Category: Misc.

Playing with @buzzumi – did a video chat with @betascience discussing metagenomics

Buzzumi looks pretty nice.  Was really easy to set up and get running and worked easily for a private video chat.  Going to try to use it for a webinar next.  Ignore the comments by Russell in the chat … 

Buzzumi

Evolution pumpkins – from Darwin to Woese

OK I know I am a geek, but I do think these came out pretty well …

“I think” in honor of Darwin

Woese Tree of Life

——–
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.

——–

Fun with a $1300 3D printer – featuring @ryneches in my lab

Just a quick one here.  I am posting some links to videos and blog posts about efforts by a student in my lab – Russell Neches – to use 3D printing to help with carrying out high throughput studies of microbial diversity. Basically the idea is that we can use new very cheap 3D printer technologies to help with normalizing sample volumes by printing in essence micro titer dishes with variable well depth. For more on this see some of the links/videos/etc below:  

From Russell’s blog:

Some of Russell’s videos

Aggie TV news story about Russell’s work on this:

——–
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.

——–

Further proof of the ascendancy of microbes: 2011 NSF "biodiversity" grants mostly focused on microbes

As if the readers of this blog needing any more proof of the ascendancy of microbes and microbiology. Well, regardless, here is more. The NSF Announced recipients of the 2011 grants on “Dimensions of Biodiversity” – see The National Science Foundation (NSF) News Diversity of Life on Earth: NSF Awards Grants for Study of Dimensions of Biodiversity

And the recipients are strongly biased towards microbes relative to the general past patterns at many funding agencies.
Microbial focused awards:
Title: Pattern and process in marine bacterial, archaeal, and protistan biodiversity, and effects of human impacts
PI (Principal investigator): Jed Fuhrman, University of Southern California
Summary: Very little about marine microbial systems is understood, despite the fact that these diverse groups dominate cycling of elements in the oceans. Fuhrman and colleagues will compare heavily affected harbor regions with relatively pristine ocean habitat in the Los Angeles basin to understand patterns and relationships in marine microbial communities.

Title: Diversity and symbiosis: Examining the taxonomic, genetic, and functional diversity of amphibian skin microbiota
PI: Lisa Belden, Virginia Polytechnic Institute & State University
Summary: All animals host internal and external symbiotic microbes; most cause no harm and many are beneficial. This study seeks to understand the regulation of microbial communities on the skin of amphibian species, and how they may limit infection by a chytrid fungus that has decimated many amphibian populations around the globe.

Title: Lake Baikal responses to global change: The role of genetic, functional and taxonomic diversity in the planktonPI: Elena Litchman, Michigan State University
Summary: Microscopic plant- and animal-like plankton are the first links in aquatic food chains. This project will study the planktonic food web of the world’s largest, oldest, and most biologically diverse lake–Lake Baikal in Siberia–to predict how native vs. non-native plankton in this ecosystem will respond to accelerating environmental change


Title: Functional diversity of microbial trophic guilds defined using stable isotope ratios of proteinsPI: Ann Pearson, Harvard University
Summary: Studying the ecological interactions among microbes is difficult given their immense diversity and the scale of observation. This project will use isotopic ratios of carbon, nitrogen, hydrogen and sulfur produced during microbial metabolism to link microbes to their roles in biogeochemical and ecosystem processes. This novel approach will contribute to an understanding of what maintains diversity in microbes and, by extension, the roles microbes play in ecosystems.


Title: An integrated study of energy metabolism, carbon fixation, and colonization mechanisms in chemosynthetic microbial communities at deep-sea ventsPI: Stefan Sievert, Woods Hole Oceanographic Institution
Summary: The 1977 discovery of deep-sea hydrothermal vent ecosystems that obtain energy not through photosynthesis, but via inorganic chemical reactions greatly expanded the perception of life on Earth. However, there has been limited progress since then in understanding their underlying microbiology and biogeochemistry. This project will establish an international research program to better understand these deep-sea ecosystems and to place them in a global context.


