Fall, 2015

Plant Ecophysiology – Biology 2210 (or ES 2223)

Marcus Hirn

Professor Barry Logan Laboratory Instructor: Jaret Reblin

Lecture: MWF: 10:30 – 11:25AM Laboratory: Wed. or Thurs.: 1:00 - 3:55PM Banister 106 Druckenmiller 222

Barry Logan Jaret Reblin Hawthorne-Longfellow 214 Druckenmiller 222A 725-3944 725-3166(w) & 443-8089(h) [email protected] [email protected] Office Hours: Tues. 4-5PM & Wed. 9-10AM Mon. 9:30-10:30AM & Tues. 2-3PM (or other times by appointment) (or other times by appointment)

Prerequisites: Biology 1102, 1109 or recommendation of Biology Department

Fall, 2015 Plant Ecophysiology – Biology 2210 (or ES 2223)

Texts: Plant Physiology and Development, 6th edition (Taiz, et al.); Physiological Ecology of North American Desert Plants (Smith, et al.). These texts will be supplemented by articles and book chapters shared as PDFs (placed in a repository on the course Blackboard site). A reading schedule will be posted to the course Blackboard site.

Course Description: Examines the functional attributes of plants and the manner in which they vary across the plant kingdom by the processes of evolution and acclimation. Topics of focus include photosynthesis and protection against high-light stress, the acquisition and distribution of water and mineral nutrients, and environmental and hormonal control of development. Special topics discussed may include plant parasitism, carnivory, the origins and present state of agriculture, plant responses to global climate change, plant life in extreme environments, and the impacts of local land-use history on plant communities. Contemporary research instrumentation is used in weekly laboratories, some conducted in the field, to enable first-hand exploration of phenomena discussed in lecture. Includes an optional excursion to three of the North American deserts of the Southwest (the Sonoran and Mojave Deserts and the Great Interior Basin) during Thanksgiving vacation.

Inquiry in the Natural Sciences & Mathematical, Computational and Statistical Reasoning requirements: This course can be completed to satisfy either the INS or MCSR Distribution Requirements. This course is dedicated to understanding plant function, distribution and responses to the environment. We will pursue this through lecture; guided problem solving and critical thinking; reading and discussion of journal articles describing original research, review articles & chapters and books; field excursions; and lab exercises designed to offer you experience with contemporary research instrumentation and authentic research opportunities. As such, we will meet (more than) the goals of INS courses through just about every element of the course. Our discussions of published data will focus on the interpretation of data presented graphically and on rigorous assessment of statistical analyses. Our explorations of aspects of plant function, particularly those relating to plant water relations, will be quantitative in nature. The greater share of our lab exercises will involve quantitative data collection and analyses. Throughout the course we are “applying general tools of mathematics and statistics” and thus meeting the goals of the MCSR requirement.

Excursion to the Desert Southwest: During Thanksgiving Break, Jaret and I will lead an optional trip to three of the four deserts of the American Southwest. We will travel to the Great Interior Basin, the Mojave and Sonoran Deserts and Biosphere II, which houses some of the largest controlled-environment climate change studies on earth. Our focus will be on the relationship between environmental conditions and plant functional biology, human impacts on desert environments, and the effects of natural climate cycles and global change desert natural and human communities. We will be joined by desert ecophysiologists along the way. The trip is subsidized by the College, although there may be participant monetary contributions expected, depending upon one’s financial aid status. More information on the trip will be forthcoming in lecture.

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Grading: Grades will be determined based upon a 1000 pt. system, composed of the following components (described below):

Points Mid-term #1 90 Mid-term #2 140 Final exam 250 Article summaries (2X40) 80 Friday Forum 90 Laboratory assignments 350 Total 1000 Participation & Involvement The “X” Factor

Exams: Exams will encompass material presented in lecture and lab (although the emphasis will be upon lecture material). The second mid-term and the final exam will be cumulative. Exams include questions that require you apply concepts discussed in class to novel scenarios or to synthesize material from more than one lecture. On all questions I am searching for correct, complete, clear and concise answers.

Article summaries: On three occasions during the semester we will be joined by Skype by a researcher in the field and I will ask you to read an article of theirs in advance. For two of these (your choice which) I will ask you to write a summary of the article. This need only be 1 ½ to 2 pages in length (double-spaced). In it you should summarize the experiments and findings, discuss whether the experimental results completely support the findings, and offer your overall impressions of the study and unanswered questions you are left with.

