Tag: Misc.

Crosspost from http://microBE.net: New, massive volumes on #metagenomics coming out soon

For those interested in microbial diversity and/or metagenomics there are two volumes that are coming out soon that are of interest:

Edited by Frans J. de Bruijn these two volumes are the most comprehensive coverage of metagenomics out there right now. The chapters are almost overwhelming (full disclosure, I have two chapters in here – both of which are republications of Open Access papers I have published on metagenomics).  See below for full chapter lists.

Order from Amazon:

Volume I: Metagenomics and Complementary Approached

  • 1. Introduction (Frans J. de Bruijn).
  • Background Chapters.
    • 2. DNA reassociation yields broad-scale information on metagenome complexity and microbial diversity (V. Torsvik).
    • 3. Diversity of 23S rRNA genes within individual prokaryotic genomes (Zhiheng Pei).
    • 4. Use of the rRNA operon and genomic repetitive sequences for the identification of bacteria (A. Nascimento).
    • 5. Use of different PCR primer-based strategies for characterization of natural microbial communities (James Prosser).
    • 6. Horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plants Astragalus luteolus and Astragalus ernestii in Sichuan, China (Xiaoping Zhang).
    • 7. Amplified rDNA restriction analysis (ARDRA)for identification and phylogenetic placement of 16S-rDNA clones (Menachim Sklarz).
    • 8. Clustering-based peak alignment algorithm for objective and quantitative analysis of DNA fingerprinting data (Satoshi Ishii).
  • The Species Concept.
    • 9. Population genomics informs our understanding of the bacterial species concept (Margaret Riley).
    • 10. Genome analysis of Streptococcus agalactiae: Implication for the microbial “pan-genome” (Rino Rappuoli).
    • 11. Metagenomic insights into bacterial species (Kostas Konstantinidis).
    • 12. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology (Erko Stackebrandt).
    • 13. Metagenomic Approaches for the Identification of Microbial Species (David Ward).
  • Metagenomics.
    • 14. Microbial Ecology in the age of metagenomics (Jianping Xu).
    • 15. The enduring legacy of small rRNA in microbiology (Susan Tringe).
    • 16. Pitfalls of PCR-based rRNA gene sequence analysis:  an update on some parameters (Erko Stackebrandt).
    • 17. Empirical testing of 16S rRNA gene PCR primer pairs reveals variance in target specificity and efficacy not suggested by in silico analysis (Sergio Morales and Bill Holben).
    • 18. The impact of next-generation sequencing technologies on (meta)genomics (George Weinstock).
    • 19. Accuracy and quality of massively parallel DNA pyrosequencing (Susan Huse and David Mark Welch).
    • 20. Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes (Jonathan Eisen).
    • 21. Comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library (C. Manischan).
    • 22. Metagenomic libraries for functional screeing (Svein Valla).
    • 23. GC Fractionation Allows Comparative Total Microbial Community  Analysis, Enhances Diversity Assessment, and Facilitates of Minority Populations of Bacteria (Bill Holben).
    • 24. Enriching plant microbiota for a metagenomic library construction (Ying Zeng).
    • 25. Towards Automated Phylogenomic Inference (Wu and Eisen).
    • 26. Integron first gene cassettes: a target to find adaptive genes in metagenomes (Christine Cagnon).
    • 27. High-resolution metagenomics: assessing specific functional types in complex microbial communities (Christoserdova).
    • 28. Gene-targeted –metagenomics (GT-metagenomics) to explore the extensive diversity of genes of interest in microbial communities (J. Tiedje).
    • 29. Phylogenetic screening of metagenomic libraries using homing endonuclease restriction and marker insertion (Torsten Thomas).
    • 30. ArrayOme- & tRNAcc-facilitated mobilome discovery: comparative genomics approaches for identifying rich veins of novel bacterial DNA sequences (Hong-Yu OU).
    • 31. Sequence-Based Characterization of Microbiomes by Serial Analysis of Ribosomal Sequence Tags (SARST) (Zhongtang Yu).
  • Consortia and Databases.
    • 32. The metagenomics of plant pathogen-suppressive soils (J.D. Van Elsas).
    • 33. Soil Metagenomic Exploration of the Rare Biosphere (Pascal Simonet and Timothy Vogel).
    • 34. The BIOSPAS consortium: Soil Biology and agricultural production (Luis Wall).
    • 35. The Human Microbiome Project (George Weinstock).
    • 36. The Ribosomal Database Project: sequences and Software for high-throughput rRNA analysis (J. R. Cole, G. M. Garrity and Jim Tiedje).
    • 37. The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes (Folker Meyer).
