Eisen Lab Blog

Future of Academic Publishing Panel discussion tomorrow at Noon – 1pm

Interdisciplinary Graduate and Professional Student Symposium,
entitled The Future of Academic Publishing. We’ll here from a variety of perspectives on existing and emerging models of publishing and what the future might hold.

  1. Don Strong, Editor in Chief of the journal of Ecology
  2. Meredith Niles, PhD student in Ecology and Evolution and Science Lobbyist in Sacramento and DC,
  3. William Gunn, Director of Outreach for Mendeley Research Networks
  4. Karthik Ram, Postdoctoral scholar at UC Berkeley and Open Science advocate
  5. Colin Cunliff, PhD student in Physics

From Noon to 1pm in the ARC ballroom

Phylogenetic analysis of metagenomic data – Mendeley group …

Just a little plug for a Mendeley reference collection I have been helping make on “Phylogenetic and related analyses of metagenomic data.” If you want to know more about such studies you can find a growing list of publications at they group collection. http://www.mendeley.com/groups/1152921/_/widget/29/10/

Phylogenetic and related analyses of metagenomic data is a group in Biological Sciences on Mendeley.

——–
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.

——–

Kimmen Sjolander talk, May 1st, 12pm, 1005 GBSF

Machine learning methods for protein function and structure prediction

Kimmen Sjölander
Associate Professor
Berkeley Phylogenomics Group
University of California, Berkeley
http://phylogenomics.berkeley.edu

May 1, 2012, 12:00 p.m.
1005 GBSF Auditorium

Abstract: Theodosius Dobzhansky, the noted geneticist and evolutionary biologist, is famous for having said “Nothing makes sense except in the light of evolution.” In this talk, I will discuss the explicit use of evolution as a fundamental principle in bioinformatics, using machine learning methods in combination with information from protein structure and evolution to improve the power and specificity of a number of bioinformatics tasks, including prediction of protein structure and function, ortholog identification, functional site prediction, and simultaneous estimation of multiple sequence alignments and protein superfamily phylogenies. Because many of these methods require expertise and/or computational resources not available to most experimental biologists, we provide pre-calculated
phylogenetic trees for gene families in the PhyloFacts database. PhyloFacts 3.0 is a phylogenomic database of gene families across the Tree of Life. Each PhyloFacts family contains a multiple sequence alignment, phylogenetic tree, predicted orthologs, predicted pathway associations and experimental and other annotation data. As of April 26, 2012, PF 3.0 contains >7.3M protein sequences from >99K unique taxa (including strains) across >92K families.

Finally, I will describe our work on a fully automated system for high-throughput functional annotation of genomes and for taxonomic and functional annotation of metagenome (environmental sample) datasets. This system, which we call FAT-CAT (for Fast Approximate Tree Classification) uses hidden Markov models placed at internal nodes of PhyloFacts trees to classify sequences to different levels of functional hierarchies. Subtree nodes are annotated automatically using data available for sequences descending from those nodes, allowing both functional and taxonomic inference for sequences classified to those nodes. The PhyloFacts Phylogenomic Database is available at http://phylogenomics.berkeley.edu/phylofacts/.

Kimmen Flyer.pdf

Nice use of PacBio sequencing to characterize methyltransferase specificity

Figure 1.


Rich Roberts just pointed me to this cool paper on which he is a co-author: Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing.  The paper was published in Nucleic Acids Research and is from Robert’s group at New England Biolabs and Jonas Korlach’s and others at Pacific Biosciences. What is cool is that they used the timing of the real time DNA sequencing to identify bases in particular DNA fragments that were methylated.  And this then allowed them to determine the specificity of particular methyltransferases (first tested on ones with known activity and then on ones with unknown activity).  This highlights one of the unique features of PacBio sequencing – because the method watches DNA replication in real time – if something alters the timing of the replication process – this can possibly be leveraged to detect alterations in DNA chemistry (e.g., methylation, DNA damage, etc).  Folks at PacBio have been promoting the methylation detection capabilities of their system for some time but I guess I did not get that interested in it because I viewed it is analogous to many other tools to quantify methylation.  But with this paper I now realize that the PacBio approach (and perhaps those of other methylation detection systems) are not just about quantifying methylation status on average across a set of DNA pieces, but can also be very specific as to exactly which bases are methylated.  And this in turn can be used to define specificity for a variety of unknown methyltransferases. ResearchBlogging.org Clark, T., Murray, I., Morgan, R., Kislyuk, A., Spittle, K., Boitano, M., Fomenkov, A., Roberts, R., & Korlach, J. (2011). Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing Nucleic Acids Research, 40 (4) DOI: 10.1093/nar/gkr1146

——–
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.

