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December 2013
Happy New Year!

The faculty, students and staff of BioFrontiers are looking forward to an exciting 2014. From research, symposiums and seminars, all in the name of science, our calendars are filling up with some amazing events.

Make sure you look at our upcoming events (to the right on this page) for dates, locations and times. Additional information on all our events can be found on our website too.

We appreciate all your support this year, and we are looking forward to sharing more of our stories with you in the new year.
JSCBB Mini Symposium encourages collaboration
JSCBB's Butcher Auditorium hosted a full house for the 
JSCBB Mini Symposium.

It looks a lot like the other buildings on the CU-Boulder campus, with its rustic Italian-inspired tile roof and red brick, but the Jennie Smoly Caruthers Biotechnology Building (affectionately known by its inhabitants as JSCBB) is something quite different. It was designed to support those scientists and engineers whose research was driving them into other academic areas, and who wanted to use the best tools from other disciplines to do their work. This building houses engineers, biologists, chemists, biochemists, computer scientists and physicists. These are the CU faculty that speak "interdisciplinar-ese".

 

In a building where a biochemist can have barbecue with a biofuels expert, good ideas are bound to proliferate. The challenge is getting these dedicated researchers away from their labs and talking to each other. It takes conversation to initiate collaboration. To help this process along, the JSCBB Mini Symposium was born.

 

The JSCBB Mini Symposium took place on July 29 with 15 faculty members presenting on topics that spanned from biomarkers for cancer, to tissue engineering, biofuels and the microbiome. Faculty members represented the groups in the JSCBB: the BioFrontiers Institute, the Division of Biochemistry and the Department of Chemical and Biological Engineering. JSCBB's Butcher Auditorium was packed for all five sessions throughout the day. The second JSCBB Mini Symposium is scheduled for January 8.

 

"It's sort of like being at an international conference. We're hearing all these great talks and listening to incredible talent," says BioFrontiers Institute Director, Tom Cech. "The best part is that we never have to leave the building." Read more here

CU-Boulder student team wows judges at biology competition

When this year's iGEM team at the University of Colorado Boulder began meeting early this year, they wanted to take what they knew about biology, and use it to build something entirely new. iGEM, or International Genetically Engineered Machine, is the top synthetic biology competition in the world and after a foundation-building first year, the CU-Boulder team wanted to make an impact in 2013.

 

Thirty CU undergraduate and graduate students from a wide range of science and engineering departments worked together to design their project: "DIY Synthetic Biology," taking apart and reconstructing lab techniques and tools and improving them. Over the summer, six students completed the project. Then, these students boarded a plane to Montreal, Canada with their faculty mentor, BioFrontiers' Robin Dowell, practiced their presentation until 2:00 a.m., and competed with 52 North American teams, earning an iGEM special award and their place in the iGEM World Competition in Boston in November. The team ultimately did not place in the World competition, but left with plans to compete at a much higher level next year.

BioFrontiers' Robin Dowell

 

"There were a lot of proposals in the competition, but CU delivered an actual product," says CU iGEM Team Mentor Robin Dowell, who is an assistant professor in Molecular, Cellular and Developmental Biology and a faculty member at the BioFrontiers Institute. "The team used a lot of ingenuity; slick lab techniques that make it cheaper and easier to conduct important research. They really gave the judges a lot to talk about." 

Recent papers by our faculty 

The non-coding B2 RNA binds to the DNA cleft and active-site region of RNA polymerase II. (J Mol Biol.) - Natalie Ahn

Wnt5a Directs Polarized Calcium Gradients by Recruiting Cortical Endoplasmic Reticulum to the Cell Trailing Edge (Dev Cell) - Natalie Ahn & Kristi Anseth

Bioactive hydrogels: Lighting the way
(Nat Mater.) - Kristi Anseth

Biophysically Defined and Cytocompatible Covalently Adaptable Networks as Viscoelastic 3D Cell Culture Systems (Adv Mater.) - Kristi Anseth

Controlled local presentation of matrix proteins in microparticle-laden cell aggregates (Biotechnol Bioeng.) - Kristi Anseth

Hydrogels preserve native pheonotypes of valvular fibroblasts through an elasticity-regulated PI3K/AKT pathway (Proc Natl Acad Sci) - Kristi Anseth and Leslie Leinwand

Role of cell-matrix interactions on VIC phenotype and tissue deposition in 3D PEG hydrogels (J Tissue Eng Regen Med) - Kristi Anseth

