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About Egghead

Egghead is a blog about research by, with or related to UC Davis. Comments on posts are welcome, as are tips and suggestions for posts. General feedback may be sent to Andy Fell. This blog is created and maintained by UC Davis University Communications, and mostly edited by Andy Fell.

Of mice, flies, rice and men

January 27th, 2012 @ 3:09 pm by Andy Fell

Wednesday’s symposium on innate immunity was a big success with a capacity crowd of over 400 attendees at the UC Davis Conference Center.

The audience heard Nobel Prize winners Bruce Beutler of the University of Texas and Jules Hoffmann of the University of Strasbourg, France, talk about their work on the ‘triggers’ of immune responses in mice and insects, while UC Davis plant pathologist Pamela Ronald discussed similar mechanisms in rice plants and Luke O’Neill of Trinity College Dublin wrapped it up with a discussion of the implications for human medicine.

Slides and video from all the presentations are now available online.

Work in these very different organisms can give insights that advances human medicine. From the basic discoveries in mice, flies and even rice could come new drugs and new approaches to treat heart disease, rheumatoid arthritis, inflammatory bowel disease and other conditions.

Our immune system has two lines of defense. The innate immune system reacts first, attacking invading microbes and triggering inflammation. If that response fails, the adaptive immune system fights back with antibodies and specialized killer cells. Afterward, the adaptive immune system retains a memory that allows a more rapid and powerful response if the same virus, bacterium or parasite comes back.

Only animals with backbones, from fish to humans, have an adaptive immune system. But all animals, including insects, as well as plants, have innate immune systems.

In the 1990s, Ronald (working with rice), Hoffmann (with Drosophila flies) and Beutler (with mice) identified genes for immune receptors that triggered innate immunity in the rice, flies and mice, and found that the genes were remarkably similar despite hundreds of millions of years of evolution.

From this common trigger, plants, insects and animals develop different types of response to invaders.

Activation of the immune system is not always a good thing. It can lead to allergy, inflammatory diseases such as rheumatoid arthritis or autoimmunity, when the body starts attacking its own tissues.

In his talk, for example, Beutler described how his team, working with mice, has isolated genes related to inflammatory bowel disease, while O’Neill talked about the possibility of being able to develop drugs to treat a wide range of diseases linked to inflammation.

The symposium is an annual event sponsored by a fund created by AIDS pioneer and UC Davis professor emeritus Murray Gardner, who previewed the meeting in an interview for Sacramento Public Radio. At the beginning of the AIDS epidemic in the 1980s, Gardner helped discover viruses similar to HIV in monkeys and cats – animal models that have been of vital importance in discovering drugs to treat and prevent HIV/AIDS.

 

 

Posted in Biology, Evolution, General, Health, Nobels | Leave a comment

UC Davis, Sac City College open first community college center at a UC campus

January 12th, 2012 @ 5:26 pm by Andy Fell

Community college and university officials this week dedicated  the newly completed Sacramento City College Davis Center at UC Davis West Village. The Davis Center will open its doors to more than 2,000 students this Saturday, Jan. 14. It’s the first community college extension built on a University of California campus.

While recent years have seen a trend of universities offering courses leading to bachelor’s degrees on community college campuses, this project marks a new direction for collaboration between higher education institutions in California. Last fall, about 160 students transferred from SCC to UC Davis.

UC Davis Chancellor Linda P.B. Katehi said the new center is emblematic of the ways UC Davis is working to make it easier for California community college students to transfer to UC Davis. “We want to build bridges,” she said. “I know this center will become that bridge for more and more students.”

[Photo: Chancellor Katehi, left, with students Mitchell Laust, Leng Mut, and Andrea de la Torre. All three transferred successfully to UC Davis after studies at SCC. On the right is UC Davis Vice Chancellor for Student Affairs Fred Wood.]

New opportunities for students

SCC President Kathryn Jeffery said of the transfer possibilities for SCC students: “Our new center enhances educational opportunities for SCC students and creates a stronger likelihood that they will move more seamlessly into UC Davis or another four-year university.”

