Eisen Lab Blog

Doug Koshland “The great conspiracy: RNA and Rad51 against the genome” #UCDavis 10/29

Molecular Genetics Seminars (Fall 2012)

1022 Life Sciences Mondays at 4:10PM

October 29, 2012

“The great conspiracy: RNA and Rad51 against the genome”

Doug Koshland

UC Berkeley, Department of Microbiology

PhD Comics @phdcomics animated cartoon on #OpenAccess interview of me & Nick Shockey

I assume if you pay any attention to science satire/humor you are familiar with PhD Comics by Jorge Cham. If not, you must check it out. It is simply brilliant stuff. And thus I was completely floored when I was contacted about whether I wanted to be interviewed by Jorge for a video he was commissioned to make as part of Open Access week activities. I mean – I figging say no to almost everything these days but I said yes to this almost immediately. And so I did a phone interview with him and Nick Shockey from SPARC. And then Jorge worked his magic — and here it is.

    

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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.

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Seminar at #UCDavis: Dr. Huanming (Henry) Yang, BGI; Nov 9 from 4:10-5:00pm

Just got this:

** PLEASE DISTRIBUTE – Special Seminar: Dr. Huanming (Henry) Yang, BGI; November 9 from 4:10-5:00pm, Genome Center Auditorium #1005, Reception to follow at UC Davis

On behalf of Vice Chancellor Lewin and Professor Yilma, we are pleased to announce a special seminar by Dr. Huanming (Henry) Yang, chairman of BGI. Please distribute the following seminar announcement to others who may be interested. If you have any questions, please contact ocr@ucdavis.edu.

** Special Seminar Announcement **

Dr. Huanming (Henry) Yang

Chairman, BGI

Genomics Cannot be Done Alone:

Working together for a better world

Friday, November 9, 4:10 – 5:00 pm

1005 GBSF, Genome Center Auditorium, UC Davis

reception to follow

Hosted by the Office of Research and

The Department of Medical Microbiology & Immunology

This presentation by Huanming Yang, Ph.D., co-founder and chairman of BGI—formerly known as the Beijing Genomics Institute—provides an overview of the past, present, and future of BGI. Dr. Yang reviews the origins of BGI with the sequencing of 1% of the Human Genome Project at a time when China was unrecognized in genomic sciences. He describes the significant impact that BGI’s first-ever sequencing and sharing of the entire rice genome had on advancing rice research and its potential impact on global health. Additional breakthrough sequencing projects completed by BGI, many conducted in collaboration with the global research community, are presented. Professor Yang emphasizes BGI’s mission of sharing its extensive next-generation sequencing capacity and bioinformatics capabilities with the goal of promoting the advancement and application of global genomics.
2012Nov9-HuanmingYang-BGI.pdf.pdf

Today’s "Overselling the microbiome award" Crohn’s Disease and Bacteria

Uggh.  Just read this: Specific bacterial species may initiate, maintain Crohn’s.  Basically it reports on a paper that showed a correlation between bacterial taxa and early Crohn’s disease.  The paper makes a big deal out of showing a correlation in the severity of pediatric Crohn’s and the types of microbes found.  Good.  That is useful.  But here is the thing.  It is a $&*#($@(& correlation.  They have NO IDEA if this is the result of the CD or the cause (or both).  To go around pushing the idea that this is about bacteria initiating CD is misleading.

The news release says “The work may ultimately lead to treatment involving manipulation of the intestinal bacteria.”  True.  The work may ultimately also lead to my screaming.  Oh wait.  It did already.

For more on Overselling the Microbiome see some of my other posts

As I have said many time.  I believe the human microbiome is VERY important.  I believe it probably plays a role in all sorts of human issues – health and disease.  But we need to be careful not to be misleading about what we know and don’t know … 
——–
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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Lab meeting Oct 23rd 2012

Dongying Wu will be presenting for this week’s lab meeting. We will be meeting at the Genome Center from 1:30 to 3:30pm in room 4202

iTalk bug – help needed with partial / unclosed aiff file

Well, too long of a saga to post directly to Twitter so posting here.

Yesterday I recorded a review session for a class with iTalk https://itunes.apple.com/us/app/italk-recorder/id293673304?mt=8.  I recorded it on my iPhone 4S.

When I got home to upload the file and to convert it to an MP3 to share with the class I discovered that it seemed to not be there in the iTalk file list.

I thought – maybe I never formally “saved” the file but maybe iTalk kept the recording somewhere.

So I opened up iTunes connected to my phone and there it was in the Apps file area


I then copied the file to my desktop and no matter what I do I cannot seem to open it and /or extract audio out of it.  I have tried to open it a million ways with all sorts of desktop and online programs and nothing works.  My guess is somehow the file was not closed out correctly and thus even though it is 430 Mb it is viewed as empty by all the programs I have tried.

Anyone know a solution for this?

I have posted the file to Dropbox here.

——–
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.

——–

Plant Bio. seminar, Friday 10/19: Justen Whittall

PBGG Seminar

“Messages from the Arctic: Transcriptome analysis of an Arctic mustard flower color polymorphism”

Speaker: Dr. Justen Whittall

Santa Clara University

Friday, October 19, 2012

12:10 – 1:00 PM

1022 Life Sciences

Host: Daniel Fulop

Mouse study of fecal transplants to treat Cdiff infection

Interesting story in thge BBC News on a paper from PLoS Pathogens: BBC News – Faecal transplant clue to treating gut bug (seems that the article has disappeared – maybe they jumped the Embargo? — anyone — found another version here). In the work, researchers from the Sanger Institute infected mice with Clostridium difficile and then treated them with different combinations of microbes isolated from mouse feces. In the end they are reported to have identified a combination of six strains that was highly effective in clearing the C. difficile infections. I say “reported to have …” because I cannot find the PLoS Pathogens paper, again suggesting to me that the BBC story may have somehow jumped the embargo. Will post more when more comes out.

——–
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.

——–

Important read: Biotechniques discussion of DNA extraction in microbial studies

Very quick post here.  This is worth a read: BioTechniques – DNA Extraction: Overcoming Obstacles in Microbial Studies.  From their summary:

“What are the most efficient methods to extract microbial DNA that accurately represents the community it is isolated from? Janelle Weaver reports on efforts to identify the best methods for DNA extraction from unknown frontiers in the human body and across the globe.”

It discusses among many things this fascinating paper: Flores GE, Henley JB, Fierer N (2012) A Direct PCR Approach to Accelerate Analyses of Human-Associated Microbial Communities. PLoS ONE 7(9): e44563. doi:10.1371/journal.pone.0044563

Note – I found out about this on the Twitter

//platform.twitter.com/widgets.js

On a related note see the paper from my lab on a metagenomic simulation we did a few years ago …

PLOS ONE: Metagenomic Sequencing of an In Vitro-Simulated …

——–
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.

——–

Today at #UCDavis Dr. Harris Lewin on “Chromosome Evolution”

Today is the Joint Seminars in Molecular Biology lecture series.

Dr. Harris A. Lewin
Vice Chancellor- Research
University of California, Davis

“Chromosome Evolution”

Thursday, October 18, 2012

4:10 p.m.

1022 Life Sciences
Lewin_MtgNotice (2).doc