Tag: Misc.

Storify/Tweet Notes from Noah Fierer’s talk at UC Davis

//storify.com/phylogenomics/noah-fierer-talk-at-ucdavis-on-biogeography-of-soi.js?template=slideshow[View the story “Noah Fierer talk at #UCDavis on biogeography of soil microbes” on Storify]

Noah Fierer talk at #UCDavis on biogeography of soil microbes

Storified by Jonathan Eisen· Thu, Jan 10 2013 22:44:52

At #UCDavis tomorrow: Noah Fierer @NoahFierer on “Exploring Terra Incognita: the biogeography of soil microorganisms” http://shar.es/44O44Jonathan Eisen
Reminder – today 4 PM #UCDavis Seminar by Noah Fierer #microbes #microbiomes #biogeography #evolution #soil http://wp.me/ph9ob-RvJonathan Eisen
Awaiting talk at #UCDavis by @NoahFierer- starting in a few minutes “Exploring terra incognita – the biogeography of soil microorganisms”Jonathan Eisen
Introduction for @NoahFierer talk at #ucdavis refers to him as a self described expert on cooties .. this has to be goodJonathan Eisen
@phylogenomics @noahfierer Did you ever play the Cooties game? I did, now I’m an entomologist. Trapped.Jack C. Schultz
For more on work of @noahfierer (whose talk at #UCDavis I am live tweeting) see http://www.colorado.edu/eeb/EEBprojects/FiererLab/Jonathan Eisen
Now tweeting from @NoahFierer ‘s #UCDavis seminar “Exploring terra incognita: the biogeography of soil microorganisms” No eukaryotes tho :(Holly Bik
Fierer at #UCDavis defends referring to plants and animals as “macrobes” as better than calling small things microbesJonathan Eisen
Fierer at #UCDavis: 4000-2000 kg microbial biomass per hectare (from Fierer et al. 2009 Ecology letters)Jonathan Eisen
Fierer at #UCDavis: vast majority of soil microbial diversity undescribed, quotes Donald Rumsfeld as “patron saint of microbial ecology”Jonathan Eisen
Fierer at #UCDavis: example of Acidobacteria – up to 30% of bacteria in soil from this phylum yet only 5 described generalJonathan Eisen
Fierer at #UCDavis: using microbes to test principles of biogeography/ecology; using biogeography to learn about poorly understood microbesJonathan Eisen
Fierer at #UCDavis: in 2006 $10K = 400 bacteria IDd in each of 5 samples; 2012 $10K = > 10K bacteria IDd in each of 500 samplesJonathan Eisen
Fierer at #UCDavis: reduction in sequencing cost / increase in capacity allows 1st time biogeography studies of microbes on large scaleJonathan Eisen
Fierer: You can’t do ecology with 5 samples (old methods) – now costs have dropped, we can sequence 100s of samples to look at ecologyHolly Bik
Fierer at #UCDavis: dealing with this: “There is no biogeography of anything smaller than 1 millimeter” Bland Finlay Science 2005 vol 310Jonathan Eisen
Fierer at #UCDavis: collected soil samples from diverse biomes (tundra, desert, prairie, forest) & asked what calls “19th century” eco ??sJonathan Eisen
If the bacterial/archaeal people are doing 19th century ecology (as says @NoahFierer), then us eukaryote people are stuck in the dark ages..Holly Bik
Fierer at #UCDavis discussing Lauber et al. 2009 http://www.ncbi.nlm.nih.gov/pubmed/19502440 – ~1000 sequences per sample x 80 + samplesJonathan Eisen
Fierer at #UCDavis discussing this figure http://aem.asm.org/content/75/15/5111/F4.large.jpg from 2009 paper – where simple ordination did not distinguish samples wellJonathan Eisen
Fierer at #UCDavis now discussing Figure B from http://aem.asm.org/content/75/15/5111/F4.large.jpg saying that soil pH shows strong association w/ microbe Beta diversityJonathan Eisen
“@Dr_Bik: Fierer: You can’t do ecology with 5 samples costs have dropped, we can sequence 100s of samples 4 ecology” SORT OF. Whoo R U? $$$Jack C. Schultz
