PROKARYOTIC DIVERSITY

BIOL 4125 - SPRING 2012
1510-1630     MW     225 TUREAUD HALL

Instructor:  Brent C. Christner
Office:
  282b Life Sciences Building
Phone:
  (225) 578-1734
Email:
  xner@lsu.edu
Office hours:
  W 11:0012:00  

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., J.M. Martinko, P.V. Dunlap, and D.P. Clark. 2009. (12th or current eds.), Prentice Hall.
Amazon – 12th ed. (new - $75; used - $50 and up)

Scientific literature:
Readings from the text will be supplemented with scientific research papers 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.  Regular exams consist of multiple choice (60%), short answer (30%), and essay (10%) questions. If a student misses an exam for any reason, there will be one opportunity to makeup the exam at the end of the course.  The makeup exam will cover the same material but will be in essay format.  The final is cumulative. There will be no early or late finals administered.  The only exception is if a student has 3 or more final exams scheduled in 24 hours and a request is submitted to the Office of the University Registrar (http://appl003.lsu.edu/slas/registrar.nsf/index) by the specified university deadline. 

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 be composed of 4 sections: (i) the objective(s) of the research; (ii) the methods used to address this; (iii) a summary of the authors’ results and conclusions; and (iv) a critique of the authors’ approaches and conclusions.  Length should be 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 22 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 26 March. DO NOT place your paper in my mailbox or under the door of my office. In addition to the hard copy, you must also submit an electronic version of your paper to receive credit for the assignment.  Email this file to xner@lsu.edu with the file named using your first initial and last name in the file name (e.g. BChristner_BIO4125ResArt.doc).  The penalty for late turn in of a research paper is deduction of 10 percentage points per day.   
 
Class participation:  Student participation in class discussions is encouraged and expected.  Attendance may affect your participation grade.  

            Overall grading percentages:

 

Grading scale:

Exam I

25%

 

A

100-90%

Exam II

25%

 

B

89-80%

Final exam

25%

 

C

79-70%

Written assignment

20%

 

D

69-60%

Class participation

5%

 

F

Below 60%

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
Spring 2012
(Subject to change)

Class

Date

Activity

Readings

1

18 January (W)

Introduction and historical context

1 (1)

2

23 January (M)

Diversity: the past

6, 14, &22
(6, 11, & 18)

3

25 January (W)

Diversity: the new paradigm

14 (11)

4

30 January (M)

Microbial evolution

14 (11)

5

1 February (W)

Bioenergetics: unity in diversity

5 (5)

6

6 February (M)

Ecological diversity

23 (19)

7

8 February (W)

Overview of the Bacteria and Archaea I

15,16, & 17 (12 & 13)

8

13 February (M)

Overview of the Bacteria and Archaea II

15,16, & 17 (12 & 13)

9

15 February (W)

EXAM I

 

 

20 February (M)

MARDI GRAS

 

10

22 February (W)

Proteobacteria I
WRITTEN ASSIGNMENT TOPIC DUE

15 (12)

11

27 February (M)

Proteobacteria II

15 (12)
Giovannoni et al. (2005)a

12

29 February (W)

Proteobacteria III

15 (12)

13

5 March (M)

Phototrophic bacteria I

15 &16 (12)

14

7 March (W)

Phototrophic bacteria II

15 &16 (12)
Tomitani et al. (2006)b

15

12 March (M)

Firmicutes & Actinobacteria

16 (12)

16

14 March (W)

Bacteroidetes

16 (12)

17

19 March (M)

Spirochetes

16 (12)

18

21 March (W)

EXAM II

 

19

26 March (M)

Planctomycetes & Chlamydia
WRITTEN ASSIGNMENT DUE

16 (12)

20

28 March (W)

Deinococci

16 (12)

21

2 April (M)

Deep-branching bacteria I

16 (12)

22

4 April (W)

Deep-branching bacteria II

16 (12)
Huber et al. (1998)c

 

9 April (M)

SPRING BREAK

 

 

11 April (W)

SPRING BREAK

 

 

16 April (M)

NO CLASS

 

 

18 April (W)

NO CLASS

 

23

23 April (M)

Hyperthermophilic Archaea I

17 (13)

24

25 April (W)

Hyperthermophilic Archaea II

17 (13)
Huber et al. (2002)d

25

30 April (M)

Methanogens

17 (13)

26

2 May (W)

Halophilic Archaea

17 (13)

27

9 May (Wednesday)

FINAL EXAM 1000-1200

 

Numbers indicate chapters in Brock Biology of Microorganisms 12th ed. (11th ed.). 

Supplemental readings:

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

b Tomitani, A., et al. 2006. The evolutionary diversification of cyanobacteria: molecular-phylogenetic and paleontological perspectives. Proc. Natl. Acad. Sci., 103:5442-5447.           

c Huber, R., 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.

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