Course ID: MICR R100L Curriculum Committee Approval Date: 01/14/2015 Catalog Start Date: Fall 2015 COURSE OUTLINE

OXNARD COLLEGE

I. Course Identification and Justification: A. Proposed course id: MICR R100L Banner title: Principles of Microbiology Lab Full title: Principles of Microbiology Laboratory

Previous course id: MICR R100L Banner title: Principles of Microbiology Lab Full title: Principles of Microbiology Laboratory

B. Reason(s) course is offered: This course is required for professional degree and certificate programs such as nursing and dental hygiene; it is an elective for the biology degree. This course is transferable to the CSU and UC and provides credit in the following areas (A1 OC GE, B3 CSU GE; 5C IGETC).

C. Reason(s) for current outline revision: In this revision, prerequisites are being modified so that they are listed for each prior course in complete (Math, Biology, English, Physiology and Anatomy). Students are entering the OC Micro course without all the prerequisites because they took these courses at other schools that have different sequential prerequisite series. The textbook was also updated.

D. C-ID: 1. C-ID Descriptor: 2. C-ID Status:

E. Co-listed as: Current: None Previous:

II. Catalog Information: A. Units: Current: 2.00 Previous: 2.00

B. Course Hours: 1. In-Class Contact Hours: Lecture: 0 Activity: 0 Lab: 105 2. Total In-Class Contact Hours: 105 3. Total Outside-of-Class Hours: 0 4. Total Student Learning Hours: 105

C. Prerequisites, Corequisites, Advisories, and Limitations on Enrollment: 1. Prerequisites Current: MICR R100: Principles of Microbiology or Previous: MICR R100: Principles of Microbiology

2. Corequisites Current: MICR R100: Principles of Microbiology Previous:

3. Advisories: Current: Previous:

4. Limitations on Enrollment: Current: Previous:

D. Catalog description: Current: This is a laboratory course designed for biological science majors and students interested in the health science professions. The exercises are intended to give the students experience in the manipulation of microorganisms and exposure to current microbial techniques. Topics covered will include microscopy methods, prokaryotic and eukaryotic cell structure, microbial metabolism, genetics, recombinant DNA, and biotechnology. Previous, if different:

E. Fees: Current: $ None Previous, if different: $

F. Field trips: Current: Will be required: [ ] May be required: [X] Will not be required: [ ]

Previous, if different: Will be required: [ ] May be required: [ ] Will not be required: [ ]

G. Repeatability: Current: A - Not designed as repeatable Previous: A - Not designed as repeatable

H. Credit basis: Current: Letter Graded Only [X] Pass/No Pass [ ] Student Option [ ]

Previous, if different: Letter Graded Only [ ] Pass/No Pass [ ] Student Option [X]

I. Credit by exam: Current: Petitions may be granted: [ ] Petitions will not be granted: [X]

Previous, if different: Petitions may be granted: [ ] Petitions will not be granted: [ ]

III. Course Objectives: Upon successful completion of this course, the student should be able to: A. Demonstrate the principles of asepsis B. Operate a light microscope C. Perform standard bacteriological staining procedures D. Cultivate, transfer and maintain pure microbial cultures E. Explain an understanding of the principles of fermentation and applied microbiology F. Perform modern recombinant DNA technology methods G. Analyze the role of microbes in the biosphere H. Identify the role of normal body flora I. State an understanding of colonization and infectious disease J. Determine the identity of a simple unknown bacterium K. Discuss the role of microbiology in medicine, food production, biotechnology and agriculture

IV. Student Learning Outcomes: A. The student will have the ability to proceed stepwise biochemical laboratory tests in solving the identity of an unknown bacterium. B. The student will be capable of producing a laboratory notebook, indexed and paginated with the current semester's schedule.

V. Course Content: Topics to be covered include, but are not limited to: A. Microscopy and microbial diversity 1. Care and use of the bright-field light microscope 2. Care and use of the fluorescence microscope 3. Care and use of the phase contrast microscope 4. Observation of bacteria, microscopic eukaryotes, and blood cells (slides). 5. Observation of microscopic organisms from environmental sources B. Basic Staining Techniques 1. Gram 2. Acid Fast 3. PHB 4. Endospore 5. Flagellar 6. Fluorescent C. Microbial Growth 1. Growth 2. Measurement of Growth 3. Phases of Growth in Closed Systems 4. Maintenance of pure culture D. Nutrition and Cultivation 1. Nutritional Requirements 2. Culture Conditions 3. Media 4. Culture Characteristics E. Methods of Identification 1. Entertube II or API method 2. PCR-Sequencing 3. Standard keys utilizing biochemical tests F. Antibiotic Sensitivity Testing Methods 1. Kirby-Bauer 2. E-Test G. Quality Control Methods 1. Plate Counts 2. Coliform Testing H. Investigation of Geochemical Microbiology 1. Biogas and Alcohol production 2. Winogradsky column I. Biotechnologies 1. Transformation 2. RT-PCR 3. DNA Extraction 4. DNA Sequencing (outsourced) 5. Phage plaque assay and purification J. Immunological Assays 1. Agglutination 2. Elisa 3. Western Blot 4. Immunoprecipitation K. Eukaryotic Cell Culture 1. Cell Culture Methods L. Applied Microbiology 1. Plant Virus: TMV 2. Animal Virus: Bacculovirus 3. Microbes used in food production M. Medical and Dental Microbiology 1. Specialized media for skin, throat, and urogenital cultures 2. Specialized media for oral cultures 3. Sampling methods for determination of cancer (oral, GI, skin) N. Aseptic technique 1. Determination of disinfectant and sanitizer effectiveness 2. Operation of the laminar flow biosafety cabinet 3. Appropriate use of gloves, gowns and goggles