Title: Functional diversity of marine eukaryotic phytoplankton and their contributions to carbon and nitrogen cyclingPI: Bess Ward, Princeton University
Summary: Marine phytoplankton form the base of food webs in the ocean’s surface layers, and thus represent the first incorporation of biologically important chemicals. This project will study two north Atlantic sites in two seasons to link the genetic diversity and species composition of phytoplankton communities to the carbon and nitrogen biogeochemistry of the surface ocean.

Title: IRCN (International Research Coordination Network): A Research Coordination Network for Biodiversity of CiliatesPI: John Clamp, North Carolina Central University
Summary: Ciliates are abundant, widespread protists found in all aquatic systems on Earth. However, it is estimated that science has described only 25 percent of these ubiquitous microorganisms, mainly in western European and eastern North American waters. This cooperative project is partially supported by the Natural Science Foundation of China, and will establish an International Research Coordination Network for Biodiversity of Ciliates (RCN-BC; including researchers from the United States, China, the United Kingdom and Brazil) to broaden exploration of these important protists.

Amazingly, there are only three awards not focused on microbes:

Title: The climate cascade: Functional and evolutionary consequences of climatic change on species, trait, and genetic diversity in a temperate ant communityPI: Nathan Sanders, University of Tennessee, Knoxville
Summary: Sanders and colleagues will help us understand what mechanisms allow some species to adapt to shifts in climate, rather than migrating or going extinct. This project will reconstruct past adaptations to climate change in a foraging ant common in forests throughout the Eastern United States and sample ant nests introduced to outdoor experimental warming chambers to determine the ant’s capacity to adapt to heat stress.

Title: Integrating genetic, taxonomic, and functional diversity of tetrapods across the Americas and through extinction risk
PI: Thomas Brooks, NatureServe
Summary: Most large-scale efforts to assess biodiversity have focused on genetic, taxonomic and functional dimensions individually; it is unknown how these dimensions relate to each other. Brooks and colleagues are using a database of the 13,000 land vertebrates in the Americas to determine how changes in one dimension of biodiversity influence changes in others. Understanding how species composition influences the diversity of certain traits, for example, will improve the efficiency and effectiveness of conservation actions.

Title: Integrating dimensions of Solanumbiodiversity: Leveraging comparative and experimental transcriptomics to understand functional responses to environmental change
PI: Leonie Moyle, Indiana University
Summary: This research will highlight the role of drought and herbivore defense in driving the remarkable diversity of wild tomato species. With the economic importance of tomatoes and their relatives (such as peppers and potatoes), this study will help prepare society for the future challenges facing global food security.

And if the PIs of these grants have any sense, they will likely include some microbial studies as part of their projects.  Of course, in the end all ecosystems include a diversity of kinds of organisms, and focusing on microbes over other organisms is also a biased approach.  But we (that is, “Science”) have spent so many years ignoring the dark matter of the biological universe (the term I now use to refer to microbial diversity) that we have to focus on microbes because there is a lot of catching up to do 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.

——–

Single cell genomics even has its own software: SmashCell

Somehow I was not aware of this software called SmashCell even though it came out a while ago.  But it is worth checking out if you are interested in single-cell genomics.  There is an open access paper describing the software: SmashCell: a software framework for the analysis of single-cell amplified genome sequences.

Single cell genomics is becoming more and more important in studies of environmental microbiology as well as other fields like cancer biology.  One of the challenges with single cell genomics is that the amplification processes used to make copies of the genome from single cells are not completely accurate or efficient so you frequently end up with partial, somewhat messed up samples of genomes.  If you then sequence these amplified genomes it can be hard to make sense out of the data.  Hopefully this software may be of use to some doing this type of work.

Note – for those interested in more see this PLoS One paper I am a coauthor on:

Assembling the Marine Metagenome, One Cell at a Time

——–
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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——–
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 microbe papers from the Royal Society archives

As many be aware, the Royal Society has made their entire archive of papers available for free.  This has included some classics and has attracted a lot of attention (e.g., papers by Darwin and Franklin and others).  Well, here are some of microbial interest

First I did a search for the term bacteria and searched by date (with oldest first): and found a few of interest.

