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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.

UC Davis biosci major wins Hughes fellowship for grad school

Congratulations to Brenda Marin-Rodriguez, an undergraduate student in the UC Davis College of Biological Sciences, who has been awarded one of nine Gilliam Fellowships for Advanced Study by the Howard Hughes Medical Institute. The fellowships provide $46,500 per year for up to four years to outstanding students from underrepresented groups pursuing graduate studies in life sciences.

Marin-Rodriguez, who is from Puerto Rico, has finished her classes at UC Davis and will graduate in June, 2013. She is currently an intern in the laboratory of Catherine Dulac at Harvard University, supported by an HHMI Capstone award. After graduating, she plans to pursue a Ph.D. in molecular biology, but hasn’t settled on a specific school yet.

Marin-Rodriguez originally came to UC Davis to study Animal Science, with the aim of going to vet school. But she found that the science classes in her schools had not prepared her for college-level study.

“When I arrived as a first year undergraduate and sat down in my first real science lecture, I felt completely mystified. Fortunately, I received a lot of help and guidance from an undergraduate research program called BUSP (Biology Undergraduate Scholars Program),” Marin-Rodriguez said. She also got help through the Special Transitional Enrichment Program (STEP) and MARCUSTAR/BSHARP (Biological Scholars Advanced Research Program).

In her second year as an undergraduate, Marin-Rodriguez began working in the laboratory of the late Simon Chan in the Department of Plant Biology, where she worked on a number of research projects. Papers from some of those projects are to be published this summer.

 

Girls Who Code summer program kicks off with Girl Rising premiere

Intel Corp.’s Girls Who Code program will be coming to UC Davis this summer. Now in its second year, Girls Who Code aims to educate and inspire 13- to 17-year-old girls to pursue opportunities in technology and engineering.

UC Davis is the first university to be a Girls Who Code training site, according to Professor Ray Rodriguez, director of the Global HealthShare Initiative at UC Davis, who is coordinating the local effort.

‘This projects fits will with Global HealthShare’s mission to improve health, wellness and prosperity in the developing world, starting with health and education for girls and women.  Global HealthShare has a collaboration with a agricultural college in India who will be working with us toward this end,” Rodriguez said.

About 20 girls, 15 to 17 selected from the surrounding area will participate in the 8-week Girls Who Code class at UC Davis this summer. Other training sites nationwide include Intel, Goldman Sachs, Twitter, Google, and eBay.

Girls Who Code kicked off last Thursday, March 7 with premiere screenings of a new documentary, “Girls Rising.” The film tells the stories of nine girls growing up around the world with the voices of stars including Cate Blanchett, Anne Hathaway, Selena Gomez and Meryl Streep.  nicholas wray, sacramento photographerThe local premiere was at the IMAX Theater in Sacramento: pictured on the red carpet, from left to right are: Leroy Tripette, Intel Corporate External Affairs Manager; Christina Chin, head of Corporate Affairs; Tammy Cyphert, VP Intel Architecture Group, GM PC Client Operations and Outbound Marketing; and Rodriguez, with a check for $100,000 to support Girls Who Code at UC Davis this summer.

More: Girl Rising trailer

Rock to Renaissance musicologist wins UC Davis teaching prize

The “History of Rock” class taught by Professor Christopher Reynolds of the music department was interrupted this morning by Chancellor Linda Katehi, bringing a cake styled like a Fender electric guitar. guitar-cake-lg

Yes, Reynolds is the 2013 winner of the  UC Davis Prize for Undergraduate Teaching and Scholarly Achievement.

Established in 1986, the $45,000 prize is believed to be the largest of its kind in the country and is funded through philanthropic gifts managed by the UC Davis Foundation. The winner is selected based on the nominations of other professors, research peers, representatives from the UC Davis Foundation Board of Trustees, and students.

Reynolds’ interests in music range from “Papal Patronage and the Music of St. Peter’s, 1380-1513” (UC Press, 1995) to Beethoven (he is founding editor of the journal, Beethoven Studies), Wagner, Led Zeppelin and Jimi Hendrix, who famously set a guitar on fire on stage (not something recommended for university property, of course).

