Eisen Lab Blog

Life as an undergrad in a research lab

I would like to start by thanking Dr. Eisen for giving me the opportunity to work in his lab.  This is my first time working in an “outside of class” lab setting and I feel that this project is perfect for undergrads looking for experience in a research lab.   The two mentors helping us, David and Jenna, are great teachers and are always anxious to share their knowledge with us inexperienced ones.  They taught us basic molecular biology techniques and procedures that are used in virtually every biology related lab around the world.

At first, the work was very interesting because I had no experience working in an actual research lab surrounded by actual scientists.  I was eager to soak up knowledge and asked plenty of questions.  When it came time for independent work and growing our own cultures I felt less motivated to do this because I excited to move on to the next stage of sequencing organisms.  As such, I decided not to work with any of the organisms I found and I am hoping to work with an organism that was grown and isolated by the group.

For my independent organism to work with, I am hoping to sequence Curtobacterium flaccumfaciens, a known plant pathogen that was tracked into the human built environment.  There aren’t any projects planned to sequence this organism or its relatives, so this seems like an ideal candidate for our project.  Its potential application to the built environment includes its ability to harm plants grown in the indoors, and/or harm crop plants that could make their way into our food.  This sounds like a very interesting bacterium to study because of the REAL world effects!

After we have sequenced the genome we will add it to a database, where other ACTUAL scientists can refer to the data we submitted and make their lives a little bit easier.

Seminar 5/7 at #UCDavis Reed Cartwright “Evolutionary models of mutation & variation for genomic data”

Genetics Seminar

“Evolutionary models of mutation and variation for genomic data”

Speaker: Reed Cartwright

Arizona State University | Biodesign Institute

Monday, May 7, 2012

4:10 PM

1022 Life Sciences

UC Davis/Berkeley Joint Colloquium, 5/3. Rasmus Nielsen “Statistical Problems in Analysis of Next-Gen Sequencing Data”

The 2012 UC BERKELEY / UC DAVIS JOINT STATISTICS COLLOQUIUM

Please join us for the 2012 Berkeley / Davis Joint Colloquium. This year’s Colloquium will feature a talk at 4:10pm by Prof. Rasmus Neilsen, followed by a reception in the statistics lounge. Grad students are also invited to the Berkeley / Davis Grad Student Colloquium from 5:30-6:30pm.

Coffee: 3:30pm, Statistics lounge (MSB 4110, 4th floor)

Seminar: 4:10 pm, Colloquium Room (MSB 1147)

Reception: 5:30 pm, Statistics lounge (MSB 4110, 4th floor)

Speaker: Prof. Rasmus Neilsen

Dept of Integrative Biology & Statistics, UC Berkeley

Title: Statistical Problems in the Analysis of Next-Generation Sequencing Data

Abstract: The biological sciences have been transformed by the emergence of Next-Generation Sequencing (NGS) technologies providing cheap and reliable large scale DNA sequencing. These data allow us to address biological research questions that previously were considered intractable, but also raise a number of new statistical and computational challenges. The data contain errors that need careful attention, and the appropriate likelihood functions are usually not computationally accessible, because of the size of the data sets. I will discuss some solutions to these problems and illustrate them in the analyses of several different data sets. In one study we sequenced all protein coding genes of 2000 individuals to identify mutations associated with Type 2 Diabetes. In a second project we used similar sequencing techniques to identify the genetic causes of altitude adaptation in Tibetans. In the third study I will discuss, we sequenced the first Aboriginal Australian genome to elucidate the history and origins of Aboriginal Australians.

Graduate Student Colloquium : Please see the attached flier for details of the Graduate Student Colloquium, which will feature talks by Andrew Farris (UC Davis) and Vincent Yates (UC Berkeley).

http://www.stat.ucdavis.edu/davis-berkeley-colloquium-2012

davis berkeley colloquium 2012 flier.pdf

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.

Life in the Lab

I have choosen to work on the organism (Morganella morganii) TEU and went through the process of tagmentation and library prep. Just recently finished running it on the Pinpin machine and cleaned my DNA and now awaiting for a few more organism to be ran on the bioanalyzer. First blog post feedback needed!

Lab meeting May 2nd, 2012

Guillaume Jospin will be presenting for this week’s lab meeting. Room 6202 in the Genome Center from 1:30 to 3:30pm.

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.