications. The amended proposal will become the student's research plan. For students intending to carry out summer research projects, the advisory committee should be in place, and the proposal prepared and reviewed, and orally presented before May 22. Students intending to do fall research projects should have proposals ready for review by their advisory committees before the beginning of the fall term to facilitate organizing the proposal meeting before the September 18th deadline.

Progress report. Each student will submit a written progress report by 15. December, by which time data collection should be done or close to completion. The written report will be reviewed before the end of the exam period.

In the event that a student's progress is judged to be unsatisfactory, an early meeting of the advisory

2 committee and the student will be called and if there is no reasonable way to get the project back on track so it can be finished on time, the student will be asked to withdraw from the course. The student could then graduate with a B.Sc. (Major) upon successful completion of 6 hours of credit from courses acceptable for the Major Program in addition to the remainder of the courses in the original Honours Program. Likewise, if either the research proposal or the progress report is not submitted by the due date, nor within a reasonable time thereafter following a reminder from the advisory committee, the student will be required to withdraw from the course.

Assuming sufficient demonstrable progress in the written report, the oral presentation of the progress report will be scheduled between mid-December and before the end of the 2nd week in January. Typically meetings will occur following the Christmas break. If a student would prefer to complete the progress report meeting before Christmas break, and the advisory committee is available, the student may request a meeting in December; however, it is recommended that the student plans for this early and submits the request to the HTC chair well before the 15 December deadline.

Thesis. The thesis should be written in accordance with the guidelines given below. All theses will be orally examined and defended at the Honours Thesis Symposium, to be held before the beginning of final examinations in the Spring Term (April).

Oral thesis examination (defense). The thesis examination committee will consist of a Chairperson (one member of the Honours Thesis Committee or departmental designate) and three examiners: the advisor(s), a member of the Honours Thesis Committee, and the additional committee member. Two of the three examiners must be regular faculty members in the department. At the defence, the student should present a summary of the thesis and its findings in a 12-minute talk. After the oral presentation, each student will be questioned orally on the thesis for about 5 to 10 minutes by each examiner. Each examiner will independently evaluate the written thesis, the oral presentation and the student's responses to examiners' questions.

Departmental thesis copy. The examining committee will agree upon any final editorial corrections that the student should make to the submitted thesis document. Major substantive changes are not permitted at this stage. One final corrected copy of the thesis should then be submitted to the course coordinators after the spring examination period. This copy will be bound by the Department and be made available to interested readers.

GRADING: The course grade for each student will be assigned on the basis of evaluations from the student's advisor(s) and advisory or thesis examination committee members. Marks will be given for:

1. The research proposal (including oral presentation) = 10% 2. The progress report (including oral presentation) = 15% 3. The conduct of the research (evaluated by the advisor(s) only) = 15% 4. The thesis as a written document = 50% 5. The oral thesis presentation = 5% 6. The oral thesis examination = 5% 100%

Note: All marks with the exemption of items 3 are evaluated by each member of the thesis examination committee. Resultant values will be a mean of the marks submitted by each of these committee members. The written proposal, progress report, research conduct, thesis document, oral thesis presentation and examination will be evaluated by both advisor and co-advisor, and their grades will be averaged. In the event of an advisor being unable to attend the oral defense of the thesis research, the co-advisor will submit that portion of the grade.

Midterm evaluation: Students will receive written evaluations with assigned marks from their advisory committees after both the research proposal review meeting and the progress report review meeting.

Plagiarism and cheating: Students should be careful to attribute properly the sources of ideas and information used in their written and oral presentations. Plagiarism carries severe penalties – see relevant discussion in the University of Manitoba Undergraduate Calendar. Students uncertain as to what constitutes plagiarism should consult their advisors or other staff members. Note: In cases where students have prepared written reports for other courses on a similar research topic (e.g. BIOL 3100), they are not allowed to resubmit this work in its original form (this is called “duplicate submission” and is outlined under Cheating, Plagiarism and Fraud according to the following: http://umanitoba.ca/student/resource/ student_advocacy/cheating_plagiarism_fraud.html). This text must be paraphrased.

GUIDELINES FOR WRITING THE RESEARCH PROPOSAL: The Honours Thesis research proposal should be no more than 6 to 12 written pages in length (excluding figures and tables) and be double-spaced. The following points should be covered, preferably in the order given. These do not represent required section headings for your proposal, however. Before you begin to write, you should consult with your advisor to determine if all of these points are relevant to your proposal and if there are any additional items that should be included.

Introduction (2 - 3 pages) → summarize the literature background and context of your proposed research, i.e. what is known about the topic → cite only the most relevant literature to justify your research question (i.e. this should not be an exhaustive review which is more appropriate for the final thesis document) → describe the relevance of the proposed research to your field of inquiry → explicitly state your research objectives or question(s), possibly recasting as a testable hypothesis

Proposed Research Activities (4 - 9 pages) → this is the main body of your proposal → the material presented here will provide the focus for discussion during your proposal review

This section will form the basis for the Materials and Methods section of your final thesis document and should include details about the: i) Study design → how will your study organisms be obtained and/or maintained? → apparatus – how will your equipment and experiments be set up? (include figures if applicable) → field site description (if applicable) → pertinent Animal Care Protocols and collection permits (if required). ii) Experimental protocol → what is your experimental unit? → what traits or variables will be measured? → how will measurements be made? (include modifications to published techniques) 4

→ what control observations will be made? → how many treatments / replicates / samples will be measured, and in what order? iii) Data presentation and processing (tables and other formats) → how do you plan to present your data at the end of your field work / experiment? → what mathematical transformations or formulae will you apply, and why? iv) Proposed statistical analysis → which tests will be performed and why? → statistical considerations (e.g. power, number of replicates).

Literature Cited → the style adopted by the Canadian Journal of Zoology or Botany will be the accepted standard (see "Instructions to Authors" on the journal webpages). Please be consistent.

GUIDELINES FOR WRITING THE PROGRESS REPORT:

The written progress report should concisely describe and analyze the scientific findings of the project to date for the advisory committee. A suitable outline should include: 1. Introduction (more thorough and comprehensive than in the proposal document) 2. Research objectives and hypothesis 3. Methods and Materials (should be nearly complete; describe any problems encountered together with detailed modifications from the original proposal). 4. Results (brief summary of your analyzed data; you should make reference to tables and figures here). This section should include tables and graphs of the results 5. Preliminary Discussion, including comparisons with published literature 6. Outlook and timeline (can be in table format) for successful completion of project 7. Literature cited 8. Appendix if required This report should emphasize mainly the results obtained in the various experiments, wherever possible through a preliminary graphical or tabular presentation of data and some assessment of their statistical significance. This presentation should be integrated with a brief discussion comparing the results obtained with the outcomes expected on the basis of relevant literature. The adequacy of the experimental design should be assessed, on the basis of the experience gained. Any difficulties experienced with particular experiments should be described, and their implications for the project's successful completion should be explained.

GUIDELINES FOR WRITING THE THESIS:

The thesis should follow the University of Manitoba graduate theses in format. It should begin with:

1. A title page (not numbered), as follows:

......

The title of the thesis

Author's Name

A thesis submitted to the Department of Biological Sciences, University of Manitoba, in partial fulfilment of the requirements for the course BIOL 4100 (Honours Thesis) for the degree of Bachelor of Science (Honours)

©Month, year

......

2. An abstract of 200 - 300 words summarizing the problem, methods, results and conclusions (numbered page i - sequential small Roman numerals follow)

3. Acknowledgements (page ii) – submitted only in the final (post-defence) thesis version

4. Table of Contents (beginning on a new page)

5. List of Tables (beginning on a new page, see note regarding placement of Tables)

6. List of Figures (beginning on a new page, see note regarding placement of Figures) This should be followed by the main body of the thesis. Text should be Times New Roman, size 12 font and double-spaced (no more than 3 lines per inch). Figure legends, tables and references may be single- spaced; references should then be separated by a blank line. Margins should be 1 inch at the top, bottom and right-hand edges of the page, and 1.5 inches at the left to allow for binding.

7. Introduction (beginning on page 1 - sequential Arabic numerals hereafter), outlining questions and hypotheses addressed, in the context of all relevant literature

8. Materials and Methods

9. Results

10. Discussion

11. Literature Cited The style adopted by the Canadian Journal of Zoology (see http://www.nrcresearchpress.com/page/cjz/ authors#Manuscriptguidelines) or the journal Botany (http://www.nrcresearchpress.com/page/cjb/ authors#Themanuscript) will be the accepted standard. Note: The student, on request of the advisor, may prepare the thesis to conform to a different format, used by another refereed journal in the discipline of the thesis; in this case, the format should be identified in advance and made available to the student's thesis examination committee.

Tables and Figures may be either: a) placed at the end of the thesis after the Literature cited or b) integrated into the body of the thesis. Large figures should be placed on separate pages in the text just after each is first cited. The figure legend may be printed below the figure on the same page (this page would be numbered sequentially with the text), or the legend may be placed on the preceding page facing the figure (in this case, the page with the legend receives a number but the page with the figure does not). Smaller figures might be inserted in the running text. Tables should likewise be interleaved and paginated in sequence with the text after they are first cited.

Students should consult with their advisory committee regarding placement of tables and figures.

12. Appendices (if necessary)

In case of other questions regarding format, the course coordinators may be consulted. Alternatively recent Honours Theses (available in the Buller Conference/Coffee Room; 528 Buller Building) may be used as guides. There is no set minimum/maximum limits on thesis length, however past documents have typically ranged in length from 30 to 80 pages (main body, including figures, tables and references). Keep in mind that length is not an indicator of quality and concise, well-written documents will make it much easier for your committee to appreciate the significance of your findings.

GUIDELINES FOR ORAL PRESENTATIONS:

The following guidelines refer specifically to the three oral presentations in the Honours Thesis course. The goal of these presentations is to summarize your research plans or results prior to discussion and to provide visual aids to assist that discussion. The presentation should be concise and approximately 12 minutes in duration for the research proposal and progress report, and no more than 12 minutes in duration for the thesis defence. It is important to discriminate between essential and nonessential information in preparing formal presentations with strict time limits. Though you should focus on your own research plans or results, you should remember that the course coordinators sitting on your advisory committee are probably initially unfamiliar with your specific field of research.

The following is a suggestion on how to organize your oral presentations:

1. Allow 1 to 2 minutes for each visual aid presented. 2. The first visual should have your name and the title of your research project. 3. The second visual is optional and may contain a general outline of your presentation and provide a ‘road-map’ of what you will present. 4. The next visual contains the background material and the research question(s) being posed. 5. The remaining visuals should deal with: 3

→ the details of research materials and design (for the research proposal) → the results obtained (for the progress report and thesis defence) and → the conclusions drawn from the results (for the defence). 6. Text visuals should: → be in large type (24-point or greater) or neatly hand written; avoid ‘fancy’ fonts and distracting animations → contain no more than 15 lines per page (preferably less) → be formatted as an outline or as complete but distinct sentences (no paragraphs). 7. Table visuals should: → have columns and rows clearly labelled (include sample sizes and statistical analysis where appropriate) → indicate (throughout the presentation) how the data relate to the experimental design. 8. Figure visuals should: → indicate expected or observed relationships → have axes and measurement units clearly labelled (include sample sizes and statistical relationships where appropriate). 9. Diagrams, maps and images should: → be clearly labelled to indicate features relevant to your research → include an indication of scale.

Note: It must be clear that you understand the background of your proposed study and the methods/experimental design you intend to use. Make sure that you understand the given time- frame of the study and the overall feasibility of the project.

BIOL 4212: SYSTEMATICS AND BIOGEOGRAPHY OF FISHES 3 CREDITS, WINTER 2016

LECTURES: M, W, F 9:30–10:20 am, Room 401 Biological Sciences Building LABS: T 2:30–5:25 pm, W240 Duff Roblin Building

INSTRUCTOR & OFFICE HOURS: Dr. Margaret Docker 505B Buller Building 204-474-8831; [email protected] W, F 1:30–2:30 pm or by appointment

COURSE DESCRIPTION: This course will explore the diversity of the world's 25,000+ species of fishes. A primarily phylogenetic organization will be followed as we trace the evolution of fishes over their 600-million-year history. Patterns of marine and freshwater geographic distribution will be presented, as well as modern methods and concepts associated with phylogenetic systematics and phylogeography. A brief history of ichthyology, important rules of zoological nomenclature, and legislation dealing with the conservation of native fishes in Canada will also be covered.

