Microbial Ecology, Proteogenomics & Computational Optima.

DOE Genomes to Life Center at Harvard/MIT/BWH/MGH

PoloniesCollaborating Principal investigators:
George Church, Sallie Chisholm, Martin Polz, Roberto Kolter, Fred Ausubel, Raju Kucherlapati, Steve Lory, Steve Gygi, Mike Laub

May 2002 Proposal:   Introduction. Goal 1: Protein complexes & Mass Spectrometry Goal 2: Regulatory Networks and RNA quantitation. Goal 3: Microbial Communities, Tn tags, Single Cell Activity Multiplexing, and biofilms Goal 4: Computational models on the edge of optimality & 4D cell models Conclusion/Management/Bibliography

Scheduled Full Project Meetings on 3rd Wed of each month at noon. (exceptions indicated by *) Location: NRB 258 (77 Ave Pasteur)
Tue 21-Nov-2006 *** 8:30 to 3 PM GTL-BR Center meeting
Wed 15-Nov-2006 12 to 2 PM GTL-BR call followed by Ari Friedland & Jim Collins on "BioCounters"
Jul-2006 to Oct 2006 Weekly Conference calls on DOE GTL Bioenergy Reasearch Center Proposal
Wed 21-Jun-2006 12 to 2 PM Ethanol production, resistance, economics.
Wed 17-May-2006 12 to 2 PM Engineering Algae (Wayne Curtis, Penn State).
Wed 19-Apr-2006 12 to 2 PM Enabling Bio-Energy (continued from last time)
Wed 15-Mar-2006 12 to 2 PM Discussion of GtL grant renewal (George et al.).
Wed 15-Feb-2006 No Boston Meeting. 2006 GtL Meeting in Bethesda.
Wed 18-Jan-2006 12 to 2 PM Ben Kirkup & Nick Reppas on "Lab evolution of growth rate". David Sarracino "Microbial Proteomics for Boston GtL".
Wed 16-Nov-2005 12 to 2 PM Farren Isaacs, George Church on Lab evolvution of aptamer-regulators, rRNA-mRNA specificity, and semi-synthetic bacterial communities.
Wed 19-Oct-2005 12 to 2 PM No Boston meeting. GSAC Meeting in SC.
Wed 21-Sep-2005 12 to 2 PM Kun Zhang & Adam Martiny on single cell sequencing.
Thu 11-Aug to 12-Aug-2005 all day Prochlorococcus Diel Jamboree
Wed 15-Jun-2005 12 to 2 PM Andy Tolonen, Adam Martiny, Maureen Coleman, Jorge Frias-Lopez on Prochlorococcus RNA data analyses (handling subpar repeats and amplification).
Wed 18-May-2005 12 to 2 PM Xiaoxia Lin & Aaron Brandes on Metabolic modeling.
Wed 20-Apr-2005 12 to 2 PM George Church on DOE Synthetic Biology Projects.
Wed 16-Mar-2005 12 to 2 PM Jeremy Zucker on "Adopt an Organism" (annotation) project
Wed 7-9-Feb-2005 Annual DOE GTL meeting in DC.
New publications from center members:
Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, & Church GM (2004) Accurate Multiplex Gene Synthesis from Programmable DNA Chips. Nature 432: 1050-4.
Rocap et al. 2003. Genome divergence in two Prochlorococcus ecotypes reflects Oceanic niche differentiation. Nature. 2003 Aug 28;424(6952):1042-7. Epub 2003 Aug 13.
Sullivan et al. 2003. Cyanophage infecting the oceanic cyanobacterium, Prochlorococcus. Nature. 2003 Aug 28;424(6952):1047-51.

DOE reports: GTL Facility for Whole Proteome Analysis

Summary of the five DOE GTL Centers:
  • ORNL /PNNL/Sandia/U.NC/U.UT:   Identification and Characterization of Protein Complexes (Rhodopseudomonas, Shewanella)
  • Harvard /MIT/BWH/MGH:   Microbial Ecology, Proteogenomics and Computational Optima. (Prochlorococcus, Pseudomonas, Caulobacter).
  • LBNL /Sandia/ORNL/UCB/U.MO/U.WA/Diversa:   Rapid Deduction of Stress Response Pathways in Metal/Radionuclide Reducing Bacteria (Shewanella, Desulfovibrio)
  • U.MA-Amherst /TIGR/ANL:   Analysis of the Genetic Potential and Gene Expression of Microbial Communities Involved in the in situ Bioremediation of Uranium and Harvesting Electrical Energy from Organic Matter (Geobacter)
  • Sandia /ORNL/LBNL/LANL/NCGR/UCSB/U.MI/TMSI/Scripps/UIUC:   Carbon Sequestration in Synechococcus:   From Molecular Machines to Hierarchical Modeling
    DOE GTL Chlorophyll Cavender-Bares, K. S. Frankel, and S. W. Chisholm. (1988) A dual-sheath flow cytometer for shipboard analyses of phytoplankton communities from the oligotrophic oceans.  Limnol. Oceanogr. 43:1383-1388.

