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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.

Hybrid “super mosquito” resistant to insecticide-treated bed nets

Interbreeding of two malaria mosquito species in the West African country of Mali has resulted in a “super mosquito” hybrid that’s resistant to insecticide-treated bed nets.

“It’s ‘super’ with respect to its ability to survive exposure to the insecticides on treated bed nets,” said medical entomologist Gregory Lanzaro of UC Davis, who led the research team.

The research, published Jan. 6 in the Proceedings of the National Academy of Sciences, “provides convincing evidence indicating that a man-made change in the environment — the introduction of insecticides — has altered the evolutionary relationship between two species, in this case a breakdown in the reproductive isolation that separates them,” said Lanzaro, who is director of the Vector Genetics Laboratory and professor in the Department of Pathology, Microbiology and Immunology in the School of Veterinary Medicine.

“What we provide in this new paper is an example of one unusual mechanism that has promoted the rapid evolution of insecticide resistance in one of the major malaria mosquito species.”

Anopheles gambiae, a major malaria vector, is interbreeding with isolated pockets of another malaria mosquito, A. coluzzii. Entomologists initially considered them as the “M and S forms” of Anopheles gambiae. They are now recognized as separate species.

"AnophelesGambiaemosquito" by James D. GathanyOriginal uploader was Kpjas at en.wikipedia - Originally from en.wikipedia; description page is/was here.The Public Health Image Library , ID#444. Licensed under Public Domain via Wikimedia Commons - http://commons.wikimedia.org/wiki/File:AnophelesGambiaemosquito.jpg#mediaviewer/File:AnophelesGambiaemosquito.jpg

Anopheles gambiae mosquito by James D. Gathany. The Public Health Image Library , ID#444.

The insecticide resistance came as no surprise. “Growing resistance has been observed for some time,” Lanzaro said. “Recently it has reached a level at some localities in Africa where it is resulting in the failure of the nets to provide meaningful control, and it is my opinion that this will increase.”

Lanzaro credits insecticide-treated nets with saving many thousands, probably tens of thousands of lives in Mali alone. The World Health Organization’s World Malaria Report indicates that deaths from malaria worldwide have decreased by 47 percent since 2000. Much of that is attributed to the insecticide-treated bed nets.

However, it was just a matter of time for insecticide resistance to emerge, medical entomologists and epidemiologist agree. Now there’s “an urgent need to develop new and effective malaria vector control strategies,” Lanzaro said. A number of new strategies are in development, including new insecticides, biological agents — including mosquito-killing bacteria and fungi — and genetic manipulation of mosquitoes aimed at either killing them or altering their ability to transmit the malaria parasite.

First author on the paper is Laura Norris, a postdoctoral scholar in the UC Davis Department of Entomology and Nematology who was supported by a National Institutes of Health training grant awarded to Lanzaro. She has since accepted a position with the President’s Malaria Initiative in Washington, D.C.

Other co-authors include, at UC Davis, Anthony Cornel, Yoosook Lee, Bradley Main and Travis Collier; and Abdrahamane Fofana of the Malaria Research and Training Center at the University of Bamako, Mali. Three grants from the National Institutes of Health funded the research.

Lanzaro has researched mosquitos in Mali for 24 years with Cornel, who is an associate professor in the UC Davis Department of Entomology and Nematology and headquartered at the UC Kearney Agriculture and Research Center, Parlier. Both are graduate student advisors in the department, training medical entomologists of tomorrow.

Contributed by Kathy Keatley Garvey.

Unraveling root growth control network

Green shoots are a sign of spring, but growing those shoots and roots is a complicated process. Now researchers at UC Davis and the University of Massachusetts Amherst have for the first time described part of the network of genetic controls that allows a plant to grow.

Plant stems and roots are built around xylem, long, hollow cells that act both as plumbing — carrying water and minerals around the plant — and as structural material. The structural strength of xylem comes from a secondary cell wall, inside the outer cell wall, which is made either of helical fibers or of perforated sheets. This secondary cell wall is made from three molecules: cellulose and hemicellulose, which are essentially sugars, and lignin, which provides strength.

