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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.

End the U.S. innovation deficit, universities urge

A new video recently released online draws attention to the “Innovation Deficit” and the need for federal investments in research and education to support economic growth and American leadership in science and technology.

The video was produced at Colorado State University for the Association of Public and Land-grant Universities (APLU) and the Association of American Universities (AAU), both organizations to which UC Davis belongs. It’s part of a continuing campaign, including a website and Twitter feed, to draw attention to the negative effects of budget cuts and sequestration on federally-funded research.

“Investment in higher education is investment in economic growth,” wrote Chancellor Linda P. B. Katehi in an op-ed last December. “UC Davis alone accounts for 70,000 jobs and $7 billion in economic activity each year. Cutting off funding to our colleges and universities means fewer jobs, fewer dollars going to small businesses and fewer of the highly educated workers essential to our state’s economy.”

Katehi cited research on childhood asthma and agricultural diseases as just two areas where federally-funded research at UC Davis has had a direct impact on the well-being of Californians.

UC Davis has certainly benefitted from these federal investments in education and research, with a 335 percent increase in overall research funding since 1995. The campus still managed to increase research funding in the fiscal year ended June 30, 2013, to $754 million, and the federal government is still the largest single sponsor of research at UC Davis, at $356 million in 2012-13. Yet within those figures, federal funding fell by about $45 million.

The UC Davis Office of Research has set up a bridge funding program for researchers who have lost, or are about to lose, their primary extramural funding. The bridge program will provide up to $100,000 for a maximum of one year, allowing projects to continue and key staff to be retained while the investigator applies for new external grants.

Vice Chancellor for Research Harris Lewin also has established the Interdisciplinary Frontiers Program, investing $14.5 million in one-time internal funds to seed 20 new interdisciplinary research themes on campus in science, engineering, humanities and arts that could grow into major research centers and attract major external grants in the future.

In addition to APLU and AAU, the video was sponsored by a list of business and educational associations: Aerospace Industries Association, American Association for the Advancement of Science, American Council on Education, American Heart Association, Association of American Universities, Association of Public and Land-grant Universities, Business-Higher Education Forum, Council on Competitiveness, Federation of American Societies for Experimental Biology, Information Technology & Innovation Foundation, Semiconductor Industry Association, Task Force on American Innovation, The Science Coalition, and United for Medical Research.

UC Davis student team selected for national solar competition

A team of students from UC Davis has been selected to compete in the U.S. Department of Energy Solar Decathlon 2015. As competitions go, it’s a marathon, not a sprint: the  teams will have until Fall, 2015 to design, build and test their solar-powered homes at the test site at UC Irvine.

“Our team is very excited at the opportunity to compete in the Solar Decathlon in 2015. We plan to build an affordable zero net energy house that will serve as a prototype for commercialization of housing units for transient populations in the U.S.,” said Professor Frank Loge of the UC Davis Department of Civil and Environmental Engineering, who is coordinating the project, via e-mail.

“Our project builds upon UC Davis’ agricultural heritage and extensive working experience in zero net energy design and operation. Our project is a direct challenge to the notion that sustainable living is the province and concern of urban elites. To make a difference, ZNE must work for everyone and our project is an effort to make this sentiment a reality,” Loge said.

Loge said that the solar decathlon team will be composed of undergraduate and graduate students, lead by faculty and staff from many units across campus, including the Colleges of Engineering, Agricultural and Environmental Sciences, Letters and Science, the Graduate School of Management, and the School of Medicine. The core team will be composed of 20 students that will compete in the competition in October 2015, but over the course of the competition the project will touch many more students at the undergraduate and graduate level.

This is the first time UC Davis has taken part in the competition.

Details of the 2015 competition are to be announced today (Feb. 13) at an event at UC Irvine.

“As President Obama made clear in the State of the Union address, we need an all-of-the-above energy strategy that creates a safer and more sustainable planet, while ensuring American students and workers have the skills they need for the challenging jobs of today and tomorrow,” said Deputy U.S. Secretary of Energy Daniel Poneman in a news release.

“The Solar Decathlon provides the next generation of America’s architects, engineers, and entrepreneurs with the real world experience and training they need to strengthen U.S. innovation and support new, clean sources of energy.”