Some students who have already made that transfer were on hand for the dedication.

Although the regimentation of high school rubbed Mitchell Faust, 25, the wrong way, the Sacramento resident said he knew he wanted a four-year degree. Faust earned three Associate in Arts degrees in English, Liberal Arts and Social Sciences at SCC. A Transfer Admissions Agreement helped him meet the requirements to transfer to UC Davis, where he is studying English and African American and African Studies. Faust remembers walking one day from the community college’s old Davis Center, where he took classes in philosophy and Western civilization, to the UC Davis campus. “The second I stepped on campus, it was really exciting,” he said. He is on track to graduate from UC Davis in June, and just completed applications to programs for master’s and doctoral studies.

A native of Peru and resident of Florida, Andrea de la Torre, 22, came to Sacramento to intern at a church. She ended up living across the street from Sacramento City College. De la Torre’s time interning and working at Sacramento’s St. John’s Shelter Program for Women and Children motivated her to complete two Associate in Arts degrees in sociology and social studies at the college in May and seek a four-year degree. She transferred to UC Davis in fall 2011 and is now studying part time in pursuit of a sociology major in organizational studies. She wants to manage a nonprofit. De la Torre became a U.S. citizen in December. She said having a community college center located on a four-year campus can not only make things easier but also serve as a motivation. “It’s good to be close to what you want to do. It keeps you focused on what you want.”

Sacramento City College and UC Davis are important steps on Leng Mut’s journey from a ruralvillage in Cambodia to chemical engineering studies and research. A farmer’s daughter, Mut, 32, worked as factory sewer, domestic maid and cook before coming to the United States in 2004. At Sacramento City College, Mut studied English as a second language and, through a Transfer Admissions Agreement, met the requirements to come to UC Davis. She enrolled at UC Davis last fall as a chemical engineering major, and is participating in the McNair Scholars and MURALS programs that prepare students for graduate studies. She is now applying to present her research on the toxicity of carbon nanotubes at the undergraduate research conference at UC Davis this spring.

Doubling space

Phase one of the SCC Davis Center spans 20,000 square feet and includes a learning resource center, computer lab, classrooms, and administrative and student services spaces. Future phases of the SCC Davis Center will include additional classrooms, a bookstore and laboratory spaces.

The SCC Davis Center has had a number of homes since it was established in 1968. The new building will be more than twice the size of the current location in South Davis.

UC Davis’ Katehi said the center’s place on campus “also underscores the strong spirit of partnership that helped create West Village as a model of sustainability and innovation.”

UC Davis West Village is the largest planned zero net energy community in the country, designed to generate as much energy as it consumes in the course of a year. The community includes housing for students, faculty and staff; a recreation center; and commercial space.

“West Village offers a unique environment for students: close to the student culture and activities at UC Davis, close to the many exciting projects of the Energy Efficiency Center, and in the midst of a neighborhood that is itself a living laboratory,” said Don Palm, dean of the SCC Davis Center.

In addition to high-tech, sustainable spaces and flexibility for future programs, the SCC Davis Center is designed to LEED Silver certification standards. LEED certified facilities are designed, constructed and operated using a more sustainable approach.

Construction for the $7.4 million center is funded by the Los Rios Community College District with Measure A bond proceeds, as approved by Sacramento voters in the 2002 election.

The center’s strategic presence on the UC Davis campus comes as a timely homage to the California Master Plan for Higher Education, which recently celebrated its 50th anniversary. The 1960 document provided a framework for the concerted growth of community colleges as well as University of California and California State University campuses.

Posted in Education, General | Leave a comment

Dogs are from China, Cats are from Iraq

December 19th, 2011 @ 1:24 pm by Andy Fell

A new genetic study from the UC Davis School of Veterinary Medicine shows that Western dog breeds are descended from animals that originated in Southeast Asia, rather than in the Middle East or Europe as previously thought. An earlier study of the genetics of cats, however, shows that they originated in the ‘Fertile Crescent’ of the Middle East, running from the Eastern shore of the Mediterranean through Turkey and Iraq.