Researchers interested in making biofuels from plants would like to get the sugars out of plant material without interference from too much lignin.

UC Davis graduate student Mallorie Taylor-Teeples and postdoctoral researcher Miguel de Lucas, working with Siobhan Brady, assistant professor of plant biology at UC Davis, Sam Hazen at U. Mass Amherst and others, cloned 50 genes involved in producing cellulose, hemicellulose and lignin in the lab plant Arabidopsis and screened them for interactions with more than 460 transcription factors, or genes that turn other genes on or off.

With help from UC Davis computer scientist Ilias Tagkopoulos and colleagues at the UC Davis Genome Center, the researchers were able to construct a network showing how the different genes and transcription factors are connected to each other. The results were published online Dec. 24 by the journal Nature.

“This is the first time that such a network has been worked out at this level in a plant,” Brady said. “It helps us think about how these networks are engineered and controlled.”

Notably, the network contains a large number of “feed-forward loops,” Brady said. In an example of a feed-forward loop, transcription factor X acts on factor Y, which in turn acts on gene Z. But X can also act directly on Z. Such systems are well-known in other control networks, reducing random “noise” and allowing precise coordination of different steps without a central core regulator.

The researchers were also able to study how the system reacts to different types of environmental changes. For example depriving root cells of iron promotes lignin production, which increases iron uptake. But exposing cells to salt causes a different response in which xylem cells proliferate to increase water transport.

Understanding the network of controls that influences lignin, cellulose and hemicellulose content might eventually help plant breeders create varieties best suited for harvesting for biofuel production, Brady said.

The findings grew out of more than seven years work, based on a wide range of data from genetics and plant physiology to computer science and drawing on the resources and expertise of the UC Davis Genome Center as well as U. Mass Amherst, UC Berkeley, the Cold Spring Harbor Laboratory, the U.S. Department of Agriculture laboratory in Ithaca, New York, UC San Diego and the University of Cambridge. Funding was provided by the U.S. Department of Energy, National Institutes of Health, National Science Foundation, USDA, the Royal Society (U.K.), UC Davis and the Hellman Foundation.

More information: Seeing the wood and the trees (Nature News & Views)

Wine cork or screwcap? It depends on aging

The winter holidays have brought many occasions to celebrate with wine and notice the variety of closures now being used to seal wines. As the New Year kicks off, you may find yourself wondering which type of closure is the best and whether that choice is consistent for all wines.

Andrew Waterhouse, professor and wine chemist in the UC Davis Department Viticulture and Enology, offers some research-based advice in an article recently published in The Conversation, an online publication written by academics.

The optimal wine closure depends largely on how long that wine will be allowed to age in the bottle, he advises. Will you be drinking the wine within two years of its production or will it be held in the bottle – either in the winery or at your home – for several years to maximize the flavor?

Andrew Waterhouse's lab at UC Davis studies wine chemistry.

Andrew Waterhouse’s lab at UC Davis studies wine chemistry.

“The way a bottle is sealed will directly affect how much oxygen passes into the wine each year. That will directly affect the aging trajectory and determine when that wine will be at its “best,” writes Waterhouse.

He points out that there are three types of closures now used to seal wines: natural corks made from the bark of the cork oak tree or technical corks (made of an aggregate of natural cork particles), screw caps, and synthetic corks made from plastic.

While natural corks carry the very small (1 to 2 percent) chance of causing a moldy flavor and aroma in the wine known as “cork taint,” the natural corks have proven to be the most effective in keeping oxygen out of the bottled wine over a number of years, Waterhouse reports.

“For the regular wine you might purchase for dinner this weekend or to keep for a year or two, any of these closures are perfectly good, while the manufactured closures avoid taint,” he writes. “In fact, your choice is more a matter of preference for opening the bottle. Do you want the convenience of twisting off the cap, or do you want the ceremony of removing the cork?”

