Eisen:Research

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(General research areas -- Phylogenomics and the Origin of Novelty)
(Model systems for studying novelty)
Line 40: Line 40:
* '''The genomics and evolution of carbon fixation.''' We use the evolution of carbon fixation as a model for studying the origin and evolution and processes and pathways.  Our work includes genomic studies of  the reverse TCA cycle  (e.g., [http://www.pnas.org/cgi/content/full/104/28/11784 here], [http://www.pnas.org/cgi/content/full/99/14/9509 here] and [http://www.ncbi.nlm.nih.gov/pubmed/9595663?ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum here]),  methylotrophy ([http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0020303 here]), Carboxydotrophs (e.g., [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010065 here]),  plastid evolution and/or the Calvin cycle (e.g.,  [http://www.pnas.org/cgi/content/full/102/20/7315 here], [http://www.nature.com/nature/journal/v419/n6906/abs/nature01097.html here], [http://www.nature.com/nature/journal/v415/n6872/abs/415630a.html here], [http://www.nature.com/nature/journal/v402/n6763/abs/402761a0.html here], [http://www.nature.com/nature/journal/v408/n6814/abs/408796a0.html and here]), and chemosynthetic symbionts ([http://www.sciencemag.org/cgi/content/full/315/5814/998 here], [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1577710 here]).
* '''The genomics and evolution of carbon fixation.''' We use the evolution of carbon fixation as a model for studying the origin and evolution and processes and pathways.  Our work includes genomic studies of  the reverse TCA cycle  (e.g., [http://www.pnas.org/cgi/content/full/104/28/11784 here], [http://www.pnas.org/cgi/content/full/99/14/9509 here] and [http://www.ncbi.nlm.nih.gov/pubmed/9595663?ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum here]),  methylotrophy ([http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0020303 here]), Carboxydotrophs (e.g., [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010065 here]),  plastid evolution and/or the Calvin cycle (e.g.,  [http://www.pnas.org/cgi/content/full/102/20/7315 here], [http://www.nature.com/nature/journal/v419/n6906/abs/nature01097.html here], [http://www.nature.com/nature/journal/v415/n6872/abs/415630a.html here], [http://www.nature.com/nature/journal/v402/n6763/abs/402761a0.html here], [http://www.nature.com/nature/journal/v408/n6814/abs/408796a0.html and here]), and chemosynthetic symbionts ([http://www.sciencemag.org/cgi/content/full/315/5814/998 here], [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1577710 here]).
-
= Model systems for studying novelty =
 
-
In our studies of the origin of novelty, we focus on a few fey biological systems and questions that are excellent model systems for studying novelty. These include
 
-
* '''Phylogenomics and the tree of life.'''  In order to get a full appreciation of microbial diversity and genomics we needs to understand more about the poorly studied branches in the tree of life. To help with this, we have been involved in multiple projects to generate genome sequence data from novel branches on the tree of life including:
 
-
** An NSF Tree of Life program to sequence and characterize genomes from phyla of bacteria for which there are no complete genomes available. For more information see http://www.tigr.org/tol
 
-
** An NSF-NIH funded project to sequence the genome of Tetrahymena thermophila a model ciliate.  See our paper [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040286 here]
 
-
** A new project at JGI to create a [http://www.jgi.doe.gov/programs/GEBA/pilot.html Genomic Encyclopedia of Bacteria and Archaea]
 
-
* '''The evolution of intracellular symbioses.'''  One of the simplest ways for organisms to acquire new functions is to engage in symbioses with other species. Perhaps the most pervasive symbioses leading to new functions are those involving the plastid and mitochondria organelles of eukaryotes. In addition, there are 1000s of other symbioses between eukaryotes and intracellular bacteria at various stages of evolution. We are interested in characterizing a diversity of such symbioses to better understand what the rules are for these symbioses to evolve.  Examples of our projects include:
 
-
** A collaboration with Nancy Moran's lab on studying the genomes of the symbionts inside the glassy winged sharpshooter. See PLoS Biology paper [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040188 here]
 
-
** A collaboration with JGI and the lab of Colleen Cavanaugh (my undergraduate advisor) on the chemosynthetic symbionts found in the giant clam Calyptogena magnifica. See paper [http://www.sciencemag.org/cgi/content/full/315/5814/998 here]
 
-
** A collaboration with the lab of Scott O'Neill on the first Wolbachia genome. See paper [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0020069 here].  See other lab papers on Wolbachia: [http://www.ncbi.nlm.nih.gov/pubmed/11812492?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum BAC from Brugia Wolbachia], [http://www.ncbi.nlm.nih.gov/pubmed/17684235?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum letter about Wolbachia classification]
 
-
* '''The functioning of communities of microbes in nature.''' For many years, we have asked questions about the origin of novelty in the context of analysis of the genome sequences of microbial species that have been grown in pure culture in the laboratory. In the last few years we have shifted much of our focus to using genome sequencing to study microbes directly in their natural habitats. We are working on methods to characterize such microbial communities and are applying these methods to characterize some model microbial communities:
 