UC Davis researchers lead by Ben Sacks, director of the Canid Diversity and Conservation Group in the UC Davis Veterinary Genetics Laboratory, with collaborators in California, Taiwan, Israel and Iran, studied genetics markers from hundreds of domestic and wild dogs including Western pure-breds, dogs from Middle Eastern villages and Australian dingoes.

“The two most hotly debated theories propose that dogs originated in Southeast Asia or the Middle East,” Sacks said in a UC Davis news release. The study is published in the journal Public Library of Science (PLoS) One.

“In contrast to those theories, our findings suggest that modern European and American dogs are overwhelmingly derived from dogs that were imported from Asia since the silk trade, rather than having descended directly from ancient dogs native to Europe,” he said.

In 2008, veterinary genetics professor Leslie Lyons published a study showing that modern cat breeds likely originated in the Middle East, where agriculture began. Perhaps cats were domesticated to hunt mice and rats in grain stores by the Tigris, while the ancestors of modern dogs trekked west from China to trade silk and spices with Europe. That paper was published in the journal Genomics.

Posted in Biology, Evolution, General, History, Veterinary Medicine | Leave a comment

Deaf sign language users pick up faster on body language

December 15th, 2011 @ 11:23 am by Andy Fell

Deaf people who use sign language are quicker at recognizing both signs and other gestures than hearing non-signers, according to a new study from researchers at UC Davis and UC Irvine published online Dec. 6 in the journal Cognition.

“There are a lot of anecdotes about deaf people being better able to pick up on body language, but this is the first evidence of that,” said David Corina, professor in the UC Davis Department of Linguistics and Center for Mind and Brain.

Corina and graduate student Michael Grosvald, now a postdoctoral researcher at UC Irvine, measured the response times of both deaf and hearing people to a series of video clips showing people making American Sign Language signs or ‘non-language’ gestures, such as stroking the chin.

“We expected that deaf people would recognize sign language faster than hearing people, as the deaf people know and use sign language daily, but the real surprise was that deaf people also were about 100 milliseconds faster at recognizing non-language gestures than were hearing people,” Corina said.

This work is important because it suggests that the human ability for communication is modifiable and is not limited to speech, Corina said. Deaf people show us that language can be expressed by the hands and be perceived through the visual system. When this happens, deaf signers get the added benefit of being able to recognize non-language actions better than hearing people who do not know a sign language.

The study supports the idea that sign language is based on a modification of the system that all humans use to recognize gestures and ‘body language,’ rather than working through a completely different system, Corina said.

One implication is that deaf persons may be quite adept at picking up on subtle visual traits in the actions of others — which may be useful for some sensitive jobs, such as airport screening, Corina said.

The research was supported by grants from the National Institutes of Health and National Science Foundation.

Posted in Uncategorized | Leave a comment

Closing in on the ‘God particle’

December 13th, 2011 @ 11:49 am by Andy Fell

Image from the CMS. Copyright CERN

Physicists are closing in on the Higgs boson, the missing piece of the Standard Model of particle physics — but they aren’t quite there yet.

UC Davis physics professor Mani Tripathi said that although not yet conclusive, the results so far were a “shot in the arm” for the thousands of young scientists working on the project.

“The students and postdocs have been working very hard and such positive developments keep the enthusiasm level high,” he said.

Two international teams of thousands of scientists working at the Large Hadron Collider in CERN, Switzerland presented their latest results today. The ATLAS and CMS experiments have made progress in narrowing the energy range at which the Higgs could exist, but have yet to pin it down with enough statistical precision, or “five sigma” in mathematical jargon.

“The fact that the results from two different experiments, CMS and ATLAS, have an excess at basically the same mass, around 125 GeV, is very exciting,” said UC Davis physicist John Conway, who is a collaborator on the CMS experiment.