But for long aging, only natural corks have a proven record of protecting the wine from unwanted oxygen, so would be the closure of choice. Waterhouse notes that long-term evaluations of synthetic corks and screw caps are needed to accurately judge their suitability for extended aging of more than 10 years.

Contributed by Pat Bailey

2015 Butterfly hunt is on!

Not the best day for it, but Prof. Art Shapiro is once again launching his “Beer for Butterfly” challenge. Find the first live Cabbage white butterfly in Sacramento, Yolo or Solano County and Shapiro will stand you a pitcher of beer (or cash equivalent if the winner is under age or doesn’t drink).

Win a pitcher of beer for the first live Cabbage White Butterfly (Pieris rapae) collected in Sacramento, Yolo or Solano County in 2015.

Your animal must be collected OUTDOORS and turned in ALIVE at the Evolution and Ecology Department Office, 2320 Storer Hall, UC Davis, with FULL DATA (exact location and date and time of collection and your contact information, preferably e-mail). If you collect it when the office is closed, keep it alive in a refrigerator (DO NOT FREEZE!) until you can deliver it. Other species are not eligible. An EVE staff member will certify that it is alive when received and take your data. The prize is a PITCHER OF BEER, your brand, or equivalent in cash if you do not drink or are under age.

In previous years winners have been collected between Jan.1 and Feb.22. Prof. Shapiro is the sole judge.

Shapiro has been running this competition (which he almost always wins) for over 40 years now, revealing information on a changing climate as well as year-to-year changes in butterfly populations.

More: Art Shapiro’s butterfly site

 

New X-ray technique for surfaces

Surfaces are very interesting to material scientists. The reactions that happen at the point where inside and outside meet, and elements interact with other chemicals or radiation, are important for developing new technology for batteries, fuel cells or photovoltaic panels, for catalysts for the chemical industry, and for understanding environmental chemistry and pollution. Now researchers at UC Davis and the Advanced Light Source at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory have combined two existing methods techniques to come up with a new method for studying surfaces with X-rays. This new technique is called SWAPPS, for Standing Wave Ambient Pressure Photoelectron Spectroscopy.

Using SWAPPS, scientists can probe the properties of surfaces with X-rays.

Using SWAPPS, scientists can probe the properties of surfaces with X-rays.

“SWAPPS enables us to study a host of surface chemical processes under realistic pressure conditions and for systems related to energy production, such as electrochemical cells, batteries, fuel cells and photovoltaic cells, as well as in catalysis and environmental science,” says Charles Fadley, a physicist who holds joint appointments with Berkeley Lab’s Materials Sciences Division and UC Davis, where he is a Distinguished Professor of Physics. “SWAPPS provides all the advantages of the widely used technique of X-ray photoelectron spectroscopy, including element and chemical-state sensitivity, and quantitative analysis of relative concentrations of all species present. However with SWAPPS we don’t require the usual ultrahigh vacuum, which means we can measure the interfaces between volatile liquids and solids.”

Fadley is one of three corresponding authors of a paper, with Hendrik Bluhm of the Berkeley Lab’s Chemical Sciences Division and Slavomír Nemšák, now with Germany’s Jülich Peter Grünberg Institute, describing SWAPPS in Nature Communications.

X-rays probe surfaces

In terms of energies and wavelengths, X-rays serve as excellent probes of chemical processes. Fadley’s group at ALS originally developed standing wave photoelectron spectroscopy, which uses X-rays to probe buried surfaces, while a team including Bluhm developed high ambient pressure photoelectron spectroscopy, which made it possible to use X-ray spectroscopy under pressures and humidities similar to those encountered in natural or practical environments. The new technique combines the best features of both. That means the researchers can probe the composition of surfaces and interfaces with unprecedented resolution under the conditions where batteries, fuel cells or other devices actually work.

Says Fadley, “We believe SWAPPS will deliver vital information about the structure and chemistry of liquid/vapor and liquid/solid interfaces, in particular the electrical double layer whose structure is critical to the operation of batteries, fuel cells and all of electrochemistry, but which is still not understood at a microscopic level.”

