UCSF Bioengineering

From MRSA, to vampire squid, to "funding cuts," The Guardian has your last minute, science-inspired Halloween costumes covered. Peer review is pretty good and scary, but we're just not so sure if that last one is funny...

UC San Francisco Bioengineer Tejal Desai, PhD, talks with Sally Rockey, PhD, deputy director for extramural research at the NIH 

Biomedical research has had numerous impacts on U.S. health in the past few decades:

The cancer rate is falling about 1 percent a year

Death rates for cardiovascular disease have dropped 60 percent in the last half-century

And HIV therapies are enabling people in their 20s infected with the virus to live to age 70 and beyond

But all that progress is under attack, according to Dr. Sally Rockey, deputy director for extramural research at the National Institutes of Health (NIH), a theme she regularly discusses on her blog, Rock Talk. Last week she visited UC San Francisco's Mission Bay campus and spoke of the impact of funding on the biomedical sciences. 

"We cannot afford ... to let science get ahead of us," Rockey said in her talk. "We still have to be at the cutting edge, we have to promote new programs and we have to remain innovative." 

And that's just what the NIH is doing. Several new programs are in the works, including "Transforming Translation," which aims to repurpose abandoned compounds from drug companies for wider use. 

While funding is always in the forefront of a researcher's mind, and the NIH will continue to be a prime source of funding, our bioengineers are forging onward, bolstered by funding opportunities through UCSF's Clinical and Translational Science Institute (CTSI), the California Institute for Quantitative Biosciences (QB3) at UCSF, and the robust Research Grants Program through the University of California. 

As Rockey said: "This is a time like never before. ... we have to take advantage of this." Indeed we do.

Today at 12pm! Watch the livestream of the Chancellor's State of UCSF address & hear what this talk of a big gift to the basic sciences is all about! Tweet questions to #ucsf2013 

Did you know holography took shape in the mid-twentieth century, with experiments in microscopy? Of course, the development of the laser helped, too. Check out the whole story via the video below!  

For Patsy Babbitt and her lab at UC San Francisco's Mission Bay campus, sequence and structure are nothing without function. Her primarily computational lab is home to a few bioengineers with a penchant for statistical models. As we celebrate the ten year anniversary of our Mission Bay campus this year, we thought it fitting to have a look back on the archives to see what some of our faculty were up to. 

You never know what you'll find, like the fact that Patsy really wanted to be an archaeologist:

"In a way I'm still the archaeologist I wanted to be. I search through evidence about the evolutionary past and make predictions."

Every week we peel one hard-working grad student away from the lab for a quick Q&A to learn a little bit more about the people crazy passionate enough to work in one of the UC San Francisco labs while they get their PhD in Bioengineering through the UC Berkeley/UC San Francisco Graduate Program in Bioengineering. Today we have Jeffrey Yunes, a graduate student in the Babbitt Lab where he researches informatics-based approaches to the computational prediction of protein function. Jeffrey received his BS in Computer Science in 2006 from the Georgia Institute of Technology and then went on to write warehouse optimization software for Amazon.com for three years before returning to academia to pursue his PhD. Read on to see how dinosaurs, space, and math tricks got Jeffrey to where he is today. Thanks, Jeffrey!  

When did you first realize you loved science?

I grew up loving dinosaurs, space, math tricks, Capsela, and computers. (I don't remember which one was introduced to me first, but thank my parents for doing so.) As I got older, I realized that the more math and science I learned, the better I was at making stuff. In college, I grew excited by the prospects of applying computer science to biological data.

What brought you to UC San Francisco?

Many factors led me to the Joint Graduate Group: the access to faculty across both campuses; the high caliber classes in bioinformatics, computer science, and statistics; the flexible curriculum; and lots of potential advisors working in bioinformatics- all in a place I wanted to be!

When you’re not hard at work in the lab, how do you spend your time?

The entrepreneurial spirit and accompanying resources in the San Francisco Bay Area are unparalleled. There are biotech hackerspaces, prototyping studios, technical workshops, and release parties. That being said, I like to work on side projects; I just released a mobile app, and have been dabbling in decentralized cryptocurrencies. I also like to exercise and participate in one-off events in the area.

What’s the coolest thing about your current research in bioengineering?

Sometimes, I'm exploring how to model relationships between protein sequence and function. Other times, I'm mustering weak signals in homologous protein sequences to identify how a protein became pathogenic. I get to learn the latest machine learning algorithms and take part in interdisciplinary collaborations. The work changes every day, and I'm always learning new stuff and becoming a better scientist.

If you could give one piece of advice to someone thinking about a graduate program in bioengineering or a related field, what would it be?

The PhD program is a huge part of bioengineering at UCSF, and so we’re taking some time to get real students to answer real questions about the program. Have a question that you’d like answered? Just ask us.

Doing a little pre-research for our Dogpatch walk -- we wanted to make sure we didn't miss anything! -- we came across this amazing peek inside the neighborhood on San Francisco Travel and written by the folks over at The Bold Italic. We promise to post some of our own pictures soon, but in the meantime, we think you'll like this vicarious trek around the neighborhood. 

We've reached our first goal!!! We're going to the @bayareascience!! thank you all! #education #science @indiegogo http://t.co/xZjV2Wdvzm

A few weeks ago we brought you two consecutive Five Questions columns from Michael Sachs and Harrison Liu, two of the guys behind LegoScope, an educational tool made of - you guessed it -- legos, designed to make microscopy more accessible. Today the team is launching their first IndieGoGo campaign to crowdfund for their upcoming launch of their new LegoScope design.

The LegoScope was born out of a partnership between UC San Francisco and IDEO about a year ago, and their prototype is ready for some real world play. Their goal is to unveil their newest design at the Bay Area Science Festival Discovery Day on November 2, 2013 at AT&T Park in San Francisco. The event attracts over 30,000 science-loving kids and parents annually. Guests who stop by the LegoScope booth will be able to build their own LegoScope from lenses, adapters, and LEGO bricks that the team provides. Kids (and, let's face it, adults, too!) can then head over to their second table to use their new microscopes to get up close and personal with zebrafish, worms, and other fun creatures. "This booth will be a way for us to test our designs, solicit feedback, and give us a strong foundation to begin bringing LegoScope to classrooms and parents," the team says on their website.

Intrigued? Help them out. Head over to their IndieGoGo page to see a video of the LegoScope in action, learn more about the project, and lay your claim to a little piece of microscopy future. Do it for the kids.