“When the results are combined in the coming weeks, the significance of this excess will be quite strong.  It won’t be the golden “five sigma” for discovery, but I think that there is every reason to believe this is the start of the exploration of the Higgs boson at the LHC.  There is much to do, and in the next year we’ll learn a lot more about it!”

“Of course it is exciting that both ATLAS and CMS see excesses consistent with the expectations for a SM (Standard Model) Higgs boson (or one that is close to SM-like) at 125 GeV (Giga electron-volts).  That they see such excesses consistent with the same mass persuades me that this is very unlikely to be a statistical fluctuation,” said UC Davis Professor Jack Gunion, who literally wrote the book — first published in 1983 — on how to hunt down the Higgs.

“It is quite striking that two independent experiments both find excess of events in the same region. This overlap is over and above the fact that various decay channels of the Higgs also find excesses in the same region.  If this is all a coincidence, nature is too cruel on us physicists!” Tripathi said. 

The Higgs particle is the missing piece of the Standard Model of particle physics, which effectively explains the behavior of the particles that make up the visible universe. The existence of the Higgs boson was proposed in the 1960s by British physicist Peter Higgs to explain why particles have mass. If Higgs bosons exist, according to theory, they can only appear for a fleeting time from extremely high energy collisions between other particles. The Large Hadron Collider, the most powerful particle accelerator ever built, was designed to produce these high energy collisions and identify the particles that spill out of them.

However, in recent years physicists and astronomers have discovered that most of the universe is made up of ‘dark matter’ and ‘dark energy’ that does not appear to be made of the same matter and energy as our visible universe. There is also a long-standing problem of reconciling the Standard Model, which deals with extremely small particles, with General Relativity, which describes the behavior of gravity on an extremely large scale.

Conclusively identifying — or ruling out — the Higgs boson would help physicists confirm or reject the various theories that aim to unify the Standard Model and Relativity or attempt to address dark matter and dark energy.

“Theoretically, if you accept a SM-like Higgs at 125 GeV, then this discards about 80 percent of the theories out there and strongly constrains many others.  If other types of new physics are seen (nothing so far) or strongly limited, the theoretical possibilities will become even more constrained,” Gunion said.

A number of UC Davis physicists are working on the Large Hadron Collider, especially at the CMS experiment which is run primarily by U.S. scientists.

Read my 2008 feature about the convergence of cosmology and particle physics for UC Davis magazine.

More information:

CERN press release

John Conway blogs on “Making the Higgs sausage”

 

 

Posted in Astronomy and space, General, Physical sciences, Technology | Leave a comment

Routing brain traffic for maximum alertness

December 7th, 2011 @ 2:40 pm by Andy Fell

A new UC Davis study shows how the brain reconfigures its functional connections to take best advantage of our knowledge of situations and minimize distractions.

“In order to behave efficiently, you want to process relevant sensory information as fast as possible, but relevance is determined by your current behavioral goals,” said Joy Geng, assistant professor of psychology at the UC Davis Center for Mind and Brain. For example, a flashing road sign alerts us to traffic merging ahead; or a startled animal might cue you to look out for a hidden predator.

When concentrating on a specific task, it’s helpful to reconfigure brain networks so that task-relevant information is processed most efficiently and external distractions are reduced, Geng said.

Geng and coauthor Nicholas DiQuattro, then a staff researcher and now a graduate student at UC Davis, used functional magnetic resonance imaging to study brain activity in volunteers carrying out a simple test. They compared their results to mathematical models to infer connectivity between different areas of the brain.

The subjects had to look for a letter ‘T’ in a box and say which way up it was by pressing a button. They were also presented with a ‘distractor:’ another letter T in a box, but rotated 90 degrees (see figure).

The distractor was either similar in appearance to the target, or brightened to be more attention-getting.

Subjects did better in trials with an ‘attention-getting’ distractor than a less obvious one, and lit up specific areas of the brain as it integrated the top-down signal from the brain – ‘the brighter object is going to be a distractor’ – with the bottom-up contextual signal – ‘here’s the brighter object.’

