Biology 367 Course Description and Syllabus

The Biology of Microorganisms (Microbial Diversity and Applied Microbial Biotechnology) California State University San Marcos Spring Semester 2008 January 19 - May 16

"Emerald Pool" Hot Spring at Black Sand Basin, Yellowstone National Park

Lecture: WF 11:30-12:45 AM Laboratory: W 1-2-50 PM

F 1-1:50 PM

Instructor: Dr. Thomas Wahlund Department of Biological Sciences

Science Hall 2: Room 131 Phone 750-8042

Email: twahlund@csusm.edu

Office Hours: MTR 1:00-2:00 PM or by appointment

Microbiology & Biotechnology at Cal State San Marcos

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COURSE DESCRIPTION AND PREREQUISITES The history of microbiology goes back well over 100 years, and what was once defined as "the study of microorganisms" has now evolved to the point where a single definition is difficult, if not impossible, to compose. Microbiology is truly an interdisciplinary endeavor. Microbiology provided the means by which the first fundamental questions of molecular biology could be addressed. It was microbiologists who developed recombinant DNA technology, and these techniques in turn have profoundly transformed the field of biochemistry. In fact, disciplines such as molecular genetics and molecular biology arose from the laboratories of microbiologists, and applied aspects of this research have spawned a tremendous number of companies under the umbrella we now call The Biotechnology Industry. We will spend a considerable amount of time in both lecture and in lab investigating applied aspects of microbiology, an area wherein one looks for the unusual occurrence: a microbe that produces a novel antibiotic, a parasitic microbe that specifically infects and destroys a particular pest, or extreme environment microbes that may provide novel sources of enzymes, or metabolic pathways. This course is designed for upper division majors in biology and biochemistry and presents a selection of topics from the field of microbiology, especially bacteriology. The lectures will cover topics involving prokaryotic structure and function; ecological and physiological diversity of bacteria; growth and control of microorganisms; genetics of bacteria and viruses; microorganisms of medical and economic significance; and human applications of microbiology and biotechnology. COURSE OBJECTIVES The study of these prokaryotic cells (bacteriology) is a foundation for many of the sub-disciplines of microbiology, including mycology, virology, immunology, medical microbiology, food and industrial microbiology. Knowledge of the prokaryotes is applied in the foods, pharmaceutical, and biotechnological industries, in the diagnosis, treatment, and prevention of diseases of plants and animals, and in our understanding of biogeochemical processes in the biosphere. Understanding the biology of microorganisms has led to some of the most important advancements in medicine, food science and agriculture during our civilization. The interdisciplinary field of applied microbial biotechnology is making dramatic progress in the areas of medicine, the chemical industry, agriculture, and environmental science. In addition, prokaryotic cells have been used for some of the most significant experiments ever done in the biological sciences in basic areas of research such as genetics, molecular biology, biochemistry and physiology. TEXTBOOK Required: Madigan, M.T, J.M. Martinko, and J. Parker. Brock: Biology of Microorganisms (BOM), 11th ed. Prentice-Hall, Inc. Englewood Cliffs, New Jersey. 2002 (12th ed, due out in spring 2008, but not in time for this class!). Suggested Reference: Glazer A.N. and H. Nikaido. Microbial Biotechnology: Fundamentals of Applied Microbiology, 2nd ed., Cambridge University Press2, 2007 (ISBN 978-0-521-84210-5 hardback). An excellent reference text for your library. It is highly recommended that you have regular access to the BOM text. There will be suggested readings in this textbook that directly support, verify or explain topics which are presented in lecture. Some of these readings may provide important background material that you are already supposed to know but need to review for maximal comprehension and integration of lecture material. (1) Many of the lecture topics are expanded and explained in the text, and additional references are given. Some subjects not covered at all in the lectures are dealt with in some detail in the text. Students are encouraged to become familiar with the organization of the textbook and its range of contents in order to use it effectively. It is modern and scientifically up to date and is arguably the best textbook in the field; it is used in several advanced Microbiology courses at universities all over the world. Required readings for the course are listed in the lecture outline syllabus below. LABORATORY MANUAL Wahlund, T.M. 2008. Biology 367. Biology of Microorganisms: Laboratory Manual. University Readers, San Diego, CA.

The laboratory exercises in the manual cover topics ranging from medicine, biotechnology, ecology, immunology, and clinical and diagnostic microbiology. It must be stressed, however, that each exercise will be supplemented with in-lab research activities not contained in the manual. Students will be required to investigate many topics in more depth, analyze their results, and present their findings to their peers. As such, it is recommended that the student have a firm background in chemistry, molecular genetics and molecular biology, and some background understanding of basic biochemical pathways. The laboratory exercises and topics are listed in the laboratory outline syllabus below.

