Archive for the 'Highlight Reel' Category

Review of the 2013 MCDB Retreat

October 28, 2013

Guest post by Jessica Vera

This year’s MCDB retreat (my third as a grad student in the department) was held in Vail, CO. Before getting into the science of it all, I just need to say that we were blessed with some spectacular weather and beautiful fall mountain scenery. Everything went off without a hitch and a thanks must be given to Robin Dowell and Gia Voeltz as well as Eric Hedl (IT) and Kathy Lozier(Admin) for their efforts in organizing the retreat. This being my third retreat, and quite possibly my last, I found myself getting nostalgic and thinking of previous retreat experiences. I was a first year when I first attended my first MCDB retreat, and as such little was required of me other than to attend the talks and check out some posters. My first retreat was also Robin’s first retreat and it was there that I distinctly remember meeting her for the first time. Little did I know that some six months later I would be joining her lab.

Each lab in the department is allotted a 20 minute talk during the retreat. I would like to elaborate on two such talks. First, Eric Davis of the Shen lab gave a talk entitled ‘Genome-wide analysis of gene-trap insertions and essential genes in human cells’. This was a continuation of work presented in his MMB talk just one week prior. What I like about his project is that he has utilized very new techniques to address lingering questions in the field of GPI-anchored protein trafficking. He has been mutagenizing a human haploid lymphoblast cell line via gene-trap insertion and then putting these cells under various selective conditions. He then performs next-gen sequencing to locate gene-trap insertion sites and identify genes involved in mediating the selected phenotype. At the retreat he specifically focused on his analytical methods for finding statistically significant hits in his experiments. I know firsthand how challenging certain aspects of his project can be and I am impressed with the quality of his work and with how he presented it to the department at large.

Second, I was happy to have caught James Orth’s talk ‘Follow the SINE: selective inhibitors of nuclear export as anti-cancer agents’. Being that James is a new assistant research professor in the department, I confess having known little about his research until the retreat. He is making use of the cell cycle biosensor system named FUCCI which allows for single cell assignment and monitoring of cell cycle progression via fluorescence microscopy. This system provides a good basis for exploring the effects of anti-cancer drugs. I predict this system may also prove useful to many other MCDB research labs!

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2013 iGEM Team Wins Gold in Toronto!

October 15, 2013

Guest post By Joe Rokicki

I woke up 36 hours ago during Boulder’s first snow storm of the year, just in time to get to DIA and catch a flight with five undergraduates, one other graduate student and one faculty member who would be representing CU at the North American Regionals of the International Genetically Engineered Machines Competition (iGEM). Now, I’m sitting at a bar in an airport in Toronto with our newly Gold Medal decorated, special award winning and world championship qualifying team and we are trying to figure out how we are going to get to Boston to compete on the world stage.

This is the story of our whirlwind, international journey from zeros to heroes.

Last spring, a team of about 20-30 undergraduates and graduate students began meeting weekly at the new JSCBB building to discus the possibilities of a newish branch of science called “Synthetic Biology”. The way I define synthetic biology is this: Traditional biology is all about pushing the frontiers of what is known. It’s about finding new pathways, new mechanisms, new enzymes, new patterns and formulating new hypotheses. Synthetic biology is something fundamentally different. Instead of pushing the frontiers of what is known about the natural world, synthetic biology is about taking what is ALREADY known and applying it in a way that nobody has ever tried before. It is about engineering biology into solutions for real world problems. The iGEM competition is a forum for undergraduates, mentored by graduate students and faculty, to spend a summer in the lab working on a real synthetic biology project of their choosing and seeing what they can accomplish in that short amount of time.

Past examples of iGEM projects are as varied as they are awesome: Bactoblood, an arsenic biodetector, resveratrol beer etc. (Descriptions of them all are online at www.igem.org.)

This year, our team decided on a project theme of “DIY Biology.” It was a hard summer of characterizing low cost versions of common lab protocols such as DNA purification and DNA gel extractions, validating methods for recycling common lab consumables such as miniprep columns and agarose gels, and developing low cost methods of homebrew, small batch enzyme production. Our team then put together a poster and a presentation and flew to the North American iGEM regionals in Toronto to see how their work would stack up against the other 52 teams from all over North America.

The reception couldn’t have been warmer. There probably aren’t many people in North America who get pumped up about new methods of low cost enzyme purification or hacking miniprep columns but the attendees at the regional competition were riveted.