Fierer et al. refs http://aem.asm.org/content/75/15/5111/F3.large.jpg from 2009 paper that shows good relationship between soil pH and alpha diversityJonathan Eisen
Fierer at #UCDavis: their soil data did not show any obvious relationship to latitude, mean annual temp, or other variables looked atJonathan Eisen
Fierer at #UCDavis: their data showing relationship between pH and microbial diversity could have been due to some feature related to pHJonathan Eisen
Fierer at #UCDavis: looked at soil microbes in one biome in arctic and still had correlation with pH and diversityJonathan Eisen
Fiere at #UCDavis: refs. http://www.nature.com/ismej/journal/v4/n10/full/ismej201058a.html where even in controlled system (Rothamsted Research) pH & microbial diversity correlatedJonathan Eisen
Does pH itself drive soil microbial assemblages, or aluminum toxicity (Al and pH closely linked)? We don’t know yet says @NoahFiererHolly Bik
At #UCDavis @NoahFierer: discussing PNAS 2012 Soil paper http://www.pnas.org/content/early/2012/12/05/1215210110.full.pdf – metagenomics of VERY different soil samplesJonathan Eisen
At #UCDavis @NoahFierer: in soil metagenomic data only ~ 20% of reads could be annotated (i.e., function predicted)Jonathan Eisen
At #UCDavis @NoahFierer: in soil metagenomic data there is a weak ++ correlation between 16S PD and functional diversityJonathan Eisen
At #UCDavis @NoahFierer: desert soils VERY different from other soils in beta diversity of taxa & functionsJonathan Eisen
At #UCDavis @NoahFierer: looked are which genes were driving the major differences beta. soils in deserts & other locationsJonathan Eisen
At #UCDavis @NoahFierer quotes Willa Cather “elsewhere the sky is the roof of the world but here the earth was the floor of the sky”Jonathan Eisen
. @NoahFierer heads to 19th century graveyards to sample native prairie grass habitats for soil microbes. One of least disturbed sites..Holly Bik
At #UCDavis @NoahFierer refs paper that modelled distributions of Sasquatch http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2009.02152.x/abstractJonathan Eisen
At #UCDavis @NoahFierer discussing collaborative work w/ Josh Ladau from UCSF http://docpollard.com/jladau/index.html (who I collaborate w/ too)Jonathan Eisen
At #UCDavis @NoahFierer says “Microbial ecology needs more Ecologists” (emphasizes the capital EJonathan Eisen
At #UCDavis @NoahFierer: Ecology needs more microbial ecologyJonathan Eisen
Pleas frm @NoahFierer: Microbial ecology needs more Ecologists–lots of data out there, not being fully used, & lots of reinvention of wheelHolly Bik
At #UCDavis @NoahFierer: ecological restoration projects need to consider microbes as part of the storyJonathan Eisen
“@phylogenomics: @NoahFierer: ecological restoration projects need to consider microbes as part of the story” or quit stupid reconstructionJack C. Schultz
“@phylogenomics: At #UCDavis @NoahFierer says “Microbial ecology needs more Ecologists” (emphasizes the capital E” ) Brilliant!Jack C. Schultz
@phylogenomics Lots of reasons reconstruction is purely subjective, starting with “which era do we reconstruct?”. Not “science”Jack C. Schultz
@phylogenomics For a different take (e.g., why is YOUR reconstruction THE reconstruction?) see http://www.amazon.com/Invasion-Biology-Oxford-Mark-Davis/dp/0199218765Jack C. Schultz
Both true! – MTs: “@phylogenomics: At #UCDavis @NoahFierer: Ecology needs more MICROBIAL ecology” &”Microbial ecology needs more Ecologists”Gavin Collins
@jackcschultz sure some restoration projects have issues but the “not science” accusation makes you sound sillyJonathan Eisen
——–
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.

