1. Welcome to Introduction to Bioinformatics Monday, 28 February 2005 Introduction to Research Projects

2. Prochlorococcus MED4 Prochlorococcus SS120 CO 2 Fixed C N2N2 Fixed N Trichodesmium erythraeum Crocosphaera watsonii Wolfgang Hess, U. Freiburg Brian Palenik, Scripps Eric Webb, Woods Hole Rakefet Schwarz, Bar Ilan U Jon Zehr, UC Santa Cruz Oceanic Cyanobacteria

3. Differentiation by N 2 -Fixing Cyanobacteria Peter Wolk, Michigan St Jim Golden, Texas A&M Terry Thiel, U. Missouri-St.Louis Mike Summers, Cal State-Northridge Jack Meeks, U California-Davis

4. Cyanobacterial Genomes You Chen, Texas A&M James Godde, Monmouth Peter Wolk, Michigan St Jack Meeks, U California-Davis AATAAAGCTTTACAAACCAAACTCTGGCTTCAATTGTGTAACCCAAGCTTT GATTCTTTCCTCTGTTAAATCGGATTGATTATCTTCATCAAGGGCAAGACC TACAAATTTACCATCACGAACAGCTTTAGACTCACTGAATTCATAACCTTC TGTAGGCCAATAGCCAACTGTTTCACCACCATTTTCTGAAATTTTTTCCTC TAGAATACCGCAACACTATCACCACCAAACTCCTTCTGAATTATTTCTGAT TCAGTTTGGGTATTGCCTGTTTGAGTACCAAAAAATAAACCAATATTAGAC AATAAAGCTTTACAAACCAAACTCTGGCTTCAATTGTGTAACCCAAGCTTT GATTCTTTCCTCTGTTAAATCGGATTGATTATCTTCATCAAGGGCAAGACC TACAAATTTACCATCACGAACAGCTTTAGACTCACTGAATTCATAACCTTC TGTAGGCCAATAGCCAACTGTTTCACCACCATTTTCTGAAATTTTTTCCTC TAGAATACCGCAACACTATCACCACCAAACTCCTTCTGAATTATTTCTGAT

5. RNA-mediated Gene Regulation in Synechococcus PCC 7942 Circadian rhythm You Chen Texas A&M C Crp 5’-GTGAGTTAGCTCACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN 3’-CACTCAATCGAGTGNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN lacZ RNA Polymerase

6. RNA-mediated Gene Regulation in Synechococcus PCC 7942 Circadian rhythm You Chen Texas A&M ??? 5’-GTGAGTTAGCTCACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN 3’-CACTCAATCGAGTGNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN photosynthesis RNA Polymerase

7. RNA-mediated Gene Regulation in Synechococcus PCC 7942 You Chen Texas A&M ??? 5’-GTGAGTTAGCTCACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN 3’-CACTCAATCGAGTGNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN photosynthesis RNA Polymerase Genomic search for potential regulatory RNA molecules

8. RNA-mediated Gene Regulation in Anabaena PCC 7120 Peter Wolk Michigan State U Heterocyst differentiation - N

9. RNA-mediated Gene Regulation in Anabaena PCC 7120 Peter Wolk Michigan State U - N Genomic search for potential regulatory RNA molecules

10. Factors mediating patterned differentiation by Anabaena PCC 7120 Jim Golden Texas A&M Heterocyst differentiation

11. Motifs regulating akinete expression in Nostoc punctiforme Mike Summers Cal State-Northridge Dark + fructose heterocyst akinetes

12. Motifs regulating akinete expression in Nostoc punctiforme Mike Summers Cal State-Northridge Dark + fructose Search for sequence patterns upstream from akinete-specific genes

13. Generalized motif discovery in small marine cyanobacteria Wolfgang Hess U Freiburg Dark + fructose

14. Generalized motif discovery in small marine cyanobacteria Wolfgang Hess U Freiburg Prochlorococcus MED4 Prochlorococcus SS120 Prochlorococcus MIT9313 Synechococcus WH8302

15. Function prediction by conserved gene position in marine cyanobacteria Jon Zehr U California-Santa Clara Why not more? CO 2 N2N2 sugar NH 3 - Limitation by iron - Limitation by nitrogen Fe-related ??

16. Motifs governing expression of iron- related genes in marine cyanobacteria Eric Webb Woods Hole Why not more? CO 2 N2N2 sugar NH 3 - Limitation by iron - Limitation by nitrogen Fe-related

17. Genome families of Nostoc punctiforme compared to smaller cyanobacteria Jack Meeks U California-Davis ? heterocyst Symbiosis with plants 9.1 Mb Prochlorococcus 1.7 Mb Why is the Nostoc genome so large?

18. Characterization of nitrogenase complexes in Anabaena variabilis Terry Thiel U Missouri-St. Louis heterocyst N2N2 NH 3 nitrogenase Molybdenum Vanadium

19. Characterization of nitrogenase complexes in Anabaena variabilis Terry Thiel U Missouri-St. Louis Vanadium What genes encode each machine? Where did they come from?

20. Protein quorum sensing signals between marine cyanobacteria Rakefet Schwarz Bar Ilan U ? Vs

21. Protein quorum sensing signals between marine cyanobacteria Rakefet Schwarz Bar Ilan U ? Vs What proteins mediate communication between cyanobacteria?

22. Protein quorum sensing signals between marine cyanobacteria Brian Palenik Scripps Ocean. Inst. What signals determine protein transport through membranes?

23. Unusual repeated sequences in genomic DNA James Godde Monmouth College Tandem repeats Dispersed repeats CRISPRs What is the mechanism by which CRISPRs propagate?