The researchers used the technique to probe an experimental system of sodium and cesium hydroxide, layered on iron oxide (hematite).

“We determined that the sodium ions are located close to the iron oxide/solution interface, while cesium ions are on average not in direct contact with the solid/liquid interface,” Bluhm says. “We also discovered that there are two different kinds of carbon species, one hydrophobic, which is located exclusively in a thin film at the liquid/vapor interface, and a hydrophilic carbonate or carboxyl that is evenly distributed throughout the liquid film.”

In their Nature Communications paper, the authors say that future time-resolved SWAPPS studies using free-electron laser or high-harmonic generation light sources would also permit, via pump-probe methods, looking at the timescales of processes at interfaces on the femtosecond time scale.

“The range of future applications and measurement scenarios for SWAPPS is enormous,” Fadley says.

In addition to Fadley, Bluhm and Nemšák, other authors of the paper describing SWAPPS were Andrey Shavorskiy, Osman Karslioglu, Ioannis Zegkinoglou, Peter Greene (UC Davis), Edward Burks (UC Davis), Arunothai Rattanachata (UC Davis), Catherine Conlon, (UC Davis) Armela Keqi (UC Davis), Farhad Salmassi, Eric Gullikson, See-Hun Yang and Kai Liu (UC Davis).

This research was primarily funded by the Department of Energy’s Office of Science. The Advanced Light Source is a DOE Office of Science User Facility.

Adapted from an original story by Lynn Yarris, LBL.

More information:

Read the original story from Lawrence Berkeley Lab

Advances in electron microscopy reveal secrets of HIV and other viruses

UC Davis researchers are getting a new look at the workings of HIV and other viruses thanks to new techniques in electron microscopy developed on campus.

The envelope (or Env) protein of HIV is a key target for vaccine makers: it is a key component in RV144, an experimental vaccine that is so far the only candidate to show promise in clinical trials. Also called gp120, the Env protein associates with another protein called gp41 and three gp120/gp41 units associate to form the final trimeric structure. The gp120 trimer is the machine that allows HIV to enter and attack host cells.

Professor R. Holland Cheng’s laboratory at UC Davis has previously shown how the gp120 trimer can change its conformation like an opening flower. The new study, published in Nature Scientific Reports Nov. 14, shows that a variable loop, V2, is located at the bottom of the trimer where it helps to hold gp41 in place — and not at the top of the structure, as previously thought.

New visualization of the V2 variable loop of the HIV Env protein (red) puts it at the bottom of the structure. (Cheng lab)

New visualization of the V2 variable loop of the HIV Env protein (red) puts it at the bottom of the structure. (Cheng lab)

“This challenges the existing dogma concerning the architecture of HIV Env immunogen,” Cheng said.

Making a vaccine against HIV has always been difficult, at least partly because the proteins on the surface of the virus change so rapidly. Better understanding the structure of the gp120/Env trimer could help in finding less-variable areas of these proteins, not usually exposed to the immune system, which might be targets for a vaccine.

Understanding viral entry

A second pair of back-to-back papers from Cheng’s lab uses new techniques in electron microscopy to probe how some common viruses hijack normal cellular processes to enter cells.

Cheng’s lab has pioneered techniques in cryoelectron microscopy. Traditionally electron microscopy has relied on coating or impregnating samples with heavy metal elements. Cryoelectron microscopy uses extremely low temperatures to freeze biological structures in place instead.

By taking multiple images from slightly different angles and reconstructing them with computers, Cheng has been able to produce three-dimensional images of viruses and virus proteins and particularly, virus-infected cells.

However, because of the way electrons are scattered from samples, cryoelectron microscopes can only use a limited range of angles, creating a “missing wedge” in imaging infected cells. In one of the papers recently published in the journal PLOS One, Lassi Paavolainen and colleagues present a new statistical technique to reconstruct this missing data with no prior knowledge of the sample.