    • C. C. Pode

      •  

    • and E. Ray Lankester

    Experiments on the Development of Bacteria in Organic InfusionsProc. R. Soc. Lond. January 1, 1872 21:348–358;doi:10.1098/rspl.1872.0069

    1 January 1872 research-article Experiments on the Development ofBacteria in Organic Infusions C. C. Pode E. Ray Lankester The Royal Society is collaborating with JSTOR to digitize, preserve, and extend access to Proceedings of the Royal Society of London. http://www.jstor.org ?
    • H. Charlton Bastian

    Further Observations on the Temperature at WhichBacteria, Vibriones, and Their Supposed Germs Are Killed When Exposed to Heat in a Moist State; and on the Causes of Putrefaction and FermentationProc. R. Soc. Lond. January 1, 1872 21:325–338;doi:10.1098/rspl.1872.0067

    1 January 1872 research-article Further Observations on the Temperature at Which Bacteria, Vibriones, and Their Supposed Germs Are Killed When Exposed to Heat in a Moist State; and on the Causes of Putrefaction and Fermentation…
    • H. Charlton Bastian

    Note on the Origin of Bacteria, and on Their Relation to the Process of PuterfactionProc. R. Soc. Lond. January 1, 1872 21:129–131;doi:10.1098/rspl.1872.0030

    1 January 1872 research-article Note on the Origin of Bacteria, and on Their Relation to the Process of Puterfaction H. Charlton Bastian The Royal Society is collaborating with JSTOR to…
    • H. Charlton Bastian

    On the Temperature at Which Bacteria, Vibriones, and Their Supposed Germs are Killed When Immersed in Fluids or Exposed to Heat in a Moist StateProc. R. Soc. Lond. January 1, 1872 21:224–232;doi:10.1098/rspl.1872.0048

    1 January 1872 research-article On the Temperature at WhichBacteria, Vibriones, and Their Supposed Germs are Killed When Immersed in Fluids or Exposed to Heat in a Moist State H. Charlton Bastian…
    • Arthur Downes

      •  

    • and Thos. P. Blunt

    Researches on the Effect of Light upon Bacteria and other OrganismsProc. R. Soc. Lond. January 1, 1877 26:488–500;doi:10.1098/rspl.1877.0068

    1 January 1877 research-article Researches on the Effect of Light upon Bacteria and other Organisms Arthur Downes Thos. P. Blunt The Royal Society is collaborating with JSTOR to digitize, preserve, and…
    • J. Burdon Sanderson

    Remarks on the Attributes of the Germinal Particles of Bacteria, in Reply to Prof. TyndallProc. R. Soc. Lond. January 1, 1877 26:416–426;doi:10.1098/rspl.1877.0063

    1 January 1877 research-article Remarks on the Attributes of the Germinal Particles of Bacteria, in Reply to Prof. Tyndall J. Burdon Sanderson The Royal Society is collaborating with JSTOR to digitize, preserve, and extend…
    • J. Cossar Ewart

    The Life-History of Bacterium Termo and Micrococcus, with Further Observations on BacillusProc. R. Soc. Lond. January 1, 1878 27:474–480;doi:10.1098/rspl.1878.0086

But these were not old enough for me.  So  I decided to search for “Leeuwenhoek” and found a treasure trove – posted below.  I am not going to get anything done for the net few days am I?
    • Anth Van Leeuwenhoek

    A Letter from Mr. Anth. Van Leeuwenhoekconcerning the Seeds of Plants, with Observations on the Manner of the Propagation of Plants and AnimalsPhil. Trans. January 1, 1693 17:700–708;doi:10.1098/rstl.1693.0026