——–

Notes from talk by Stephen J. O’Brien at #UCDavis

Stephen O’ Brien talked at UC Davis a few days ago. I met with him in the afternoon before his talk. It was one of the more interesting discussions I have had in a long time. He has done some very interesting and important work (e.g., comparative genomics, HIV, feline evolution) though most of what we talked about was not work per se (e.g., we talked a lot about baseball and big cats since my kids are obsessed with big cats).

Anyway, below is a “Storification” of tweets from his talk. Best part – he signed a copy of his Tears of the Cheetah: The Genetic Secrets of Our Animal Ancestors book with a dedication to my kids.
//storify.com/phylogenomics/steven-j-o-brien-talk-at-ucdavis-on-ccr5-hiv-aids.js?template=slideshow[View the story “Steven J. O’ Brien talk at #UCDavis on CCR5/HIV/AIDS” on Storify]

Steven J. O’ Brien talk at #UCDavis on CCR5/HIV/AIDS

Storified by Jonathan Eisen· Mon, Jan 07 2013 20:12:09

Today at #UCDavis Stephen O Brien on “Three Decades of Genomics and AIDS” http://pic.twitter.com/dQG4tBsoJonathan Eisen
Can’t wait for talk at 4 PM today at #UCDavis Genome Ctr by Stephen O’Brien on “Three Decades of Genomics and AIDS” http://pic.twitter.com/dQG4tBsoJonathan Eisen
@phylogenomics Wow! Interesting topic. Wish I was attending.Setor Amuzu
As an evolutionary biologist am jealous of name of Obrien’s “Theodosius Dobzhansky Center for Genome Bioinformatics” http://shar.es/4vIBYJonathan Eisen
@phylogenomics any podcasts available?Cuquis R
SJ Obrien – head of new Dobzhansky Inst – intro by Harris Lewin, discussing how Dobzhansky finished his career here at #UCDavis:Jonathan Eisen
Lewin point out that Steven O Brien has been called the Indiana Jones of Genomes (e.g.., http://www.genomenewsnetwork.org/articles/2004/03/19/tears.php ) #ucdavisJonathan Eisen
Lewin: Steven O’ Brien is also one of the coordinators of the genome 10K project http://genome10k.soe.ucsc.edu/participants #UCDavisJonathan Eisen
Steven O Brien launching into his talk at #ucdavis http://pic.twitter.com/RTadoUJmJonathan Eisen
O’Brien at #UCDavis: Giving props to T. Dobzhansky and his pioneering work on population geneticsJonathan Eisen
O’Brien at #UCDavis: discussing how population genetics help lead to many whole fields/areas incl. conservation genetics, DNA forensics, etcJonathan Eisen
Stephen J. O’Brien: is on Plagues and people Contagion Genomics & Beyond. 3 areas: Gene Discovery, Conservation Genetics, DNA forensicsDawei Lin
O’Brien at #UCDavis: began work on AIDS epidemic partly as model for way to connect human genetics and infectious diseaseJonathan Eisen
O’Brien at #UCDavis: close to 30 million people have died of AIDS and close to 30 million more are infected w/ HIV & disease still spreadingJonathan Eisen
@Curosik don’t think soJonathan Eisen
O’Brien at #UCDavis: heterogeneity in progression in HIV led him to try to use advances in human genetics to look for AIDS restrictive genesJonathan Eisen
SJO: Oct. 1996 AIDS quilt is a symbol of the pandemic disease with 40K Tabard Emblems on that day at the Capitol Hill.Dawei Lin
O’Brien at #UCDavis: early in AIDS epidemic got access to samples from different groups of people to test role of human genes in progressionJonathan Eisen
O’Brien at #UCDavis: looked for genetic variation in AIDS resistance, progression rate, outcomes, response to HAART therapyJonathan Eisen
O’Brien at #UCDavis: in 1996 5 groups discovered that CCR5 (a G coupled seven transmembrane receptor) was target of HIV for cell entryJonathan Eisen