VI. Lab Content: A. Microscopy and microbial diversity 1. Care and use of the bright-field light microscope 2. Care and use of the fluorescence microscope 3. Care and use of the phase contrast microscope 4. Observation of bacteria, microscopic eukaryotes, and blood cells (slides). 5. Observation of microscopic organisms from environmental sources B. Basic Staining Techniques 1. Gram 2. Acid Fast 3. PHB 4. Endospore 5. Flagellar 6. Fluorescent C. Microbial Growth 1. Growth 2. Measurement of Growth 3. Phases of Growth in Closed Systems 4. Maintenance of pure culture D. Nutrition and Cultivation 1. Nutritional Requirements 2. Culture Conditions 3. Media 4. Culture Characteristics E. Methods of Identification 1. Entertube II or API method 2. PCR-Sequencing 3. Standard keys utilizing biochemical tests F. Antibiotic Sensitivity Testing Methods 1. Kirby-Bauer 2. E-Test G. Quality Control Methods 1. Plate Counts 2. Coliform Testing H. Investigation of Geochemical Microbiology 1. Biogas and Alcohol production 2. Winogradsky column I. Biotechnologies 1. Transformation 2. RT-PCR 3. DNA Extraction 4. DNA Sequencing (outsourced) 5. Phage plaque assay and purification J. Immunological Assays 1. Agglutination 2. Elisa 3. Western Blot 4. Immunoprecipitation K. Eukaryotic Cell Culture 1. Cell Culture Methods L. Applied Microbiology 1. Plant Virus: TMV 2. Animal Virus: Baculovirus 3. Microbes used in food production M. Medical and Dental Microbiology 1. Specialized media for skin, throat, and urogenital cultures 2. Specialized media for oral cultures 3. Sampling methods for determination of cancer (oral, GI, skin) N. Aseptic technique 1. Determination of disinfectant and sanitizer effectiveness 2. Operation of the laminar flow biosafety cabinet 3. Appropriate use of gloves, gowns and goggles VII. Methods of Instruction: Methods may include, but are not limited to: A. Short lectures using computer data and the blackboard/whiteboard to explain the procedures of microscopy, staining, dilutions, biochemical analysis, genetics, virology, immunology and recombinant DNA technologies. B. Laboratory exercises completed individually for solving the unknown bacterial sample or in groups of two or more for performing other exercises. C. The use of computer slides, overheads, video and other media to illustrate recombinant DNA technologies and other conceptually difficult topics D. Structured one-on-one interactions with students to support, monitor, and evaluate progress in completing a laboratory notebook, computer data presentation and laboratory methods related to sterile techniques, staining and solving the bacterial unknown. E. Use of a student generated laboratory book and/or report assignments and presentations to help create a study guide for efficient examination preparation. F. A pre-examination practice lab practical to familiarize student with the exam mode. G. Daily oral quizzing, group discussion and student driven current events sections of the class. H. A detailed review of the material as a take home assignment before students have been given the opportunity to take a test with similar material.

Other methods of instruction:

I. Short lectures using computer data and the blackboard/whiteboard to explain the procedures of microscopy, staining, dilutions, biochemical analysis, genetics, virology, immunology and recombinant DNA technologies. J. Laboratory exercises completed individually for solving the unknown bacterial sample or in groups of two or more for performing other exercises. K. The use of computer slides, overheads, video and other media to illustrate recombinant DNA technologies and other conceptually difficult topics L. Structured one-on-one interactions with students to support, monitor, and evaluate progress in completing a laboratory notebook, computer data presentation and laboratory methods related to sterile techniques, staining and solving the bacterial unknown. M. Use of a student generated laboratory book and/or report assignments and presentations to help create a study guide for efficient examination preparation. N. A pre-examination practice lab practical to familiarize student with the exam mode. O. Daily oral quizzing, group discussion and student driven current events sections of the class. P. A detailed review of the material as a take home assignment before students have been given the opportunity to take a test with similar material.

VIII. Methods of Evaluation and Assignments: A. Methods of evaluation for degree-applicable courses: Essays [X] Problem-Solving Assignments (Examples: Math-like problems, diagnosis & repair) [X] Physical Skills Demonstrations (Examples: Performing arts, equipment operation) [ ]

For any course, if "Essays" above is not checked, explain why.