    • 38. The EBI Metagenomics Archive, Integration and Analysis resource (Apweiler).
  • Computer Assisted Analysis.
    • 39. Comparative metagenome analysis using MEGAN (Suparna Mitra and Daniel Huson).
    • 40. Phylogenetic binning of metagenome sequence samples (Alice C. McHardy).
    • 41. Gene prediction in metagenomic fragments with Orphelia: A large scale machine learning approach (Katharina Hoff).
    • 42. Binning metagenomic sequences using seeded GSOm (Sen-Lin Tang).
    • 43. Iterative read mapping and assembly allows the use of a more distant reference in metagenomic assembly (Bas E. Dutilh).
    • 44. Ribosomal RNA identification in metagenomic and metatranscriptomic datasets (Li).
    • 45. SILVA: comprehensive databases for quality checked and aligned ribosomal RNA sequence data compatible with ARB (Frank Gloeckner).
    • 46. ARB; a software environment for sequence data (Wolfgang Ludwig).
    • 47. The Phyloware Project: A software framework for phylogenomic virtue (Daniel Frank).
    • 48. Metasim- A sequencing simulator for genomics and metagenomics (Daniel Richter).
    • 49. ClustScan: an integrated program package for the detection and semi-automatic annotation of secondary metabolite clusters in genomic and metagenomic DNA datasets (Daslav Hranueli).
    • 50. MetaGene; Prediction of prokaryotic and phage genes in metagenomic sequences (Noguchi).
    • 51. primers4clades, a web server to design lineage-specific PCR primers for gene-targeted metagenomics (Pablo Vinuesa).
    • 52. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes (Y. Ye).
    • 53. ESPRIT: estimating species richness using large collections of 16S rRNA data (Yijun Sun).
  • Complementary Approaches.
    • 54. (Meta) genomics approaches in systems biology (Manuel Ferrer).
    • 55. Towards “focused metagenomics”: a case study combining DNA stable-isotope probing, multiple displacement amplification and metagenomics (J. Colin Murrell).
    • 56. Galbraith, E. A., D. A. Antonopoulos, K. E. Nelson, and B. A. White . Suppressive subtractive hybridization reveals extensive horizontal transfer in the rumen metagenome (Bryan White).
  • Microarrays.
    • 57. GeoChip: A high throughout metagenomics technology for dissecting microbial community functional structure (J. Zhou).
    • 58. Phylogenetic microarrays (PhyloChips) for analysis of complex microbial communities (Eoin Brodie).
    • 59. Phenomics and Phenotype MicroArrays: Applications Complementing Metagenomics (Barry Bochner).
    • 60. Microbial persistence in low biomass, extreme environments: The great unknown (Kasthuri Venkateswaran).
    • 61. Application of phylogenetic oligonucleotide microarrays in microbial analysis (Nian Wang).
  • Metatranscriptomics.
    • 62. Isolation of mRNA from environmental microbial communities for metatranscriptomic analyses (P. Schenk).
    • 63. Comparative day/night metatrancriptomic analysis of microbial communities in the North Pacific subtropical gyre (Rachel Poretski).
    • 64. The “double RNA” approach to simultaneously assess the structure and function of environmental microbial communities by meta-transcriptomics (Tim Urich and Christa Schleper).
    • 65. Soil eukaryotic diversity, a metatranscriptomic approach (Marmeisse).
  • Metaproteomics.
    • 66. Proteomics for the analysis of environmental stress responses in prokaryotes Ksenia Groh, Victor Nesatyy and Marc Suter).
    • 67. Microbial community proteomics (Paul Wilmes).
    • 68. Synchronicity between population structure and proteome profiles: A metaproteomic  analysis of Chesapeake Bay bacterial communities (Feng Chen).
    • 69. High-Throughput Cyanobacterial Proteomics: Systems-level Proteome Identification and Quantitation   (Phillip Wright).
    • 70. Protein Expression Profile of an Environmentally Important Bacterial Strain: the Chromate Response of Arthrobacter sp. strain FB24 (K. Henne).
  • Metabolomics.
    • 71. The small molecule dimension: Mass spectrometry based metabolomics, enzyme assays, and imaging (Trent R. Northen).
    • 72. Metabolomics: high resolution tools offer to follow bacterial growth on a molecular level (Lucio Marianna and Philipp Schmitt-Kopplin).
    • 73. Metabolic profiling of plant tissues by electrospray mass spectrometry (Heather Walker).
    • 74. Metabolite identification, pathways and omic integration using online databases and tools (Matthew Davey).
  • Single cell analysis.
    • 75. Application of cytomics to separate natural microbial communities by their physiological properties (Susann Müller).
    • 76. Capturing microbial populations for environmental genomics (A. Pernthaler/Wendeberg).
    • 77. Microscopic single-cell isolation and multiple displacement amplification of genomes from uncultured prokaryotes (Peter Westermann).