O’Brien at #UCDavis: looked for CCR5 mutations in cohorts of patients w/ HIV & found that homozygous mutations were protectiveJonathan Eisen
SJO: CCR5 is the binding target for HIV. People with CCR5 delta with a 32 peptide deletions do not have HIV infections.Dawei Lin
O’Brien at #UCDavis: those people heterozygous for CCR5 deletions showed slower progression of HIV infectionJonathan Eisen
@phylogenomics would love to see the stats methods on thatLewis Lab
@Lewis_Lab seems to be relatively old data …Jonathan Eisen
Obrien at #UCDavis: many scientists occasionally like to do more than publish in a good journal, some would like to translate to bedsideJonathan Eisen
SJO: People study genes about infectious diseases should not stop at publishing on a good journal, should bring it to the bedside.Dawei Lin
Obrien at #UCDavis: re: delta32 mutation in CCR5 and modifies Dobzhansky “nothing in medicine makes sense except in light of evolution”Jonathan Eisen
Obrien at #UCDavis: discussing how frequency of CCR5 delta32 mutation has increased rapidly over time; suggest this is due to ++ selectionJonathan Eisen
@phylogenomics I’m not seeing any open access/open data reports.Lewis Lab
Obrien at #UCDavis: 20 mutations in CCR5 have been found outside of delta32 mutation; 18/20 are amino acid changing; suggests ++ selectionJonathan Eisen
SJO: 1/5 people now is CCR5 delta 32 carriers. There are 22 variants. 18 of them changes peptides.Dawei Lin
Obrien at #UCDavis: Suggests something influenced CCR5 mutations prior to AIDS epidemic (admits much of his theories on this controversial)Jonathan Eisen
OBrien at #UCDavis now reading from Tears of the Cheetah http://www.amazon.com/Tears-Cheetah-Genetic-Secrets-Ancestors/dp/0312339003 his book on genetics / genomicsJonathan Eisen
O’Brien at #UCDavis: suggests that bubonic plague may have influenced CCCR5 mutation frequencies over timeJonathan Eisen
O’Brien at #UCDavis: discussing plague epidemic in 1665 and 1666 (reading from his book)Jonathan Eisen
@phylogenomics that got me the statistical test I was looking for–thanks. I don’t find the article very intuitive, thoughLewis Lab
O’Brien at #UCDavis: discussing their estimates of the age of the CCR5 delta 32 mutations by looking at the size of the linkage groupJonathan Eisen
O’Brien at #UCDavis: estimates of the date of the origin of the spread of the CCR5 delta 32 mutation is correlated w/ plague epidemicJonathan Eisen
O’Brien at #UCDavis: many many waves of plague epidemics over time (though he notes many other possible epidemics also at same general time)Jonathan Eisen
@phylogenomics thanks. This is a good case study for the stats class.Lewis Lab
“@phylogenomics O’Brien suggests that bubonic plague may have influenced CCCR5 mutation frequencies” No doubt a 1-2 insC mutation.Donald Atkinson
SJO: Conspiracy theories of black death cause CCR5 mutation hike, which mostly found in Caucasians.Dawei Lin
O’Brien at #UCDavis: refs a 2004 Nature study of mice w/ CCR5 delta 32 homozygous mutation; -/- have 90+% reduction in Y.pestis uptakeJonathan Eisen
O’Brien at #UCDavis: after 9/11 & anthrax attack collaborated w/ people to look at smallpox infection in CCR5 delta 32 mutant cellJonathan Eisen
“The O’Brien at #UCDavis” stream of tweets by @phylogenomics is fascinating. Must-read for biology folks.Rob Quarles
@phylogenomics What is his book? I show the PBS vid he was in few years ago to my molec epi class each year to discuss CCR5/plague/HIVTara C. Smith
O’Brien at #UCDavis: many other viruses have been screened for whether they make use of CCR5Jonathan Eisen
@phylogenomics thanks for tweets re O’Brien lecture. Say hi to Steve for me!Kathy Belov