Weekly labs will focus on fish identification and classification, emphasizing identification of fishes from Manitoba and other parts of Canada. The diversity of worldwide fishes will be studied using the departmental fish collection. Given that a field trip will not be feasible during the winter, there may be a class trip (e.g., to the zoo or Fort Whyte’s “Aquarium of the Prairies”) near the end of the semester to allow you to see and identify live fishes. You will be expected to maintain an electronic lab “notebook” with well- labelled photographs and/or illustrations; this notebook is intended to provide you with a lasting guide to the identification and classification of the fishes we examine in the laboratory. You will be graded on your electronic notebook (see below).

TEACHING & LEARNING PHILOSOPHY: I will do my best to create a comfortable atmosphere for learning, present the material in an organized manner, and be open to questions and constructive feedback. I expect you to be ready to explore new ideas, participate fully in class exercises, ask for clarification when needed, and to complete assignments by the class deadline. If you cannot meet a deadline, please discuss it with me as soon as possible. Work that is handed in late without sufficient documentation will be docked 10% per day.

Lecture outline notes will be posted before the lecture on UM Learn (listed in the order presented and by topic under “Files”). These are NOT intended to replace the lectures, but are meant to: 1) allow you to review upcoming material in advance of the lecture; 2)

1 ease your note taking during lectures; and 3) serve as a reference in the absence of a required Fish Systematics textbook. You are encouraged to supplement these with notes taken during class and, if useful, photographs (e.g., from the internet).

GRADING SCHEME: Midterm Test (Fri, Mar 4, during lecture) 10% Midterm Lab Test (Tues, Feb 23, during lab) 10% Research Paper (Fri, Apr 1, 5:00 pm) 15% Lab Final (Tues, Apr 5, during lab, or TBD)* 15% Electronic Lab “Notebook” (due at Final Lecture Exam) 15% Pop Quizzes, Mini-assignments, Participation 5% Final Lecture Exam (TBA) 30%

*Lab Final will be held during the usual lab period on Tues, Apr 5, unless the class unanimously would prefer to have it closer to the lecture final exam (i.e., during the final exam period) so that students can study for both exams at once

ELECTRONIC LAB NOTEBOOK: You will be putting together an electronic compilation of our laboratory exercises, supplemented with photographs or other materials that will provide you with a lasting guide to the identification and classification of the fishes we examine in the laboratory. There is no set format, but you will be graded for completeness, organization, and presentation. Organization and annotation is key; the goal is for you to be able to find the information you need when you need it. You have until the final exam to finalize your notebook because putting the finishing touches on it will likely help you study for the exam (but I may ask to see “sneak previews” of it intermittently during the semester as part of your “pop quizzes, mini-assignments, participation” mark).

REQUIRED TEXTBOOK: Stewart, K. and D.A. Watkinson. 2004. Freshwater Fishes of Manitoba. University of Manitoba Press (also in Reference section in Elizabeth Dafoe Library QL 626.5 M3 S74).

REFERENCE TEXTBOOK: Barton, M. 2007. Bond’s Biology of Fishes, 3rd edition. Brooks Cole (available on Reserve in Science Library and I have multiple copies that I am happy to loan out).

OTHER USEFUL REFERENCES AND MATERIALS: BOOKS Nelson, J.S. 2006. Fishes of the World, 4th Edition. John Wiley and Sons, Hoboken, N.J. Scott, W.B. and E.J. Crossman. 1973. Freshwater Fishes of Canada. Bulletin 184, Fisheries Research Board of Canada (on Reserve in Science Library).

ONLINE REFERENCE MATERIAL: Catalog of Fishes. California Academy of Sciences, the authorative reference for taxonomic fish names (www.calacademy.org/scientists/projects/catalog-of-fishes); searchable online database (“Search the catalog”) great resource for determining current (valid) taxonomic names and authorities FishBase (http://www.fishbase.org/); searchable database with species summaries providing information on classification, distribution, general biology, and conservation status Page, L.M., H. Espinosa-Pérez, L.T. Findley, C.R. Gilbert, R.N. Lea, N.E. Mandrak, R.L. Mayden, and J.S. Nelson. 2013. Common and Scientific Names of Fishes from the United States Canada and Mexico, 7th Edition. American Fisheries Society Special Publication No. 34 (see http://fisheries.org/docs/pub_fish_names.pdf for searchable online version).

OTHER STUFF: Deadline for late registration: January 19, 2016 Last Date for voluntary withdrawal: March 18, 2016

ACADEMIC HONESTY: Plagiarism or academic dishonesty will not be tolerated in this course. All students should be familiar with the University of Manitoba’s website on academic dishonesty: http://umanitoba.ca/faculties/science/undergrad/resources/webdisciplinedocuments.html

BIOL 4212: SYSTEMATICS AND BIOGEOGRAPHY OF FISHES TENTATIVE SCHEDULE:

Chapter references are from Barton (2007), Bond’s Biology of Fishes, 3rd edition M T (Lab) W F Jan 6 Jan 8 Course Introduction History of Ichthyology (Chapter 1) Jan 11 Jan 12 Jan 13 Jan 15 Fish Anatomy Lab 1: Introduction, Fish Fish Anatomy, Cont’d Taxonomy and (Chapter 3) Anatomy Nomenclature (Chapter 1) Jan 18 Jan 19 Jan 20 Jan 22 Nomenclature, Cont’d Lab 2: Myxini to Systematics Jawless Fishes Chondrichthyes (Chapter 4) (Chapter 5) Jan 25 Jan 26 Jan 27 Jan 29 Jawless Fishes, Cont’d Lab 3: Sarcopterygians Chondrichthyes Chondrichthyes, Cont’d and basal (Chapter 6) Actinopterygians Feb 1 Feb 2 Feb 3 Feb 5 Chondrichthyes, Cont’d Lab 4: Ostariophysi I Introduction to the Basal Actinopterygians: (the milkfish and Telostomes; Chondrosteans, minnows) Sarcopterygians (Chapter “Holosteans” 7) (Chapter 8) Feb 8 Feb 9 Feb 10 Feb 12 Introduction to the Lab 5: Ostariophysi II Elopomorphs Clupeomorphs Teleosts; (suckers, characiformes, (Chapter 9) (Chapter 9) Osteoglossomorphs knifefishes, catfishes) (Chapter 9) Feb 15 Feb 16 Feb 17 Feb 19 ---MID-TERM BREAK--- --MID-TERM BREAK------MID-TERM BREAK------MID-TERM BREAK-- Feb 22 Feb 23 Feb 24 Feb 26 Ostariophysans MIDTERM LAB TEST Ostariophysans, Cont’d Ostariophysans, Cont’d (Chapter 10) (10%) Feb 29 Mar 1 Mar 2 Mar 4 Introduction to the NO LAB NO LECTURE MIDTERM TEST (10%) Euteleosts; “Protacanthopterygii” (Chapter 11) Mar 7 Mar 8 Mar 9 Mar 11 Protacanthopterygii, Lab 6: Salmonids: Taxonomic Esociforms and Basal Cont’d Protacanthopterygii Problems Neoteleosts (Chapter 12)

M T (Lab) W F Mar 14 Mar 15 Mar 16 Mar 18 Paracanthopterygii Lab 7: Deepsea Conservation of Native Conservation of Native (Chapter 13) Neoteleostei, Fishes in Canada: Fishes in Canada, Paracanthopterygii, and COSEWIC (Committee on Cont’d basal Actinopterygii the Status of Endangered Wildlife in Canada) and SARA (Species at Risk Act) Mar 21 Mar 22 Mar 23 Mar 25 Acanthopterygii: Lab 8: Percomorpha I Acanthopterygians: GOOD FRIDAY Mugilomorphs, Percomorphs NO LECTURE Atherinimorphs (Chapters 14, 15) (Chapter 15) Mar 28 Mar 29 Mar 30 Apr 1 Acanthopterygians: Lab 9: Percomorpha II, Perciforms, Cont’d Acanthopterygians: Perciforms Review Final Percomorphs (Chapter 16) (Chapter 17) ESSAY DUE (15%) Apr 4 Apr 5 Apr 6 Apr 8 Biogeography of Fishes: Lab 10: Class Trip or Pleistocene Glaciation Course Wrap-Up Introduction LAB FINAL* and Postglacial Dispersal LAST CLASS (Chapter 29) of Fish

*Lab Final will be held during the usual lab period on Tues, Apr 8, unless the class unanimously would prefer to have it closer to the lecture final exam (i.e., during the final exam period) so that students can study for both exams at once

BIOL 4212: SYSTEMATICS AND BIOGEOGRAPHY OF FISHES Research Paper: Due Friday, April 1, 5:00 pm (15%)

You may write your research paper on A) an aspect of fish systematics or phylogenetics that has recently been or is currently under debate or B) the biology and conservation status of a species of freshwater fish in Manitoba. An essay on fish systematics (option A) can be entered into the competition for the “Leon Provancher Prize in Systematic Zoology “ in April; a report on one of the freshwater fishes of Manitoba (option B) could form the basis of a status report for COSEWIC (the Committee on the Status of Endangered Wildlife in Canada). See below for details, and I encourage you to discuss your ideas with me—both prior to finalizing your topic and throughout the writing process.

A. Fish Systematics: Reconsideration of Phylogenies Topic: Our existing classifications are hypotheses about the interrelationships of different fish taxa. The purpose of this research paper is to give you an appreciation for the fact that these hypotheses are subject to revision. This is especially true with the advent of molecular techniques (particularly DNA sequencing) that have allowed the phylogenies of many taxa, constructed previously using traditional morphological characters, to be tested with an independent character set.

Your research paper will re-examine the phylogeny of a fish taxon that has recently been or is currently under debate. Some questions that are particularly vexing to fish systematists and that we will discuss to some extent in class are: • Are the living agnathans monophyletic? • What is the relationship among the major elasmobranch lineages? • What is the relationship between the clupeomorphs and the ostariophysans? • Is Paracanthopterygii a monophyletic group? Any of these four topics would make a good essay; there are plenty of recent references available. You may also choose to write on another fish taxon of interest to you, provided that there is an interesting systematics question associated with this group. Ideally, you will choose a taxon that will allow you to evaluate phylogenies generated using both morphological and molecular data sets.

In your research paper, you’ll need to outline the traditional classification or classifications (in many cases, even before the use of molecular techniques, different classification schemes were proposed based on different morphological characters or on different interpretations of these characters), what some of the associated problems or conflicts are, and how they have been addressed recently with new data or new interpretations. If you are including papers that use molecular data sets, you are not expected to understand all the intricacies of the molecular analyses, but you should understand the results as well as the limitations of these data.

Samples: I have posted a few sample papers on UM Learn that use molecular data to help resolve previously debated fish phylogenies. These are all research papers (i.e.,

6 they have generated their own data to help resolve previously debated fish phylogenies), but they might help you get started. In contrast, to these original (primary) research papers, however, you will be writing a brief review summarizing the findings of other authors.

Length and Number of References: Your essay should be approximately 2500–3500 words (approximately 7–10 pages, double-spaced) plus tables and figures, but there is no hard-and-fast page limit or requirement. You will definitely want to include tables and/or figures. You’ll want to draw on more than just a few references (in particular, make sure you look up and cite the previous papers cited by others and not just repeat what is written in the most recent study). When you include the papers specific to your taxon and some general phylogenetic papers that you’ll need for background information, I would expect at least 10 references. The goal is to synthesize information from multiple sources, and not just summarize the findings of one or a few papers.