He has also collected thousands of copies of sheet music of songs composed by women, which he has donated to the University Library.

Read more here.

 

 

Bioengineered cartilage: low oxygen makes it stronger

A new study published this month by Kyriacos A. Athanasiou’s lab in the Biomedical Engineering Department at UC Davis has shown for the first time that depriving cartilage cells of oxygen at just the right time increases collagen crosslinks and doubles the tensile properties of engineered cartilage.

Healthy cartilage allows joints to move freely, but injured cartilage cannot heal itself and leads to debilitating conditions. Cartilage is composed largely of interlinked collagen fibers that give it strength and resilience. Athanasiou and his team want to produce engineered cartilage tissue that could restore damaged cartilage in humans.

Lately, emphasis has been placed on enhancing collagen type and quantity to improve the mechanical properties of engineered cartilage. However, not much attention has been placed on promoting collagen crosslinking in the engineered tissues, either in cartilage or in other, collagen-rich tissues whose primary function is biomechanical.

The new study by Eleftherios Makris, Jerry Hu, and Athanasiou shows that collagen tensile properties can be improved without affecting collagen type or quantity by enhancing crosslinks through reducing oxygen levels at the right time. They showed that hypoxia upregulates  an enzyme called LOX, which crosslinks collagen. Reducing the cell’s oxygen exposure to 4 percent makes the LOX gene about 20-times more active, leading to more crosslinks and significant increases in engineered cartilage’s mechanical properties.  These benefits were only seen when hypoxia was applied during the third and fourth weeks of neotissue development.

“Since collagen is produced mostly during the early phases of neocartilage development, applying hypoxia too early disrupts its formation. We realized that, to improve the tensile properties of engineered cartilage, hypoxia should be applied after collagen already exists and is ready to be crosslinked,” Makris explained.

The study suggests that previous work using hypoxia has seen mixed success because it had not been clear that hypoxia can be both beneficial and detrimental, depending on when it is applied.  The researchers believe that hypoxia during the early collagen synthesis phase activates the maturation process in the tissue, promoting collagen crosslinking but also blocking the synthetic process of the cells, resulting in low collagen. This, in turn, leads to poor biomechanical properties.

By applying hypoxia after the correct types of collagen are already present, crosslinks were induced without compromising collagen content. Since most of the body’s tissues contain collagen, this work might inform researchers interested in engineering other tissues.

Contributed by Holly Ober, Department of Biomedical Engineering

UC Davis Physics, Milton Gardner and the President of China

Wednesday afternoon I joined a delegation of Chinese journalists, including the China News Service and People’s Daily, visiting UC Davis as they met with faculty and students of the Physics Department. Earlier, the group had lunch with Winston Ko, dean of mathematical and physical sciences, and met with Chancellor Linda Katehi.

Why are the Chinese media interested in UC Davis Physics? Apart from the growing scientific collaborations and flow of international students, there is an interesting little tale that links the Chinese leadership and the campus.

Milton Gardner was one of the original three faculty members of the UC Davis Department of Physics when it was formed in 1953. Gardner was born in China, where his parents were missionaries, and spent the first years of his life there before moving back to the U.S. in 1911. Towards the end of his life, he often spoke of the village where he was born, “Guling” but was never able to return there. Gardner’s widow, Elizabeth tried to fulfill his wish by visiting the village, but was not able to find it.

A Chinese student who had lodged with the Gardners identified the village as being near Fuzhou in Fujian province. He wrote an article on the story that was published in the People’s Daily. The story caught the eye of the party chief of Fuzhou, Xi Jinping, who arranged for Elizabeth Gardner to finally visit Guling in 1992 and meet childhood friends of her late husband.

Xi Jinping went on to rise through the Chinese leadership. In February last year, as Vice President of the People’s Republic, he visited the U.S. where he recounted the story. In November 2012, Xi became General Secretary of the Chinese Communist Party and is expected to succeed Hu Jintao as President this year.

Professor emeritus Joe Kiskis told the delegation some anecdotes about Gardner as a teacher. Kiskis took Gardner’s introductory physics class as an undergraduate at UC Davis in the 1960s. The professor was fond of setting “fiendishly difficult” pulley problems that challenged students to grasp fundamental concepts, Kiskis recalled, and was exacting in how students wrote up and presented their work.