Obrien at #UCDavis: delta 32 mutations in CCR5 may lead to higher risk to West Nile virus …Jonathan Eisen
SJO: people with homozygous CCR5 delta mutations are susceptible to West Nile virus, not HIV.Dawei Lin
Obrien at #UCDavis: looking back to 1996 b/c this is when HAART therapy for HIV was startedJonathan Eisen
Obrien at #UCDavis: showing slide from Tony Fauci of FDA Approved antiretroviral drugs; now many new drugs going after CCR5 interactionJonathan Eisen
@phylogenomics cool! I will order it.. Thanks for the link!Cuquis R
@phylogenomics thanks!Tara C. Smith
Obrien at #UCDavis: discussing “The Berlin Patient” (see http://articles.latimes.com/2012/jul/27/news/la-heb-hiv-cure-aids-meeting-20120727); had AML; prognosis bad; bone marrow tplant from CCR5delta32Jonathan Eisen
OBrien at #UCDavis: 2008 Gero Hitter – the doctor for “The Berlin Patient” shows up at AIDS conference; news finally comes out in WSJ 2008Jonathan Eisen
Obrien at #UCDavis: here is the WSJ news story about The Berlin Patient http://online.wsj.com/article/SB122602394113507555.htmlJonathan Eisen
Obrien at #UCDavis: says the story of the Berlin patient is an anecdote; emphasizes it is one patient; need more information / data / casesJonathan Eisen
Obrien at #UCDavis: refs SciAm article http://www.scientificamerican.com/article.cfm?id=blocking-hivs-attack where gene therapy for HIV patients reported; he’s skeptical about peer reviewJonathan Eisen
Obrien at #UCDavis: some researchers have been looking at how CCR5 might influence Graft Versus Host Disease (see http://www.nejm.org/doi/full/10.1056/NEJMc1209665)Jonathan Eisen
Obrien at #UCDavis refs new Nature paper showing CCR5 is a receptor for MRSA leukotoxin (see http://www.sciencedaily.com/releases/2012/12/121214191518.htm)Jonathan Eisen
@KathyBelov will do …Jonathan Eisen
SJO: Patients with bone marrow transplants with CCR5 negative genotypes remain HIV free without drug treatments. A potential breakthrough.Dawei Lin
Obrien at #UCDavis giving props to George W. Bush for PEPFAR program http://www.pepfar.gov http://www.avert.org/pepfar.htmJonathan Eisen
Obrien at #UCDavis: OBrien ends his talk by thanking the patients who have provided samples cc: @rebeccasklootJonathan Eisen
Question at Obrien talk at #UCDavis: is CCR5 delta 32 the only restriction mutation? Obrien says yes but not yet translated to bedsideJonathan Eisen
Comment at talk by Obrien at #UCDavis: primate center at UCDavis played a major role in work on HIVJonathan Eisen
Comment at Obrien talk at #UCDavis: says to students in crowd that you have heard a talk about thinking which most people don’t do anymoreJonathan Eisen
@phylogenomics Nice. He definitely saw importance of donor appreciation/respect differently than most in the early days.Rebecca Skloot
@phylogenomics I wanna know what happened to his amazing frozen zoo at NCI! Hope he took it w/him; he worried re who would take care of itRebecca Skloot
@RebeccaSkloot he did not discuss this …Jonathan Eisen
Love @phylogenomics tweets on O’Brien’s talk at #UCDavis. Everything he said on CCR5/HIV/Berlin pt is right up my alley.Nathalia Holt
My kids are very happy w/ autographed copy of “Tears of the Cheetah” Steven O Brien gave me after his talk at #ucdavis http://pic.twitter.com/SCEh5AXkJonathan Eisen
As follow up to post about “Tears of a cheetah” – my kids are a bit obsessed w/ big cats … http://pic.twitter.com/M82V4fiHJonathan Eisen
@phylogenomics How do the cats get along with all the microbes?Cindy Manson
@CynthiaManson1 extremely well http://pic.twitter.com/joOoehUWJonathan Eisen
——–
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.

