Microbial Genetics genomics

1. Microbial Geneticsgenomics

2. Class demographics 200 level (sophomore) course Majors in Biology, Biotechnology and those applying for professional programs (Pharmacy school, PA, etc) Have taken Intro to Cell and Molecular Biology as freshmen.

3. Learning Objectives Addressed • Students will be able to explain how genetic variation impacts microbial functions • Students will be able to explain the mechanism of how cells, organisms and major metabolic pathways evolved (TOUCHES ON THIS SUBJECT) • Students will be able to interpret data and apply to new concepts

4. 6 4 2 MONDAY Lecture on genomics, discussion of paper after group brainstorm, evaluation note card FRIDAY Group work comparing Thurs assignment, class discussion on other models Learning outcomes 1, 2, 3 WED In class exercise creating dotplot of E.coliK12 vsE.coli o157H7 Learning outcomes 1, 2, 3 IN CLASS 5 SUNDAY Read assigned paper, questions Learning outcome #1 TUESDAY Dot plot tutorial, vocab LAB THURS research genes associated with inversion, LAB Learning outcome 1, 2, 3 3 SAT/SUN Survey of CCR7 1 7 OUT OF CLASS

5. Comparative genomics of xylose-fermenting fungi for enhanced biofuel production 1 Dana J. et al aDepartment of Genetics, University of Wisconsin, Madison, WI 53706; bGreat Lakes Bioenergy Research Center, Madison, WI 53706; cUS Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; dBiomass Conversion Research Laboratory, Department of Chemical Engineering and Materials Science, Michigan State University, Lansing, MI 48910; and eGreat Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 Edited by Chris R. Somerville, University of California, Berkeley, CA, and approved July 5, 2011 (received for review February 24, 2011) Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant within hemicellulose creates specific challenges for microbial biofuel production from cellulosic material. Although engineered strains of Saccharomyces cerevisiae can use the pentose xylose, the fermentative capacity pales in comparison with glucose, limiting the economic feasibility of industrial fermen- tations. To better understand xylose utilization for subsequent mi- crobial engineering, we sequenced the genomes of two xylose- fermenting, beetle-associated fungi, Spathasporapassalidarum and Candida tenuis. To identify genes involved in xylose metabo- lism, we applied a comparative genomic approach across 14 Asco- mycete genomes, mapping phenotypes and genotypes onto the fungal phylogeny, and measured genomic expression across five Hemiascomycete species with different xylose-consumption pheno- types. This approach implicated many genes and processes involved in xylose assimilation. Several of these genes significantly improved xylose utilization when engineered into S. cerevisiae, demonstrat- ing the power of comparative methods in rapidly identifying genes for biomass conversion while reflecting on fungal ecology. bioenergy | genome sequencing | transcriptomics

6. Lecture Monday • How do the genomes of prokaryotes differ from that of eukaryotes • Discuss the principles of comparative genomics and evolution • Discuss the main points of the assignment paper • Few fungi can ferment xylose, suggest picked up ability through evolution • Tie into previous lectures on metabolism • FORMATIVE ASSESSMENT Pass out an evaluation card. • What was the main point of this lecture? • RELATES TO LEARNING OBJECTIVES 1, 2

7. Out of class assignment before lecture 2 3 • Learn vocabulary list: insertion, deletion, frameshift, etc • Read about dotplots.

8. IN CLASS LECTURE TWO • Review main points from Monday (5 minutes) • In class assignment: • Compare E.coli K12 and E.coliO157:H7 using cmr.jcvi.org

9. http://genomevolution.org/wiki/index.php/2011_BSA_Workshop

11. Lecture three • Discuss the research the students did about the genes associated with the inversion and whether they contribute to the pathogenicity of E.coli O157:H7 • Relate to paper discussed • Brainstorm in groups other times when microbes can pick up genes from others and how it can give them an advantage or disadvantage’ • Ex: antibiotic resistance • FORMATIVE ASSESSMENT Post a survey of Remember, Summarize, Connect on Blackboard to do as homework. • RELATES TO LEARNING OBJECTIVES 1,2, 3

12. Summative Assessment: graded in class assignment Align the genomes two other organisms and have the class analyze them A. What is a dot plot? Why is it used? B. What can you conclude about this dot plot? C. What genes are located in the (inversion, duplication, etc)? D. Of what value to the organism would it be for it to have this….

13. Extension • Identify a lab that can be associated with gene variation • Ex: Luria doublet, antibiotic resistance, mutagenesis

14. How were the learning objectives addressed through the assignments? • Discuss how genetic variation impacts microbial functions • Paper presents the selection of bacteria • Comparative genomic exercise demonstrates that E.coli 0157 contains a gene associated with toxin production. • Students had to analyze the data and bring it to the next level. • Students had to research E.coli0157:H7

15. How were the learning objectives addressed through the assignments? • Explain how cells, organisms and major metabolic pathways evolved from early prokaryotes • Comparative genomics exercise demonstrated that E.coli 0157:H7 acquired a gene that may be associated wiith toxin production. • Ties into xylose-fermenting fungi paper • Ties into conjugation, transformation, transposon, phage-mediated mutagenesis/gene delivery to be discussed in Evolutionlecture the following week

16. http://labrat.fieldofscience.com/2010/12/levels-of-evolution.htmlhttp://labrat.fieldofscience.com/2010/12/levels-of-evolution.html