One component of the project, a protein tag which reversibly precipitates in the presence of calcium, was successfully cloned, characterized and submitted to iGEM headquarters. This part (“bioBrick’’) was deemed so promising that it was awarded the “Best New Part, Engineered” award at the competition. We were the only team at the Regionals awarded this prize. The project as a whole was rated among the best in North America and a CU team, for the first time, was invited to present at the World iGEM Finals in November along with the best teams from Europe, Asia and Latin America.

I couldn’t be more proud of our team. A video of our team’s presentation and a description of their project is available on the iGEM.org website. Make sure you root for the Buffs in November and feel free to contact iGEM@colorado.edu with any questions about the iGEM program at CU.

The ASBMB Special Symposia on Evolution and Core Processes in Gene Regulation

August 30, 2013

The ASBMB Special symposia on Evolution and Core Processes in Gene Regulation was held at the University of Chicago July 25–28, 2013.   The meeting promised, ” Organisms have evolved a diverse set of mechanisms to orchestrate the expression of their genes. The core machinery of gene expression is both instrumental to this process but is also subject to the ever changing needs required to survive and reproduce. This special symposium aims to bring together current perspectives on regulatory evolution with mechanistic insights into gene expression.”    A diverse crowd was in attendance with backgrounds in evolution, molecular biology, computers science, mathematics, developmental biology, and likely others.

In general, the goal of the meeting was to highlight efforts aimed at understanding general truths that underly the evolution of transcriptional regulation.  lya Ruvinsky, one of the organizers,  categorized efforts into two broad approaches:  1) studying individual cases or 2) generating large datasets.   His talk described an exceptionally elegant example of the individual loci approach.   Aviv Regev gave a nice talk on the power and capabilities of the large data approach.   While many of the talks fell into those two broad categories, there were also a number of talks focused on improving our understanding of transcription itself including discussions of pausing (Julia Zeitlinger and Robert Landick), structure (Zachary Burton and Seth Darst), and splicing fidelity (Jonathan Staley).
Overall, the meeting showcased an exceptional lineup of talks, but I’ll only highlight a few here:

 

  • Saeed Tavzoie kicked off the meeting with a nice talk that highlighted two recent papers.  First, he summarized his 2008 work on how can can predict upcoming environment changes (doi: 10.1126/science.1154456) and then discussed their more recent work (doi:10.1371/journal.pgen.1003617) highlighting the value of loss of function mutations in adaptation.
  • Barack Cohen gave a talk on his recently published (doi: 10.1073/pnas.1307449110) work on Crx recognition using high throughput report assays.   This work highlights how little we understand about the sequence context necessary around a motif to give rise to both binding and expression.
  • There were several good talks on modeling.  My favorite two were David Arnosti, who spoke on their quantitative modeling framework for looking at enhancer function and evolution, and Zeba Wunderlich, whose model focuses on patterns of divergence between Drosophilia species (doi:10.1038/msb.2012.35).
  • Ian Dworkin highlighted how important genetic background is to phenotype.   This work has since been published (doi:10.1371/journal.pgen.1003661).
  • John Reinitz talked about how function is conserved in the face of non-conservation of sequence  (doi:10.1371/journal.pgen.1003243).

 

2013 Summer Journal Club in the Dowell Lab

August 23, 2013

Guest post By Justin Freeman

This summer, the Dowell Lab continued its annual tradition of temporarily converting our standing lab meeting into a weekly journal club. Lab members took turns selecting papers they found interesting, controversial, or particularly relevant and assigned them for weekly reading. Given our diverse backgrounds and research interests, we read pretty widely this summer. Topics ranged from stickleback evolution to mathematical models for quantifying RNA-seq data. Here’s what we read, discussed, and sometimes argued about…
We hope you enjoy these papers as much as we did!

Mouse genomic variation and its effect on phenotypes and gene regulation
Statistical inferences for isoform expression in RNA-Seq
CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
Translating dosage compensation to trisomy 21
A ncRNA Modulates Histone Modification and mRNA Induction in the Yeast GAL Gene Cluster
The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb
The Genomic Basis of Adaptive Evolution in Threespine Sticklebacks
Functional Roles of Enhancer RNAs for Oestrogen-Dependent Transcriptional Activation
Genome-Wide Analysis of in vivo Translation with Nucleotide Resolution Using Ribosome Profiling
Extensive Transcriptional Heterogeneity Revealed by Isoform Profiling

Quick Guides

January 6, 2010

PLoS Computational Biology has published a series of “Education” articles lately that are useful for those entering Bioinformatics / Computational Biology. Even seasoned veterans might find a nugget or two in these:

A Quick Guide for Developing Effective Bioinformatics Programming Skills

A Quick Guide to Organizing Computational Biology Projects