Friday Forum: Most weeks at precisely 10:31AM on Friday we will answer a question concerning the lecture material of the previous three meetings. Successful completion of Friday Fora indicates that you are keeping up with the material and that you are present and on-time for Friday lecture. Friday forums also give me an opportunity to offer you input on your strategies for answering questions in a lower stakes setting outside of the exam context.

Laboratory assignments; See below. These will be described in detail in lab.

Participation & involvement; The success of this course, both collectively and for you as individuals, hinges on your active participation. Lectures and labs require your preparation and input. If you show up for lectures and labs mentally keen and full of zeal and curiosity and a willingness to engage, then we will all enjoy the course more fully and come away with a meaningful appreciation for plants and plant function. When assigning grades to those students who find themselves “on the borderline,” we will give serious consideration to their degree of participation and involvement.

We will not set numerical standards for grades until the end of the course; however, please feel free to make an appointment to discuss how you are doing, if you like.

A passing grade in Plant Physiology requires passing knowledge of the subject matter, as reflected by exam scores. An average exam score of 60% or above may be required for passing this course.

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Lecture syllabus Date Topic Photosynthesis Sept. 4 Introductions, Overview, Photosynthesis: Broad strokes 7 Light gathering & Electron transport 9 Light gathering & Electron transport 11 Photoprotection 14 Photoprotection & The Calvin cycle 16 The Calvin cycle 18 Sunflecks 21 Translocation Water & Nutrients 23 Introduction & The properties of water 25 Exam #1 28 The soil-plant-atmosphere continuum (S.P.A.C.) 30 S.P.A.C. Oct. 2 S.P.A.C. 5 Xylem cavitation 7 Xylem cavitation 9 Redwood ecophysiology & The limits to tree height 12 Fall Break 14 The limits to tree height 16 No Class 19 Occult precipitation and its uses 21 Photorespiration & C4 23 C4 & CAM 26 Desert ecophysiology 28 Desert ecophysiology 30 Exam #2 Mineral nutrition & The soil microenvironment Nov. 2 Mineral uptake & Mycorrhizae 4 Alternative modes of gathering nutrients 6 Nitrogen fixation 9 Anthropogenic nitrogen fixation and the Green Revolution 11 Genetically modified plants 13 Genetically modified plants 16 Elevated CO2 & Global change 18 Elevated CO2 & Global change 20 Plants in winter 23 Plants in winter 25 Thanksgiving Break 27 Thanksgiving Break Growth & Development 30 Plant growth at the cellular level Dec. 2 Phytochromes 4 Selected examples of plant hormones 7 Tree die off 9 Plant parasites 11 Plant parasites

Dec. 16 Final Exam – 9:00AM

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Laboratory Schedule Week Laboratory 1 Augbeginnin 31 No Lab 2 Septg 7 Photosynthetic Oxygen Exchange & Light Response Curves 3 Sept 14 Photoprotection & Plant Pigments - Carotenoids & Anthocyanins

4 Sept 21 Chlorophyll Fluorescence 5 Sept 28 Field Excursion 6 Oct 5 Hydraulic Conductivity of Woody Plant Stems 7 Oct 12 Hydraulic Conductivity of Woody Plant Stems 8 Oct 19 Data Analysis for Water Relations Labs 9 Oct 26 Plant Ecophysiology Research Projects 10 Nov 2 Plant Ecophysiology Research Projects 11 Nov 9 Plant Ecophysiology Research Projects 12 Nov 16 Scientific Writing 13 Nov 23 Thanksgiving Break – No Lab – Class Trip 14 Nov 30 Field Excursion – Parasitic Plants 15 Dec 7 No Lab – Paper Preparation

Laboratory Policy Laboratory attendance is mandatory. You must discuss any pending conflicts with the instructor in advance. Under some circumstances we may allow you to switch between sections on a given week, if that will eliminate a conflict, but this is not to be considered a generally accepted practice.

Read the laboratory before coming to lab. This will ease the flow of the lab session for you, the instructor, and your lab-mates.

Many of the lab exercises require that you work in groups. However, each individual is expected to keep track of his/her group’s data and, when necessary, data generated by the entire class. You are expected to complete assignments individually. You could be assessed a point penalty for turning in assignments after their due date.