B. Typical graded assignments (methods of evaluation): 1. A laboratory lab book entry and/or report will be required for the topics listed in the course content section and include notations on staining bacteria (Gram, simple, acid fast, spore, flagella, ete.), observation of living prokaryotes and eukaryotes, biochemical tests to determine identity of the unknown, PCR of the unknown. The lab book is double indexed with a table of contents and additional listing of tests used to solve the unknown. 2. Laboratory exams will cover the major content areas and include written questions, projected video data in lieu of a lab practical and essay style answers. 3. Physical skills demonstrations include sterile technique, Gram stain, sterile transfer and tests used for the completion of the identification of the unknown. 4. An end of term data presentation consisting of a minimum of five slides that is presented to the class is expected of each student. Each slide is referenced as to its source. As an example starting point, it is suggested that content is derived from information from the CDC related to clinical or over the counter rapid diagnostic tests for determination of microbial identity. These have an 18 month development to market cycle within the FDA so new tests are available each semester. Kits for detection of Southeast Asian HPAI A H5N1 avian flu and the 2009 A H1N1 swine flu are examples of recently developed and unevenly distributed clinical tools. Additional information can be inferred from the US Patent office (or more conveniently, Google patents) to determine the molecular basis for the rapid diagnostic test of choice. Most outpatient or over the counter rapid diagnostic kits are PCR ELISA or Western based assays - the very techniques the students have performed in lab from scratch using off the shelf reagents. An example data presentation is graded on the basis of the student’s ability to provide data slides on disease symptoms as initially presented clinically, detection using the above mentioned diagnostic, the kit procedure, the molecular basis for the kit test (including required auxiliary equipment) and conclusion. The basis of grading is a combination of essay style in-class exams, multiple-choice exams, take home essay exams, and writing assignments including a research presentation. The grading is determined on the basis of class averages, including the use of the functions of the average and standard deviation. A level students are typically in the percentage area above the first standard deviation while B students are between the first standard deviation and the mean. C grades and lower fall below the mean while D and F grades are reserved for incomplete data sets and those performing less than one standard deviation below the average.

C. Typical outside of classroom assignments: 1. Reading a. Beyond the required laboratory texts, students will be required to consult peer-reviewed journals on the Internet for source information on microbiological methods. The site www.ncbi.nlm.nih.gov contains the PubMed database where review articles can be located. Other sources of information for locating diagnostic tests for rapidly determining disease identity include Google patents, the www.cdc.gov, and the www.who.gov and FDA literature on approved diagnostic tests. It is particularly important that the student understand that many classical methods of microbiology are being augmented by newer tests based on biotechnology principles. 2. Writing a. Laboratory reports are prepared prior to the laboratory reporting periods in the lab book. They are completed after the observation period before being turned in to the instructor for grading. 3. Other a. The preparation of a PowerPoint presentation related to a diagnostic method or other aspect of microbiology is an expectation of the course. IX. Textbooks and Instructional Materials: A. Textbooks/Resources: 1. Leboff, M. J., and Pierce, B. E. (2010). Microbiology: Laboratory Application and Theory (3rd/e). Colorado Morton. 2. Leboff, M. J., and Pierce, B. E. (2012). Microbiology Laboratory Theory & Application, Brief (2nd/e). Morton. 3. John G. Holt PhD. Bergey's Manual of Systematic Bacteriology. Lippincott Williams & Wilkins (This is the most current version) , 01-01-1994. 4. "Earth Microbiome." Argonne National Laboratory, First ed. Description: http://www.earthmicrobiome.org/ This is a website sponsored by a US Government agency to assist with the determination of unknown microorganisms using DNA sequencing. Components ("16S and 18S DNA primers") are specifically identified on the website that are used in the Oxnard College laboratory for PCR amplification and DNA sequencing (by Sanger or Illumina technology). 5. Pubmed review and primary literature from the site: www.ncbi.nlm.nih.gov 6. Blast Program www.ncbi.nlm.nih.gov Blast is a program used to identify matching DNA sequences in a database of microorganisms. The students produce a DNA from an unknown bacteria using the PCR method. The PCR "fragment" is sent by mail for DNA sequencing and the identity of the sequence is returned by email. The sequence can then be used to probe the Blast database for a match to known microorganisms (thus providing identity). B. Other instructional materials: 1. A myriad of slides, culture plates and extracts of live cultures 2. Microscope, PCR machine, Gel Electrophoresis and other standard lab equipment 3. Computer projection, Internet Based Animations and Video

X. Minimum Qualifications and Additional Certifications: A. Minimum qualifications: 1. Biological Sciences (Masters Required) B. Additional certifications: 1. Description of certification requirement: 2. Name of statute, regulation, or licensing/certification organization requiring this certification:

XI. Approval Dates Curriculum Committee Approval Date: 01/14/2015 Board of Trustees Approval Date: 01/14/2015 State Approval Date: Catalog Start Date: Fall 2015

XII. Distance Learning Appendix A. Methods of Instruction Methods may include, but are not limited to: B. Information Transfer Methods may include, but are not limited to: Course ID: 1637