Welcome to Introduction to Bioinformatics Monday, 28 February 2005 Introduction to Research...
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Transcript of Welcome to Introduction to Bioinformatics Monday, 28 February 2005 Introduction to Research...
Welcome toIntroduction to Bioinformatics
Monday, 28 February 2005
Introduction to Research Projects
Prochlorococcus MED4
Prochlorococcus SS120
CO2
Fixed C
N2
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
Differentiation by N2-Fixing Cyanobacteria
Peter Wolk, Michigan StJim Golden, Texas A&MTerry Thiel, U. Missouri-St.LouisMike Summers, Cal State-NorthridgeJack Meeks, U California-Davis
Cyanobacterial Genomes
You Chen, Texas A&MJames Godde, MonmouthPeter Wolk, Michigan StJack Meeks, U California-Davis
AATAAAGCTTTACAAACCAAACTCTGGCTTCAATTGTGTAACCCAAGCTTTGATTCTTTCCTCTGTTAAATCGGATTGATTATCTTCATCAAGGGCAAGACCTACAAATTTACCATCACGAACAGCTTTAGACTCACTGAATTCATAACCTTCTGTAGGCCAATAGCCAACTGTTTCACCACCATTTTCTGAAATTTTTTCCTCTAGAATACCGCAACACTATCACCACCAAACTCCTTCTGAATTATTTCTGATTCAGTTTGGGTATTGCCTGTTTGAGTACCAAAAAATAAACCAATATTAGACAATAAAGCTTTACAAACCAAACTCTGGCTTCAATTGTGTAACCCAAGCTTTGATTCTTTCCTCTGTTAAATCGGATTGATTATCTTCATCAAGGGCAAGACCTACAAATTTACCATCACGAACAGCTTTAGACTCACTGAATTCATAACCTTCTGTAGGCCAATAGCCAACTGTTTCACCACCATTTTCTGAAATTTTTTCCTCTAGAATACCGCAACACTATCACCACCAAACTCCTTCTGAATTATTTCTGAT
RNA-mediated Gene Regulation in Synechococcus PCC 7942
Circadian rhythmYou ChenTexas A&M
C
Crp
5’-GTGAGTTAGCTCACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CACTCAATCGAGTGNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
lacZ
RNA Polymerase
RNA-mediated Gene Regulation in Synechococcus PCC 7942
Circadian rhythmYou ChenTexas A&M
???
5’-GTGAGTTAGCTCACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CACTCAATCGAGTGNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
photosynthesis
RNA Polymerase
RNA-mediated Gene Regulation in Synechococcus PCC 7942
You ChenTexas A&M
???
5’-GTGAGTTAGCTCACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CACTCAATCGAGTGNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN
photosynthesis
RNA Polymerase
Genomic search for potential regulatory RNA molecules
RNA-mediated Gene Regulation in Anabaena PCC 7120
Peter WolkMichigan State U Heterocyst differentiation
- N
RNA-mediated Gene Regulation in Anabaena PCC 7120
Peter WolkMichigan State U
- N
Genomic search for potential regulatory RNA molecules
Factors mediating patterned differentiation by Anabaena PCC 7120
Jim GoldenTexas A&M Heterocyst differentiation
Motifs regulating akinete expression in Nostoc punctiforme
Mike SummersCal State-Northridge
Dark+
fructose
heterocyst akinetes
Motifs regulating akinete expression in Nostoc punctiforme
Mike SummersCal State-Northridge
Dark+
fructose
Search for sequence patterns upstream from akinete-specific genes
Generalized motif discovery in small marine cyanobacteria
Wolfgang HessU Freiburg
Dark+
fructose
Generalized motif discovery in small marine cyanobacteria
Wolfgang HessU Freiburg
Prochlorococcus MED4Prochlorococcus SS120Prochlorococcus MIT9313Synechococcus WH8302
Function prediction by conserved gene position in marine cyanobacteria
Jon ZehrU California-Santa Clara
Why not more?
CO2 N2
sugar
NH3
- Limitation by iron- Limitation by nitrogen
Fe-related??
Motifs governing expression of iron-related genes in marine cyanobacteria
Eric WebbWoods Hole
Why not more?
CO2 N2
sugar
NH3
- Limitation by iron- Limitation by nitrogen
Fe-related
Genome families of Nostoc punctiforme compared to smaller cyanobacteria
Jack MeeksU California-Davis
?heterocyst Symbiosis
with plants
9.1 Mb
Prochlorococcus
1.7 Mb
Why is the Nostoc genome so large?
Characterization of nitrogenase complexes in Anabaena variabilis
Terry ThielU Missouri-St. Louis
heterocyst
N2
NH3nitrogenase
Molybdenum
Vanadium
Characterization of nitrogenase complexes in Anabaena variabilis
Terry ThielU Missouri-St. Louis
Vanadium
What genes encode each machine?Where did they come from?
Protein quorum sensing signals between marine cyanobacteria
Rakefet Schwarz Bar Ilan U
?
Vs
Protein quorum sensing signals between marine cyanobacteria
Rakefet Schwarz Bar Ilan U
?
Vs
What proteins mediate communication between
cyanobacteria?
Protein quorum sensing signals between marine cyanobacteria
Brian PalenikScripps Ocean. Inst.
What signals determine protein transport through
membranes?
Unusual repeated sequences in genomic DNA
James GoddeMonmouth College
• Tandem repeats
• Dispersed repeats• CRISPRs
What is the mechanism by which CRISPRs propagate?