ENVIRONMENTAL MICROBIOLOGY BIOL 424 CRN 85424 FALL 2012 t
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Days and Times: Tuesday and Thursday, 2:10-­‐3:30pm Location: All Classes – EE Just Hall, Rm 209 Prerequisites: General Biology BIOL 101/102, Genetics BIOL 200, and General Microbiology BIOL 220 Credit Hours: 4 Instructor: Courtney J. Robinson, Ph.D., Assistant Professor, Dept. of Biology Office: EE Just Hall Rm 222 Lab: EE Just Hall Rm 239 Email: courtney.robinson@howard.edu Office Phone: 202-­‐806-­‐6953 Office Hours: Monday 2-­‐4, Wednesday 3-­‐5, and by appointment Course description: This course will include exploration of microbes’ interactions with their biotic and abiotic environments. We will discuss scientific articles from journals such as Applied and Environmental Microbiology. The articles will examine bacterial survival and diversity in a number of habitats through the use of traditional microbiological and molecular techniques. A key assignment in the course is a project focused on the characterization of environmental isolates. Text: Brock Biology of Microorganisms, 13th ed. Madigan, Martinko, Stahl and Clark Pearson Benjamin Cummings, Publisher, 2012 Additional readings will be assigned in class General rules, regulations and procedures: 1. Safety: It is important that all students familiarize themselves with the safety rules as outlined here and as described during the course. There is absolutely no eating, chewing gum, or drinking in the laboratory. We will be using an open flame, so please tie long hair back, do not wear scarves, baseball hats, long flowing sleeves, etc. in the laboratory. Do not wear open-­‐toed shoes, or shorts. Report accidents of ANY kind to your instructor. 2. Grading: EXAMS (three worth 150 pts each) 450 QUIZZES (5 worth 10 pts each) 50 LAB NOTEBOOK 50 JOURNAL CLUB / DISCUSSION 100 LAB REPORT 150 PRESENTATION 100 TOTAL POINTS 1000 ,
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**NOTE THAT THE INSTRUCTOR OF THIS COURSE RESERVES THE RIGHT TO DEVIATE FROM THIS SYLLABUS AT HER DISCRETION ** 3.
Exams: There are no makeup exams except in extraordinary cases (as determined by the instructor) and such cases must be presented with the necessary documents (to be determined by the instructor based on the nature of the situation). The laboratory exams will be essay, short answer, multiple-­‐choice, true/false and may include a practicum component emphasizing correct execution of techniques used throughout the semester. The exam will consist of material from mini-­‐
lectures at the beginning of laboratory, material covered in the resource guide, and material from text assignments or assigned reference materials. 4.
Quizzes: Both unannounced and announced quizzes will be given during the semester and can cover any information covered in the course. There are absolutely no makeup quizzes. 5.
Lab Notebook: This is a research-­‐based course. You must maintain a research notebook in order to document your activities and so that scientists who come behind you can repeat your experiments. Your notebook will be collected at various (mostly unannounced) times throughout the semester and will be graded on completeness, and ease of understanding. ep
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Lab Report and Presentation: The lab report (Profiles of Environmental Isolates) and oral presentation (~ 15min) will inform the audiences of each project’s progress and the student-­‐
scientist’s findings up to that point. Each student must generate his or her own original lab report. A separate document will outline details as to how the lab report and oral presentation are generated. Students are encouraged to show the instructor his/her presentation slides at least one week before the presentation in order to get feedback in preparation for the actual seminar. The presentation will be graded by the instructor (80% of the grade) and other students in the class (20% of the grade). 7.
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Journal Club / Discussion: During certain class periods students will be expected to participate in discussions facilitated by the instructor. Discussions can cover a number of topics, including, but not limited to: information from the previous class period, and reading assignments. During Journal Club each student will informally and briefly (8 min at the very most) present a scientific article of the student’s chosing that focuses on some aspect of environmental microbiology – the topic can be related or unrelated to class activities, as long as it obviously connects to environmental microbiology. The presenting student must have read the article in its entirety and be prepared to answer questions from classmates and the instructor. Students will be graded on level and quality of participation. Students should report/describe: Late Assignments: All assignments must be submitted in-­‐person, at the beginning of the class period at which it is due. On the date the assignments are due, one (1) point will be docked per hour the assignment is late. Assignments submitted after their due dates will be docked 10 points for each calendar day they are late. Blackboard: Students are responsible for accessing Blackboard. Announcements, assignments and electronic versions of most of the material used in this course will be posted to Blackboard. Grades for the course will be maintained on Blackboard. ity
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the name of the journal, the authors’ names and affiliations, title of paper, the goal of the paper/hypothesis, key experiments and their results (not data, but results), the conclusions drawn by the authors, conclusions drawn by themselves, and critiques, and suggestions for new experiments ow
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10. Open laboratory time: There may be times when your attendance in lab is required outside of the normal class period. Students will not be permitted access to the lab without supervision. Open lab time will be announced via Blackboard. Other times can be requested, if necessary. **NOTE THAT THE INSTRUCTOR OF THIS COURSE RESERVES THE RIGHT TO DEVIATE FROM THIS SYLLABUS AT HER DISCRETION ** 11. Tips on how to do well: a.