Format: Your paper will be written in essay format, not as a lab report or regular journal article (i.e., without Materials and Methods or Results). However, you can (in fact, are encouraged) to subdivide your paper into appropriate sections (e.g., introduction, traditional taxonomy and problems, molecular phylogeny, conclusions, remaining unresolved questions). Please follow the style used in the Journal of Fish Biology. For guidance on how to write a review article (essay) rather than a research article (lab report) and to use as your template for formatting, I would encourage you to look at one or more of the following review articles from this journal:  Bergstad (2013) North Atlantic demersal deep-water fish distribution and biology: present knowledge and challenges for the future. Journal of Fish Biology 83: 1480–1507  Gozlan et al. (2010) Current knowledge on non-native freshwater fish introductions, Journal of Fish Biology 76: 751–786  Neuenfeldt et al. (2013) Analysing migrations of Atlantic cod Gadus morhua in the north-east Atlantic Ocean: then, now and the future. Journal of Fish Biology 82: 741–763  Sutton (2013) Vertical ecology of the pelagic ocean: classical patterns and new perspectives. Journal of Fish Biology 83: 1508–1527. PDFs of these articles on posted on UM Learn. These articles are not are addressing phylogenetic questions, but serve as good examples for scientific review papers. Also look at the formatting guidelines in this journal’s “Instructions to Authors.” As you are aware, each journal has its own format for citing references (in the text and in the full literature citations) and other general formatting conventions (e.g., in this journal, figure captions are placed below the figure and table captions are placed above the table; tables should not contain any vertical lines). Pay careful attention to these.

Leon Provancher Prize in Systematic Zoology: This prize is awarded to a student who has either prepared an outstanding zoological collection, has undertaken a systematics research project of merit, or has been nominated for an outstanding performance on a suitable course assignment from a 200– 400 level zoology systematics or taxonomy-related course. Three awards are given out

7 per year; the deadline is sometime in April. See: https://umanitoba.ca/faculties/science/departments/bio_sciences/admin/awards.html

B. Biology and Conservation Status of Manitoba Fishes Topic: This option will give you an opportunity to learn more about the basic biology of one of Manitoba’s freshwater fishes (or, with permission from me, a species found elsewhere in Canada), its distribution in the province and the rest of Canada, its population sizes and trends, habitat availability and trends, and threats to this species, as well as learning more about the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) and the process by which species status reports are written. A status report is a comprehensive technical document that compiles and analyzes the best available information on a wildlife species' status in Canada, and it forms the starting point for the COSEWIC Assessment Process (e.g., to help determine if a species is endangered or threatened).

You will prepare a COSEWIC status report for one species that occurs in Manitoba, preferably from the high or mid-priority candidates (Group 1 or Group 2) from COSEWIC’s Candidate Wildlife Species list for Fishes (freshwater). For a list of candidate species, see: http://www.cosewic.gc.ca/eng/sct3/index_e.cfm. For sample status reports, see: http://www.sararegistry.gc.ca/search/advSearchResults_e.cfm?stype=doc&docID=18 or those I have posted on UM Learn. In your status report, however, you do not need to write a “Technical Summary” or “Status and Reason for Designations” section.

Length and Number of References: The length of your status report and number of references will depend on the species chosen, but will likely be approximately 20 pages long (double-spaced). I would expect at least 10–15 references.

Format: Follow the instructions for the preparation of COSEWIC status reports http://www.cosewic.gc.ca/htmldocuments/Instructions_e.htm or use previous status reports as your template (“learn by example”). Note, however, that the style desired by COSEWIC is “evolving” (e.g., they now ask that common names be capitalized). If the instructions for authors differ from the format in previous reports, use the instructions for authors (which are more current).

Call for Bids to Prepare COSEWIC Status Reports: Generally each fall, COSEWIC posts a call for bids on their website, soliciting bids for the preparation of status reports for high-priority species. Professional or other biologists can submit a bid (often for $6,000–8,000 ) for one of these species. Contractors generally have 6–12 months to write the status report; your research paper could conceivably form the basis for a full status report. You can register to receive notification of upcoming calls for bids to prepare status reports. See: http://www.cosewic.gc.ca/eng/sct2/index_e.cfm

Biology of Mammals - BIOL 4218 Lecture Syllabus Fall, 2015

1:00-2:15 TTh 301 Biological Sciences Building

Instructor: Dr. Jane Waterman Office: 424 Biological Sciences Bldg Phone: 204-272-1678 Email: [email protected] Office hours: By appointment

Course description: This course is will explore the global diversity of mammals. You will build a solid understanding of major aspects of mammalian biology that have made them so successful, including their evolution, distribution, physiology, ecology, behaviour and evolution. The goal is for you to have exposure to current research in mammalogy and to develop your abilities in independent, critical thought.

Textbooks: Required: 1. Feldhamer, G.A., Drickamer, L.C. , Vessey, S.H., Merritt, J.F., Krajewski, C. 2007. Mammalogy: Adaptation, Diversity, Ecology. 3rd Edition. John Hopkins University Press: Baltimore, MA. Amazon.ca $102-$130Cdn. Used from $70-$172. Also available on Google books (but not every page is in there). 2. Martin, R., Pine, R., DeBlase, A. 2011. A Manual of Mammalogy with Keys to Families of the World. 3rd Edition. Waveland Press ISBN-10: 1577667689; ISBN-13: 978-1577667681. Amazon.ca $55.14Cdn.

Recommended: Knox Jones, J., Manning, R.W. 1992. Illustrated Key to Skulls of Genera of North American Land Mammals. Texas Tech University Press, Lubbock, TX. Amazon.ca $13.66Cdn. OR: Glass, BP, Thies, M.L. 1997. 3rd ed. A Key to the Skulls of North American Mammals. Check out: http://www.shsu.edu/~bio_mlt/SkullKey.html#ORDERING to order a copy. Dr. Thies charges $17 plus $2 in shipping and it has to be ordered directly. It takes a few weeks to get this manual.

Course Webpage: I will be posting my pdf lectures and other handouts on the course website in D2L.

Grading: Midterm I 15% Midterm II 15% Final Exam** 25% Mammalian Species Account 15% Laboratory 30%

**The cumulative final will be during the December examination period

Grades (A-F) will be assigned as 90+ A+ 80-89 A 76-79 B+ 70-75 B 66-69 C+ 60-65 C 50-59 D 0-49 F

Important Lecture Dates: Species Account topic Oct 1st Exam I. Oct.15th Species Account Draft Nov 3rd Exam II. Nov. 17th Species Account Final Dec 3rd

Mammalian Species Account: Species accounts are monographs that provide a detailed synthesis about what is known about a particular species, including form, function, taxonomy, ecology and conservation status. The species accounts published by the American Society of Mammalogists (http://www.asmjournals.org/perlserv/?request=index-html) are very very detailed and can take a few years to write. However, the Animal Diversity Website of the University of Michigan Museum of Zoology (http://animaldiversity.ummz.umich.edu/site/index.html) publishes species accounts on their website. These accounts are not as detailed as those from the ASM. In this course, you will be responsible for the writing of a species account. These online species accounts provide a database of knowledge that can be used by researchers, teachers and students who access the site. You will need to register for a species account first (https://animaldiversity.ummz.umich.edu/workspaces/), and then after you log in you will be able to access a list of species (from the wish list of the ADW) and you will be required to choose a species and write up the species account for this species. Instructions for writing the accounts can be found at: http://animaldiversity.ummz.umich.edu/site/teach/contributor_guidelines.html and we will go over the details in class. A Species Account Draft is due Nov. 3rd and is worth 1% of the 15%.

Class information: I will only accept late assignments for two days after they are due (10% deducted per day late). After 2 days I will not accept the assignments. My policy for missed assignments: You must inform me, IN WRITING, ASAP if you will be or have missed a class where an assignment is due or there is an exam. If you have a valid reason to miss class, then you will be allowed to hand in the work. However if you wait to let me know you will not be allowed to make up assignments unless you have a doctor’s note. ALL papers must be typed.

Lecture Exams: You will have two midterms exams and one final. Exams may consist of fill in the blank, short answer and essay. Remember, I emphasize critical thinking and synthesis. Questions primarily cover material from the lectures, but also include assigned chapters. Midterm exams are not cumulative but the final exam is cumulative. If you have a problem with the scheduling of any of these exams, you must come and see me at least two weeks before the exam is scheduled. If you miss the midterm and you have a valid excuse (documented injuries, illnesses etc.) there is no makeup exam. You will instead take a final exam worth 45%. 2

General sequence of lectures: The topics slated for coverage in the lecture portion of the course are listed below. I will be giving more detailed information (specific lecture topics, chapter readings, papers) online at the D2L website for this course.

Week Topics 1 Introduction 2 What is a mammal? Origins 3 Form/function 4 Environmental adaptations; reproduction 5 Monotremes & Marsupials 6 Exam I, Marsupials & Eutherians 7 Eutherians – Bats, elephant shrew etc.. 8 Eutherians – Primates; edentates, carnivores 9 Eutherians – Rodents & rabbits 10 Eutherians - Elephants and relatives; Ungulates 11 Exam II 12 Social behaviour, mating systems 13 Population & community ecology 14 Parasites & diseases; conservation

Guest Speakers: I have invited some guest speakers to contribute to our lectures during the semester. Being faced with different speakers will be challenging as far as note taking goes, but the benefits of hearing from these speakers will be immense, as they can give us insights into current research and methodologies in mammalogy, beyond my expertise and that of the textbook.

List of Speakers (dates are tentative) Nov 3rd. Dr. Stephen Peterson, Assiniboine Zoo (carnivores) Nov. 12th. Dr. Steve Ferguson, Freshwater Institute, DFO (marine mammals) Nov. 19th Dr. Susan Lingle, Dept. Biology, University of Winnipeg (deer/coyote) Dec 3rd. Dr. Chris Enright, Assiniboine Park Zoo (parasites & diseases)

Laboratory You will be receiving more information on the lab in the first lab next week (lab meeting time is Tues., 2:30-5:25pm in W230 Duff Roblin Bldg.). Please note that on September 29th we will be meeting downtown at the Manitoba Museum for a tour of the research collections with Dr. Randy Mooi (Curator of Zoology) and Janis Klapecki (Collections Manager).

Online information on Mammalogy: These websites and online journals are wonderful places to find literature or other information about mammals.

Websites: University of Michigan Animal Diversity Web- Mammals http://animaldiversity.ummz.umich.edu/site/accounts/information/Mammalia.html

Mammal Species of the World edited by Wilson & Reeder 3 http://www.bucknell.edu/msw3/

The Field Museum, Chicago. About the Museum’s Mammal Collections. http://www.fieldmuseum.org/expeditions/stanley/about.html

The National Museum of Natural History, Smithsonian Institution. The North American Mammals includes photographs, range maps, and field guides. http://www.mnh.si.edu/mna/

Museum of Vertebrate Zoology, U of California, Berkeley website http://mvz.berkeley.edu/

American Society of Mammalogists Mammals on the Internet site: http://www.mammalsociety.org/links/index.html

Mammalian Species site: http://www.asmjournals.org/perlserv/?request=index-html

Key to the Skulls of North Dakota Mammals http://www.npwrc.usgs.gov/resource/mammals/skulls/

Journals (not all online or in the U of M library): Journal of Mammalogy Mammal Review Mammalian Biology (Zeitschrifte fur Saugetierkunde) Mammalia (International Journal of the Systematics, Biology and Ecology of Mammals) Journal of Mammalian Evolution Australian Mammalogy Hystrix (Italian Journal of Mammalogy) Marine Mammal Science Journal of Marine Animals and their Ecology Aquatic Mammals Journal of Cetacean Research & Management Latin American Journal of Aquatic Mammals

BIOL 4220 MARINE BIODIVERSITY 2015 FALL Course Syllabus

Instructor: Dr. Gail Davoren, Office: Rm W371 Duff Roblin Building, Phone: 474-7497, email: [email protected]

Office Hours: by appointment. Lecture: Tuesday, Thursday: 1130-1245 Course website: UM Learn Text: no required textbook for this course Recommended Readings: 1. Norse, E.A. and L.B. Crowder. 2005. Marine Conservation Biology: the Science of Maintaining the Sea’s Biodiversity. (on Reserve in the Science and Technology Library – 2hr loan; eBook available through UofM Library) Lectures will be supplemented with references to current research and review papers to develop skills in critically analyzing the primary scientific literature.