    …1693 research-article A Letter from Mr. Anth. Van Leeuwenhoekconcerning the Seeds of Plants, with Observations…of the Propagation of Plants and Animals Anth Van Leeuwenhoek The Royal Society is collaborating with JSTOR…
    • Anth. Van. Leeuwenhoek

    An Extract of a Letter from Mr. Anth. Van.Leeuwenhoek, containing Several Observations on the Texture of the Bones of Animals Compared with That of Wood: On the Bark of Trees: On the Little Scales Found on the Cuticula, etc.Phil. Trans. January 1, 1693 17:838–843;doi:10.1098/rstl.1693.0050

    …research-article An Extract of a Letter from Mr. Anth. Van.Leeuwenhoek, containing Several Observations on the Texture of the Bones…the Little Scales Found on the Cuticula, etc. Anth. Van.Leeuwenhoek The Royal Society is collaborating with JSTOR to digitize…
    • Anthony Van Leeuwenhoek

    An Extract of a Letter from Mr. Anthony VanLeeuwenhoek, to the R. S. Containing His Obseruations on the Seeds of Cotton, Palm, or Date-Stones, Cloves, Nutmegs, Goose-Berries, Currans, Tulips, Cassia, Lime-Tree: On the Skin of the Hand, and Pores, of Sweat, the Crystalline Humour, Optic Nerues, Gall, and Scales of Fish: and the Figures of Seueral Salt Particles, etc.Phil. Trans. January 1, 1693 17:949–960;doi:10.1098/rstl.1693.0073

    …research-article An Extract of a Letter from Mr. Anthony VanLeeuwenhoek, to the R. S. Containing His Obseruations on the Seeds of…the Figures of Seueral Salt Particles, etc. Anthony VanLeeuwenhoek The Royal Society is collaborating with JSTOR to digitize…
    • Anthony van Leeuwenhoek

    Part of a Letter from Mr. Anthony van Leeuwenhoek, F. R. S. Concerning the Eyes of Beetles, etc.Phil. Trans. January 1, 1698 20:169–175;doi:10.1098/rstl.1698.0026

    1 January 1698 research-article Part of a Letter from Mr. Anthony vanLeeuwenhoek, F. R. S. Concerning the Eyes of Beetles, etc. Anthony van Leeuwenhoek The Royal Society is collaborating with JSTOR to digitize, preserve, and…
    • Anthony van Leeuwenhoek

    A Letter from Mr Anthony Van Leeuwenhoek, F. R. S. concerning Spiders, Their Way of Killing Their Prey, Spinning Their Webbs, Generation, etcPhil. Trans. 1700 22:867–881;doi:10.1098/rstl.1700.0088

    …research-article A Letter from Mr Anthony Van Leeuwenhoek, F. R. S. concerning Spiders, Their Way of Killing…Spinning Their Webbs, Generation, etc Anthony van Leeuwenhoek The Royal Society is collaborating with JSTOR…
    • Antony van Leeuwenhoek

    A Letter from Mr Antony van Leeuwenhoek, F. R. S. to Mr Chamberlaine, concerning the Causes of the Different Tastes of Waters and Edge of RazorsPhil. Trans. 1700 22:899–903;doi:10.1098/rstl.1700.0093

    …research-article A Letter from Mr Antony van Leeuwenhoek, F. R. S. to Mr Chamberlaine, concerning the…Tastes of Waters and Edge of Razors Antony van Leeuwenhoek The Royal Society is collaborating with…
    • Antony van Leeuwenhoek

    Part of a Letter from Mr Antony van Leeuwenhoek, concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of FrogsPhil. Trans. 1700 22:509–518;doi:10.1098/rstl.1700.0013

    1700-1701 research-article Part of a Letter from Mr Antony vanLeeuwenhoek, concerning the Worms in Sheeps Livers, Gnats, and Animalcula in the Excrements of Frogs Antony van LeeuwenhoekThe Royal Society is collaborating with JSTOR to digitize…
    • Anthony van Leeuwenhoek

