Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Seminar: Ed Lewis Friday at 12 #UCDavis “Infection behaviors of parasitic nematodes: The story of the slithering herd”

This week’s Animal Behavior Graduate Group seminar:

Dr. Edwin Lewis, Departments of Entomology and Nematology, UC Davis

Infection behaviors of parasitic nematodes: The story of the slithering herd

Friday, May 4th, 12:10 in 194 Young Hall

Coffee and cookies will be available

Dr. Lewis’ website: http://nematology.ucdavis.edu/faculty/lewis/

My research program is wide-ranging in the scope of the questions asked and in the taxa that are studied. There is, however, a common thread to the work that takes place in my laboratory; we seek to understand why and how organisms find, recognize, assess and exploit resources. We ask questions about how insects and nematodes make decisions about resource utilization and what the fitness outcomes of the decisions are. To answer these kinds of questions, we engage in studies of behavior, population ecology, community ecology and evolutionary biology with several groups of insects, nematodes and bacteria. There are also intentional links to more practical pursuits including biological control of crop pests, predicting the impact of crop management on pest and beneficial organisms and restoration ecology. I see no difference between what is traditionally called “basic” and “applied” research, thus the links of nearly all of the work in the laboratory to agricultural or environmental concerns is explicit.

Workshop: Tools & Workflows for RNA-Seq Analysis, Berkeley, June 30

Berkeley *Seq I: Tools and Workflows for RNA-Seq Analysis
Saturday, June 30, 2012
9 a.m. – 5 p.m.
105 Stanley Hall
University of California, Berkeley

EVENT WEBSITE

REGISTER BY JUNE 7

Berkeley *Seq I, the inaugural workshop on analysis of Next Generation sequencing data at UC Berkeley, will take place on June 30, 2012. This first year, the workshop is being organized by Lior Pachter and will focus on analytical tools and workflows for RNA-Seq experiments. The one-day meeting features a morning of talks, an on-site lunch, and afternoon live demonstrations of Cufflinks and eXpress software packages.

Sponsored by the California Institute for Quantitative Biosciences (QB3) and the Berkeley Center for Computational Biology (CCB). >
>

CPB Seminar May 1 “Predicting the structure & dynamics of phytoplankton communities w/ functional traits”

CPB Seminar Series: Spring 2012

When: Tuesdays, 4:10 – 5:30PM

Where: 1022 Life Sciences Building

May 1: Kyle Edwards, Postdoctoral Research Associate Michigan State University

Title: “Predicting the structure and dynamics of phytoplankton communities with functional traits”

Interested in presenting a seminar? Please contact jjstachowicz@ucdavis.edu.

Additional seminar information: http://cpb.ucdavis.edu/Seminars.html.

MIC 291 – Dr. Ned Ruby – May 2, 2012

MIC 291: Selected Topics in Microbiology

Hosted by MGG students

Dr. Ned Ruby
Professor, Medical Microbiology and Immunology
University of Wisconsin, Madison

“The squid-vibrio symbiosis: thinking about bacteria as individuals”

Wednesday, May 2, 2012
4:10 pm
1022 Life Sciences
Ruby 5-2-12.pdf

Dear Frontiers Journals – I am sick of your SPAM and I want nothing to do with you

Dear Frontiers Journals

Repeated unsolicited emails with no means to unsubscribe oneself (such as the one excerpted below) are SPAM. I like some aspects of the Frontiers journals but your email system has to be changed. I will not submit to or review for your journals until you make some commitment to stopping SPAMMING scientists.

Dear Dr Eisen, The article submission deadline for the Frontiers Research Topic, for which you received a call for participation, is approaching. If you are planning to submit a manuscript and you anticipate any delay beyond the deadline, please inform the Topic Editors and the Frontiers Editorial Office so they can manage the delay. If you have not yet responded to the call for participation or have not yet committed to a submission and you are planning to submit a manuscript, please let us know by responding to this message.

PS – the article alerts also have to stop. For F#*$@( sake clean up your act.

——–
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.

——–

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.

——–