Most of the class was made up of engineering majors rather than physics undergraduates, Kiskis went on. Gardner would tease the engineers, claiming that the engineers “just wanted a formula so they could turn a handle and get a result.”

On his retirement in 1968, the Society of Engineering Students presented Gardner with a slide rule, equipped with hand crank, mounted on a plaque declaring Gardner an “honorary engineer.”

This slide rule was presented to Prof. Milton Gardner on his retirement in 1968 by the Student Engineering Society.

This slide rule was presented to Prof. Milton Gardner on his retirement in 1968 by the Student Engineering Society.

Clues to chromosome crossovers

Neil Hunter’s laboratory in the UC Davis College of Biological Sciences has placed another piece in the puzzle of how sexual reproduction shuffles genes while making sure sperm and eggs get the right number of chromosomes.

The basis of sexual reproduction is that a fertilized egg gets half its chromosomes from each parent — sperm and eggs each contributing one partner in each pair of chromosomes. We humans have 23 pairs of 46 chromosomes: so our sperm or eggs have 23 chromosomes each.

Before we get to the sex part, though, those sperm and eggs have to be formed from regular body cells that contain twice as many chromosomes. That happens through a specialized type of cell division, meiosis.

During meiosis, the couples in each pair of chromosomes have to, well, couple by “crossing over” with each other. Each chromosome pair must become connected by at least one crossover so that when the couples separate, they are delivered to separate sperm or egg cells.

These crossovers also mean that chromosomes can exchange chunks of DNA with each other, shuffling the genetic deck for the next generation. But if too few crossovers are formed, gametes end up with the wrong number for chromosomes, a situation that can cause infertility, pregnancy miscarriage or chromosomal diseases such as Down Syndrome.

Large-scale studies of human genetics have shown that the number of crossovers formed during meiosis is under genetic control. Moreover, women that make more crossovers tend to have more children. One gene suggested to control crossover numbers in humans, called Rnf212, is the subject of a new study by UC Davis researchers lead by Professor Neil Hunter.

Hunter studies how crossovers form and chromosomes separate at the UC Davis Department of Microbiology & Molecular Genetics and the Comprehensive Cancer Center. In 2009, he was awarded an early career fellowship from the Howard Hughes Medical Institute.

Chromosome pairs entwined during meiosis. Green spots show the location of RNF212. (Neil Hunter/UC Davis)The latest paper from Hunter’s lab, published Feb. 10 in Nature Genetics, shows that Rnf212 is essential for crossing-over in mammalian cells. Crossovers form by a process called homologous recombination, in which chromosomes are first broken and then repaired by coupling with a matching template chromosome. Although hundreds of recombination events are started in each cell, only one or two crossovers will form between any given pair of chromosomes.

“There isn’t a special, predetermined site for a crossover. It can occur just about anywhere along a chromosome. But there has to be at least one and there always is,” Hunter said.

In a series of experiments in mouse cells, graduate student April Reynolds, Hunter and colleagues found that the RNF212 protein defines where crossovers will occur by binding to just one or two recombination sites per chromosome where it triggers the accumulation of the protein machinery that actually carries out the cutting and splicing of DNA.

Mice that lacked the gene for RNF212 were sterile. Mice that had one working copy of the gene were fertile, but on careful examination there were fewer crossovers formed while sperm and eggs were being made than in normal mice, potentially reducing fertility. It’s possible that this might be tied to some causes of infertility in humans.

It remains unclear how each pair of chromosomes always manages to crossover at least once. But Hunter says he is, “convinced that RNF212 holds the key to understanding this unique problem in chromosome biology.”

The full author list of the paper is: April Reynolds, Huanyu Qiao, Ye Yang, Jefferson Chen, Neil Jackson, and Kajal Biswas, all in Hunter’s laboratory at UC Davis; J Kim Holloway, Cornell University; Frédéric Baudat and Bernard de Massy, Centre National de Recherche Scientifique, Montpellier, France; Jeremy Wang, University of Pennsylvania; Christer Höög, Karolinska Institutet, Stockholm, Sweden; Paula Cohen, Cornell University; & Neil Hunter.