Wavelength-Controlled Photocleavage for the Orthogonal and Sequential Release of Multiple Protein (Angew Chem Int Ed Engl.) - Kristi Anseth

Promiscuous RNA binding by Polycomb repressive complex 2 (Nat Struct Mol Biol.) - Tom Cech

RNA Seeds Higher-Order Assembly of FUS Protein (Cell Rep.) - Tom Cech

Environmental structure and competitive scoring advantages in team competitions (Sci Rep.) - Aaron Clauset

Retrospective reflections of a whistleblower: Opinions on misconduct responses. (Account Res) - Robin Dowell

Advancing Our Understanding of the Human Microbiome Using QIIME. (Methods Enzymol.) - Rob Knight

Alterations in the Gut Microbiota Associated with HIV-1 Infection. (Cell Host Microbe) - Rob Knight

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system (Elife) Rob Knight

Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. (Science) - Rob Knight

The amphibian skin-associated microbiome across species, space and life history stages. (Mol Ecol.) - Rob Knight

Events
Save the dates for 
these events:
 
JSCBB Mini Symposium II
Jan 8, All Day
JSCBB - Butcher Audi. (A115)
 
BioFrontiers Seminar
Jim Wells
UCSF - Mission Bay
Mar 11, 4:00 pm
JSCBB - Butcher Audi. (A115)
 
BioFrontiers Seminar
Steve Quake
Stanford University
April 8, 4:00 pm
JSCBB - Butcher Audi. (A115)
 
BioFrontiers Seminar
L. Mahadevan
Harvard University
May 13, 4:00 pm
JSCBB - Butcher Audi. (A115)
 
JSCBB Mini-Symposium III
May 23, All Day
JSCBB - Butcher Audi. (A115)
 
BioFrontiers Symposium on 
Large Datasets & Genomics
May 28, All Day
JSCBB - Butcher Audi. (A115) 
 
BioFrontiers Special Seminar - 
Butcher Awardee
Richard Axel
Columbia University
Oct 7 - 7:00 pm
Location TBD
IQ Bio Blog: 
Science is Hard
 
Joey Azofeifa is a second-year graduate student in the IQ Biology program.
Joey Azofeifa is a second-year, computer science graduate student in the IQ Biology program.

It must be said that I have had a very difficult time writing this blog-post. The reason, after a few too many cups of coffee, came clear to me: Science is Hard (and I worried if that's what I should tell my readers). Certainly there are intellectual struggles in Science, the esoteric aspects of an algorithm, and the even more enigmatic explanations of it on StackOverflow, can be mind-numbingly painful. But the real reason that Science is Hard (at least from the perspective of a lowly and naïve graduate student) circumvents "advanced" material and is better understood as an emotional one.

 

At the point of a really innovative thought, the scientist exists outside the documented, outside the history. At such an apex, he or she is met with a flurry of emotions: motivation, passion, strength and, to a degree, reluctance. But why feel the fear? Did Richard Feynman feel the fear? Albert Einstein? Probably. No, definitely. Any truly original moment identifies the thinker as different and such a separation from the comfort of the known begets questions of assuredness, obligation and failure. And so, Science is Hard because the very nature of Science is to innovate, push-past and discover and these struggles bring along the unwelcome feelings of separation.

 

As someone who works at the interface of computer science and biology, let me tell you: I feel the fear. Not because I would presume to have had something truly original but because such an interface is so new, untouched and foreign that every step is fraught in new territory. New textbooks are created every year to describe the field of "bioinformatics" but with very little collective agreement. Why? Well I think there are just so few foundational principles for bioinformatics that consensus still waits; I mean it's a chaotic, free-for-all. 

 

Within this spinning cacophony, innovation is ripe for the picking and this reason (among others) motivated a move from a background in biology to a graduate degree in computer science. Should I emphasize my thesis again? I think so: Science is Hard. The move away from the comfortable pleasures of a biological background was/is hard. But don't worry, here is the silver lining: it has been a wildly rewarding experience.

 

Without going into the gory details of my 2-hour nights of sleep, eye's glazed by a terminal screen and the quiet jitters of too much caffeine, I can honestly say I am glad to have taken the plunge into computer science. Not only because the field of bioinformatics is "hot" but such a transition highlights the whole purpose of Science: to stand outside the comfortable.     Read more here

 

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