BIOL 4125 - SPRING 2008
13:40-15:00     TTh     E131 HOWE-RUSSEL

Instructor:  Brent C. Christner
Office:  282b Life Sciences Building
Phone:  (225) 578-1734
Email:  xner@lsu.edu
Office hours:  W 11:00–12:00
 

Prerequisite: 
BIOL 2051 – General Microbiology

Course content:
• Biology of the Bacteria and Archaea
• Evolution, diversity assessment, systematics, and ecology
• Emphasis on molecular approaches

Text:
Recommended: Madigan, M.T. and J.M. Martinko. 2005. Brock: Biology of Microorganisms (11th or current eds.), Prentice Hall.

Scientific literature:
Readings from the text will be supplemented with scientific research papers and reviews that will be posted on the course website.  For many students, these papers will be their first exposure to scientific literature.  Reading a scientific paper is not like reading a text book.  One goal of this course is to develop your ability to digest the content of and critically evaluate scientific literature.

Grading:
Exams: There will be 3 exams.  A missed exam can only be made up if official documentation is provided that clearly indicates circumstances beyond a student’s control.  Notes from a family member or friend are not acceptable.  The makeup will be an essay exam and cover all material in the course. 
Written assignment:  All students must submit a critical analysis of a research paper focusing on some aspect of microbial diversity.  Papers are to be based on published research articles from journals such as Applied and Environmental Microbiology, Environmental Microbiology, and International Journal of Systematic and Evolutionary Microbiology.  The paper should include a summary of the (i) methods and (ii) results, and (iii) a critique of the approach used and authors’ conclusions.  Length should be at least 3 full double-spaced pages (1 inch margins) using 12-pt Times New Roman font.  Each student must choose a research article and submit a pdf version to me (email to xner@lsu.edu; subject line BIOL4125 research article) by 19 February.  Come see me during my scheduled office hours if you need help selecting an article.  A hard copy of your paper is due in class on 13 March. DO NOT place your paper in my mailbox or under the door of my office.  The penalty for late turn in of a research paper is deduction of 10 percentage points per day.  Graduate students: see below for additional requirements. Plagiarism examples.  
Class participation:  Student participation in class discussions is encouraged and expected.  Attendance may affect your participation grade.

Additional requirements for graduate credit: Graduate student exams will be different (i.e., contain more essay questions) and will be graded on different standards from those designed for undergraduate students.  Graduate students are also required to submit a research paper of at least 5 pages in length.  The paper should focus on a topic rather than a specific research article.  Email me your research paper topic by 19 February.  As with exams, graduate student research papers will be evaluated separately from the rest of the class.  Grades for graduate students will be straight scale, meaning there will be NO curve or rounding of the final grade.  To obtain a passing grade (i.e., C or higher), graduate students must accrue at least 70% of the possible points in the course.

Other course information:
Email and internet access are required for the course.  Students should check the course site and read their email regularly.
Lecture slides:  The instructor will supply a hard copy of the lecture slides for each class.  An electronic copy (pdf version) of these notes will be made available on the course website.
Attendance will be documented but is not directly factored into the final grade.
Study hint:  The LSU Center for Academic Success (CAS; http://appl003.lsu.edu/slas/cas.nsf/index) exists to help students do well in their classes.  At their web site, consider taking their “Test Your Learning Style” to see how you learn best.

Code of Student Conduct:
Students are expected to adhere to the Code of Student Conduct, which can be accessed at: http://appl003.lsu.edu/slas/dos.nsf/$Content/Code+of+Conduct?OpenDocument.  University regulations on academic misconduct will be strictly enforced and violators will be referred immediately to the Dean of Students.

Students with disabilities:
If a student has a disability which may require accommodation, you should immediately contact the office of Services for Students with Disabilities to officially document the needed accommodation.  The instructor must be presented with this documentation during the first week of class.

To make our time together as valuable as possible:
·   Attend all scheduled classes and arrive on time.
·   Come prepared to discuss the material.
·   Please turn off cell phones and refrain from sending text messages, checking email, or any other behavior that might be disruptive to other students.
·   If you have trouble concentrating on the lecture because of a distraction, quietly ask those responsible for the distraction to stop. If the distraction continues, please let me know.
·   Please contact me immediately if you have any problem which is preventing you from performing satisfactorily in this class.

TENTATIVE course calendar
(Subject to change) 

^† Numbers indicate chapters in Brock Biology of Microorganisms (11^th ed.). 

Supplemental readings:
The copyright of the respective articles are with the corresponding publishers and the files are provided for academic use only.

Giovannoni et al. 2005. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1242-1245.

Tomitani et al. 2006. The evolutionary diversification of cyanobacteria: molecular-phylogenetic and paleontological perspectives. PNAS 103:5442-5447.

Huber et al. 1998. Thermocrinis ruber gen. nov., sp. nov., a pink-filament-forming hyperthermophilic bacterium isolated from Yellowstone National Park. Appl. Environ. Microbiol. 64:3576-3583.

Huber et al. 2002. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63-67.