The new work shows that the brain doesn’t always “ramp up” to deal with the more salient situation, Geng said. Instead, it changes how traffic moves through the existing hard-wired network — rather like changing water flow through a network of pipes or information flow over a computer network in order to maximize efficiency.

The study is published in the Dec. 7 issue of the Journal of Neuroscience.

Posted in Biology, Health, Neuroscience, Psychology | Leave a comment

Learn about superconductivity at Emergent Universe

December 2nd, 2011 @ 10:28 am by Andy Fell

The online exhibit Emergent Universe has opened a new virtual wing, on ‘Superconductivity.’ Opened in 2009, Emergent Universe aims to encourage young people to learn about “emergence,” complex behaviors that arise from interactions of simple parts, and develop an “emergent perspective.” The site is sponsored by the Institute for Complex Adaptive Matter, based at UC Davis.

The new wing, “Resistance is futile,” uses animations, videos and text to show the science, history and potential uses of superconductivity, which occurs when the electrical resistance of a material drops to zero. Superconductors are already used to build powerful magnets for medical imaging devices and bullet trains. As scientists discover new materials that are superconductors at higher temperatures, they could find even more uses — for example rebuilding the electrical grid so that energy can be sent long distances with little or no loss of power. They could also be used to tell the difference between a cargo of kitty litter and an atomic bomb.

Included in the exhibit is this video of a flash mob at the University of Washington, illustrating how electrons start to move in synch as a conducting material reaches superconducting temperatures.

This year marks the hundredth anniversary of the discovery of superconductivity by scientists in Leiden, the Netherlands.

The site was designed and built by Suzi Tucker, a former chemistry professor at UC Davis, with interactive designer Stephen Hartzog and scientific input from Pines, UC Davis physics professor Daniel Cox, and other members of the Institute for Complex Adaptive Matter.

 

Posted in Computer science, Education, Energy, Engineering, General, Materials science, Physical sciences | Leave a comment

UC Davis a leader for women in Chemistry

November 29th, 2011 @ 3:57 pm by Andy Fell

A survey by Chemical & Engineering News Magazine features the UC Davis Department of Chemistry as one of the Top 5 Departments for Female Faculty among big spenders on chemistry research. With 10 female assistant, associate and full professors out of 40, UC Davis chemistry ranks on the Top Five for both the number of female faculty and by percentage.

Unfortunately, the overall figures are not good. C&E News reports that women held only 17 percent of the tenured and tenure-track positions at U.S. universities in 2010–11, up from 16 percent in the previous two years. C&E News notes that the figures have grown slowly but steadily from 10 percent in 2000-1, when the magazine began collecting data.

About 39 percent of graduate students in chemistry are women, according to National Science Foundation data cited in the article.

Back in 2007, I wrote about how both two UC Davis departments — Chemistry and Chemical Engineering and Materials Science — are national standouts in recruiting and retaining women faculty.

Posted in Chemistry, General | Leave a comment

Students take home trophy in synthetic biology competition

November 17th, 2011 @ 12:31 pm by Andy Fell

A team of four UC Davis undergraduates took home the trophy for best entry in their track at the Internationally Genetically Engineered Machine competition held at MIT Nov 5-7.

While other UC Davis students enter competitions to engineer cars or bridges, iGEM is an annual competition for undergraduate students working with life itself — in the new field of synthetic biology. Competing teams get a basic kit of parts and use them to build circuits that work in living cells.

The team members are, with majors (from the left): Nick Csicsery, biological systems engineering; Keegan Owsley, biomedical engineering; Aaron Heuckroth, microbiology and classics; and Tim Fenton, cell biology.

Going to the weekend competition was “one of the best weekends of my life,” Heuckroth said in an email.