Volume 2: Metagenomics in Different Habitats

  • 1. Introduction (Frans J. de Bruijn).
  • Viral Genomes.
    • 2. Viral metagenomics (Shannon Williamson).
    • 3. Methods in Viral Metagenomics (Thurber).
    • 4. Metagenomic contrasts of viruses in soil and aquatic environments (Eric Wommack).
    • 5. Biodiversity and biogeography of phages in modern stromatolites and thromolites (Christelle Desnues).
    • 6. Assembly of Viral Metagenomes from Yellowstone Hot Springs Reveals Phylogenetic Relationships and Host Co-Evolution (Thomas Schoenfeld).
    • 7. Next-generation sequencing and metagenomic analysis; a universal diagnostic tool in plant pathology (Ian Adams).
    • 8. Direct Metagenomic Detection of Viral Pathogens in Human Specimens Using an Unbiased High-throughput Sequencing Approach (T. Nakaya).
  • The Soil Habitat.
    • 9. Soil based Metagenomics (R. Daniel).
    • 10. Methods in Metagenomic DNA, RNA and Protein Isolation from Soil (P. Gunasharan).
    • 11. Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications (Mark Liles).
    • 12. Application of PCR-DGGE and metagenome walking to retrieve full-length functional genes from soil (Morimoto).
    • 13. Actinobacterial diversity associated with Antarctic Dry Valley mineral soils (Cowan).
    • 14. Targetting major soil-borne bacterial lineages using large-insert metaenomic approaches (G. Kowalchuk).
    • 15. Novelty and uniqueness patterns of rare members of the soil biosphere (M. Elshahed).
    • 16. Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters (Holben WE).
    • 17. The Antibiotic Resistance: Origins, Diversity, and Future Prospects (Gerard Wright).
  • The Digestive Tract.
    • 18. Functional Intestinal Metagenomics (Michael Kleerebezem).
    • 19. Assessment and improvement of methods for microbial DNA preparation from fecal Samples (M. Hattori).
    • 20. Role of dysbiosis in inflammatory bowel diseases (Johan Dicksved).
    • 21. Culture independent analysis of the human gut microbiota and its activities (Kieran Tuohi).
    • 22. Complete genome of an uncultured endowsymbiont coupling nitrogen fixation to cellulolysis with protest cells in termite gut (Hongo).
    • 23. Cloning and identification of genes encoding acidic cellulases from metagenomes of buffalo rumen (Feng).
  • Marine and Lakes.
    • 24. Microbial diversity in the deep seas and the underexplored “rare biosphere” (David Mark Welsch and Susan Huse).
    • 25. Bacterial Community Structure and Dynamics in a Seasonally Anoxic Fjord (Steven J. Hallam).
    • 26. Adaptation to nutrient availability in marine microorganisms by gene gain and loss (A. Martini).
    • 27. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities (Jack Gilbert).
    • 28. Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a lacustrine ecosystem (Didier Debroas).
    • 29. Metagenomics of the marine subsurface: the first glimpse from the Peru Margin, ODP Site 122 (Jennifer Biddle).
    • 30. A targeted metagenomic approach to determine the ‘population genome’ of marine Synechoccus (D. J. Scanlan).
    • 31. Diversity and role of bacterial integron/gene cassette metagenome in extreme marine environments (Hosam Easa Elsaied and Akihiko Maruyama).
  • Other Habitats.
    • 32. The Olavius algarvensis metagenome revisited: lessons learned from the analysis of the low diversity microbial consortium of a gutless marine worm (Nicole Dubulier).
    • 33. Microbiome diversity in human saliva (Ivan Nasidze).
    • 34. Approaches to understanding population level functional diversity in a microbial community (D. Bhaya).
    • 35. A functional metagenomic approach for discovering nickel resistance genes from the rhizosphere of an acid mine drainage environment (JOSE Gonzales –Pastor).
    • 36. The Microbiome of Leaf-cutter Ant Fungus Gardens (Garret Suen).
    • 37. Diversity of archaea in terrestrial hot springs and role In ammonia oxidation (Chuanlun Zhang).
    • 38. Colinization of nascent, deep-sea hydrothermal vents by a novel Archaeal and Nanoarchaeal assemblage (S. Craig Cary).
    • 39. Analysis of the Metagenome from a biogas-producing microbial Community by means of Bioinformatucs Methods (Andreas Schlueter).
    • 40. Amplicon pyrosequencing analysis of endosymbiont population structure (Colleen Kavahagh).
    • 41. Investigative bacterial diversity along alkaline hot spring thermal gradients by barcoded pyrosequencing (Scott Miller and Michael Welzer).
    • 42. Genetic characterization of microbial communities living at the surface of building stones (J. C. Salvado).
    • 43. Novel aromatic degradation pathway genes and their organization as revealed by metagenomic analysis (Kentaro).
    • 44. Functional screening of a wide host-range metagenomic library from a wastewater treatment plant yields a novel alcohol/aldehyde dehydrogenase (Wexler).
    • 45. Aromatic hydrocarbon degradation genes from chronically polluted Subantarctic marine sediments (H. M. Dionisi).
    • 46. Isolation and characterization if alkane hydroxylases from a metagenomic llibrary of Pacific deep-sea sediment  (Fengping Wang).
  • Biocatalysts and Natural Products.
    • 47. Emerging Fields in Functional Metagenomics and its Industrial Relevance  – Overcoming Limitations and Redirecting the Search for Novel Biocatalysts (Wolfgang Streit).
    • 48. Carboxylesterases and Lipases from Metagenomes (Chow and Wolfgang Streit).
    • 49. Expanding small molecule functional megenomics through parallel screening of broad host-range cosmid environmental DNA libraries in diverse Proteobacteria (Sean Brady).
    • 50. Biomedicinals from the microbial metagenomes of marine invertebrates (Walter Dunlap).
    • 51. Molecular characterization of TEM-type beta-Lactamases identified in Cold-seep sediments of Edison Seamount (South of Lihir Island).
    • 52. Identification of Novel Bioactive Compounds from the Metagenome of the Marine (David Lejon).
    • 53. Functional Viral Metagenomics and the Development of New Enzymes for DNA and RNA Amplification and Sequencing (Thomas Schoenfeld).
  • Summary.
    • 54. Future of metagenomics, metatranscriptomics, metabolomics, metaproteomics and single cell analysis: A perspective (J. Tiedje).
    • 55. Darwin in the 21st Century: Natural Selection, Molecular Biology, and Species Concepts (Francisco Ayala).
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Sequence/short read archive (SRA) back from the dead