    Part of a Letter from Mr Anthony van Leeuwenhoek, F. R. S. to the Pablisher, concerning Several Microscopical ObservationsPhil. Trans. 1700 22:903–907;doi:10.1098/rstl.1700.0094

    1700-1701 research-article Part of a Letter from Mr Anthony vanLeeuwenhoek, F. R. S. to the Pablisher, concerning Several Microscopical Observations Anthony van Leeuwenhoek The Royal Society is collaborating with JSTOR to digitize…
    • Anthony van Leeuwenhoek

    Part of Two Letters from Mr Anthony Van Leenwenhoek, F. R. S. concerning Worms Pretended to be Taken from the TeethPhil. Trans. 1700 22:635–642;doi:10.1098/rstl.1700.0042

    …Two Letters from Mr Anthony Van Leenwenhoek, F. R. S. concerning Worms Pretended to be Taken from the Teeth Anthony van Leeuwenhoek The Royal Society is collaborating with JSTOR to digitize, preserve, and extend access to Philosophical Transactions…
    • Antony van Leeuwenhoek

    Part of a Letter from Mr Antony van Leeuwenhoek, F. R. S. concerning Green Weeds Growing in Water, and Some Animalcula Found about ThemPhil. Trans. 1702 23:1304–1311;doi:10.1098/rstl.1702.0042

    1702-1703 research-article Part of a Letter from Mr Antony vanLeeuwenhoek, F. R. S. concerning Green Weeds Growing in Water, and Some Animalcula Found about Them Antony van LeeuwenhoekThe Royal Society is collaborating with JSTOR to digitize…

    • Anthony van Leeuwenhoek

    A Letter from Mr Anthony Van Leeuwenhoek, F. R. S. concerning the Barks of TreesPhil. Trans. 1704 24:1843–1855;doi:10.1098/rstl.1704.0056

    1704-1705 research-article A Letter from Mr Anthony VanLeeuwenhoek, F. R. S. concerning the Barks of Trees Anthony vanLeeuwenhoek The Royal Society is collaborating with JSTOR to digitize, preserve, and extend access to Philosophical Transactions (1683-1775). http://www.jstor.org ?
    • Anthony van Leeuwenhoek

    A Letter from Mr Anthony Van Leeuwenhoek, F. R. S. concerning the Figures of the Salts of CrystalPhil. Trans. 1704 24:1906–1917;doi:10.1098/rstl.1704.0069

    1704-1705 research-article A Letter from Mr Anthony VanLeeuwenhoek, F. R. S. concerning the Figures of the Salts of Crystal Anthony van Leeuwenhoek The Royal Society is collaborating with JSTOR to digitize, preserve, and extend access…
    • Antony van Leeuwenhoek

    A Letter from Mr Antony Van Leeuwenhoek, F. R. S. to John Chamberlain, Esq; S. R. S. concerning Tobacco AshesPhil. Trans. 1704 24:1740–1748;doi:10.1098/rstl.1704.0037

    1704-1705 research-article A Letter from Mr Antony VanLeeuwenhoek, F. R. S. to John Chamberlain, Esq; S. R. S. concerning Tobacco Ashes Antony van Leeuwenhoek The Royal Society is collaborating with JSTOR to digitize, preserve, and extend…
    • Antony van Leeuwenhoek

    A Letter from Mr Antony Van Leeuwenhoek, F. R. S. concerning the Flesh of Whales, Crystalinc Humour of the Eye of Whales, Fish, and Other Creatures, and of the Use of the Eye-LidsPhil. Trans. 1704 24:1723–1730;doi:10.1098/rstl.1704.0035

    1704-1705 research-article A Letter from Mr Antony VanLeeuwenhoek, F. R. S. concerning the Flesh of Whales, Crystalinc Humour…Other Creatures, and of the Use of the Eye-Lids Antony van Leeuwenhoek The Royal Society is collaborating with JSTOR to digitize…
    • Antony van Leeuwenhoek