——–

Twisted tree of Life Award #13: Press release from U. Oslo on new protozoan

Wow.  Just got pointed to this press release Rare protozoan from sludge in Norwegian lake does not fit on main branches of tree of life (hat tip to Bill Hooker).  It is a long PR.  And it is riddled with many examples of evolutionary mumbo jumbo – each of which on their own could win a Twisted Tree of Life Award here.  And together, well, I am just going to give it one award – the Twisted Tree of Life Award #14.

Here are some statements that are, well, dubious, and/or painful.

  • Biologists all over the world have been eagerly awaiting the results of the genetic analysis of one of the world’s smallest known species, hereafter called the protozoan, from a little lake 30 kilometer south of Oslo in Norway.
    • Wow – really?  All over the world?
    • And why not tell us what the F#&$# it is?  Where is the name of the organism?  WTF?
  • When researchers from the University of Oslo, Norway compared its genes with all other known species in the world, they saw that the protozoan did not fit on any of the main branches of the tree of life. The protozoan is not a fungus, alga, parasite, plant or animal.
    • That is right.  There are five main branches on the tree of life.  Fungi.  Alga.  Parasites.  Plants. And animals.  Uggh.
  • His research group studies tiny organisms hoping to find answers to large, biological questions within ecology and evolutionary biology, and works across such different fields as biology, genetics, bioinformatics, molecular biology and statistics
    • Yes, and I study tiny organisms to answer small questions.
  • Life on Earth can be divided up into two main groups of species, prokaryotes and eukaryotes. The prokaryote species, such as bacteria, are the simplest form of living organisms on Earth. 
    • Yup, two main groups.  As of 40 f3$*@# years ago.
  • The micro-organism is among the oldest, currently living eukaryote organisms we know of. It evolved around one billion years ago, plus or minus a few hundred million years.
    • OMG.  This is a MODERN ORGANISM.  It did not evolve a billion years ago.  It is no older than ANYTHING ELSE ON THE PLANET.  AAAAAARRRGH.
  • The tree of life can be divided into organisms with one or two flagella
    • What?
    • The tree of life can also be divided into organisms with one or two penises.  
  • Just like all other mammals, human sperm cells have only one flagellum. Therefore, humankind belongs to the same single flagellum group as fungi and amoebae.
    • I don’t even know what to say here.
  • The protozoan from Ås has four flagella. The family it belongs to is somewhere between excavates, the oldest group with two flagella, and some amoebae, which is the oldest group with only one flagellum.
    • Wow – no prior description of the major groups of eukaryotes and now we use excavates (kind of technical) and amoebae (not technical).  Translation error?
    • But even w/ translation issues still very strange.
  • Were we to reconstruct the oldest, eukaryote cell in the world, we believe it would resemble our species. To calculate how much our species has changed since primordial times, we have to compare its genes with its nearest relatives, amoebae and excavates,” says Shalchian-Tabrizi.
    • What?  Their species has been around since primordial times?  What?  That is one really old cell. 
  • The protozoan lives off algae, but the researchers still do not know what eats the protozoan. 
    • Why does something have to eat it?
  • The protozoan was discovered as early as 1865, but it is only now that, thanks to very advanced genetic analyses, researchers understand how important the species is to the history of life on Earth
    • Very advanced?  Like, what? Sequencing?  
  • The problem is that DNA sequences change a lot over time. Parts of the DNA may have been wiped away during the passing of the years. Since the protozoan is a very old species, an extra large amount of gene information is required
    • What?  Since it is old they need more DNA? What?
I could go on and on.  I won’t.  But I will say one last thing that drives me crazy.  There is no paper attached to the press release in any way I can tell.  So all we are left with is this very very very very bad PR.  Ugh.
——–
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.