The program challenges 20 collegiate teams to design, build, and operate solar-powered houses that are cost-effective, energy-efficient, and attractive. The winner of the competition is the team that best blends affordability, consumer appeal, and design excellence with optimal energy production and maximum efficiency.

The first five competitions (2002, 2005, 2007, 2009 and 2011), were held on the National Mall in Washington, D.C. The 2013 competition was held in Orange County Great Park in Irvine, Calif. and the 2015 competition returns to the same location.

The Solar Decathlon enhances public understanding of how to save money at home with clean energy solutions available today and provides students with training and hands-on experience to prepare them for the clean energy workforce. Since 2002 the Solar Decathlon has involved 132 collegiate teams with nearly 20,000 participants, pursuing a multidisciplinary approach to study the requirements for designing and building energy-efficient, solar-powered houses.

In September 2011, UC Davis officially opened West Village, a 200-acre community designed to house 3,000 UC Davis students and 500 staff and faculty in apartments and single-family homes. Developed by a public-private partnership between UC Davis and West Village Community Partnership, a joint venture of Carmel Partners from San Francisco and Urban Villages from Denver, it is the largest planned zero net energy community in the U.S. It is on track to demonstrate, for the first time, that zero net energy is practical on a large scale.

More: news release from the U.S. Department of Energy

Social or Stinky? New study reveals how animal defenses evolve

When people see a skunk, the reaction usually is “Eww,” but when they see a group of meerkats peering around, they often think “Aww.”

Why some animals use noxious scents while others live in social groups to defend themselves against predators is the question that biologists Tim Caro of the University of California, Davis and Theodore Stankowich of California State University, Long Beach  and sought to answer through a comprehensive analysis of predator-prey interactions among carnivorous mammals and birds of prey.

Their findings appear in the online edition of the journal Evolution.Who me, stinky? Photo by Jennifer Hunter.

“The idea is that we’re trying to explain why certain antipredator traits evolved in some species but not others,” said Stankowich, who noted that this study not only explains why skunks are stinky and why banded mongooses live in groups but also breaks new ground in the methodology of estimating predation risks.

Caro, Stankowich and Paul Haverkamp, a geographer who recently completed his Ph.D. at UC Davis, collected data on 181 species of carnivores, a group in which many species are small and under threat from other animals. They ran a comparison of every possible predator-prey combination, correcting for a variety of natural history factors, to create a potential risk value that estimates the strength of natural selection due to predation from birds and other mammals.

They found that noxious spraying was favored by animals that were nocturnal and mostly at risk from other animals, while sociality was favored by animals that were active during the day and potentially vulnerable to birds of prey.

“Spraying is a good close-range defense in case you get surprised by a predator, so at night when you can’t detect things far away, you might be more likely to stumble upon a predator,” Stankowich said.

Conversely, small carnivores like mongooses and meerkats usually are active during the day which puts them at risk from birds of prey. Living in a large social group means “more eyes on the sky” in daytime, when threats can be detected further away.

The social animals also use other defenses such as calling out a warning to other members of their group or even mobbing together to bite and scratch an intruder to drive it away.

The project was a major information technology undertaking involving plotting the geographic range overlap of hundreds of mammal and bird species, but will have long-term benefits for ongoing studies. The researchers plan to make their database, nicknamed the “Geography of Fear,” available to other researchers.

Swedish laurels for physics professor

Charles Fadley, distinguished professor of physics at UC Davis and the Lawrence Berkeley National Laboratory, has been awarded an honorary doctorate by Uppsala University, Sweden. Fadley was one of four recipients of honorary doctorates in science and technology presented Jan. 24 at Uppsala, which was founded in 1477.

“His work, not least his synchrotron-light-based spectroscopic studies of surfaces, magnetic materials, and nanostructures, has inspired researchers around the world and at Uppsala,” according to the citation, which also noted Fadley’s service on two campus-wide research assessments at the Swedish university, in 2007 and 2011.