Prerequisites: BIOL 2300 (ZOOL/BOTN 2370; 002.237, 001.237), AGEC 2370 (065.237), BIOL 2390 (ZOOL 2290, 002.229; BOTN 2280, 001.228).

Overview: This course is designed to introduce students to key principles of ecology, evolution, sociology and economics that form the multidisciplinary field of Conservation Biology. Emphasis is on the ecological and evolutionary principles that govern the threats to biodiversity in marine ecosystems around the globe. Students will be exposed to multiple perspectives on important scientific issues in marine conservation, with a focus on the impacts of fisheries activities. The purpose of this course is to increase your understanding of the concepts and theories underlying the field of Marine Conservation Biology, which is critical for increasing awareness and effective management of marine resources. This class includes lectures, library research, written assignments, student-led debates and discussions on timely, controversial issues. The course will also emphasize practical solutions, primarily better fisheries management and marine protected areas.

Assessment and Grading: Assignments are designed to raise awareness of current issues in Marine Conservation Biology and will develop skills in the practical application of ecological theory to marine biodiversity-related issues. Assignments are designed to gain valuable experience in critical thinking, oral and written communication skills, and scientific debating. The first part of the course will involve introductory and background lectures, followed by a midterm exam. Near the end of the first month, students are required to submit one paragraph to summarize the debate topic (Argument Abstract) along with one key reading to be assigned to the class. During the second part of the course, each week will consist of an introductory lecture on the topic (Tuesday) for the debate in the following class (Thursday). There will be 6-7 debates on the topics listed below, dependent on class size. For each debate (Thursday), students are required to read assigned scientific papers and to submit a Debate Report at the start of class, consisting of a 1-2 page typed list of 3 points of evidence from both sides of the debate with one different supporting reference for each argument (see below How to Prepare Debate Reports). Late Debate Reports will not be accepted, however, each student is only required to hand in a report for 4 of the 6-7 debates. Each student is required to lead one class debate by (1) giving a 10 minute oral presentation to introduce the argument and points of evidence for their side of the debate, and (2) facilitating and stimulating debates (see below How to Debate). Each student will also complete a Marine Conservation Biology in Winnipeg assignment (see details below). See below for assignment grades and weighting. Because of the time-sensitive nature of the work, 10 % will be deducted each day for late assignments.

Note: Each student must sign up to lead one side of a debate. Debate assignments are determined on a first come, first serve basis. The topics chosen may be modified or augmented by the debate leaders with instructor approval.

Evaluation/Assignments: Exams/Assignments Percentage Deadline

Argument Abstract & Assigned Reading 5 September 29 Mid-term Exam 30 October 15 Debate Reports (4 at 5% each)* 20 Oral Presentation & leading debate 20 Marine Conservation Biology in Winnipeg 15 December 8 Debate Participation ** 10 TOTAL 100 * Debate reports are due at the START of each debate class. ** Debate participation is determined by the amount of involvement during class debates and discussions. The last day of registration is September 23, 2015. The last day for voluntary withdrawal is November 18, 2015.

IMPORTANT NOTICES: The Faculty of Science and The University of Manitoba regard acts of academic dishonesty in quizzes, tests, examinations, laboratory reports or assignments as serious offences. Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another individual, using answers provided by tutors, plagiarism, and examination personation. Note: cell phones, pagers, PDAs, MP3 units or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations. Penalties that may apply, as provided for under the University of Manitoba's Student Discipline By- Law, range from a grade of zero for the assignment or examination, failure in the course, to expulsion from the University. The Student Discipline By-Law may be accessed at: http://umanitoba.ca/admin/governance/governing_documents/students/discipline/index.html. Examinations can only be missed on medical and compassionate grounds recognized by the Faculty of Sciences. Deferred exams may be written ONLY upon presentation of an original (i.e., not photocopied) copy of a doctor’s certificate.

Lecture Topics / Debate Schedule Week of: Sept 7 Introduction

Sept 14 History and need for Marine Conservation Biology?

Sept 21 What is biodiversity and why is it important?

Sept 28 History of Fisheries Science. Human Dimensions. Species At Risk ARGUMENT ABSTRACT Act.

Oct 5 Fisheries as a selective pressure. Better fisheries management.

Oct 12 End of the line MIDTERM EXAM

Oct 19 By-catch DEBATE 1

Oct 26 Bottom Trawling DEBATE 2

Nov 2 Marine Pollution (Oil) DEBATE 3

Nov 9 Bioinvasions DEBATE 4

Nov 16 Mariculture (Aquaculture) DEBATE 5

Nov 23 Race to fish DEBATE 6

Nov 30 Marine protected areas DEBATE 7

Dec 7 Marine Conservation Biology in Winnipeg

2 DEBATES Students will research an important conservation topic. Choose a topic from the list below. These topics can be modified with permission from the instructor.

How to Debate Scientific debates differ from normal debates, whereby every argument must be backed by a peer-reviewed scientific publication. The goal is to argue a perspective based on objective scientific evidence only (not emotion). Therefore, students must do their own library research to gather evidence that provides support for and against a particular debate topic.

General Format: Each student must sign up to lead one side of one debate. During the debate, the two debate leaders will summarize their argument and primary points of evidence for their side of the debate question. All remaining students will be randomly assigned to one of the two sides being debated that day. This means that ALL students must be familiar with both sides of the debate and, thus, are expected to do the assigned readings for each debate, as well as contribute to group discussions and debates. The two teams will meet with the debate leaders for up to 15 minutes to discuss their position and share information from readings and other information that they may have found. The debates will be fairly informal and follow a standard debate format: 10 minute presentations by leaders of each side, rebuttal, discussion, concluding remarks, and vote (see details below).

Debate Details: (1) Preparation: o Student debate leaders must choose a perspective to argue regarding a current threat to marine biodiversity (see Debate Topic List). They must focus the debate topic and define key terms with instructor approval. o The debate leaders will write one paragraph to summarize the debate topic, their argument points, and key points of evidence (Argument Abstract). Debate leaders will also provide one key reading. This is due by September 29 and will be posted on the course website 1 week before each debate. The assigned reading and the argument abstract will guide and focus other students during preparation for the debate and while conducting the literature search for the Debate Report. o These assigned readings are required reading for ALL students in the course, despite whether handing in a Debate Report. Students must find and read supplemental scientific papers to use as evidence for both sides of each debate question when writing Debate Reports (see posted examples). o Student debate leaders AND the entire class will search for scientific papers on the debate topic using the University of Manitoba e-library article databases (e.g. BIOSIS Previews) and other sources (e.g. Google Scholar).

(2) Debate (Thursdays): o Student debate leaders will introduce their side of the argument in a 10 min oral presentation (Powerpoint). o After the presentation, all students will be randomly assigned to one side of the debate. Debate leaders will have up to 15 minutes to discuss and arrange key arguments and evidence with their team. o The rebuttal period will be 10 minutes for each team. The rebuttal will start with an Introduction by the debate leader, who will summarize the key points that will be covered in the rebuttal. The debate leaders will then choose students on their team to make the rebuttal points (ensuring that everyone who wants to speak has a chance). Remember, each statement must be backed by a specific publication or data set. The debate leader will then conclude by summarizing the key rebuttal points. o After the rebuttal period, we will have a class discussion for 10 minutes, followed by a class vote.

How to Prepare Debate Reports Each student participant is required to submit a Debate Report, consisting of 1-2 page typed list of 3 different arguments for each side of the debate topic, with one supporting reference for each argument. Debate Reports are due at the start of class in which the debate will be held. References should be in the Canadian Journal of Zoology format (see handout). References must be from peer-reviewed publications or unpublished technical reports (web page addresses and popular press articles are not allowed). You may use any references except those that are assigned required reading and only one reference per statement. Therefore, you should have a minimum of 6 different references per debate report. Please use the example Debate Reports posted on the website as a guide.

Marine Conservation Biology in Winnipeg Assignment The purpose of this assignment is to increase awareness of Marine Conservation issues in Winnipeg. In this assignment a mini-poster/pamphlet (Powerpoint, 8.5 x 11 inches) will be constructed to inform the people of Winnipeg about a marine conservation issue and what they can do to reduce their impact on marine ecosystems. These should be written in layman’s terms to be accessible to the general public (e.g. scientific terms defined as appropriate), but should provide information on the science underlying the conservation issue. Posters should catch the attention of the reader; clearly outline the marine conservation issue (provide enough information for a person of the general public to understand the issue) and why people should care (especially Winnipegers!); plus provide key references that refer people to further readings on the issue, including 1-2 relevant scientific papers, websites, etc. Posters must be clearly laid out and font size must be large enough to read when printed out on 8.5 x 11 inch paper. The amount of text should be limited and images are very important (careful of copyright laws!). Example projects are posted on the course website and on Dr. Davoren’s office door.

All students will present their poster (5 min oral presentation) during lecture on the last day of classes (December 8) as if presenting to an audience of the general public. Remember that the presentation is meant also to inform Winnipegers about the marine conservation issue they have chosen and should outline the general information presented on the poster. After the presentation, students will hand in one colour hard copy of the poster (8.5 x 11 inches) along with an electronic version of the poster (PDF only). The top three final posters will be uploaded to Davoren Lab, University of Manitoba Facebook page for the public to access.

4 DEBATE TOPICS

1. Are gear modifications, fisheries closures, or consumer management the best solution to by-catch? By-catch of non-target species by fishers is a major global threat to marine biodiversity. Some fisheries catch orders of magnitude more non-target species than target species (e.g. tropical shrimp fishery). This results in population declines of these non-target species, often long-lived species that are highly vulnerable to extinction (e.g. seabirds, sharks, sea turtles, marine mammals). Many solutions have been suggested and tried, including (1) modifications to the fishing gear or fishing methods to reduce the catch of non-target species; (2) fisheries closures in areas of high by-catch; and (3) increasing public awareness of commercial species that result in high by-catch to curtail consumer demand for these species. Choose one of these three solutions and provide evidence that it is the best method to minimize by-catch. To assess this, consider the following questions: Is there evidence that gear modifications or altered fishing methods have been effective in reducing by-catch of non-target species? If so, what impact does this have on the fishing industry for the target species? Are fisheries closures at certain times and places effective at reducing by-catch? Is there technology available to determine spatial and temporal shifts in high by-catch areas to make this method effective? Is there evidence that increased public awareness (e.g. ‘by-catch safe’ certification) reduces the consumption (and therefore demand) on target species associated with high by-catch? Is this effective at minimizing by-catch?

2. Will a ban on bottom trawling in international waters (‘high seas’) be effective at protecting marine biodiversity? Most scientists and managers agree that bottom trawling is destructive and has large impacts on benthic communities as well as the species that rely on these communities, either as food or habitat. There is, however, considerable debate over the best strategy to minimize the impacts. Choose the ‘yes’ or ‘no’ side and provide evidence that a ban is or is not the best method to reduce the impact of bottom trawling. To assess this, consider the following questions: Would a complete ban on bottom trawling in coastal and international waters be economically feasible? In other words, would the fishing industry of certain countries be economically sustainable if bottom trawling was banned? Is bottom trawling detrimental to benthic communities in all habitat types? If not, would it be more effective to close sensitive habitats to trawling? A good place to start: Deep Sea Conservation Coalition website: http://www.savethehighseas.org/index.cfm

3. Do infrequent, high magnitude (‘episodic’) oil spills have more of an impact on marine biodiversity than frequent, low magnitude (‘chronic’) spills? (Marine Pollution) The recent blowout of British Petroleum’s Deepwater Horizon drilling platform in the Gulf of Mexico, USA (April 2010) has revived the debate of whether offshore (deep) oil drilling should be banned in the United States and elsewhere. While these and other large oil spills (e.g. Exxon Valdez, Alaska, 1989) receive high media attention, small, chronic ‘leaks’ from oil drilling/exploration platforms and pipelines as well as deliberate dumping from ships go unnoticed. As oil is less dense than water, it immediately spreads as a thin layer on the ocean’s surface, principally impacting seabirds that live year round on the surface. Choose episodic or chronic spills and provide evidence that it has more of an impact on marine biodiversity than the other. To assess this debate question, consider the following questions, with a primary focus on the impacts of these types of oil spills on seabirds: O What is the relative magnitude of oil pollution from episodic versus chronic sources? O What is the evidence of the magnitude of impact of episodic versus chronic sources of oil pollution on seabirds? O Does the magnitude of an oil spill equal its impact? Is the magnitude of oil spilled as important as the frequency of small amounts of oil (i.e. one a large episodic spill versus many small spills)?