    • Prochlorococcus sectionsProchlorococcus SEM

    Relevant publications:
    Badarinarayana et al. 2001 Nature Biotechnology 19: 1060-5. Selection analyses of insertional mutants using subgenic-resolution arrays.
    Drenkard & Ausubel 2002 Nature 416:740-3 Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation.
    Dudley et al. 2002 Proc. Nat. Acad. Sci. USA 99:7554-7559. Measuring absolute expression with microarrays using a calibrated reference sample and an extended signal intensity range.
    Hogan & Kolter 2002 Science 296: 2229-32 Pseudomonas-Candida interactions: an ecological role for virulence factors.
    Laub et al. 2002 Proc Natl Acad Sci USA. 99: 4632-7. Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle.
    Licklider et al. 2002 Anal Chem 74: 3076-83. Automation of nanoscale microcapillary liquid chromatography-tandem mass spectrometry with a vented column.
    Sokurenko et al. 2001 Nucleic Acids Res 29:E111 Detection of simple mutations and polymorphisms in large genomic regions.
    Ting et al. 2002 Trends Microbiol 10: 134-42 Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies.
    Rocap G, Distel DL, Waterbury JB, and Chisholm SW (2002). Resolution of Prochlorococcus and Synechococcus ecotypes using 16S-23S rDNA Internal Transcribed Spacer (ITS) sequences. Applied & Environmental Microbiol. 68(3): 1180-1191.
    Hess WR, et al. (2001). The photosynthetic apparatus of Prochlorococcus: Insights through comparative genomics. Photosynthesis Research 70: 53-71.
    Thompson et al. 2002 Nucleic Acids Res. 30: 2083-8. Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'.

    Previous meetings:
    Wed 11-Sep-2002* 12 to 2 PM Prochlorococcus, oligonucleotide arrays and related experiments. Coordinating RNA and protein samples. Overall project milestones and budgets.
    Wed 20-Nov-2002 12 to 2 PM Cell and circadian cycles, metabolic monitoring and modeling, proteogenomics, sequencing genomes, and environmental sampling.
    Wed 15-Jan-2003 12 to 2 PM Modeling and Measures.
    Wed 26-Feb-2003* 12 to 2 PM Pseudomonas PA01 sequence annotation & utilization.
    Wed 19-Mar-2003 12 to 2 PM Time series data analyses
    Wed 16-Apr-2003 12 to 2 PM Prochlorococcus homologous recombination
    Wed 21-May-2003 no meeting (ASM meeting)
    Wed 18-Jun-2003 12 to 2 PM Community projects & Modeling themes
    Wed 16-Jul-2003 12 to 2 PM "Retreat-format" meeting. One brief talk for each PI
    Wed 17-Sep-2003 12 to 2 PM Lory, Jaffe, Leptos (Proteomics)
    Wed 15-Oct-2003 12 to 2 PM Steffen (Native complexes), open discussion,
    Wed 19-Nov-2003 12 to 2 PM John Aach on Microbial Community Computational Modeling.
    Wed 17-Dec-2003 12 to 2 PM Dan Lee on Pseudomonas Genome Annotation & Proteomics
    Wed 21-Jan-2004 12 to 2 PM Debbie Lindell & Matt Sullivan on "Phage Photosynthetic genes"
    Wed 18-Feb-2004 12 to 2 PM Dat Nguyen on "Toward automatic proteomics & biological pathways"
    29-Feb to 2-Mar 2004 National DOE-GtL meeting in DC.
    Wed 17-Mar-2004 12 to 2 PM George Church, Xiaoxia Lin, Jeremy Zucker protein complexes & Metabolomics
    Wed 21-Apr-2004 12 to 2 PM Open discussion of Proteomics 12 to 2 PM
    Wed 16-Jun-2004 12 to 2 PM Prochloroccus time series
    Wed 15-Sep-2004 12 to 2 PM Jake Jaffe & Matt Wright on Prochlorococcus & Pseudomonas Proteomics and Proposed Caulobacter chromosome project.
    Wed 17-Nov-2004 12 to 2 PM New methods for sequencing single cells and possible application to Prochloroccus and/or Vibrio species.
    Wed 15-Dec-2004 12 to 1:30 PM Adam Martiny & George on Ocean sample single cell sequencing.
    Tue 11-Jan-2005 2:30 to 4 PM (MIT48-3rdfl) Eric Zinser RNA diel data.
    Wed 19-Jan-2005 12 to 1 PM Kyriacos Leptos on Quantitative Mass-spectrometry.

    Related meetings:
    10 to 12-Feb-2003: 2003 Genomes to Life Workshop in Arlington, VA.
    16 to 18-Sep-2002: DOE & Japan Bioindustry Association Systems Biology of Useful Microorganisms Tsuruoka (Mike Laub) 


    This page was updated 23-Apr-2005 by GMC