The presentation, complete with laurel wreaths, marks the “first and last occasion” of Fadley wearing a white tie and tails, he says (unless, we assume, he wins another major prize presented in Scandinavia). Luckily, there is photographic evidence:

Fadley_Tokura_Uppsala_Jan2014

 

Charles Fadley, left with Yoshinori Takura of Tokyo University, who also received an honorary doctorate.

Fadley has had a long association with Sweden, beginning with postdoctoral research in 1969. He was elected to the prestigious Royal Society of Sciences at Uppsala in 2009.

Policy makers, scientists agree: Water to dominate natural resource issues

A survey of scientists and policy makers identifies water supply as the most pressing environmental issue facing the U.S.. The results, published Feb. 5 in the journal BioScience, come as California suffers its worst drought in nearly half a century.

The survey, by Erica Fleishman of the John Muir Institute of the Environment at UC Davis and Murray Rudd the University of York, England, asked managers, policymakers and their advisers, and scientists to rank a series of questions on the environment and natural resources based on their applicability to policy.

A question on the water supply necessary to sustain human populations and ecosystem resilience was ranked as having the greatest potential, if it was answered, to increase the effectiveness of policies related to natural resource management in the U.S..

The survey found no evidence of differing priorities between academics and government employees, or between scientists (either government of academic) and policymakers.

The question emerged from a previous collaboration among decision makers and scientists that yielded 40 research questions that most reflected the needs of those with jurisdiction over natural resources. That research also was published in BioScience.

The 602 respondents included 194 policymakers, 70 government scientists, and 228 academic scientists.

Other questions that were ranked as of high importance to policy included those on methods for measuring the benefits humans receive from ecosystems; the effects of sea-level rise, storm surge, erosion and variable precipitation on coastal ecosystems and human communities; and the effect on carbon storage and ecosystem resilience of different management strategies for forests, grasslands, and agricultural systems.

DNA repair protein is a three-way zipper

New work from UC Davis explains how a protein motor named Rad54 helps both to form and to break down the “displacement loop,” or D-loop, a key intermediate in the important DNA repair pathway, homologous recombination.

Formation of the D-loop allows a cell to use a broken or damaged DNA molecule to locate and synthesize lost sequence from an intact “donor” DNA molecule containing the same sequence. The cell needs to do this in order to maintain its genome, and it is therefore of crucial importance in understanding the origins of cancer and birth defects.

“It’s a big step for the field because it’s been unclear what Rad54 does,” said Wolf-Dietrich Heyer, professor in the Departments of Microbiology and Molecular Genetics and of Molecular and Cellular Biology in the College of Biological Sciences and at the UC Davis Comprehensive Cancer Center. Heyer is coauthor of the paper published Jan. 30 in the journal Molecular Cell, along with graduate student William Douglass Wright.

Before DNA can be copied from the donor molecule, the damaged and donor DNA molecules have to find each other. A protein called Rad51 is responsible for lining a DNA strand and stretching it like a spring, so that the bases that make up the genetic code (A, C, G and T) can flip outwards.

During the search for the template from which to copy the missing information, Rad51 also stretches the donor DNA to match it to the broken DNA forming a unique three-stranded structure, the D-loop.

It’s been known that Rad54 both assists Rad51 in forming the D-loop and also disrupts D-loops, but until now it has not been clear how that happens.

Wright used purified DNA molecules with filaments of Rad51 to show that Rad54 acts as a pump that pushes a strand of the damaged DNA and a strand of the donor molecule through itself to create double-stranded DNA, knocking off Rad51 as it does so. Rad54 moves along DNA in the direction in which it detects Rad51.

In other words, presented with three-stranded DNA stretched open by Rad51, Rad54 moves along it, knocking out the Rad51 so that the structure can snap back into its normal form. Two strands are pushed together, but at the same time, another part of the Rad54 protein is in contact with the third strand of DNA, which is displaced.

graph abstract1So Rad54 is acting as a three-way zipper: it brings together two strands of DNA, while at the same time it separates a third strand of DNA that would otherwise interfere.

“This model consolidates both Rad51 removal and DNA zippering functions into one step,” Heyer said. It also helps place Rad54 in a class of other proteins that act as DNA pumps, for example during bacterial cell division.

The work was supported by grants from the National Institutes of Health, and a fellowship to Wright from the Tobacco-Related Disease Research Program.