——–

Reading in detail Carl Woese’s 1998 "Manifesto on Microbial Genomics" for the first time …

I am a bit stunned by this paper from Carl Woese in 1998 which I was aware of but have not read in detail until now: ScienceDirect.com – Current Biology – A manifesto for microbial genomics

I re-discovered it because I am making a compilation of papers by Woese in relation to the tribute page I have set up.  And the title (a manifesto about microbial genomics) combined with the date (1998 – early in the genome sequencing era) struck me as something worth looking at.  Plus I knew others (e.g., Phil Hugenholtz, Nikos Kyrpides, …) had mentioned this paper to me so I figured – hey – how about actually reading it in detail.  And fortunately it is freely available at the Current Biology web site (not sure why that is actually).  Anyway – what I found in the paper is basically an argument for much of my career from 1998-2008.

Some choice lines in here but the crux is as follows

The first order of business in microbial genomics should be a phylogenetically representative genomic screen of the microbial world. In other words, all the major microbial taxa and their subdivisions — which are the major source of biological diversity on Earth — should be represented by several genome sequences. There are now more than 30 recognized major eubacterial taxa — each the phylogenetic equivalent of a eukaryotic kingdom — and at least half that number in the (far less well characterized) Archaea; not to mention the yet-to-be-discovered kingdoms among the unicellular eukaryotes.

This basically lays out the Tree of Life project I co-ran at TIGR and the Genomic Encyclopedia of Bacteria and Archaea project I co-ran / run at the DOE JGI.

The ending is perfect

This is not the place to go into the specifies of which microbial genomes would be most useful. I would suggest, however, that a phylogenetic tree hang on the wall of every laboratory in which microbial genomes are being sequenced — for inspiration.

Somehow I had missed the crux of this paper until now.  I think it is worth reading by everyone out there working on microbes and/or their genomes.

Oh – and here is the compilation of Woese’s papers I am making in Mendeley.

http://www.mendeley.com/groups/2940711/papers-by-carl-woese/widget/21/3/

——–
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.

——–

Water Chemistry 10 Commandments

So for this aquarium project we have been doing a ton of water chemistry (over 50 hours so far).  Along the way we’ve learned a number of lessons the hard way and so have written up a set of “Water Chemistry 10 Commandments”.  I’m posting them here for both the current students or for anyone else doing water chemistry analysis.

1. Wear gloves! (seriously… reagents include mercury, corrosives, and carcinogens)

2. Double-check all reagents!!! For example “sulfuric acid” ≠ “sulfamic acid”.  Likewise “phosphorus” ≠ “phosphate”.

3. Be sure your measurement is within the range of the test.

4. Be sure to keep track of “ppm” versus “ppb”!

5. Replace the cap of each solution immediately! Spills are expensive, hazardous, and annoying.

6. Rinse all glassware with the sample to be measured before conducting an assay

7. Always rinse everything between measurements and assays.   The pH meter should be rinsed in tapwater, everything else should be rinsed in DI water.

8. Dilutions should be performed with DI water.  Be sure to measure the concentration of whatever you’re testing in the DI water first so that you can subtract the background.  The blank needs to be of the diluted solution as well!

9. Keep cuvettes clean!  Clean before each use… wipe with a Kimwipe immediately before placing in detector.

10. If you get an anomalous measurement: do it again twice more.  Sometimes things really do change but if you’ve been getting ammonia measurements between .5ppm and 1ppm for days and then all of a sudden you see 25ppm… it’s worth making absolutely sure!

RIP Carl Woese: Collecting posts / notes / other information about my main science hero here

My tribute to Carl Woese 12/30/12

Sadly, Carl Woese has passed away.  I am collecting some links and posts about him here in his memory.  He was without a doubt the person who most influenced my career as a scientist.

