Welcome to Introduction to Bioinformatics Monday, 28 February 2005

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Welcome toIntroduction to BioinformaticsMonday,
28 February 2005
Introduction to Research Projects
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Oceanic Cyanobacteria
Wolfgang Hess, U. Freiburg Brian Palenik,
Scripps Eric Webb, Woods Hole Rakefet Schwarz,
Bar Ilan U
Jon Zehr, UC Santa Cruz
CO2
N2
Prochlorococcus MED4
Prochlorococcus SS120
Fixed C
Fixed N
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Differentiation by N2-Fixing Cyanobacteria
Peter Wolk, Michigan St Jim Golden, Texas
AM Terry Thiel, U. Missouri-St.Louis Mike
Summers, Cal State-Northridge Jack Meeks, U
California-Davis
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Cyanobacterial Genomes
AATAAAGCTTTACAAACCAAACTCTGGCTTCAATTGTGTAACCCAAGCTT
TGATTCTTTCCTCTGTTAAATCGGATTGATTATCTTCATCAAGGGCAAGA
CCTACAAATTTACCATCACGAACAGCTTTAGACTCACTGAATTCATAACC
TTCTGTAGGCCAATAGCCAACTGTTTCACCACCATTTTCTGAAATTTTTT
CCTCTAGAATACCGCAACACTATCACCACCAAACTCCTTCTGAATTATTT
CTGATTCAGTTTGGGTATTGCCTGTTTGAGTACCAAAAAATAAACCAATA
TTAGAC AATAAAGCTTTACAAACCAAACTCTGGCTTCAATTGTGTAACC
CAAGCTTTGATTCTTTCCTCTGTTAAATCGGATTGATTATCTTCATCAAG
GGCAAGACCTACAAATTTACCATCACGAACAGCTTTAGACTCACTGAATT
CATAACCTTCTGTAGGCCAATAGCCAACTGTTTCACCACCATTTTCTGAA
ATTTTTTCCTCTAGAATACCGCAACACTATCACCACCAAACTCCTTCTGA
ATTATTTCTGAT
You Chen, Texas AM James Godde, Monmouth Peter
Wolk, Michigan St Jack Meeks, U California-Davis
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RNA-mediated Gene Regulation in Synechococcus PCC
7942
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RNA-mediated Gene Regulation in Synechococcus PCC
7942
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RNA-mediated Gene Regulation in Synechococcus PCC
7942
Genomic search for potential regulatory RNA
molecules
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RNA-mediated Gene Regulation in Anabaena PCC 7120
- N
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RNA-mediated Gene Regulation in Anabaena PCC 7120
Genomic search for potential regulatory RNA
molecules
- N
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Factors mediating patterned differentiation by
Anabaena PCC 7120
Jim GoldenTexas AM
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Motifs regulating akinete expression in Nostoc
punctiforme
Mike SummersCal State-Northridge
Darkfructose
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Motifs regulating akinete expression in Nostoc
punctiforme
Search for sequence patterns upstream from
akinete-specific genes
Mike SummersCal State-Northridge
Darkfructose
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Generalized motif discovery in small marine
cyanobacteria
Wolfgang HessU Freiburg
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Generalized motif discovery in small marine
cyanobacteria
Wolfgang HessU Freiburg
Prochlorococcus MED4Prochlorococcus
SS120Prochlorococcus MIT9313Synechococcus WH8302
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Function prediction by conserved gene position in
marine cyanobacteria
CO2
N2
NH3
sugar
Jon ZehrU California-Santa Clara
Why not more?
?
?
Fe-related
- Limitation by iron
- Limitation by nitrogen
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Motifs governing expression of iron-related genes
in marine cyanobacteria
CO2
N2
NH3
sugar
Eric WebbWoods Hole
Why not more?
Fe-related
- Limitation by iron
- Limitation by nitrogen
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Genome families of Nostoc punctiforme compared to
smaller cyanobacteria
?
Jack MeeksU California-Davis
Why is the Nostoc genome so large?
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Characterization of nitrogenase complexes in
Anabaena variabilis
N2
NH3
Terry ThielU Missouri-St. Louis
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Characterization of nitrogenase complexes in
Anabaena variabilis
What genes encode each machine?Where did they
come from?
Terry ThielU Missouri-St. Louis
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Protein quorum sensing signals between marine
cyanobacteria
?
Rakefet Schwarz Bar Ilan U
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Protein quorum sensing signals between marine
cyanobacteria
What proteins mediate communication between
cyanobacteria?
?
Rakefet Schwarz Bar Ilan U
Vs
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Protein quorum sensing signals between marine
cyanobacteria
Brian PalenikScripps Ocean. Inst.
What signals determine protein transport through
membranes?
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Unusual repeated sequences in genomic DNA
What is the mechanism by which CRISPRs propagate?
James GoddeMonmouth College