“Real Revolutionaries Carry a Banjo:” Jesse Drew on Pete Seeger

Jesse Drew of the Cinema and Technocultural Studies program at UC Davis met legendary musician Pete Seeger several times, most recently during filming of his documentary, “Open Country.” Seeger died Jan. 27, and Prof. Drew just posted a remembrance, “Real Revolutionaries Carry a Banjo.”

Seeger should be considered a founder of country music, Drew argues:

Not folk music, mind you, as that has been around for some time. Coun­try music. Nashville, I believe, owes Pete a statue in the cen­ter of town.

Read the whole article here.

Seeger also recorded an intro for Davis community radio station KDRT:

 

UC Davis engineer works on Google’s smart contact lens for diabetics

Google recently announced that its Google[x] lab is working on a novel contact lens that could help people with diabetes monitor their blood sugar, by measuring glucose levels in tears.

Stephen O’Driscoll, a professor of electrical and computer engineering at UC Davis’ College of Engineering, is contributing to the project during a leave of absence at Google[x].

This contact lens can help diabetics monitor their blood glucose. (Google image).

This contact lens can help diabetics monitor their blood glucose. (Google image).

“We have heard some pretty moving reactions to the publicity from those suffering with diabetes and from their loved ones,” O’Driscoll wrote in an email. “There are still some questions to answer and work to do but such feedback is a big motivation to get this completed.”

This project builds on work begun at the University of Washington by Brian Otis and Babak Parviz, both now working at Google[x]. O’Driscoll worked on part of the integrated circuit design and led the wireless design.

O’Driscoll’s expertise is in designing circuits for use in biomedical devices that can be implanted or worn on the body. In 2013, he received a prestigious early career award from the National Science Foundation to support his work on electronics for implantable devices.

Previous innovations from the Google[x] lab include the Google driverless car and the Google Glass augmented reality headset. “It’s a dream location for an engineer,” O’Driscoll says.

O’Driscoll said he was grateful to the university, the College of Engineering and his department for giving him the opportunity to take an unpaid leave at Google.

“It has been a great experience to contribute to a device which may change many people’s lives for the better and to work with the resources that allow us to turn a research concept into a viable device. Those experiences will, I hope, enrich me as an engineering researcher and teacher,” he said.

A native of Ireland, O’Driscoll worked as a design engineer at Cypress Semiconductor in San Jose before completing his master’s and doctorate degrees at Stanford University. He joined the faculty at UC Davis in 2009.

New anthrax-killing virus from Africa is unusually large

From a zebra carcass on the plains of Namibia in Southern Africa, an international team of researchers has discovered a new, unusually large virus (or bacteriophage) that infects the bacterium that causes anthrax. The novel bacteriophage could eventually open up new ways to detect, treat or decontaminate the anthrax bacillus and its relatives that cause food poisoning. The work is published Jan. 27 in the journal PLOS One.

The virus was isolated from samples collected from carcasses of zebras that died of anthrax in Etosha National Park, Namibia. The anthrax bacterium, Bacillus anthracis, forms spores that survive in soil for long periods. Zebras are infected when they pick up the spores while grazing; the bacteria multiply and when the animal dies, they form spores that return to the soil as the carcass decomposes.

Photo: Vultures gather at a zebra carcass (Holly Ganz/UC Davis)
zebra_carcass

While anthrax is caused by a bacterium that invades and kills its animal host, bacteriophages, literally “bacteria eaters” are viruses that invade and kill bacterial hosts.

The first thing the team noticed was that the virus was a voracious predator of the anthrax bacterium, said Holly Ganz, a research scientist at the UC Davis Genome Center and first author on the paper.

Photo: The Tsamsa phage is unusually large (SEM by Jochen Klumpp/ETH Zurich) tsamsa_virus

They also noticed that the new virus, named Bacillus phage Tsamsa, is unusually large, with a giant head, a long tail and a large genome, placing it among the largest known bacteriophages.

Tsamsa infects not only B. anthracis but also some closely related bacteria, including strains of Bacillus cereus, which can cause food poisoning. Sequencing the genome allowed researchers to identify the gene for lysin, an enzyme that the virus uses to kill bacterial cells, that has potential use as an antibiotic or disinfecting agent.