5 4. Are pre-invasion (prevention) or post-invasion (eradication, biocontrol) measures the best solution to marine bioinvasions? Bioinvasions are now common on land and in freshwater and marine systems. Invasive species often have wide ranging impacts at the community and ecosystem-levels, by altering habitat structure, eliminating or displacing native species and ultimately having cascading effects throughout food webs. Invasive species are thought to be responsible for ~$138 billion annually in lost revenue and management costs in the US alone. There are two main solutions to this issue, including prevention of the spread of invasive species (pre- invasion measures) and eradication or biocontrol once a non-native species has invaded an area. Choose one of these solutions and provide evidence that it is the best method to minimize the impacts of invasive species. To assess this, consider the following questions: Is there evidence that humans can effectively stop the spread of invasive species? What mitigation measures and technology are available to stop the spread of invasive species? Are these measures cost-effective in relation to eradication efforts? Is there evidence that humans can effectively eradicate an invasive species? How long does it take to notice the presence of an invasive species? Is this important for the eradication of invasive species?

5. Will mariculture solve the overfishing problem? There is a growing consensus that aquaculture is necessary to support the growing population of humans on Earth. One perceived advantage to aquaculture is that it reduces overfishing of wild populations. However, many stocks of small forage fish are being overfished to feed the fish we farm. In North America, salmon are key species for both commercial (wild) catches and farming. Choose the ‘yes’ or ‘no’ side and provide evidence that mariculture will or will not solve the overfishing problem. (NOTE: We are not debating how mariculture influences wild populations (e.g. waste discharge, disease transfer to wild) but whether mariculture will stop overfishing!). To assess the debate question, consider the following questions, with a primary focus on salmon species: Is there evidence that mariculture currently reduces catch rates? Is there evidence that replacing fisheries with mariculture results in the recovery of overfished stocks? Is there evidence that mariculture will reduce overfishing in the future? For instance, is there evidence of new technology that will allow a reduction in catch fisheries to feed farmed fish?

6. Are catch shares the best approach to reduce overfishing? (Race to fish) Many fisheries scientists argue that better fisheries management is the best tool to protect marine biodiversity. As MPAs/MRs do not reduce fishing effort and the “race to fish” (Tragedy of the Commons), they simply displace fishing effort and do not deal with the root of the problem. The best way to minimize this ‘race to fish’, however, is a hot topic of debate. In class, we illustrate many ways to better manage fisheries through two examples: the Bristol Bay Salmon Fishery and the Maine Lobster Fishery. These strategies included fishers rights, or catch share incentives. An example of this is Individual Transferable Quota (ITQ). Choose the ‘yes’ or ‘no’ side and provide evidence that catch shares is or is not the best method to reduce overfishing. To assess this debate question, consider the following questions: Is there evidence that catch shares reduce the “race to fish”, overfishing or lead to sustainable fisheries? Is there evidence against this? Is there evidence that catch shares increase or decrease ecosystem-based management (e.g. reduce discards, by-catch)?

7. Do the challenges of enforcing Marine Protected Areas/Marine Reserves make them ineffective (i.e. ‘paper parks’)? Marine protected areas are often considered one of the best tools to protect marine biodiversity. Protected areas are considered an ecosystem-based tool that safeguards biodiversity, habitats and species interactions within food webs, while overcoming the issues that plague single-species management (e.g. uncertain population sizes), typical of fisheries science. One of the main challenges is enforcement, whereby managers of the protected areas must enforce its boundaries (e.g. stop fishing). If this challenge cannot be overcome, these areas simply become ‘paper parks’ and will not meet their objective of maintaining biodiversity. Choose the ‘yes’ or ‘no’ side and provide evidence that the challenges of enforcing MPAs/MRs do or do not make them ineffective. To assess this debate question, consider the following questions: 6 Is there technology available to enforce MPAs/MRs? Is this being implemented in the world (i.e. is it cost effective)? Are there limitations to this technology? What are the costs of enforcing MPA/MRs boundaries using this technology? How do these costs compare to fisheries subsidies and other fisheries management costs? Is enforcement necessary? Is there evidence that fishers comply with MPA boundaries if educated on the potential benefits of the MPA?

7 Winter Term

Applications of Population Ecology in Fisheries and Wildlife BIOL 4310

The objective of this course is to develop skills in the application of quantitative methods used in the study of current ecological issues and experience in the use of mathematical software (SCILAB, a freely available MATLAB-like language) to support this goal.

INSTRUCTOR Dr. Darren Gillis Office: W361 Duff Roblin Bldg. Phone: 474-9683 (messages) Office Hours: By Appointment Email: [email protected] (e-mail or phone) LECTURES: MWF, 11:30-12:20, 401 Biological Sciences

WORKSHOPS: Thursdays , 2:30-5:00 p.m., W346 Duff Roblin TEXTBOOK: Williams,B. , Nichols,J., Conroy,M. 2002. Analysis and Management of Animal Populations. Academic Press. (recommended – detailed overview of most lecture material)

COURSE SYNOPSIS: Lectures will involve the presentation of underlying theory, its discussion, demonstration of its application, and proof-of-concept exercises. The core of the course is formed by the material practiced in the workshops. Evaluation will be based upon assignments, participation and performance in class and workshops, a midterm and a final examination. Material covered includes: Probability Distributions, Estimation of Population Size (Mark-Recapture, Catch & Catch Rate, Line Transects), Study Design, Stock-Recruitment, Biomass Dynamics, Delay Difference, Fleet Dynamics, VPA, Statistical Catch at Age, Multispecies Analysis, Optimization, and PVA.

COURSE DEADLINES AND HOLIDAYS: February 15 – 19 READING WEEK Wed. February 24 MIDTERM Fri. March 18 VW Deadline April 8 End of Classes

EVALUATION: Please note that all assignments are due AT THE BEGINNING OF THE LECTURE PERIOD. In-class exercises MUST BE COMPLETED as and when directed by the instructor. All tardy work will be penalized 10% immediately following the time due, and then an additional 10% per day (24h starting after the deadline), with the exception of verifiable compassionate or medical reasons. Late assignments MUST BE turned into the Biological Sciences General Office (BSB 212), addressed to Dr. Gillis, between 9:00-16:00 Mon. - Fri. Under no circumstances will assignments be “slipped under the door”. These are often lost (recycled) before I have an opportunity to see them. If I do find them, they will be accessed an additional day later – sorry, this is the only way to stop it.

In-class performance and participation 10% Assignments (3 in total) 30% Midterm Examination: 20% Final Examination (cumulative): 40%

Plagiarism and cheating are serious academic offences. Please consult your calendar for regulations and penalties. Copying any intellectual aspect of another student's work is plagiarism. Please refer to the Faculty website on Acts of Academic Dishonesty: http://umanitoba.ca/faculties/science/undergrad/resources/webdisciplinedocuments.html for more details.

BIOL 4312 ANALYSIS OF BIOLOGICAL COMMUNITIES

COURSE CALENDAR DESCRIPTION: COURSE OUTLINE: A survey of methods and approaches to the analysis INTRODUCTION of biological and environmental data containing many Attributes, variables, nature of data; multivariate data variables. analysis/objectives; multivariate data sets in biology. INSTRUCTOR: MULTIVARIATE DATA SETS IN BIOLOGY Dr. N. Kenkel, Professor Basic data matrix: variables x individuals; more complex Buller Building, Room 432 data matrices; geometric representation of data. Office telephone: 474-6889 Email: [email protected] NATURE OF VARIABLES Website: http://home.cc.umanitoba.ca/~kenkel/ Variables and choice; four measuring scales; redundancy, noise/error, outliers, nonlinear response, LECTURES: commonness vs rarity; underlying distribution: data September 10 - December 9, 2015 (Fall Term 2015). transformation. Tuesdays and Thursdays, 8:30 - 9:45 AM. QUANTITATIVE VARIABLES: VARIANCE Types of quantitative variables; mean,variance, covari- TEXTBOOK: ance and correlation. BIOL 4312/7540 Course Notes (Fall 2015, Updated and Revised Edition), available at University Bookstore. QUALITATIVE VARIABLES: ENTROPY Qualitative (nominal) variables; entropy, mutual en- IMPORTANT DATES: tropy, coherence coefficient. Oct. 8, 2015: NO CLASS. SPECIES DIVERSITY Oct. 12, 2015: Thanksgiving Day, no classes. Concepts of diversity; species richness and measures Nov. 11, 2015: Rembrance Day, no classes. of heterogeneity; measures of evenness. Nov. 18, 2015: VW deadline. MEASURES OF ASSOCIATION MARKING SCHEME: Similarity and distance; covariance/correlation matrices; Midterm Examination (Oct. 29, 2015): 30% binary measures; metric and semi-metric measures. Assignment 1 (due Oct. 27, 2015): 10% Assignment 2 (due Dec. 8, 2015): 10% NUMERICAL CLASSIFICATION Purpose and approaches to classification; hierarchical- Final Examination (December, 2015): 50% agglomerative cluster analysis; K-means clustering. ATTENDANCE: PRINCIPAL COMPONENT ANALYSIS (PCA) The University of Manitoba Academic Regulations state Concepts of dimension reduction; principal component that “Regular attendance is expected of all students in analysis: graphical; eigenvalues/eigenvectors. all courses” (Undergraduate Calendar 2015-2016). CORRESPONDENCE ANALYSIS (CA) PLAGIARISM AND CHEATING: Correspondence analysis: analytical method; PCA vs. Plagiarism, cheating or impersonation in the completion CA; detrended correspondence analysis (DCA). of assignments, and at examinations, are very serious NONMETRIC MULTIDIMENSIONAL SCALING offences. Refer to the University of Manitoba Aca- Conceptualization and analytical approach; use and demic Regulations Section 7 (Undergraduate Calendar limitations of NMDS as an ordination method. 2015-2016) for definitions and penalties. MULTIPLE DISCRIMINANT ANALYSIS COPYRIGHT: Conceptualization and method; interpretation and Lectures and displays delivered or provided in the hypothesis testing. course, including written, visual or audio recording thereof, are subject to copyright owned by Dr. N. Kenkel. CANONICAL MODELS AND METHODS It is prohibited to record or copy by any means, in any Canonical correlation (CANCOR): canonical weights, format, openly or surreptitiously, in whole or in part, structure correlations; redundancy analysis (RDA): any of the lectures or materials provided or published constrained PCA; canonical correlation analysis (CCA): in any form during or from this course. constrained CA. BIOL 4362 Behavioural Ecology & Cognitive Ethology

Instructor: Dr. James F. Hare: 222 Biological Sciences Building; 474-6379 e-mail: [email protected] Office Hours: by appointment (send e-mail to arrange a date & time you prefer)

Lecture: 401 Biological Sciences Building: Slot 10; T, TR 1300 - 1415 hrs Optional Text: Dugatkin, L.A. 2013. Principles of Animal Behavior, 3rd Ed. New York, W.W. Norton & Company. 648 pp. Supplementary Reading: Sherman, P.W. & Alcock, J. 2013. Exploring Animal Behavior – Readings from American Scientist 6th Ed. Sunderland, Sinauer Associates, 372 pp. **(and papers listed by major topics on course web site)

Lab/Tutorial: 304 Biological Sciences Building: Slot 21; M 1430 - 1715 hrs Web Page: http://home.cc.umanitoba.ca/~harejf/BIOL4362/ Teaching Assistant: Ms. Amélie Roberto-Charron: 207 Biological Sciences Building; e-mail: [email protected]

Overview: Behavioural Ecology and Cognitive Ethology (BIOL 4362) builds upon principles introduced in Animal Behaviour (BIOL 3360), addressing aspects of mating and parental behaviour at both the proximate and ultimate levels of causation. Communication – an integral aspect of those processes – will be examined in detail, providing further insight into the intimate relationship between behavioural evolution and the environment. The pivotal nature of communication systems prompts a consideration of "code breaking" in interspecific exploitation, particularly social parasitism. Further, communication leads naturally into the topic of animal intellect, where we will explore recent developments in the field of cognitive ethology. Throughout the course, lectures from active researchers will be incorporated to reinforce major topics, while three laboratory exercises coincident with major topics from lecture will focus on methodological aspects of collecting, analyzing and presenting behavioural data.

