Celebrating Strengths & Preparing for Our Future: 3rd Annual CRSB Meeting, Fall 2015

Preparing for Our Future

Because we had a successful site review in May of 2015, funding looks good to finish out the five year grant, ending in Summer 2017.  At the same time trends indicate that this type of collaborative funding is changing – so we also talked about our strengths as a scientific community to prepare ourselves for long term sustainability in that future funding environment, and brainstorm ways to be responsive to feedback – for different funding arrangements and possibilities, as things move forward.

In that vein, on September 4th, 2015 – our larger membership and advisory teams came together to hear the very latest science in our labs and in our larger community, as well as to talk about our fourth and fifth NIGMS P50 grant years, and farther out.  Nearly fifty members attended including a shooting star list of speakers and poster presenters:

Marina Volegova – Cate Lab, Functional characterization of eIF3a in relation to non-canonical translation initiation

Kevin Doxzen – Doudna Lab, Structural insights into a novel prokaryotic argonaute 

Meghan Zubradt – Weissman Lab, DMSseq 2.0: Steps toward single-molecule mRNA structure determination

Harold Pimentel – Pachter Lab, Quantification and analysis of RNA transcripts

David Weinberg – UCSF Faculty Fellow, Guest Presenter, New lessons from an old RNA:Revisiting the post-transcriptional silencing of unspliced HAC1 mRNA

Poster Presenters:

Amy R. Eisenberg Brar Lab, Translation elongation regulation in budding yeast meiosis

Stephen Floor Doudna Lab, Tunable protein synthesis by transcript isoforms in human cells

Tania L. Gonzalez Hammond Lab, Tight, inducible regulation of plant immune responses by combining promoter and suicide exon elements

Shintaro Iwasaki Ingolia Lab, Rocaglamide A converts RNA helicase eIF4A into a sequence-specific translational repressor

Yeon Lee Hammond & Rio Labs, Systems Level Analysis of Alternative Pre-mRNA Splicing: The roles of RNA structure and RNA Chaperone Proteins

James Peter Brook Lloyd Brenner Lab, Characterizing the regulation of splicing factors by alternative splicing and nonsense-mediated mRNA decay

Ryan Muller Rio & Hammond Labs, Cas9-Mediated Manipulation of Alternative Splicing

Mia Pulos & Luisa Tacca Cate & Ingolia Labs, Pathways under eIF3-directed translational regulation

Dan Santos Weissman Lab, Investigating protein multi-functionality and translational regulation using ribosome profiling

Duane Smith Cate Lab, Modulation of calcineurin signaling by dysregulation of non-essential eIF3 subunits

2015 Undergrad CRSB-Amgen Fellows

Paige Diamond, Mentor – Faculty – Dr. Gloria Brar Brar Lab, Systematic identification of alternative ORF translation in meiotic yeast cells

Lauren A. Thurlow; Mentor – Dr. Audrone Lapinaite Cate & Doudna Labs, A Fluorescently Labelled dCas9 for Imaging Endogenous RNAs In Vivo




Talented Undergraduates Make a Difference in the Labs: Paige Diamond & Lauren Thurlow

We had the great fortune to have two outstanding undergraduate scholars visit our campus and CRSB labs this summer – Lauren Thurlow and Paige Diamond as part of the Amgen and CRSB sponsored Summer Fellowship program. Here is a little of what they had to say about their experience.

Thank you Paige and Lauren for your hard work! Also – big thank you to our very busy scientists in our labs – especially, Drs. Gloria Brar, Audrone Lapinaite – for stepping up to be mentors.

DSC_2673 DSC_2681

“As a scholar in the 2015 CRSB summer program, I had the privilege to work with Dr. Gloria Brar on a project focused on the systematic identification of alternate ORF translation in meiotic yeast cells. Working in this lab, I was exposed to innovative research methods and gained technical skills and knowledge which surpassed those obtained at my home institution, Drake University. Through the program, I was provided the opportunity to attend the National Centers for Systems Biology Conference where I gained increased awareness of the variety of research currently underway in the field of systems biology and was able to present a poster on our research to a diverse crowd of professionals. The UC- Berkeley community is vibrant and beautiful.  Organized social activities allowed us to take advantage of what the area has to offer– a bike ride across the Golden Gate Bridge was definitely a highlight.  Overall, I am deeply grateful for this experience, particularly for valuable insight into an advanced research program and the high-quality mentoring received throughout, but also for many new friends and colleagues.” Paige Diamond, Amgen CRSB 2015 Fellow, Mentor: Dr. Gloria Brar, Brar Lab

DSC_1044 Lauren and Paige in the labs.

“Before participating in the CRSB Scholars Program, all I had was a passion for nucleic acids research. Now I have the experience and connections to back it up. The program has helped me prepare for graduate school and define my goals for the future – all while working on one of the best molecular biology campuses in the world.” Lauren Thurlow, Amgen CRSB 2015 Fellow, Mentor: Dr. Audrone Lapinaite, Cate-Doudna Lab

Straight Math Talk from CRSB Faculty, Professor Lior Pachter

Check out Professor and CRSB Faculty, Dr. Lior Pachter’s fascinating blog and twitter feed.  He talks about analytical tools in the quantitative biosciences, about math, and some of the deeper philosophical questions from the math arena.  He even hits upon the important question of how and what to teach our young people during their K-12 years, in a thoughtful discussion of common core standards by grade level. Check out this and more, here.

Follow Professor Pachter on Twitter

Follow Professor Pachter’s Blog

2015 Fall Seminar Series: CRSB Faculty, Ming Hammond & Visiting Professor, Robert Batey

CRSB Faculty, Professor Ming Hammond kicked off the Fall 2015 Organic/ChemBio Seminar series  on Tuesday, September 15th presenting, “Exploiting riboswitches to study and manipulate bacterial signaling.”

Keep an eye out for Professor Robert Batey, Tuesday, October 13th presenting, “Structure and mechanism of riboswitches and their application to synthetic biology” from University of Colorado-Boulder.

Time & Location: 11 am – Noon, 120 Latimer Hall

CRSB Has Strong Showing at National Conference

The Center for RNA Systems Biology (CRSB) had a strong showing at the July 2015 National Centers for System Biology Conference in Albuquerque, New Mexico.  Our team presented on Center activities, and shared the latest exciting research through flash presentations and posters.


Left to right:  James Peter Brook Lloyd (back row); Paige Diamond; Marina Volegova;
Center Director, Jamie Cate; Lauren Thurlow, Stephen Floor; Faculty, Ming Hammond; Brigid Acuña.


3rd Annual Re-Writing Genomes Symposium

August 24th, 2015
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