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Tuesday 1 8/23/12 Thursday 8/28/12 Tuesday 8/30/12 Thursday 9/4/12 Tuesday 3 9/6/12 Thursday 9/11/12 Tuesday 4 9/13/12 Thursday 9/18/12 Tuesday 5 9/20/12 Thursday 9/25/12 Tuesday 6 Study/Project Day -­‐ No Class 9/27/12 Thursday Study/Project Day -­‐ No Class 10/2/12 Tuesday 7 2 Course overview Overview of Microorganisms -­‐ Chapters 1-­‐5 Lab: Review of laboratory safety Overview of Microorganisms -­‐ Chapters 1-­‐5 Lab: Streaking bacteria, bacterial morphologies, Gram staining Overview of Microorganisms -­‐ Chapters 1-­‐5 Lab: Endospore stain, motility, taxes (tentative) Methods in Microbial Ecology -­‐ Chapter 22 Reading Assignment – Microbial Interactions: Little et al Annual Review of Microbiology Vol. 62: 375-­‐401 Lab: Review of dilution plating, plating soil on selective media, isolation of antibiotic producers Microbes in the Environment – Chapter 23 -­‐ 24 Seminar: Ed DeLong http://www.yada-­‐yada.co.uk/Blackwell/SFAM2009/SfAM2009.html Discussion of Reading Assignment: Annu Rev, Little et al Lab: Isolation of antibiotic producers continued, review of biochemical tests Microbes in the Environment – Chapter 23 -­‐ 24 Reading Assignment – Host Microbe Interactions: Eydal et al The ISME Journal (2009) 3, 1139–1147 Lab: Isolation of antibiotic producers continued, review of biochemical tests Microbial Symbioses – Chapter 25 Seminar: Willem de Vos http://www.yada-­‐yada.co.uk/Blackwell/SFAM2011/SFAM2011.html Brief Exam Review Discussion of Reading Assignment: Eydal, et al Lab: Isolation of antibiotic producers continued ,
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read and be thoroughly familiar with this syllabus read text/assignments before coming to class do not wait until the last day before exams to go over the study materials, or seek help 12. CHEATING WILL NOT BE TOLERATED. ANYONE CAUGHT CHEATING WILL BE DEALT WITH ACCORDING TO THE RULES OF THE COLLEGE OF ARTS AND SCIENCES. 13. In compliance with the law (Section 504, Rehabilitation Act and the American with Disabilities Act, "ADA"), Howard University is committed to providing its disabled students with reasonable accommodations. In accordance with this policy, students in need of accommodations due to a disability should contact the Office of the Dean for Special Student Services for verification and determination of reasonable accommodations as soon as possible after admission to the University, or at the beginning of each semester. The Office of the Dean for Special Student Services can be reached at (202) 806-­‐2420. COURSE SCHEDULE ar
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EXAM #1 (all of the above) The Bacteria – Chapters 17 -­‐ 18 Project Outline – Profiles of Environmental Isolates Randomly select environment type Lab: Check plates, isolation of antibiotic producers continued The Bacteria – Chapters 17 -­‐ 18 **NOTE THAT THE INSTRUCTOR OF THIS COURSE RESERVES THE RIGHT TO DEVIATE FROM THIS SYLLABUS AT HER DISCRETION ** 10/4/12 ep
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10/9/12 Thursday Tuesday 8 tm
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10/11/12 Thursday 9 10/18/12 Thursday 10/23/12 Tuesday 10 10/25/12 Thursday 10/16/12 Tuesday t
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Reading Assignment – Workplace Microbial Communities and Human Impact: Murat et al Appl. Environ. Microbiol. January 2012 vol. 78 no. 1 34-­‐41 Sample Site and Experimental Design Due Journal Club Lab: begin isolation of microorganisms if possible Vectorborne and Soilborne Microbial Pathogens – Chapter 34 Reading Assignment – Microbial Bioremediation: Kostka et al Appl. Environ. Microbiol. November 2011 vol. 77 no. 227962-­‐7974 Discussion: Reading Assignment Murat et al. Lab: Open lab, continue isolation of microorganisms Journal Club Lab: Open lab, continue profiling isolates Wastewater Treatment, water purification and waterborne Microbial Diseases – Chapter 35 Discussion: Reading Assignment Kostka et al. Lab: Open lab, continue profiling isolates Journal Club Lab: Open lab, continue profiling isolates 11 11/1/12 Thursday 11/6/12 Tuesday 12 11/8/12 Thursday 11/20/12 Tuesday 14 11/22/12 Thursday Presentations Presentations Lab: FINAL LAB, RECORD FINAL OBSERVATIONS, NOTEBOOKS WILL BE COLLECTED à Make sure to photocopy pgs necessary to complete lab report THANKSGIVING RECESS -­‐ NO CLASS LAB REPORTS DUE EXAM #3 (all of the above) U
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Exam Review 11/27/12 Tuesday ow
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10/30/12 Tuesday EXAM #2 (all of the above) Journal Club Lab: Open lab, continue profiling isolates Presentation Review – Randomly select presentation date Reading Assignment -­‐ Viral Diversity: Ng et al PLoS ONE 6(6): e20579. doi:10.1371/journal.pone.0020579 Lab: Open lab, continue profiling isolates Journal Club Lab: Open lab, continue profiling isolates Discussion: Reading Assignment Ng et al. Lab: Open lab, continue profiling isolates **NOTE THAT THE INSTRUCTOR OF THIS COURSE RESERVES THE RIGHT TO DEVIATE FROM THIS SYLLABUS AT HER DISCRETION **