Eisen:Research

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Research)
(General research areas -- Phylogenomics and the Origin of Novelty)
Line 26: Line 26:
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 [http://genomics.ucdavis.edu/ U. C. Davis Genome Center].  Dr. Eisen has appointments in the [http://www-eve.ucdavis.edu/ Section of Evolution and Ecology] and the [http://www.ucdmc.ucdavis.edu/medmicro/ Department of Medical Microbiology] at [http://www.ucdmc.ucdavis.edu/medmicro/ U. C. Davis] and an Adjunct Appointment at the [http://www.jgi.doe.gov/ Joint Genome Institute], where he runs a small "Phylogenomics" group.
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 [http://genomics.ucdavis.edu/ U. C. Davis Genome Center].  Dr. Eisen has appointments in the [http://www-eve.ucdavis.edu/ Section of Evolution and Ecology] and the [http://www.ucdmc.ucdavis.edu/medmicro/ Department of Medical Microbiology] at [http://www.ucdmc.ucdavis.edu/medmicro/ U. C. Davis] and an Adjunct Appointment at the [http://www.jgi.doe.gov/ Joint Genome Institute], where he runs a small "Phylogenomics" group.
-
= General research areas -- Phylogenomics and the Origin of Novelty =
+
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:
-
*'''Mechanisms of novelty generation.''' A major component of our work involves using genome sequences to better understand the mechanisms by which new processes originate in microbes. Mechanisms in which we are interested include lateral DNA transfer, gene duplication and divergence and invention of new genes.
+
 
-
* '''Evolvability.'''  In addition, we are particularly interested in constraints and biases in the use of these novelty generating mechanismsThese constraints and biases generate differences in evolvability both within genomes and between individuals and speciesFor example, we are interested in differences in DNA repair and recombination processes between species and how these shape mutation rates and patterns.   
+
* '''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 [http://www.tigr.org/tol see here] and GEBA (A Genomic Encyclopedia of Bacteria and Archaea)  [http://www.jgi.doe.gov/programs/GEBA/pilot.html here]
-
* '''Predicting organisms biology from their genome sequences.''' One of the major goals behind our work in studies of the origin of novelty is to use this information to improve our ability to make predictions of the biology of organisms from their genome sequences. Examples of our work in this area include:
+
 
-
** We were the first to outline a phylogenetic approach to functional prediction generally known as phylogenomics (e.g., [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=7651832 Eisen, 1995]; [http://www.ncbi.nlm.nih.gov/pubmed/9334711?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Eisen et al, 1997], [http://www.genome.org/cgi/content/full/8/3/163 Eisen, 1998])
+
* '''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 evolveExamples of our past projects on this topic include studies of symbionts of the  glassy winged sharpshooter [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040188 here], chemosynthetic symbionts (e.g., [http://www.sciencemag.org/cgi/content/full/315/5814/998 here]), Wolbachia ([http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0020069 wMel genome], [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]).
-
** We have used and developed methods for predicting function using phylogenetic profiling (e.g., [http://www.pnas.org/cgi/content/full/99/14/9509 Eisen et al. 2002], [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010065 Wu et al 2005], [http://www.ncbi.nlm.nih.gov/pubmed/12167367?ordinalpos=20&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Eisen and Wu, 2002])
+
 
-
* '''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.
+
* '''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  [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050082 Review], [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050016 GOS Proteins]; [http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0050077 GOS Survey]; [http://www.ncbi.nlm.nih.gov/pubmed/15001713?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Sargasso metagenomics], [http://www.ncbi.nlm.nih.gov/pubmed/11832943?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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., [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=7651832 Eisen1995]; [http://www.ncbi.nlm.nih.gov/pubmed/9334711?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum Eisen1997], [http://www.genome.org/cgi/content/full/8/3/163 Eisen1998] [http://www.pnas.org/cgi/content/full/99/14/9509 Eisen2002], [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010065 Wu2005], [http://www.ncbi.nlm.nih.gov/pubmed/12167367?ordinalpos=20&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum 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., [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 =  
= Model systems for studying novelty =  

Revision as of 17:50, 15 July 2011


Home        Contact        Internal        Lab Members        Publications        Research        Talks       



Contents

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).

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 here
    • A new project at JGI to create a 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 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 here
    • A collaboration with the lab of Scott O'Neill on the first Wolbachia genome. See paper here. See other lab papers on Wolbachia: BAC from Brugia Wolbachia, 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:
  • The genomics and evolution of carbon fixation

Recent News

More information

Personal tools