The work was supported by NIH and HHMI.

Ithaca school robotics team builds augmented reality sandbox on UC Davis design

A high school robotics team in Ithaca, New York has built their own augmented reality sandbox, based on the model built by Oliver Kreylos and colleagues at UC Davis’s Keck Center for Active Visualization in Earth Sciences (KeckCAVES). A video of the UC Davis sandbox went viral last year, attracting over one and half million views to date.

The sandbox uses a Kinect controller from a Microsoft Xbox game console and a digital projector to read contours on real sand and project images such as contours or flowing water onto the sand.

“The sandbox teaches geology and topography to younger children,” Ithaca High senior Mike Guo told the Ithaca Journal, “and older kids can appreciate and explore the technical side of the simulation.”

Local kids try out the sandbox built by Ithaca High School students based on a UC Davis design.

Local kids try out the sandbox built by Ithaca High School students based on a UC Davis design.

The Ithaca students plan to donate the sandbox to a local science education center.

KeckCAVES team members are thrilled others are using their design.

“This is a great example of how small scientific outreach projects here at Davis can have positive impacts on kids on the other side of the country,” said Magali Billen, a professor of geophysics at UC Davis and a member of the KeckCAVES team.

Professor Louise Kellogg noted that a high school in Perth, Australia has also built a sandbox. The UC Davis team plans to install sandboxes at three science centers nationwide: the ECHO Center at Lake Champlain, Vermont; the Lawrence Hall of Science in Berkeley; and at the Tahoe Environmental Research Center at Lake Tahoe.

More information about the UC Davis AR sandbox.

Want to build your own? How-to videos available here.

Here’s the original video of the UC Davis sandbox.

 

Six elected as Fellows of the American Physical Society

Congratulations to six faculty members from the Department of Physics have been elected as Fellows of the American Physical Society. They are:

Professor Nemanja Kaloper: For numerous and imaginative contributions to theoretical cosmology, particularly for his pioneering work in the physics and cosmology of “braneworlds” or theories involving extra dimensions of the universe. Kaloper has also made important contributions to theories of early universe inflation and dark energy.

Professor Lloyd Knox: For his work on studying the cosmic microwave background.

The Planck Space Observatory

The Planck Space Observatory

Knox currently leads the US team for the Planck observatory, a space telescope launched in 2009 to study microwave radiation that dates back to the beginning of the universe. He also works with the South Pole Telescope team measuring signals he predicted over the past 15 years.

Professor Kai Liu: For his work on magnetic effects in nanomaterials, including contributions to the understanding of magnetoresistance effects, exchange bias, and magnetization reversal in magnetic nanostructures.

Professor Sergej Savrasov: For his innovative design and implementation of electronic structure algorithms and software, and for his many contributions to a microscopic understanding of superconductors, magnetic materials, and strongly correlated electron systems.

Professor Robert Svoboda: For his numerous contributions to the study of the neutrino, and development of technologies for neutrino detection. His contributions include the first observation of neutrinos from the supernova SN1987A, and development of large underground neutrino detectors such as the Irvine-Michigan-Brookhaven detector in the U.S. and the Super-Kamikande and Kamland experiments in Japan, that have resulted in the definitive discovery of neutrino oscillations.

Professor Gergely Zimanyi: For contributions to the theory of strongly correlated systems, vortices, and magnetic hysteresis in materials.

Fellows are elected for exceptional contributions to the physics enterprise. Election as a fellow is an honor signifying recognition by one’s peers.

UC Davis tech incubator admits three new startups

Three new UC Davis startup companies working in clean hydrogen production, chip-scale magnetic sensors and tissue engineering have been admitted to the Engineering Translational Technology Center at the College of Engineering.

Woodall Tech, Inc.