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GENOMICS/PROTEOMICS BIOINFORMATICS TERM PROJECT A semester research project (100 points) will be undertaken by students working in pairs (your lab partner). Details of this project will be given in class and will in part depend upon the results from your amplification and cloning of antibiotic resistance genes from the environment. GRADING CRITERIA Two hourly exams (100 points each) will be given during the semester (see Lecture Schedule) along with a comprehensive final exam (200 points). The final can count for as much as one-half, or as little as one fourth of your final lecture exam grade. This is because your score on the final will be divided by “2” to generate two - “one hour” exam equivalents. Along with these three exam grades, this will give you a total of 4 exam scores. The top three of these four scores will be summed to yield your lecture exam points (maximum = 300 points). This system effectively allows you to “drop” an hourly exam, therefore NO MAKEUP EXAMS WILL BE GIVEN FOR ANY REASON. All exams will consist both of objective and essay questions. You will be graded on the content of the answer that you put down on paper. I will not “interpret” what I might “think” you are trying to say since that would require a selective interpretation on my part, which I refuse to do. Full sentences, addressing only what was asked for in the question, will be the criteria for assigning points to those questions. Good communication skills and the ability to think critically are essential prerequisites for a successful career in science. The exams will also include any information covered in the laboratory component of the course. The laboratory notebook will be graded two times during the semester for a total of 150 points. Grading criteria for the laboratory notebook can be found in your laboratory manual and will be discussed in lab. Therefore, along with your term project points, the course grading criteria are summarized as follows:

Point Totals

Grade Scale

Term Exams: 2 x 100 = 200 Final Exam: 1 x 200 = 200 Laboratory Notebook = 150 Term Project = 100 COURSE TOTAL POINTS = 550

90% (495-550) = A 80% (440-494) = B 70% (385-439) = C 60 % (330-384) = D <60% (0-329) = F

Special Needs. A student with a verified disability may be entitled to appropriate academic accommodations. Please contact your instructor and/or the Disabled Student Services office in Craven Hall 5205, ext. 4905, for further assistance.

The Evolution of the Eukaryotic Cell from its Prokaryotic Ancestry

Comparison of the crystal structure of eukaryotic actin, bacterial MreB and ParM proteins. The four subdomains of actin are shown in different colors and the same colors are used for equivalent domains of the bacterial proteins. The conventional subdomain labels of actin are indicated against the ParM structure (from ASM News, December, 2003).

300

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Microbial Drug Resistance Weapons in Soil

Antibiotic resistance profiling of 480 soil-derived bacterial isolates. (A) Schematic diagram illustrating the phenotypic density and diversity of resistance profiles. The central circle of 191 black dots represents different resistance profiles, where a line connecting the profile to the antibiotic indicates resistance. (B) Resistance spectrum of soil isolates. Strains were individually screened from spores on solid Streptomyces isolation media (SIM) against 21 antibiotics at 20 µg of antibiotic per ml of medium (µg/ml). Resistance was defined as reproducible growth in the presence of antibiotic. (C) Resistance levels against each antibiotic of interest. (from Science, Vol. 311, pp. 374-377, 2006).

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TENTATIVE LECTURE SCHEDULE. SPRING 2008

Date Lecture Topic Reading 1/23 1 Overview of Microbial Diversity/Evolutionary Microbiology Ch. 2:4.1-4.4 Origin of Life and Microbial diversification 11.1-11.4 1/25 2 Evolution, Phylogeny and Taxonomy of Prokaryotes 14.2-14.4 Phylogeny of Bacteria and Archaea 12.1: 13.1

1/30 3 Structure and Function of the Prokaryotic Cell Ch. 4

2/1 4 Structure and Function of the Prokaryotic cell 4.5-4.16 2/6 5 Structure and Function of the Prokaryotic cell 6.1-6.3

2/8 6 Nutrition and Growth of Bacteria 5.1-5.3; 2/13 7 Growth of Bacterial Populations 6.4-6.16

2/15 8 Metabolic Diversity and Microbial Ecology Appendix 1A Bioenergetics 5.4-5.9 Heterotrophic metabolism: Fermentations and Respiration 5.10-5.17 2/20 9 Overview of Lithotrophic Metabolisms 17.8-17.21

2/22 FIRST EXAMINATION (covers Lectures 1-9) 2/27 10 Photosynthesis and Carbon Assimilation: An Overview 17.1-17.7

2/29 11 Genetic Engineering, Biotechnology & Industrial Micro. Ch. 7 (FYI)