Lecture Outline: Approximate # Readings From Topic of Lectures Dugatkin 3rd Edn. Introduction and Course Overview 1

Reproductive Behaviour The Evolution of Sex 1

Mating Systems 2 8 (238-255)

Human Sexual Behaviour 1 8 (256-258)

Sex Change and Sex 2 Role Reversal 2 Lecture Outline: (continued) Approximate # Readings From Topic of Lectures Dugatkin 3rd Edn. Sperm Competition 1 8 (258-263)

Mate Choice and 2 7 (200-231) Sexual Selection 2 (52-53)

Adaptive Manipulation of Sex Ratio 1

Research Lecture 1 (delayed until 25 February 2016 owing to fieldwork!) Dr. Jane Waterman: Mating Behaviour of Cape Ground Squirrels

Parental Behaviour Parental Investment: The Basics 1 2 (60-62)

Parent-Offspring Conflict 1 9 (291-295) and Dispersal

Midterm Test Tuesday February 23rd Cooperative Breeding 2 9 (279-291) 14 (462-465)

Parental Favoritism, Brood 1 9 (295-297) Reduction and Siblicide

Research Lecture 2 Dr. Scott Forbes: Parent-Offspring Conflict and the Structured Family

Communication Reasons for Communication 1 13 (418-420)

The Evolution of Honest Signals 1 13 (420-422)

Methods of Study: Determining 1 13 (422-443) the Function of Communication

Ritualization and the 1 Evolution of Signals

Natural Selection and 2 Signal Characteristics

Code Breaking and 2 Social Parasitism

Research Lecture 3 Dr. Spencer G. Sealy: Brood Parasitism by Brown-Headed Cowbirds

Animal Intellect Communication and Mental 1 (Griffin reprint) Representation: Language and Symbolic Thought

Attribution, Intentionality 1 and Theory of Mind

Physiological Evidence of 1 Thinking

Consequences of 1 Animal Consciousness

3 Lab Exercises: Laboratory and field exercises will provide hands-on experience with data collection, analysis, and interpretation of material within the context of the major themes developed in lecture. You will work in groups of 3-4 individuals for each of the 3 exercises, with data from all groups within the class forming replicates for analysis and written presentation. The first exercise will be conducted over several laboratory periods and will involve the quantification of human mating preferences, thus complementing lecture material on reproductive behaviour. Results from that exercise will be incorporated into an assignment requiring data analysis addressing both mechanistic and functional questions. The second exercise focuses on avian alarm communication. You will be introduced to the study in the lab, though data will be collected in the field over several weeks and pooled to form a class data set. Those data will also form the basis of a brief assignment where you will be required to perform statistical analyses to answer specific questions regarding alarm communication. The final exercise will involve a field exercise conducted in a single laboratory period, and if necessary, independent data collection. Data from that final exercise will be employed in an assignment similar to that undertaken in the first exercise, but will address optimality and the assessment of animal cognitive abilities.

Lab Schedule: Assignment due dates are indicated in italics: 10% will be deducted for each day an assignment is overdue. Formal lab meetings are held only for the first lab period of each lab exercise (i.e. 11 January, 1 February and 29 February for labs 1, 2 and 3 respectively). The remaining lab periods allotted to each exercise allow time for data collection and analysis.

• Lab 1: 11 January - 1 February (304 BSB) Human mate choice (assignment due 1 February)

• Lab 2: 1 February - 29 February (304 BSB Duff/Field Work) Avian alarm communication (assignment due 29 February)

• Lab 3: 29 February - 22 March (304 BSB/Field Work) Mammalian locomotion in snow (assignment due 22 March)

Evaluation: Lecture Midterm 30 (23 February) Lecture Final (cumulative) 40 (Exam Date TBA) Human Mate Choice 10 (due 1 February) Avian Alarm Communication 10 (due 29 February) Mammalian Locomotion 10 (due 22 March) 100 Voluntary Withdrawal Date: 18 March 2016

Academic Integrity: as per University Policy outlined at; http://umanitoba.ca/faculties/science/undergrad/resources/webdisciplinedocuments.html

Final Grades: ≥90 = A+ 62 - 67 = C+ 80 - 89 = A 56 - 61 = C 74 - 79 = B+ 50 - 55 = D 68 - 73 = B <50 = F BIOL 4500 Molecular Genetics of Plant Development

Instructor: Dr. Dana Schroeder (Buller 520) email: [email protected]

Analysis of plant development at the molecular level. Recent advances in model system genetics will be highlighted including seedling, root, shoot, and flower development as well as environmental responses. Prerequisite: BIOL 2500 (BOTN 2460).

Readings: Reviews and literature as provided by instructor and supplemental reserve material.

Topics: 1. Approaches to the Study of Plant Development 2. Embryogenesis 3. Seedling Development 4. Root Development 5. Shoot Development 6. Leaf Development 7. Vascular Development 8. Transition to Flowering 9. Flower Development 10. Gametogenesis & Fertilization 11. Seed and Fruit Development

Grading: Presentation 20% Participation 5% Midterm 20% Literature Review 20% Final 35%

The Presentation will consist of a 12 minute talk followed by 3 minutes for discussion. The topic will be one of the journal articles included with the course material (see chart). Articles will be selected on Monday Sept 14.

Participation grade will be based on attendance at and feedback on presentations.

The Midterm will take place in class on Friday Oct 16. The Final will be a two hour exam during the December exam period. Both will consist of interpretation and analysis of data. Review material will be provided.

The Literature Review will consist of a 6-8 page paper on recent developments on a plant developmental genetics topic which has not been covered in detail in lecture and is on a different stage of plant development than the students’ presentation. Papers are due Monday Dec 7. Possible Literature Review topics include the genetics of:

Development of cellular structures: plastids, cytoskeleton, or cell walls Development of anatomical structures: trichomes, stomata, lateral roots or root hairs Tropisms: phototropism, gravitropism, or thigmotropism Hormones: jasmonic acid, abscisic acid, brassinosteroids, gibberelic acid or salicylic acid Stress tolerance: drought, salt, cold, heat, or pathogens Stages or phenomena: germination, dormancy, apical dominance, phyllotaxy, or senescence or other topics as approved by instructor. Faculty of Science Statement on Academic Dishonesty

Acts of academic dishonesty include, but are not limited to bringing unauthorized materials into a test or exam, copying from another student, plagiarism, and examination impersonation.

Note: cell phones, pagers or electronic translators are explicitly listed as unauthorized materials, and must not be present during tests or examinations.

http://umanitoba.ca/admin/governance/governing_documents/students/868.htm

Suggested penalties assessed by the Faculty of Science for acts of academic dishonesty are available on the Faculty of Science web-page: http://umanitoba.ca/faculties/science/

All Faculty members (and their teaching assistants) have been instructed to be vigilant and report all incidents of academic dishonesty to the Head of the Department.

REGISTRATION RESTRICTIONS

PLEASE ENSURE THAT YOU THE STUDENT ARE ENTITLED TO BE REGISTERED IN THIS COURSE:

THIS MEANS THAT YOU THE STUDENT HAVE:

-the appropriate prerequisites, as noted by the calendar description, or have permission from the instructor to waive these prerequisites

-not previously taken, or are concurrently registered in this course and another that has been identified as “not to be held with”

The registration system may have allowed the student to register but it is up to the student to ensure that they have met all the requirements.

Consequences may be the student being withdrawn from the course part way through the term, or the course not used in the degree program. There will be no fee adjustment. This is not appealable.

BIOLOGY 4542: Genes and Development Winter 2016 Time and Location: Tuesdays and Thursdays 11:30-12:45 pm, 401 Biological Science Building

Recommended Texts: Gilbert, S.F. 2010. Developmental Biology, 9th edition, or Gilbert, S.F. 2013. Developmental Biology, 10th edition Sunderland, Massachusetts: Sinauer Associates; & additional readings provided by the instructor.

Instructor: Dr. Jeffrey Marcus Email: [email protected] Office: 600 Buller Building (really!)

Office Hours: Office hours by appointment only. Email the instructor with a request for a meeting and indicate several days and times when you are available. He will email you back with an appointment time. Make sure you include your full name in the email. Please note that same-day appointments may not always be available.

Course Website: The slides and supporting materials will be posted to the course website on Desire to Learn (D2L) after each lecture.

Course Description: An in-depth examination of development, emphasizing the genetic control of the cell and molecular mechanisms that direct embryogenesis and other developmental processes. The course will include examples from animals (vertebrate, and invertebrate), plants, and other model organisms for studying developmental biology. The course will consist of lectures and presentations integrating recent advances and classic experiments in selected aspects of development. Some of the course material will focus on an analysis of the current literature. This course does not have a lab associated with it.

Developmental genetics employs many different experimental approaches in diverse model organisms, resulting in what sometimes seems like overwhelming amounts of information. By studying developmental genetics in the context of the unifying themes such as the scientific method, the construction of explanatory models and metaphors, and the evolution of development, students will learn how researchers organize masses of experimental data into manageable units.

Course Grading: There will be three exams: (1) a mid-term exam (25%) held in class on February 4, (2) a second mid-term exam (25%) held in class on March 15, and (3) a final exam (35%) held during the regular exam period in April at a date and time to be established by the Registrar. The exams will be conceptually cumulative, but each will focus on subjects not covered by the other exams. There will also be a mitochondrial genome annotation assignment divided in two parts due Jan. 28 (3%) and Feb. 23 (12%).

Note: Make-up exams and extensions for assignment deadlines will only be given in cases of serious illness (medical certificate required), a death in the immediate family (written verification from a physician or a religious authority required) or a compulsory religious observance (written verification from a religious authority required).