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Assignments Due date1 Points “Review” Questions Sept. 7a 20 Photosynthesis Lab Review Sept. 14a 20

Pigments Lab Review Sept. 21a 20

Exam #1 Sept. 25 90

Fluorescence Lab Review Sept. 28a 20 Plant Ecophysiology Photo Story Sept. 28 20 (Must do 2 of 3 photo summaries) Hydraulic Conductivity Literature Summary Oct. 5a 20

Article Summary Oct. 19 40 (Must do 2 of 3 article summaries) Group Research Proposal Oct. 26 25 Plant Ecophysiology Photo Story Oct. 26 20 (Must do 2 of 3 photo summaries) Exam 2 Oct. 30 140 Hydraulic Conductivity Summary Nov. 6 55 Research Project: Draft Introduction Nov. 9a 10 Research Project: Draft Methods Nov. 16a 10

Article Summary Nov. 20 40 (Must do 2 of 3 article summaries) Research Project: Draft Results, Discussion, Title, Abstract, & Literature Cited Sections Dec. 4 30 Plant Ecophysiology Photo Story (Must do 2 of 3 photo summaries) Dec. 7 20 Article Summary Dec. 9 40 (Must do 2 of 3 article summaries) Research Project: Final Paper Submission Dec. 9 80

Friday Forum ~Weekly 90

Final Exam 250

Total 1000 points 1 We may need to adjust these due dates to suit the evolving needs of the course. If changes become necessary, you will be informed of them in lecture or lab. a These assignments are due on your lab day during the week starting on the date listed

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The Academic Honor Code [excerpted from the Student Handbook]

The success of the Academic Honor Code requires the active commitment of the College community. Bowdoin College expects its students to be responsible for their behavior on and off the campus and to assure the same behavior of their guests. Uncompromised intellectual inquiry lies at the heart of a liberal education. Integrity is essential in creating an academic environment dedicated to the development of independent modes of learning, analysis, judgment, and expression. Academic dishonesty, in or out of the classroom, is antithetical to the College’s institutional values and constitutes a violation of the Honor Code. The Academic Honor Code plays a central role in the intellectual life at Bowdoin College. Students and faculty are obligated to ensure its success.

III. Proscribed Conduct The following sections describe activities constituting breaches of the Academic Honor Code. 1. "Academic Dishonesty" includes but is not limited to (1) the receiving, giving, or using of any assistance on quizzes, tests, written assignments, examinations or laboratory assignments; (2) references to sources beyond those authorized by the instructor in preparing papers, constructing reports, solving problems, or carrying out other academic assignments; (3) inadequate citation of sources; (4) acquisition, without permission, of tests, computer files or similar material which would give the student an unfair advantage on an assignment or examination; (5) submission of academic work not a student’s own original effort; (6) use of the same work for multiple courses without prior knowledge of the receiving instructors; (7) depriving learners of access, including computer access, to library information through intentional monopolization, mutilation, defacing, unauthorized removal of books or other materials from College libraries, or purposeful failure to return library materials on a timely basis; (8) unauthorized altering of academic records (transcripts, grading sheets, Course Registration Cards, etc.).

2. A number of Bowdoin College courses employ various kinds of collaborative assignments in several different situations, including homework, laboratory reports, and in-class assignments. When preparing such course work, students should follow the individual instructor’s policy on collaboration. When the instructor permits collaboration among students, the use of another student’s work or ideas should be credited properly.

3. It is the obligation of students to be thoroughly familiar with proper citation of sources and to consult and refer to authoritative style guides for research papers. New students will receive a copy of Sources during Orientation. Students should keep this booklet for reference throughout their years at Bowdoin. The Bowdoin College Library Web site provides links to style guides at http://www.bowdoin.edu/dept/library/eref/write.html. Students are particularly encouraged to consult the MLA Style Guides, Sources, and Bibliographic Formats for Citing Electronic Information. Plagiarism is possible with any work performed in any medium and any scholarly discipline. Plagiarism involves the use, by paraphrase or direct quotation, of the published or unpublished work of another person without full and clear acknowledgment in all such scholarly work as essays, examinations, quizzes, oral/written reports, homework assignments, laboratory reports, computer programs, music scores, choreography, graphic depictions, and visual representations. Plagiarism also includes the unacknowledged use of materials prepared by another person or agency engaged in the selling of term papers or other academic materials.

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