Vincent J Denef
Affiliation: University of California
- Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteriaIan Lo
University of California, Berkeley, California 94720, USA
Nature 446:537-41. 2007....
- Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysisVincent J Denef
Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
J Proteome Res 6:3152-61. 2007..4% reduction of the initial protein coverage per 1% amino acid divergence and total identification loss at 86% AAI. Consequently, shotgun proteomics is capable of cross-strain identifications but avoids most cross-species false positives...
- Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptationVincent J Denef
University of California, Berkeley, CA 94720, USA
Environ Microbiol 11:313-25. 2009..Our findings demonstrate the power of PIGT and reveal that recombination is a mechanism for fine-scale adaptation in this system...
- Ecological distribution and population physiology defined by proteomics in a natural microbial communityRyan S Mueller
Earth and Planetary Science Department, University of California, Berkeley, CA 94720, USA
Mol Syst Biol 6:374. 2010..This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ...
- Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communitiesVincent J Denef
University of California, Berkeley, CA 94720, USA
Proc Natl Acad Sci U S A 107:2383-90. 2010..In summary, the results show how subtle genetic variations can lead to distinct ecological strategies...
- Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditionsChristopher P Belnap
Microbiology Graduate Group, Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
ISME J 5:1152-61. 2011....
- Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaeaAlexis P Yelton
Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
BMC Genomics 14:485. 2013..Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order...
- In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybridsVincent J Denef
Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA
Science 336:462-6. 2012..The ecological success of hybrid bacterial types highlights the role of evolutionary processes in rapid adaptation within natural microbial communities...
- The dynamic genetic repertoire of microbial communitiesPaul Wilmes
Department of Earth and Planetary Science, University of California at Berkeley, Berkeley, CA 94720, USA
FEMS Microbiol Rev 33:109-32. 2009..Finally, we highlight the importance of virus-host dynamics in generating and shaping within-population diversity...
- AMD biofilms: using model communities to study microbial evolution and ecological complexity in natureVincent J Denef
Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
ISME J 4:599-610. 2010..We discuss the value and limitations of tractable model microbial communities in developing molecular methods for microbial ecology and in uncovering principles that may explain behavior in more complex systems...
- Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formationSheri L Simmons
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, United States of America
PLoS Biol 6:e177. 2008..Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination...
- Persisting viral sequences shape microbial CRISPR-based immunityAriel D Weinberger
Biophysics Graduate Group, University of California, Berkeley, California, United States of America
PLoS Comput Biol 8:e1002475. 2012..By maintaining old immunities, selection may be tuning CRISPR-mediated immunity against viruses reemerging from lysogeny or migration...
- Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatilityPatrick S G Chain
Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
Proc Natl Acad Sci U S A 103:15280-7. 2006....
- Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communitiesVincent J Denef
Laboratory of Microbial Ecology and Technology, Ghent, Belgium
Environ Microbiol 5:933-43. 2003..This increase in sensitivity is important if oligonucleotide microarrays are to be used for simultaneous monitoring of a range of functions performed by different microorganisms in the environment...