News stories about Woese’s passing

Some of my posts about Woese

Woese Tree of Life pumpkin (by J. Eisen)

Storification of Tweets and other posts about his passing //storify.com/phylogenomics/rip-carl-woese.js?template=slideshow[View the story “RIP Carl Woese” on Storify]

Other posts worth reading about Woese’s passing

Some videos with Woese 





Miscellaneous

My graduate student Russell Neches used a laser to etch a picture of Carl Woese on a piece of toast.

http://www.mendeley.com/groups/2940711/papers-by-carl-woese/widget/21/3/

——–
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.

——–

Preliminary phosphate data too

Thought this one was interesting (though not surprising) as well.   Phosphorus levels are low in the in initial system (seawater and sand) and go up quite a bit once corals and established sediment are added.

chemistryfigures

Preliminary Nitrite/Nitrate data just for fun

Since we’ve been collecting all this water chemistry data I thought it’d be nice to share a bit of it.   Here you can see the nitrate and nitrate levels in Coral Pond #1 over a couple of weeks.  Levels start out low, then rise in the newly established system right up until inoculation with an stable microbial community.  At that point the nitrites head back down quickly and the nitrates continue to rise.  So question for the undergrads on the project:  Is this what we expect or not?   Why would we see this pattern?

nitrate-nitratefigure

Welcome to the Microbial Earth Project

Map of type strains.

All interested in microbes and their genomes should check out The Microbial Earth Project.  It “is an international effort to generate a comprehensive catalog from genome sequences of all the archaeal and bacterial type strains. The name of the project comes from the recognition that Earth is a predominantly a microbial planet, and by effect in order to understand life on our planet, we need to understand how microbial life works.”

There are some 10,000 described type strains of bacteria and archaea.  Not really a lot given that there are probably millions upon millions of species of bacteria and archaea.  But it is what we have available to us in terms of the formally described and accepted species for which there is an available cultured strain.

At this site you can do things like “Adopt a Type Strain” or view a cool “Map of the type strains“.

The Steering Committee for the project is

Much of the real work being done by Nikos Kyrpides, George Garrity, and others though I am very pleased to be a member of the Steering Committee.   One of my key jobs will be to get the word out early and often.  Hence this post.

——–
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.

——–

A tale of two stoppers (one of which is a rip-off)

For the water filtration we’ve been using Supor PES membrane filters (.1um), supported using a fancy filter holder from Millipore. (both recommended by Laura Sauder from the University of Waterloo).  So far this setup has worked pretty well, although obviously a bit slow when there’s a lot of sediment in the water.   However, last night the rubber stopper that holds the thing together cracked and got sucked into the vacuum flask.  Which is pretty much a one-way trip… It’ll probably stay there forever.   So I looked at the Millipore website and they want $100 + shipping for a replacement stopper!   It’s a piece of rubber (well silicone actually) with a hole in it.  Sheesh.

So after consulting with Russell in our lab, he directed me to Central Services on campus where I bought a rubber stopper for $1.05 and they drilled the hole for free.   As a bonus, it actually fits better and is easier to use than the one that costs one hundred times as much from Millipore.

Sampling yesterday

Yesterday we did PM samples on both Coral Ponds after they were inoculated. Our rate limited step (the water filtrations) took even longer because there was so much sand in the water. The sand would collect on the filter, causing the water to pass through much slower. We didn’t filter the water from Coral Pond #2 because there was so much sand that I think the water filtrations would have been unsuccessful. We did take water samples and left them overnight so that the sand would settle and David filtered the water this morning. We did run all water chemistry tests on both Coral Ponds last night.

Because our nitrite meter only measures up to 200 ppm, I did a 1:4 dilution for the water from Coral Pond #1 and a 1:10 dilution for the water from Coral Pond #2 in order to get readings within the range. Then I multiplied to get the correct value.