3/5 12 Introduction to Molecular Genetics 8.1-8.14 3/7 13 Regulation of Gene Expression 10.1-10.14 3/12 14 Bacterial Genetics & Genetic Engineering: Overview Ch. 31

3/14 15 Prokaryotic/Eukaryotic Diversity: Selected readings from Ch.12, 13, & 14

3/19 16 Microbial Genomics: Tools for Industry and Research 3/21 17 Microbial Genomes & Genomic Cloning Techniques Ch. 15

Proteomics and Microarrays 3/26 18 Industrial Microbiology and Product Development Ch. 30

3/28 SECOND EXAMINATION (covers Lectures 10-18) SPRING BREAK (3/31 - 4/5)

4/9 19 Control of Microbial Growth & Clinical Microbiology/Immunology Physical, Chemical, and Antibiotic Methods Ch. 20

4/11 20 Antimicrobial Tests and Immunodiagnostics: Precipitation 24.1-24.4 Agglutination, Fluorescence & Clinical Applications 24.5-24.13

4/16 21 Human-Microbe Interactions 4/18 22 Normal Bacterial Flora of Animals Ch. 21 Intro. 4/23 23 Mechanisms of Bacterial Pathogenicity 21.6-21.12 4/25 24 Host Antimicrobial Defense Mechanisms 21.13-21.14

4/30 25 Epidemiology and Public Health Ch. 25 5/2 26 Biological Warfare and Biological Weapons Ch. 26; Ch. 27 Selected Microbial Diseases

5/7 27 Closing Lecture: Microbial Biotechnology and Human Health 5/9 28 Course Wrap-up and Term Projects Due

FINAL EXAM WEEK MAY ?

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Beyond penicillins. Bacteria use a peptidoglycan layer to protect themselves from osmotic stress. Synthesis of this layer proceeds in several steps. First, lipid II is synthesized in the cell. It is then transferred to the outside, where it is added to the peptidoglycan polymer by membrane-associated transglycosylase enzymes. Finally, the polymer is cross-linked via interstrand peptide bonds catalyzed by transpeptidase enzymes. Lovering et al. report the three-dimensional structure of a bifunctional transglycosylase-transpeptidase. The structure should aid development of new antibiotics targeting the transglycosylation domain. (from Science vol. 315, 2007)

Overall structure of PBP2. The modular nature of the GT51 and TP folds is shown, with the predicted position of the transmembrane region represented by a vertical blue rectangle. The active-site residues for the GT51 (lower, E171; upper, E114) and TP (S398) functionalities have their α-C atoms shown as red spheres. The GT51 domain is proposed to be at least partly submerged in the bilayer in order to access the lipid II substrate, which is consistent with observations that catalytic activity and crystallization were dependent on the presence of detergents. (from Science vol. 315, 2007)

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Tentative Schedule for Biology 367 Laboratory

Spring 2008

Week

Period

Date

Reminders

Begin

Continue

Finish

1

1

2

W 1/23

F 1/25

1.1 2.1 3.1 4.1

1.1 1.2 2.2

2

3

4

W 1/30

F 2/1

5.1 6.1 7.1

4.2

4.3

3.2 5.2 6.2

3

5

6

W 2/6

F 2/8

8.1 9.1

4.4

4.5

7.2 9.1 8.2

4

7

8

W 2/13

F 2/15

12.1/1A

4.6

5

9

10

W 2/20

F 2/22

10.1

12.2/2A

4.7

10.2

6

11

12

W 2/27

F 2/29

14.1

15.1

4.8

12.3/3A

10.2

7

13

14

W 3/5

F 3/7

13.1

12.4/4A

14.2 15.2

13.2

8

15

16

W 3/12

F 3/14

16.1

4.10

12.5/5A 14.3

10.2 15.3 16.2

9

17

18

W 3/19

F 3/21

17.1

4.11 14.4

12.6/6A

17.2

8

10

19

20

W 3/26

F 3/28

18.1

4.12 12.4

12.5 14.5

18.2

11

21

22

W 4/9

F 4/11

19.1

20.1

4.13 19.2

12

23

24

W 4/16

F 4/18

21.1

20.2

21.2

13

25

26

W 4/23

F 4/25

22.1

22.2

14

27

28

W 4/30

F 5/2

23.1

23.2

15

29

W 5/7

16

30

F 5/9

Analysis by SEM of biofilm development by E. faecalis OG1RF in the chemostat-based biofilm fermentor. Glass rods carrying biofilms were removed from the fermentor at the indicated times and processed for SEM. (see J. Bacteriol., January 2004.)