    A Letter from Mr Antony Van Leeuwenhoek, concerning the Tubes or Canals That Convey the Yellow Sap in the Herb Called Chelidonium Majus, or Celandine, etc.Phil. Trans. 1704 24:1730–1740;doi:10.1098/rstl.1704.0036

    1704-1705 research-article A Letter from Mr Antony VanLeeuwenhoek, concerning the Tubes or Canals That Convey the Yellow Sap…Called Chelidonium Majus, or Celandine, etc. Antony van Leeuwenhoek The Royal Society is collaborating with JSTOR to digitize…
    • Anthony van Leeuwenhoek

    Part of a Letter from Mr Anthony Van Leeuwenhoek, F. R. S. to John Chamberlayne, Esq; F. R. S. concerning the Vitrifyed Salts of Calcin’d HayPhil. Trans. 1704 24:1856–1859;doi:10.1098/rstl.1704.0057

    …research-article Part of a Letter from Mr Anthony VanLeeuwenhoek, F. R. S. to John Chamberlayne, Esq; F. R. S. concerning the Vitrifyed Salts of Calcin’d Hay Anthony vanLeeuwenhoek The Royal Society is collaborating with JSTOR to digitize…
    • Anthony van Leeuwenhoek

    Observations on the Seed-Vessels and Seeds of Polypodium. In a Letter from Mr Anthony VanLeeuwenhoek, F. R. S.Phil. Trans. 1704 24:1868–1874;doi:10.1098/rstl.1704.0061

    …research-article Observations on the Seed-Vessels and Seeds of Polypodium. In a Letter from Mr Anthony Van Leeuwenhoek, F. R. S. Anthony van Leeuwenhoek The Royal Society is collaborating with JSTOR to digitize, preserve, and extend access to Philosophical…
    • Anthony van Leeuwenhoek

    A Letter to the Royal Society, from Mr Anthony Van Leeuwenhock, F. R. S. concerning Animalcula on the Roots of Duck-Weed, etc.Phil. Trans. 1704 24:1784–1793;doi:10.1098/rstl.1704.0045

    …Royal Society, from Mr Anthony Van Leeuwenhock, F. R. S. concerning Animalcula on the Roots of Duck-Weed, etc. Anthony vanLeeuwenhoek The Royal Society is collaborating with JSTOR to digitize, preserve, and extend access to Philosophical Transactions…
    • Anthony van Leeuwenhoek

    Microscopical Observations on the Cortex Peruvianus: By Mr. Anthony Van Leeuwenhoek, F. R. S.Phil. Trans. 1706 25:2446–2455;doi:10.1098/rstl.1706.0056

    1706-1707 research-article Microscopical Observations on the Cortex Peruvianus: By Mr. Anthony Van Leeuwenhoek, F. R. S. Anthony van Leeuwenhoek The Royal Society is collaborating with JSTOR to digitize, preserve, and extend access to Philosophical…
    • Anthony van Leeuwenhoek

    Part of a Letter Written to Signior Antonio Magliabechi, by Mr Anthony Van Leeuwenhoek, F. R. S. concerning the Particles of Silver Dissolved in Aqua Fortis, etc.Phil. Trans. 1706 25:2425–2432;doi:10.1098/rstl.1706.0052

    …Letter Written to Signior Antonio Magliabechi, by Mr Anthony VanLeeuwenhoek, F. R. S. concerning the Particles of Silver Dissolved in Aqua Fortis, etc. Anthony van Leeuwenhoek The Royal Society is collaborating with JSTOR to digitize…
    ——–
    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.

    ——–

    Good morning #compass11

    P348


    P345 P346 P344 P350 P347 P349 P343

    See the full gallery on Posterous
    ——–
    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.

    ——–

    Good morning #compass11

    p330.mov Watch on Posterous

    P327 P326 P329 P328

    See the full gallery on Posterous
    ——–
    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.

    ——–

    More pics from CA coast at #compass11

    P243

    P241 P245 P247 P249 P251

    See the full gallery on Posterous

    p252.mov Watch on Posterous
    ——–
    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.

    ——–