Well, in February it seemed as though the Sequence/Short Read Archive was dead (see for example, End of Sequence Read Archive (SRA) – some quick notes and Though I generally love NCBI, the Sequence/Short Read Archive (SRA) seems to have issues; what do others think?)).

But now it seems as though there has been a resurrection of sorts (I guess I should have paid attention in March). See for example: SRA Home where it is stated that
“Recently, NCBI announced that due to budget constraints, it would be discontinuing its Sequence Read Archive (SRA) and Trace Archive repositories for high-throughput sequence data. However, NIH has since committed interim funding for SRA in its current form until October 1, 2011. In addition, NCBI has been working with staff from other NIH Institutes and NIH grantees to develop an approach to continue archiving a widely used subset of next generation sequencing data after October 1, 2011.
We now plan to continue handling sequencing data associated with:
RNA-Seq, ChIP-Seq, and epigenomic data that are submitted to GEO
Genomic and Transcriptomic assemblies that are submitted to GenBank
Genomic assemblies to GenBank/WGS
16S ribosomal RNA data associated with metagenomics that are submitted to GenBank
In addition, NCBI will continue to provide access to existing SRA and Trace Archive data for the foreseeable future. NCBI is also continuing to discuss with NIH Institutes approaches for handling other next-generation sequencing data associated with specific large-scale studies.”
Well I’ll be. I guess it is back at least for now.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

New #UCDavis Dean of the College of Biological Sciences: James E.K. Hildreth

Just announced a few minutes ago. The new Dean of the College of Biological Sciences at UC Davis is James Hildreth from Meharry Medical College.

