Jonathan Eisen's Lab

#Badomics word of the day, week and month: the morphome

Well, I have been avoiding the badomics meme for a little bit but cannot help getting back into it for this one. From this paper: BMC Biology | Full text | The songbird syrinx morphome: a three-dimensional, high-resolution, interactive morphological map of the zebra finch vocal organ. Yes, that is right – rolls right off the tongue – the songbird syrinx morphome.

The key sentence assigning guilt for this

“Here we present an annotated high-resolution three-dimensional (3D) morphological dataset, which we have dubbed a morphome,”

Note – I love the move for more high throughput, digital morphological data. It rocks. It will make for some interesting science. It however, does not deserve it’s own ome word.

For more on this meme see All my writings on badomics words.

H/T David Coil …

A title and figures say it all: An In-Depth Analysis of a Piece of Shit (note – a bit gross)

I had heard about this paper a few weeks ago and was just reminded about it by a friend. To understand this paper all you really need are the title and Figure 1 and 2 which are below. Enjoy.

An In-Depth Analysis of a Piece of Shit: Distribution of Schistosoma mansoni and Hookworm Eggs in Human Stool.

Figure 1. Instruction form on how to collect whole-stool samples for the study

Figure 2. Processing of stool samples according to consistency including whole-stool homogenization. Sausage-shaped-but-soft samples were processed like in (A) without taking samples from the center.

Seminar, #UCDavis, 1/10, Lizzie Wolkovich “Community assembly & disassembly under global change”

DEPARTMENT OF EVOLUTION AND ECOLOGY

RECRUITMENT SEMINAR

ECOLOGIST

Dr. Elizabeth Wolkovich

Biodiversity Research Centre Fellow

Department of Zoology

University of British Columbia, Vancouver

"Community assembly and disassembly under global change"

Thursday, January 10th, 2013

1:10pm

1022 Life Sciences Building

Wolkovich Seminar Flyer.doc

Lab meeting Jan 8th 2013

Happy new year everyone.
We will resume our lab meetings on Tuesdays from 1:30 to 3:30pm starting tomorrow Jan 8th.
Angus will be presenting in room 4202 of the Genome Center.

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/

Papers by Carl Woese is a group in Biological Sciences on Mendeley.

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!

Science for Kids: Explorit in #DavisCA

Had a great time yesterday with my kids at the Explorit museum in Davis, CA. Some pics and vids are below

Cichlids at entrance

Really nice dissecting scope / viewing scope with video monitor:

Dissecting scope

Lots of good displays on agriculture which is a good think in and around the Central Valley

Why are fertilizers important?

Are all soils the same?

Agricultural space

More activities

Really nice activity making a bracelet that reflected where water goes in the environment.

Awesome game on water flow

Really helpful staff

Sifting seeds in water or not water

Snake …

Checking out the python

Bugs:

Giant cave cockroaches

Grind your own grain:

Add grain

Floating ball

Best activity: make your own floating spider …

How spiders float

//www.youtube.com/get_player

Ball python time

Ball python

Spider display

Science for Kids: Lawrence Hall of Science in Berkeley, CA

Had a relatively nice trip to the Lawrence Hall of Science in the Berkeley hills last week with my kids. The new math exhibit was less than ideal (complicated instructions for many things, not exceptionally friendly to my five year old) but the rest was pretty nice.

I am going to try to post more and more about science for kids in the future. I was inspired a bit by getting some press coverage for being a geeky dad recently (e.g., see The Sexiest Geek Dads in the Galaxy – Io9 the New York Times had a bit about what science toys scientists used as kids and somehow I was included: These Were a Few of Their Favorite Things).

Anyway – here are some pics from the Lawrence Hall of Science. It is worth a visit if you are anywhere near Berkeley and want something to do with your kids that is sciency. We particularly enjoyed the simple star / constellation show at the planetarium.

We had a bit more fun in 2009 when we went. Not sure why it was more fun but the math exhibit was not there so maybe that was it. Some pics from 2009 are below

UCDavis Ecology & Evolution Seminar Jan 10th: Noah Fierer

:Noah Fierer from the University of Colorado Boulder
"Exploring terra incognita: the biogeography of soil microorganisms", will be on Thursday, January 10 at 4:10pm in 1003 Giedt Hall.

A few of his publications include:

Fierer, N., C.M. McCain, P. Meir, M. Zimmermann, J.M. Rapp, M.R. Silman, R. Knight. 2011. Microbial elevational diversity does not follow the biogeographical trends of plants and animals. Ecology. 92: 797-804.
Fierer, N., J.W. Leff, B.J. Adams, U.N. Nielsen, S.T. Bates, C.L. Lauber, S. Owens, J.A. Gilbert, D.A. Wall, J.G. Caporaso. in press. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. PNAS (available online)
Fierer, N., S. Ferrenberg, G.E. Flores, A. Gonzalez, J. Kueneman, T. Legg, R.C. Lynch, D. McDonald, J.R. Mihaljevic, S.P. O’Neill, M.E. Rhodes, S. Song, W.A. Walters. 2012. From animalcules to an ecosystem: application of ecological concepts to the human microbiome. Annual Review of Ecology, Evolution, and Systematics. 43:137-155.
Hulcr, J., J.B. Henley, N.R. Rountree, N. Fierer, A. Lucky, M.D. Lowman, A.M. Latimer, R.R. Dunn. 2012. A jungle in there: bacteria in belly buttons are highly diverse, but predictable. PLoS One. 7(11): e47712.
Craine, J.M., N. Fierer, K. McLauchlan, A. Elmore. in press. Reduction of the temperature sensitivity of soil organic matter decomposition with sustained temperature increase. Biogeochemistry (available online)
Fierer, N., C.L. Lauber, N. Zhou, D. McDonald, E.K. Costello, R. Knight. 2010. Forensic identification using skin bacterial communities. PNAS 107: 6477-6481.

More about his research is here.

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