Grades will be assigned using the following scale: Percentage Grade 90 -100 A+ 80 - 89 A 75-79 B+ 70-74 B 65-69 C+ 55-64 C 50-54 D 0-49 F Tentative Course Schedule (subject to change): Date Topic Notes (complete readings by date listed, other readings will be supplied by the instructor in class) January 7 Methods, models, & metaphors Gilbert, Chapter 1 January 12 Genes, switches, and modes of regulation I Gilbert, Chapter 2 January 14 Genes, switches, and modes of regulation II January 19 Methods for sequencing genes and genomes January 21 Mitochondrial genomics January 26 Signals, pathways, and programs: Cellular communication I January 28 Signals, pathways, and programs: Gilbert Chapter 3: 84-90 Cellular communication II due before class Mitochondrial genome assignment part 1 February 2 Fields: regulative & mosaic development, Gilbert Chapter 3: 102-105, Primordia and Stem Cells Chapter 4: 109-116 February 4 Midterm Exam 1 in class February 9 Drosophila Axis Formation Gilbert Chapter 6: 209-226 February 11 Vertebrate Axis Formation Gilbert Chapter 7: 295-298, 311-316 February 16, 18 No class, reading week February 23 Left-right asymmetry Gilbert Chapter 7: 316-319, due before class Mitochondrial genome assignment part 2 Chapter 6: 217 February 25 Eye Development Gilbert Chapter 9: 359-365 March 1 Heart Development Gilbert Chapter 12: 445- 453 March 3 Limb Development I Gilbert Chapter 13 March 8 Limb Development II Gilbert Chapter 15: 550- 566 March 10 Limb Development III March 15 Midterm Exam 2 in class March 17 Development of Flower Structures March 22 Evolution & Development: The Comparative Approach March 24 Evolution & Development: The Phylogenetic Gilbert Chapter 19 Approach II March 29 Computational Developmental Biology I March 31 Computational Developmental Biology II April 5 Genomics and Development April 7 Future prospects in Genes & Development

Academic Integrity: Plagiarism and Cheating: Plagiarism or any other form of cheating in examinations, term tests or academic work is subject to serious academic penalty (e.g. suspension or expulsion from the faculty or university). Cheating in examinations or tests may take the form of copying from another student or bringing unauthorized materials into the exam room (e.g., crib notes, pagers or cell phones). Exam cheating can also include exam impersonation. (Please see Section 4.2.8 on Exam Personation). A student found guilty of contributing to cheating in examinations or term assignments is also subject to serious academic penalty. To plagiarize is to take ideas or words of another person and pass them off as one's own. In short, it is stealing something intangible rather than an object. Plagiarism applies to any written work, in traditional or electronic format, as well as orally or verbally presented work. Obviously it is not necessary to state the source of well-known or easily verifiable facts, but students are expected to appropriately acknowledge the sources of ideas and expressions they use in their written work, whether quoted directly or paraphrased. This applies to diagrams, statistical tables and the like, as well as to written material, and materials or information from Internet sources. To provide adequate and correct documentation is not only an indication of academic honesty but is also a courtesy that enables the reader to consult these sources with ease. Failure to provide appropriate citations constitutes plagiarism. It will also be considered plagiarism and/or cheating if a student submits a term paper written in whole or in part by someone other than him/herself, or copies the answer or answers of another student in any test, examination, or take-home assignment. Working with other students on assignments, laboratory work, take-home tests, or on-line tests, when working together is not specifically allowed by the instructor can constitute Inappropriate Collaboration and may be subject to penalty under the Student Discipline By-Law. An assignment that is prepared and submitted for one course should not be used for a different course. This is called "duplicate submission" and represents a form of cheating because course requirements must be fulfilled through original work for each course.

personates a candidate at a competitive or qualifying examination held under the authority of law or in connection with a university, college or school or who knowingly avails him/herself of the results of such personation is guilty of an offence punishable on summary conviction. 1953- 54,c.51, s.347. Both the personator and the individual who avails him/herself of the personation could be found guilty. Summary conviction could result in a fine being levied or up to two years of imprisonment. When in doubt about any practice, ask your professor or instructor. The Student Advocacy Office, 519 University Centre, 474-7423, is a resource available to students dealing with Academic Integrity matters.

*************************************************************************************** IMPORTANT NOTES: 1. Reminder: deadline for late registration/withdrawal with no record on transcript is January 19, 2016. 2. Reminder: deadline for voluntary withdrawal is March 18, 2016. 3. Exam questions may come from the parts of the textbook indicated in this outline and from material presented during class. Questions that require detailed recall will derive primarily from lecture material. Designated readings and material covered in class will supply all of the information tested on the exams. 4. The lecture materials available on the web are incomplete. You will be responsible for additional material that will be presented during class. If you miss class for any reason, it is your responsibility to obtain the slides from the lecture you missed from the web site and the additional information presented in class from a classmate. The instructor will not provide lecture notes beyond what is available online.

Agreement Form

All students who wish to remain enrolled in BIOL 4542 are required to sign and return this form to the instructor by the third class meeting. By submitting your name on the form you are agreeing to the following statement:

"I have read the BIOL 4542 course syllabus and understand and accept its contents. I also understand that all work in this course must be my own, in my own words, and all required assignments, projects, and tests must be completed to receive a passing grade for this course. I understand that facilitating academic dishonesty such as plagiarism by another student is an academic offense for both students and both students will be penalized for such behavior. I stipulate that I have reviewed the following websites: http://umanitoba.ca/faculties/science/undergrad/resources/webdisciplinedocuments.html http://www.umanitoba.ca/student/resource/student_advocacy/cheating_plagiarism_fraud.html and understand what constitutes academic plagiarism. I further agree that is it my responsibility to withdraw or make other changes in my enrollment status, according to the policies and deadlines outlined in the University Catalog and/or Academic Calendar."

______Signature ______Print your Name ______Date ______Semester Taken

BIOL 4544 Course Syllabus - 2016

Lectures will be held in BSB 401 and labs in Duff Roblin W340.

Advanced Developmental and Cellular Biology INSTRUCTOR: Dr. Steve Whyard TEACHING ASSISTANT(S): Carlos Cruz and Cassidy Erdelyan

RECOMMENDED TEXT: None COURSE CONTENT: This course is designed to introduce students to some of the approaches and techniques used in modern cellular/developmental biology. It is primarily a laboratory-based course but will also employ tutorial style lectures on occasion in order to explore some of the more theoretical aspects of the techniques used. Although we have attempted organize laboratories that use the designated three hour time slots efficiently, the nature of the techniques used in modern cellular/developmental biology sometimes dictate that extra time may be required outside of the scheduled lab time, or not all the time allotted in lab periods will be necessary. The Wednesday lecture slot that precedes the laboratory will be used to provide the necessary background material for each lab. This is the ONLY lecture slot to be used (i.e. we will not use the Monday and Friday time slots). Be advised that extra hours or time out of the lab slot may still be required. OBJECTIVES: 1. As implied above, the main objective of this course is to give students some "hands on" experience with laboratory techniques used in modern cellular/developmental biology. We have tried to highlight techniques that are discussed in other courses (primarily Cell Biology and Developmental Biology) and/or are significant techniques currently being employed by modern research laboratories. 2. The second objective of this course is to increase the students' understanding and appreciation for how the techniques work, the kind of biological questions that can be addressed with them and what the results produced from these techniques actually tell the researcher. 3. The third objective is to introduce the students to the use of simple animal models to explore aspects of research questions in cell and developmental biology. While studies using vertebrate animals are both interesting and can be more readily translated to understanding our own human cell and developmental biology questions, it is costly to use vertebrates in studies, and where possible, more researchers are turning to simpler models for preliminary studies. For this reason, this course will rely on invertebrate models to explore some aspects of cell and/or developmental biology. The species used will vary from year to year, but may include sea urchin, the fruit fly Drosophila, various other insects, the nematode C. elegans, and the flatworm Planaria. We will not necessarily use all of these in any given year. 4. The fourth objective of this course is to provide students with opportunities to present their ideas clearly and concisely in written reports, oral presentations, and reviews of scientific publications.

Grade Assessments: Module reports (3 @ 20% each) 60% Seminar Presentation (1) 10% Short Assignments (4 @ 5% each) 20% Final Lab Report 10% Note: there is no final exam

Course Plan: The course will comprise of three modules: Module 1 – Gametogenesis and reproduction Module 2 – Cloning, Stem Cells, Transgenics discussion topics Module 3 – Innate immunity

Course Schedule:

Date Gametogenesis Cloning & Stem Cells Immunity module module module Jan 6 RNA extraction Jan 13 cDNA synth. + PCR Jan 20 Gel electrophoresis Cloning/stem cells intro and DNA purification (lecture) Jan 27 2 min talks Feb 3 Module student seminars Feb 10 Ligations + bacterial Module Report due cloning Feb 17 Midterm break Midterm break Midterm break Feb 24 Bacterial challenges; gene knockdowns Mar 2 Assessing immunity status Mar 9 Module student seminars Mar 16 RNAi knockdowns Module Report due Mar 23 Module student seminars Mar 30 Assessing gametogenesis Apr 6 Design your own RNAi Apr 25 Module Report & Final Lab Report due

Short Assignments: 1. Bioinformatics assignment: assigned Jan.13; due Jan. 20 2. Cloning and transgenic technologies: assigned Jan 20; 2 min presentations - Jan 27 3. DNA constructs assignment: assigned Feb 10; due Feb. 24 3. Design your own gene silencing construct: Assigned Mar 23; 2 min presentations on Apr 6

Final Lab Report: due Apr 25

Field Code Changed MICROTECHNIQUE BIOL 4560 Course Content and Subject Matter 2015

TEXTBOOK: " Histotechnology: A Self-Instructional Text" by Freida Carson and Christa Hladik, ASCP Press, Chicago, 3rd Edition

INSTRUCTOR: Dr. Erwin Huebner, Buller 524 (Office). 531 (Laboratory) [email protected] T.A. Bailey Rankine

Lectures: Tues and Thurs. 10 - 11:15 slot 5, Rm. 301 Biological Sciences Building Laboratory: Wed aft and evening, slots 25 and E, Buller Rm 523.

COURSE CONTENT: This is an intensive fourth year Honours level laboratory oriented course. Students are exposed to a variety of microscopic techniques used to examine the structure and function of animal tissues. The lectures and labs deal with the gamut of basic preparative methods such as fixation, dehydration and embedding as related to both light and electron microscopy. A variety of types of light microscopes, scanning probe and electron microscopes (TEM, SEM, ESEM and STEM) used for animal cell and tissue analysis will be covered. We also briefly cover some of the more experimental methods and recent advances in areas such as histochemistry, extracellular tracers, horseradish peroxidase methods, autoradiography, in situ hybridization, fluorescence microscopy, data collection including imaging, image analysis and image recording. A term paper on a specialized techniques topic is required. The laboratory component of the course involves a regular weekly scheduled lab during which the equipment and methods are presented as demonstrations. Then each student must do the lab procedures and practice the methods outside of the scheduled lab hours each week so as to gain first-hand experience. Because of the nature of the subject matter and the limitations of equipment and space there is no alternative if students are to get the hands on experience and have a foundation to build on for future work. Many of the protocols have multiple steps that can take 1 or 2 days or longer to run. Thus the time commitment for this course is unusually high compared with other 3CH courses. It is important you are aware of this at the outset and will be prepared to spend the extra time required. Each student learns the basic foundation of microtechnique methods by doing a “practical project” focused on a specific tissue or organ. To master the hands-on skills a certain amount of problem solving is essential. The project is determined by the instructor. If you have an interest in a particular tissue or project, selection will on a first-come-first-served bases from the project list. If feasible incorporating a more specialized technique may be possible in some projects. There will be one demonstration laboratory involving electron microscopy. Likely near the end of the term. We will also cover digital imaging prior to project completion. Finally, each student submits a written paper with supporting slides, images and preparations on his or her results and also presents a short oral report on the findings to the class. The course grade is based on the “project” work and report, the term paper and a lab exam. As you can see the course is extensive and ambitious in the amount of material covered and hopefully provides you with a foundation in microscopy based methods that will be of value in a variety of career paths. Lecture and Lab attendance is mandatory. Absences without special permission constitute grounds for requiring withdrawal from the course. This is essential because information on specific methods, lab equipment and special health and safety points relating to certain procedures are covered in class and not covered in the reference text.

LABORATORIES: The lab content will span a variety of topics from principles of microscopy and optical features of a variety of microscopes, specimen preparation and data presentation. Basic principles of the light microscope used as a contemporary analytical tool will be covered. Light microscope systems to be covered include: bright field, contrasting systems such as - dark field, phase contrast, polarizing, single side band, Hoffmann modulation contrast, differential interference contrast and special systems such as super resolution microscopy, light sheet microscopy, fluorescence microscopy, confocal microscopy, various scanning probe types, and various electron microscopy types. Data collection and analysis will include introduction to video microscopy, image analysis and manipulation. Tissue preparation methods will include techniques routinely used in histological, cell biological and biomedical research as well as more specialized techniques may be covered in lecture, possibly with demonstrations, pending time. We begin with consideration of the living tissue, carry on with tissue fixation and processing and end with microscopic examination and imaging. The general framework for learning and applying the techniques is in the form of specific assignments and individual projects determined by the course instructor. A written and oral project presentation is required along with representative slides and other preparations. There is one lab exam. Keys will be signed out to class members and must be returned at the class presentation at the end of term. A $50 replacement fee will be charged for any lost keys and a grade will not be assigned until your keys have been returned to the instructor.