Some tidbits about him:
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Selfish DNA, symbionts and parasites – some quick links

I was at a committee meeting yesterday for a great PhD student here at UC Davis, Michael Hornsby and the topic of selfish DNA came up.  After his meeting we sat down and looked for some new papers and review papers on the topic.  I just thought it might be of value to share some of these here:

We also discussed briefly the evolution of mutualists and parasites and here are a few papers that came up:

If anyone knows of any other good recent papers or blog posts about selfish DNA or mutualists vs. parasites please post them here.  Thanks
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

NSF requests for "conflicts of interest" lists drive me batty and seem to penalize collaborative, interdisciplinary researchers

OK, time to bitch and moan a bit.

I am working on a few proposals to the National Science Foundation where NSF asks one to include “lists of institutions, project personnel, and collaborators with Conflicts of Interest”.

Seems simple I suppose.  But not when you get down to the details.  For example I found some guidance from the NSF about this where they ask one to list coauthors, collaborators, co-editors, students, advisors, advisees, friends, relatives, and many other affiliations.

To make a very long story short.  NSF wants you to make a list of anyone who possibly should not review your grant.  And if you are involved in many large collaborative projects or teach or train a lot of students.  Well, you are screwed.  For example, if they really want me to be thorough, I would probably have to list more than 500 people.  This would include a few hundred co-authors and hundreds of collaborators (e.g., on some projects I am working on with the Joint Genome Institute there are hundreds of people involved in some way).


Why does NSF ask for this?  Apparently, to help them select reviews for grant (I note, as far as I have seen, other granting agencies do not ask for this information).  If I were to do this as thoroughly as they ask, it would probably take me 2-3 full days of work – compiling the entire list of all who I collaborate with in some way on the many large projects on which I work.  I note – they don’t just ask for a list of names.  They ask for current organizational affiliations.  I published some papers four years ago with people who I have not met and have no frigging idea where they are now.  In some cases I might be able to figure this out with google but in others it might be impossible.  Even when easy it would take many minutes of searching per person to be sure.  So with some 500 people on my list (actually, probably more) it could take many many many hours just to figure out where people are now.

Anyone heavily involved in genome sequencing would probably have a massive list to go through.  Actually anyone involved in any large scale collaborative science project would have a pretty big list.  So, in a way, NSF is punishing people who do large scale projects like this by giving us extra work to do.  If you don’t collaborate with anyone or train anyone, well, you get a free pass and have no work to do here.

Do you get the feeling I am annoyed by this?  I used to compile a relatively full list.  But I have given up making it complete.  I now do my best to list major collaborators and coauthors but even that takes a long time.  And it all seems a bit inane.  Why can’t NSF just ask reviewers to declare their conflicts like other granting agencies?

Oh, and don’t even get me started on the fact that they ask for this as an Excel spreadsheet saved in csv format.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

What’s Lurking in Your (Work) Basement

Well, sad as it may be I finally made it into the basement in the building where I have worked for five + years – the Genome and Biomedical Sciences Facility (GBSF) at UC Davis (the Genome Center is in the same building).  There, down in the basement they were having an Open House for the CMGI – the Center for Molecular and Genomic Imaging.  I knew of some of the stuff they did but had never been down to see their facility and their, well, toys.  And it was really cool.

https://picasaweb.google.com/s/c/bin/slideshow.swf

They also had a nice food spread upstairs on the first floor of our building that I discovered later.  The best part of this spread were the animal chocolates and carvings:

Anyway – just a little post here.  Oh, and they do some pretty cool science at the CMGI, including some interesting uses of CT, PET, SPECT, MRI, and more.   You just never know what you will find in the basement …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Crosspost from microBEnet: Where is metagenomic analysis heading? Hopefully in directions suggested in this paper.

Figure 3 from Raes et al. Molecular Systems Biology 7 #473  doi:10.1038/msb.2011.6 

Just a quick post here.  I have been reading this paper: Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data by Jeroen Raes et al. in Molecular Systems Biology.  This integration they try to pull off in the paper is to me where we need to move as a field (i.e., microbial ecology) in order to make full use of metagenomic data.  The paper provides a nice overview of microbial biogeography too.  Definitely worth a read.