Founded by Jerry Woodall, a distinguished professor in the Department of Electrical and Computer Engineering, Woodall Tech, Inc. discovered a proprietary bulk aluminum alloy that splits water to generate hydrogen gas, with byproducts of aluminum hydroxide and heat. The process eliminates the need for hydrogen storage and transport, mitigating the major barriers to a sustainable hydrogen economy. Initial market is the low power fuel cell industry. Woodall Tech creates and stores ultra-pure hydrogen, independently tested at 99.9993% pure, at low temperatures and pressure using a green and economical process. Aluminum, the third most abundant element on the earth’s surface, is the main component to the process that uses recyclable raw materials. Other hydrogen fuel manufacturing methods burn fossil fuels to extract the hydrogen from water and methane, emitting carbon dioxide into the atmosphere.

Picosense LLC

Founded by Prof. David Horsley and post-doctoral fellow Andre Guedes from the Department of Mechanical and Aerospace Engineering, Picosense LLC is developing highly sensitive chip-scale magnetic sensors capable of measuring picotesla magnetic signals. Picosense LLC earned a National Science Foundation Small Business Innovation Research (SBIR) Phase I Grant for $150,000.

ViVita Technologies Inc.

Founded by Prof. Leigh Griffiths from the School of Veterinary Medicine and graduate students Maelene Wong, Regina MacBarb and Jennifer Lee from the Department of Biomedical Engineering, ViVita Technologies Inc. utilizes their patent-pending technology to generate animal tissue-derived scaffolds which are compatible with the human body and repopulation by patient cells. Given the critical need for superior heart valve replacement devices, a $2.5 billion global market, ViVita initially intends to apply their technology to produce a new generation of heart valve replacements. However, with success they plan to transition into all tissues and organs of the human body. Heart, muscle, small vessel, bone, liver, and cartilage applications are all under development.

Bruce White, the co-director of ETTC and an emeritus professor of mechanical and aerospace engineering, finds pride in the center’s progression. “The rapid development of ETTC is indicative of the innovative research being done at UC Davis. These new firms, together with the six incumbent start-ups, demonstrate the breadth of research excellence at our university. The possibilities to benefit society are almost unlimited.”

Established in 2010, the center helps technology startups, based on intellectual property developed at the UC Davis College of Engineering, attract support from external financial investors. ETTC assesses the commercial potential and developmental readiness of faculty research in determining admission into the incubator. ETTC provides member companies with campus workstations close to the college’s laboratories. Furthermore the center offers support, mentorship and introduction to investors and strategic partners. Members are selected for admission into the business incubator through a review process that includes an assessment of the commercial potential of the faculty research and its readiness for commercial development.

ETTC has already successfully launched two startups: Dysonics, developer of the Rondo Player, an iTunes application that reproduces and creates three-dimensional, immersive sound for headphones; and Ennetix, Inc., a clean-tech/networking company whose software EnergyPlus reduces energy consumed by IT networks and connected systems. To date, ETTC has admitted ten startups, eight of which are still receiving guidance.

More information:

Engineering Translational Technology Center: http://engineering.ucdavis.edu/research/ettc.html

Bruce White: brwhite@ucdavis.edu

Jim Olson: jimolson@ucdavis.edu

(Contributed by Paul Dorn, College of Engineering)

Test for hormone-disrupting chemicals gets global seal of approval

A test for hormone-disrupting pollutants, originally developed at the University of California, Davis, has been approved as an international standard by the Organization of Economic Cooperation and Development as well as by the U.S. government.

“Endocrine disruptors” are chemicals that interfere with the action of hormones on cells. There has been growing concern that such chemicals, from a wide variety of products, might have an impact on both human health and the environment.

Hormones such as estrogen act on cells by triggering a receptor on the cell surface, setting off a chain of events inside the cell. The new test uses a cell line, BG1Luc4e2, which produces a glowing firefly protein called luciferase when exposed to estrogens or similar chemicals.

The test was originally created by Professor Michael Denison and colleagues at the UC Davis Department of Environmental Toxicology. It has been validated by the National Toxicology Program at the U.S. Department of Health and Human Services and by the U.S. Environmental Protection Agency, and now by the OECD.

The test is licensed to users through UC Davis, in collaboration with UC San Diego and Promega, Inc. of Madison, Wisc., and which own patents on some components of the test. Typical customers are companies that carry out environmental testing for clients.

More information

Licensing information from the UC Davis Office of Research

OECD Performance standards for test (pdf)