-
** [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 A review I wrote on environmental shotgun sequencing]
 
-
** Metagenomics of ocean microbes: [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050016 Global Ocean Sampling Protein Families]; [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050077 Global Ocean Sampling: Northwest Atlantic through Eastern Tropical Pacific]; [http://www.ncbi.nlm.nih.gov/pubmed/15001713?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Sargasso Sea metagenomics] [http://www.ncbi.nlm.nih.gov/pubmed/11832943?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Phototroph metagenomics with Ed Delong]
 
-
* '''The genomics and evolution of carbon fixation'''
 
-
** Reverse TCA cycle: Genome sequencing and evolution of Chlorobium tepidum: [http://www.pnas.org/cgi/content/full/104/28/11784 here], [http://www.pnas.org/cgi/content/full/99/14/9509 here] and [http://www.ncbi.nlm.nih.gov/pubmed/9595663?ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum here].
 
-
** Methylotrophy: [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0020303 Genome sequencing of Methylococcus capsulatus]
 
-
** Carboxydotrophs: [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010065 Genome sequencing of Carboxydothermus hydrogenoformans]
 
-
** Plastid evolution and/or Calvin cycle and genomics [http://www.pnas.org/cgi/content/full/102/20/7315 Prochloron symbionts], [http://www.nature.com/nature/journal/v419/n6906/abs/nature01097.html Plasmodium genome], [http://www.nature.com/nature/journal/v415/n6872/abs/415630a.html uncultured bugs], [http://www.nature.com/nature/journal/v402/n6763/abs/402761a0.html Arabidopsis chromosome II], [http://www.nature.com/nature/journal/v408/n6814/abs/408796a0.html Arabidopsis genome]
 
-
** Chemosynthetic symbionts [http://www.sciencemag.org/cgi/content/full/315/5814/998 Calyptogena genome], [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=1577710 Solemya symbionts]
 
= Recent News =
= Recent News =

Revision as of 16:51, 15 July 2011


Home        Contact        Internal        Lab Members        Publications        Research        Talks       



Laboratory of Jonathan A. Eisen

The Eisen Lab research focuses on understanding the genomic basis for the origin of novelty (new functions and processes) in microorganisms. For many years, studies in this area were of limited scope. However, the advent of genome sequencing has allowed one to study the origin of novelty on a more global level. The Eisen lab's main location is in the U. C. Davis Genome Center. Dr. Eisen has appointments in the Section of Evolution and Ecology and the Department of Medical Microbiology at U. C. Davis and an Adjunct Appointment at the Joint Genome Institute, where he runs a small "Phylogenomics" group.

The main overarching focus on the Eisen lab is on the mechanisms by which new functions original and in particular the causes and effects of variation in these mechanisms between taxa. Among our current research topics are:

  • Improving phylogenetic coverage of genomes. In order to get a full appreciation of microbial diversity and genomics we needs to understand more about the poorly studied branches in the tree of life. Examples of our work on this include: a past NSF Tree of Life project see here and GEBA (A Genomic Encyclopedia of Bacteria and Archaea) here
  • The evolution of intracellular symbioses. One of the simplest ways for organisms to acquire new functions is to engage in symbioses with other species. We use genomic sequencing of a diversity of such symbioses to better understand what the rules are for these symbioses to evolve. Examples of our past projects on this topic include studies of symbionts of the glassy winged sharpshooter here, chemosynthetic symbionts (e.g., here), Wolbachia (wMel genome, BAC from Brugia Wolbachia, letter about Wolbachia classification).
  • The functioning of communities of microbes in nature. For many years, we focused on studies of microbes grown in pure culture in the laboratory. Recently, we have shifted much of our focus to using genome sequencing to study microbes directly in their natural habitats. See for example Review, GOS Proteins; GOS Survey; Sargasso metagenomics, Phototroph metagenomics.
  • Computational methods for analyzing metagenomic data. We are currently working on multiple projects focusing on designing methods for analyzing metagenomic data. Our work on this includes iSEEM (a collaboration with the labs of Jessica Green and Katherine Pollard [see http://openwetware.org/wiki/ISEEM for more detail]) and a collaboration with Simon Levin and Josh Weitz as part of the DARPA Fundamental laws of Biology program.
  • Phylogenomic methods development. Embedded within all our work is the development of computational approaches in which evolutionary reconstructions and genome analyses are combined into a composite phylogenomic approach. (e.g., Eisen1995; Eisen1997, Eisen1998 Eisen2002, Wu2005, EisenWu2002)
  • The genomics and evolution of carbon fixation. We use the evolution of carbon fixation as a model for studying the origin and evolution and processes and pathways. Our work includes genomic studies of the reverse TCA cycle (e.g., here, here and here), methylotrophy (here), Carboxydotrophs (e.g., here), plastid evolution and/or the Calvin cycle (e.g., here, here, here, here, and here), and chemosynthetic symbionts (here, here).


Recent News

More information

Personal tools