——–

The Undergraduate Research Experience. . . so far

As my first REAL research experience, I had no idea what to expect.  Back in high school, I did a little research in my statistics class where I tested students’ memories based on the type of music they were listening.  Obviously, the data I collected wasn’t going to be research paper worthy.  Before I began working under the Eisen Lab, I thought to myself, “This is my chance to find some crazy new bacteria and name them after me!”  (Spoiler: None of us have yet found a novel bacteria.  Pretty disappointing, I know.)  Eventually, Winter Quarter came along and the undergrads finally began researching.

It was a pretty rough beginning for those first few weeks.  We didn’t know how to pipet – considering the only pipets we were exposed to were those plastic pipets in Chemistry labs; didn’t know the proper lab protocols for avoiding contamination; couldn’t perform a simple dilution streaking; didn’t know what was done and what needed to be done; and so on and so forth.  After finally coming up with a good system, the research went by smoothly.  And it actually has become a very fulfilling experience.  I’ve really come to appreciate the variety and unique characteristics of bacteria in the world.  Sometimes, I find myself looking at a surface and wondering what bacteria has made a home there.

Currently, each undergrad is isolating and extracting bacterial DNA from their choice of environment.  I took a couple of swabs from a restaurant’s chair, table, couch, and counter in Davis.  And I also took some swabs from a nursing home, and the Golden Gate Bridge in San Francisco.  I’m really close to submitting some of my 16S DNA in for sequencing.  I’m pretty excited to see what the results are.

Quick little slideshow summary of our work so far

I am a member of the Biological Undergraduate Scholars Program (BUSP), a science-enrichment program aimed at helping EOP students excel in their science courses and obtain research positions (thanks to them I obtained a position in Dr. Eisen’s lab, which had the added bonus of turning me into a blogger!).  I recently gave a presentation to my program coordinator and fellow second-year BUSPers that summarized the methods the Eisen undergraduates have used to isolate, purify, and analyze the 16S gene of various bacteria.  Dr. Eisen mentioned in my previous blog post that a summary of our work thus far would help our readers better understand our methodology and final goals, so I figured the presentation would be a good little placeholder until something more formal is written up

The Undergraduate Genomic Sequencing Project

I will admit that the slides are scarce on detailed information, and instead give very general descriptions. After all, I had to actually address the audience during my presentation and not just read off the slides!

Somebody ruined the party

Consider reading this first if you have no idea what we are doing

Last week I submitted 6 organisms to the UCD Sequencing Facility after several weeks of isolating and purifying their 16S genes. My initial submission of 5 organisms went somewhat smoothly, though something managed to sneak into two of my samples and mix the forward sequences I received (for each organism, we must submit enough for both a forward and a reverse reaction to be sequenced. We receive these sequences and align the complementary bases to generate a consensus sequence). I had really hoped this time would go much more smoothly than last, but unfortunately 4 of my 12 reactions, all forward reactions, were mixed and thus indecipherable.

I suspected the forward primer might have been contaminated at some point, and looking at my initial submission the only mixed reactions were forward reactions as well. Seems pretty clear to me that some little critter was able to find his way into our forward primer and rain on my alignment parade. I had hoped that I would have a larger list of organisms by this point, but here is what I have analyzed so far

  • Staphylococcus pasteuri
  • Enterobacter ?
  • Bacillus amylolequefaciens
  • Micrococcus luteus? (the most “interesting” organism I’ve found, based on GOLD results)

I brought in 5 new samples that I can hopefully begin culturing in the coming days, and in the near future I will resubmit the forward reactions that failed using a new batch of forward primer.

Lab meeting, April 25th 2012

Lizzy Wilbanks will be presenting for this week’s lab meeting with rumors of a guest appearance by Angus Chandler.
We will be meeting in the Genome center from 1:30 to 3:00pm in Room 5206.

Stajich seminar today on fungal population genomics

Genetics Seminar

“Population genomics of Batrachochytrium dendrobatidis, a fungal pathogen of amphibians”

Speaker: Dr. Jason Stajich

University of California, Riverside | Department Plant Pathology and Microbiology

Monday, April 23, 2012

4:10 PM

1022 Life Sciences