All aspects of the course are completed prior to the end of term as per the following schedule.

Tentative Lecture/Lab Schedule – Subject to change if circumstances dictate

Course Schedule and Sequence of Topics:

Sept. 10 Course introduction, objectives and approach, requirements

Sept.15-17 Lectures: Intro and Live methods, Overview tissue prep methods.

Sept.16 Lab - overview, lab-layout, equipment available, lab use rules, and safety.

Sept.22-24 Fixation and processing of tissues for paraffin embedding.

Sept.23 Lab: Fixation and tissue processing for paraffin media embedding

Sept 24-Oct 1 Fixation and processing of tissues for plastic embedding.

Sept.30 Lab: Fixation, and tissue processing for plastics.

Oct.6-8 Microtomy - microtomes, sectioning of paraffin and plastic blocks.

Oct 7 Lab: Sectioning. Also Selection of term paper topic and outline due.

Oct.13

Oct 14-15 Individual work on sectioning, project planning and project outline preparation. No formal lecture or lab.

Oct.20-22 Lectures Principles of Microscopy and Contrasting types: DF, Phase, Pol., DIC etc.

Oct. 21 Lab - Principles of BF light microscopy, microscope alignment and optics and some time for individual project work.

*LAB EXAM October 28*

Oct.24-29 Lecture – Microscopy Continued - Fluorescence, video and image processing

Nov.3-5 Lectures – Nov.4 Lab – Microscopy Continued - Fluorescence, video and image processing

Nov.10-12 Lectures – Staining theory continued

*Term PAPER DUE NOVEMBER 12

Nov. 11 No Formal lab Remembrance Day (Individual Project Work)

Nov. 17-19 Histochemistry and special methods

Nov.18 Lab – Staining and mounting of slides

Nov. 24-26 Individual Project Work

Dec.1-3 Class Demo of TEM and SEM during lecture slots

Dec. 9 Class minisymposium. Oral project presentations. Submission of written project reports, representative slide preparations, and return of keys and course materials. Time TBA

No extensions will be allowed, so it is critical you budget your time, work on the project throughout term as it is not doable in the last couple weeks!

Course Grade Allocations:

Lab Exam...... 20%

Term paper...... 20%

Laboratory project (slides and preps, overall performance in lab, oral and written reports, photomicrographs ...... 60%

Total 100%

In your work for this course you should be careful not to contravene the Universities Regulations concerning "academic dishonesty including plagiarism and cheating." Full statements can be found in the University General Calendar and Science Web Site.

Please be aware that as of September 2013, the University of Manitoba will only use a student’s university email account for official communications, including messages from instructors, department or faculty, academic advisors, and other administrative offices. http://umanitoba.ca/registrar/email_policy/

Practical Project Details:

Individual projects will be determined by discussion with the instructor and then assigned by the instructor. Availability of material, cost, feasibility, time factor and animal care guidelines are all among the factors considered in the selection of tissues available for this course.

All Projects Must Include The Following:

1. Basic Techniques: (i). Tissue fixed using two classical fixatives - Two of: buffered formalin, Bouin's, Carnoy's or other fixative - and processed for paraffin embedding media.

(ii). Tissue fixed in a contemporary aldehyde fixative (e.g.Modified Karnovsky's fix) and processed for plastic methacrylate based embedding medium.

(iii). Sectioning and staining. Paraffin (5 - 7 um) and plastic (1 - 3 um) sections prepared, mounted on glass slides and stained as follows: Paraffin sections - Hematoxylin & Eosin (H&E), a triple stain, PAS histochem staining, Feulgen histochem staining, Picro-sirius Red (Optional). Plastic sections - Toluidine blue staining, and optionalGill’s H & E.

2. Imaging of Sections: Video Microscopy - Image processing Capture, storage and processing of microscope images of your preparations using a PC based imaging system (Northern Eclipse, Empix Inc,) will be required.

3. Written Report A 15 - 25 page (typed) written report on your project must be submitted in research paper format (Introduction, Materials and Methods, Results, Discussion - or Results and Discussion combined and Conclusions, and Literature Cited). Micrographs (printed or on disc) with appropriate figure captions must be included and a representative set of properly labeled slides must be handed in with the report. ` 4. Oral Presentation A 10 - 15 minute classroom presentation will be given by each student on their particular projects . Project reports and materials must also be handed in by this time. No time extensions are possible. Room keys and all course supplies must be returned at this time. Course work will not be graded unless the keys and materials are turned in with the report.

5. Special Techniques Depending on circumstances it may be possible to demonstrate some additional special preparative techniques. Fluorescent staining of DNA may be possible in some select projects. Other prospects are TBA.

6. Academic dishonesty and discipline policies: You must note that academic dishonesty matters (such as plagiarism, submitting someone else's work, etc.) will not be tolerated and have severe consequences. http://umanitoba.ca/faculties/science/resources/Science_StatementOnAcademic DishonestyJul09.pdf

The link to the main page is: http://umanitoba.ca/faculties/science/student/webdisciplinedocuments.html

The link to the penalty table is: http://umanitoba.ca/faculties/science/resources/Discipline_Penalties_Table_ Jul09.pdf

Equipment must only be used after you have received instruction on its proper use. Do not use any equipment if you are unsure of how to use it, get help from the instructors.

Do not be wasteful. Use the minimum amounts necessary.

Lab alcohols contain poisons, human consumption is prohibited and dangerous

Remember the chemicals and procedures you are using are designed to stabilize, and kill cells and tissues!! You are composed of cells and tissues. Lab safety cannot be overstated. Remain alert, exercise care, seek help and advice when you are unsure, and report all instances where others are performing unsafely to the course instructors. When working after hours, such as evenings and weekends it is important to coordinate with another classmate or more so at all times there are at least 2 people working in the lab. Be sure to keep the lab locked at all times.

Winter 2016

PROBLEMS IN BIOLOGICAL STATISTICS BIOL 7360

COURSE INFORMATION SHEET

The objective of this course is: 1) to review the application of statistics to biological issues through reading and exercises and, 2) to complete and present the analysis of a biostatistical question. Students will be introduced to R, an open-source statistical computing program, which will provide a common quantitative environment for developing statistical concepts and applications.

INSTRUCTOR: Dr. Darren Gillis Office: Duff Roblin W361 Phone: 474-9683 (messages) Office Hours: by appointment Email: [email protected]

COURSE FORMAT: Course members will meet once a week, initially to discuss methodology (based upon text readings) and perform sample exercises (in R). Each week students will begin by handing in a sheet of three questions that they wish to discuss during class, based upon the assigned readings (they should have a second copy for their own use). We will review basic statistical concepts and methods from hypothesis testing to Linear Regression and ANOVA. Two quizzes will examine the material covered. Then each student will choose a biostatistical problem for analysis as their focus for the remainder of the course. They will present a brief proposal (oral and written) to the class prior to undertaking their analysis. At the end of the course, a more detailed presentation and report will outline the results of the analysis. To prepare you for the analysis of data outside of classes, this course emphasizes the development of analyses in novel situations. It does not aim to simply teach a specific series of statistical procedures, but rather it develops a methodology for approaching the use of new and unfamiliar statistics in research.

RESOURCES: Readings will be taken from Experimental Design and Data Analysis for Biologists by G.P. Quinn and M.J. Keough. Information and documentation on R can be found at the The Comprehensive R Archive Network (http://cran.r- project.org/). This is the distribution site for the most recent R version, online help and FAQs. In addition, much explanatory material tailored for beginners are located in the Contributed Documents section of the CRAN website. All students are responsible for regularly checking their e-mail for important class notices.

COURSE DEADLINES AND HOLIDAYS: Feb. 15-19 Midterm Break Mar. 18 VW withdrawal deadline Apr. 8 Classes End – All term work to be completed in courses without final examinations (Note: Quizzes will be announced in the previous week, approximately in the 4th and 8th weeks of class)

EVALUATION: Please note that all assigned work is due AT THE BEGINNING OF THE CLASS. A penalty of 10% per day will be deducted from all tardy work, with the exception of verifiable compassionate or medical reasons.

Participation 20% (Based Upon # Of Completed Weekly Discussions & Workshops) Quizzes (2) 20% Analysis Proposal (Oral): 10% Analysis Proposal (Written): 10% Final Report (written): 30% Final Report (presentation): 10%

Plagiarism and cheating are serious academic offences. Please consult your calendar for regulations and penalties. Copying any intellectual aspect of another student's work is plagiarism.

BIOL 7540 METHODS FOR ANALYSING BIOLOGICAL DATA

COURSE CALENDAR DESCRIPTION: COURSE OUTLINE: A survey of methods and approaches to the analysis INTRODUCTION of biological and environmental data containing many Attributes, variables, nature of data; multivariate data variables, suitable for graduate students. analysis/objectives; multivariate data sets in biology. INSTRUCTOR: MULTIVARIATE DATA SETS IN BIOLOGY Dr. N. Kenkel, Professor Basic data matrix: variables x individuals; more complex Buller Building, Room 432 data matrices; geometric representation of data. Office telephone: 474-6889 Email: [email protected] NATURE OF VARIABLES Website: http://home.cc.umanitoba.ca/~kenkel/ Variables and choice; four measuring scales; redundancy, noise/error, outliers, nonlinear response, LECTURES: commonness vs rarity; underlying distribution: data September 10 - December 9, 2015 (Fall Term 2015). transformation. Tuesdays and Thursdays, 8:30 - 9:45 AM. QUANTITATIVE VARIABLES: VARIANCE Types of quantitative variables; mean,variance, covari- TEXTBOOK: ance and correlation. BIOL 4312/7540 Course Notes (Fall 2015, Updated and Revised Edition), available at University Bookstore. QUALITATIVE VARIABLES: ENTROPY Qualitative (nominal) variables; entropy, mutual en- IMPORTANT DATES: tropy, coherence coefficient. Oct. 8, 2015: NO CLASS. SPECIES DIVERSITY Oct. 15, 2015: Thanksgiving Day, no classes. Concepts of diversity; species richness and measures Nov. 11, 2015: Rembrance Day, no classes. of heterogeneity; measures of evenness. Nov. 18, 2015: VW deadline. MEASURES OF ASSOCIATION MARKING SCHEME: Similarity and distance; covariance/correlation matrices; Midterm Examination (Oct. 29, 2015): 30% binary measures; metric and semi-metric measures. Assignment 1 (due Oct. 27, 2015): 10% Assignment 2 (due Dec. 8, 2015): 10% NUMERICAL CLASSIFICATION Purpose and approaches to classification; hierarchical- Final Examination (December, 2015): 50% agglomerative cluster analysis; K-means clustering. ATTENDANCE: PRINCIPAL COMPONENT ANALYSIS (PCA) The University of Manitoba Academic Regulations state Concepts of dimension reduction; principal component that “Regular attendance is expected of all students in analysis: graphical; eigenvalues/eigenvectors. all courses” (Undergraduate Calendar 2015-2016). CORRESPONDENCE ANALYSIS (CA) PLAGIARISM AND CHEATING: Correspondence analysis: analytical method; PCA vs. Plagiarism, cheating or impersonation in the completion CA; detrended correspondence analysis (DCA). of assignments, and at examinations, are very serious NONMETRIC MULTIDIMENSIONAL SCALING offences. Refer to the University of Manitoba Aca- Conceptualization and analytical approach; use and demic Regulations Section 7 (Undergraduate Calendar limitations of NMDS as an ordination method. 2015-2016) for definitions and penalties. MULTIPLE DISCRIMINANT ANALYSIS COPYRIGHT: Conceptualization and method; interpretation and Lectures and displays delivered or provided in the hypothesis testing. course, including written, visual or audio recording thereof, are subject to copyright owned by Dr. N. Kenkel. CANONICAL MODELS AND METHODS It is prohibited to record or copy by any means, in any Canonical correlation (CANCOR): canonical weights, format, openly or surreptitiously, in whole or in part, structure correlations; redundancy analysis (RDA): any of the lectures or materials provided or published constrained PCA; canonical correlation analysis (CCA): in any form during or from this course. constrained CA.