“I’ve never met so many dedicated, intelligent and downright awesome people in such a short time. There’s a sense of camaraderie both within and between iGEM teams that’s unlike anything else I’ve experienced as an undergrad. You work 40, 50, 60 hours a week all summer on a project that you really, earnestly care about. Getting to share that enthusiasm with other people who understand not only the subject matter but the level of effort that went it is just an amazing experience.”

The UC Davis team began work in the Spring and did most of the work over the summer quarter, working in laboratories at the UC Davis Genome Center, said faculty advisor Marc Faccioti, professor of biomedical engineering.

The summer project gave them real experience of what it’s like to have full-time research position, and seeing like-minded people excited about their work was inspiring, Csicsery said.

“After finishing iGEM this year, I feel inspired to do more research and am more passionate about biology and engineering than I was before,” he said.

The team competed in ‘foundational advances,’ one of a number of available tracks within the competition. For their project, they decided to expand the range of ‘kit parts’ available to would-be genetic engineers.

These parts consist of genes called promoters and repressors, which, rather like resistors and transistors in electronic circuits, function to turn genes on or off or turn them up or down.

With these components in hand, scientists can build circuits to make cells carry out different functions, Faccioti said. For example, a cell might be engineered to change color when exposed to pollutants, churn out a useful drug, or to digest food to make biofuels.

The new ‘parts’ will be added to the Registry of Standard Biological Parts that is available to all scientists working in synthetic biology, Faccioti said.

Also advising the team were Ilias Tagkopoulos, professor in the Department of Computer Science and at the Genome Center; and graduate students Mike Starr and Lin Huynh. The team was sponsored by Novozymes Inc., the UC Davis Colleges of Engineering and of Biological Sciences, the UC Davis Genome Center, the Department of Biomedical Engineering and Fisher Scientific Inc.

More information about the iGEM World Championship, including photos and video, is available here.

 

Posted in Biology, Biotech, Engineering, General, Technology | Leave a comment

Wrapping sorts carbon nanotubes

November 16th, 2011 @ 12:29 pm by Andy Fell

Carbon nanotube wrapper

Carbon nanotubes – sheets of carbon atoms rolled up into tiny cylinders or tubes – have many interesting properties and potential uses, for example in flexible display screens or printed circuits. Some act like conducting metals, and others are semiconductors. But when chemists make these nanotubes, the different types are usually mixed together. Now researchers at Stanford University have come up with a polymer material that can sort separate the different types of nanotubes, and with help from computational scientists at UC Davis they have been able to figure out how it works.

“It’s an example of a theory/experiment collaboration that has worked really well,” said Giulia Galli, professor of chemistry at UC Davis and a co-author on the paper, published Nov. 15 in the journal Nature Communications. Francois Gygi, professor of computer science at UC Davis, is also a coauthor on the paper by Hang Woo Lee, Zhenan Bao and colleagues at Stanford University.

“Sorting has been a major bottleneck for carbon nanotubes to be viable for practical electronics applications,” Bao said in a Stanford University news release. “This work solves the problem of separating the conducting from the semiconducting nanotubes.”

The researchers used a polymer that, when mixed with carbon nanotubes in a solvent, selectively wraps around semiconducting nanotubes but not conducting nanotubes.

The group tested nearly 200 individual nanotubes to confirm that the polymer only wraps around semiconducting tubes and not conducting tubes. To explain how the polymer wraps around the carbon nanotube, Galli and Gygi modeled the geometry of a semiconducting carbon nanotube and its polymer shell using the Qbox software written by Gygi.

According to Galli, the model provides “a theoretical explanation of how this polymer actually interacts with the nanotube.” The polymer has a long, rigid backbone, with regular arm-like molecular chains along each side. The side chains fit together like fingers, making a ribbon of polymer that wraps around the semiconducting nanotubes.

The Stanford team were then able to confirm that model through experiments.

The calculations for the modeling were carried out using computer cluster at UC Davis, as well as the National Science Foundation Teragrid supercomputers.

Stanford University news release

Posted in Chemistry, Computer science, Materials science, Nanotechnology, Physical sciences | Leave a comment