Am crossposting this from the microBEnet blog (microBEnet is the site for the microbiology of the built environment network that I am building):

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Microbiology for the public – Science at the Lesher in Walnut Creek Sponsored by DOE-JGI

Well, a month or so ago I asked people for help in planning a talk on microbes to a non sciency crowd.  I got some good suggestions and, well, I think it ended up OK.  The talk I gave was part of the JGI Science @ the Theater series in Walnut Creek.  The topic was “The Deal with Carbon: How the Earth’s Mighty Microbes Respond”  and my job was to introduce microbes to set up talks by Rachel Mackelprang (on permafrost melting) and Berkeley Lab’s Terry Hazen (on microbes and the gulf oil spill).  In the beginning, JGI debuted a short video about the carbon cycle and the Berkeley Lab Carbon Cycle 2.0 initiative, created in collaboration with Illumina Visual in Emeryville.

The best part of the whole thing was meeting John Fowler from KTVU TV.  He was great.  I have a ten minute chat with him before the talks started and he inspired and impressed me with his interest in both science and science communication (see his “Side Effects” blog here and his twitter feed here).  Another good part of this event was I got to meet Terry Hazen.  We have seen each other before at conferences but never really talked.  He is doing some very interesting work on bacteria and oil spills (see the video).  I note, I am not completely convinced by his conclusions regarding microbes being “primed” to degrade/eat the oil that was spilled into the gulf but his work is still fascinating and comprehensive.  I note – it is not just that he does interesting work.  I published a paper a few years ago with his daughter Tracy Hazen on plasmids from marine sediments and I always wanted to meet her dad.

Another good thing about the night was that some of my wife’s family came to the event.  That was inspiring in a way and kind of fun.  I think that was the first time they had seen me give a talk.

Anyway – I hope people like the talk I gave – it was my first real introduction to microbes and molecular studies of microbes to a non science audience.  So forgive me for some of the mistakes in there.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Updated Again: Compilation of articles, news, blogs about the "arsenic bacteria" NASA study

Lots of new stuff on the arsenic-bacteria front.  For those interested I am compiling some of the more useful links here:

News stories:

Blogs:
  • A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus
    • Felisa Wolfe-Simon, 
    • Jodi Switzer Blum, 
    • Thomas R. Kulp, 
    • Gwyneth W. Gordon, 
    • Shelley E. Hoeft,
    • Jennifer Pett-Ridge, 
    • John F. Stolz, 
    • Samuel M. Webb, 
    • Peter K. Weber, 
    • Paul C. W. Davies,
    • Ariel D. Anbar, 
    • and Ronald S. Oremland

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • James B. Cotner and

          •  

        • Edward K. Hall

        Science 27 May 2011: 1201943Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Rosemary J. Redfield

        Science 27 May 2011: 1201482Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • B. Schoepp-Cothenet, 
        • W. Nitschke, 
        • L. M. Barge, 
        • A. Ponce, 
        • M. J. Russell, 
        • and A. I. Tsapin

        Science 27 May 2011: 1201438Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • István Csabai and

          •  

        • Eörs Szathmáry

        Science 27 May 2011: 1201399Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Stefan Oehler

        Science 27 May 2011: 1201381Published online 27 May 2011

      • Editor’s Note

        • Bruce Alberts

        Science 27 May 2011: 1208877Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • David W. Borhani

        Science 27 May 2011: 1201255Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Steven A. Benner

        Science 27 May 2011: 1201304Published online 27 May 2011

      • Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus”

        • Patricia L. Foster

        Science 27 May 2011: 1201551Published online 27 May 2011

      • A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus

        • Felisa Wolfe-Simon, 
        • Jodi Switzer Blum, 
        • Thomas R. Kulp, 
        • Gwyneth W. Gordon, 
        • Shelley E. Hoeft,
        • Jennifer Pett-Ridge, 
        • John F. Stolz, 
        • Samuel M. Webb, 
        • Peter K. Weber, 
        • Paul C. W. Davies,
        • Ariel D. Anbar, 
        • and Ronald S. Oremland

        Science 2 December 2010: 1197258Published online 2 December 2010

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Some general tips for how to keep up w/ American Society for Microbiology Mtg #ASM2011

https://picasaweb.google.com/s/c/bin/slideshow.swf

Well, I have arrived in New Orleans for the ASM General Meeting 2011.  Some quick notes here about how people might keep up with whats going on:

Watch this or other real time streams of twitter posts

http://widgets.twimg.com/j/2/widget.js
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Follow just my posts about the Meeting:

http://widgets.twimg.com/j/2/widget.js
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Read up on some of my past reports from ASM meetings

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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