Bacteriophages are often highly specific to a particular strain of bacteria, and when they were first discovered in the early 20th century there was strong interest in them as antimicrobial agents. But the discovery of penicillin and other antibiotics eclipsed phage treatments in the West, although research continued in the Soviet Union.

“With growing concerns about antibiotic resistance and superbugs, people are coming back to look at phages,” said Ganz said.

One advantage of bacteriophages is that because they tend to be very specific, they can potentially target only “bad” bacteria while leaving beneficial bacteria unharmed. Also, phages evolve with the host and have the potential to overcome bacterial resistance, said coauthor Jochen Klumpp of the Institute of Food, Nutrition and Health, ETH Zurich.

Ganz began the work as a postdoctoral scientist on a team led by Wayne Getz, Professor of Environmental Science, Policy and Management at UC Berkeley and at the University of KwaZulu-Natal, South Africa. Sequencing of the phage genome was conducted at UC Davis after Ganz joined the laboratory of Professor Jonathan Eisen.

Ganz said that she hoped the publication of the phage’s sequence information would enable other researchers to investigate further and potentially develop applications for the phage and its proteins.

“You might use it to detect the anthrax bacillus or B. cereus; use it as an alternative to antibiotics or as part of a decontaminant,” she said.

Other authors on the study in addition to Ganz, Getz and Klumpp are: Christina Law and Richard Calendar, UC Berkeley; Martina Schmuki, Fritz Eichenseher, and Martin Loessner, ETH Zurich, Switzerland; Jonas Korlach, Pacific Biosciences, Menlo Park, Calif.; and Wolfgang Beyer, University of Hohenheim, Stuttgart, Germany. The work was supported by the NIH.

Probing hydrogen catalyst assembly, part II

Biochemical reactions sometimes have to handle dangerous things in a safe way. New work from researchers at UC Davis and Stanford University shows how cyanide and carbon monoxide are safely bound to an iron atom to construct an enzyme that can generate hydrogen gas. The work is published Jan. 24 in the journal Science.

Producing hydrogen with catalysts based on abundant metals, such as iron, is key to hopes of using hydrogen to replace carbon-based fuels. But before you can make hydrogen, you have to make the catalyst that enables the reaction –something bacteria have been able to do for millennia.

Video: Dave Britt discusses the chemistry of forming hydrogen catalysts

Jon Kuchenreuther, a postdoctoral researcher working with Professor Dave Britt, project scientist Simon George and colleagues at the UC Davis Department of Chemistry, with James Swartz and colleagues at Stanford, used a variety of analysis techniques to study the chain of chemical reactions that assembles these catalysts based on clusters of iron and sulfur atoms adorned with cyanide (CN) and carbon monoxide (CO) molecules.

“How does biology make these complicated active sites?” Britt said. “You can’t release cyanide or carbon monoxide into the cell. It turns out that it’s formed and kept on iron throughout.”

In work published in Science last year, the researchers showed that the amino acid tyrosine first binds to the iron/sulfur cluster, and is then split by the enzyme HydG to create a radical. The new paper picks up the story from there, showing that carbon monoxide and cyanide derived from the splitting of tyrosine, remain bound to the same iron atom as the tyrosine radical is removed. This iron/cyanide/carbon monoxide structure becomes part of the final cluster.

The team principally used a technique called Fourier Transform Infra Red spectroscopy to follow the process. FTIR measures vibrations in bond length, and both cyanide and carbon monoxide show strong signals with this method.

Metal atoms in biological molecules are usually bound to large structures, like amino acids or heme groups, Britt said. For metals to be bound to small molecules, like carbon monoxide and cyanide, is “some unusual chemistry by itself,” he said.

Other authors on the paper are: at UC Davis, Professor Stephen Cramer, postdoctoral researchers Jon Kuchenreuther, William Myers, Daniel Suess and Troy Stich; Vladimir Pelmenschikov, Technical University of Berlin; and Stacey Shiigi, Stanford University. The work was supported by grants from the U.S. Department of Energy.

Previously: Unique chemistry in hydrogen catalysts (news release, Oct. 2013)