In the companion paper, Pan Soonsawad and colleagues applied the new technique to study the vesicles, or small bubbles that form inside cells when a picornavirus enters. The picornaviruses are a large group that includes the viruses that cause colds, gut infections, polio, hepatitis A and the recent outbreaks of contagious hand-foot-mouth disease (HFMD) spread in infants and children of younger age in U.S. this summer.

Picornaviruses get into cells by getting themselves dragged into an endosome, or pouched-off bubble from the cell’s surface inside the cell. Then they exit the endosome and replicate their genetic material, RNA, in the cytoplasm of the host cells.

The new work shows that the endosomes are lined with host proteins called integrins, which are found in cell membranes. When integrins come close together in a membrane, they send signals into the cell. Viruses take advantage of this behavior, Cheng said. Attaching itself to a cell, the virus gathers integrins towards itself, triggering formation of an endosome.

“This virus collects integrins into a pattern so it can be ‘swallowed’ by the host cells,” Cheng said.

Once inside, the new images show the endosomes breaking up as the viruses release their genetic material into the cell, leading to massive virus replication.

Despite the illness they cause, Cheng finds the viruses have their own charm.

“The virus is beautiful, because it has its own geometry that can be reused and redesigned for the benefit of human being,” he said.

Indeed, Cheng’s laboratory has patented technology that makes use of self-assembling proteins from the coat of Hepatitis E virus, including using them to deliver drugs or vaccines or to target breast cancer.

Coauthors on the Nature Science Reports paper were Carlos G. Moscoso, Li Xing, Jinwen Hui, Jeffrey Hu, Mohammad Baikoghli Kalkhoran, Onur M. Yenigun at UC Davis; Yide Sun, Carlo Zambonelli, Susan W. Barnett, and Indresh K. Srivastava at Novartis Vaccines and Diagnostics Inc., Cambridge, Mass.; Loïc Martin, Commissariat à l’énergie atomique et aux énergies alternatives, Gif-sur-Yvette, France; Lassi Paavolainen and Anders Vahlne, Karolinska Institute, Stockholm, Sweden.

The PLOS One papers include coauthors from University of Jyvaskyla, Finland; Tampere University of Technology, Tampere, Finland; and Mahidol University, Bangkok, Thailand.

Diamonds and other treasures found in Sutter’s Mill meteorite

By Kat Kerlin

Researchers digging deeper into the origins of the Sutter’s Mill meteorite, which exploded over California’s Gold Country in 2012, have found diamonds and other “treasures” that provide important new insight into the early days of our solar system. They report their results in 13 papers in the November issue of Meteoritics & Planetary Science.

UC Davis scientists Akane Yamakawa and Qing-Zhu Yin in the Department of Earth and Planetary Sciences studied the different forms of the element chromium, called isotopes. They found that at least five different stellar sources composed of mixtures of 54-chromium-rich and -poor materials must have contributed matter to the nascent solar system four and half billion years ago. Some of these materials remained in the Sutter’s Mill meteorite.

Composite photo of the Sutter's Mill meteorite

Composite photo of the Sutter’s Mill meteorite fall.

“The formation of the solar system did not fully erase and homogenize these signatures, and Sutter’s Mill provides the clearest record yet,” said Yin, who co-led the Sutter’s Mill Meteorite Consortium with Peter Jenniskens of NASA Ames and the SETI Institute.

In primitive meteorites like Sutter’s Mill, some grains survive from what existed in the cloud of gas, dust and ices that formed the solar system. In Sutter’s Mill, the liquid water appears to have destroyed the silicate type of these, according to Xuchao Zhao of the Chinese Academy of Sciences, working with NASA and UC Davis colleagues.

Researchers in the consortium also found two, 10-micron diamond grains in the meteorite. Though too small to sparkle in a ring, they were larger than the nanometer-sized diamonds commonly found in such meteorites. Nanodiamonds are thought to originate in the atmospheres of stars. The larger diamonds found in Sutter’s Mill may have had another origin closer to home.

“We suspect that these diamonds are so-called xenoliths,” said Yoko Kebukawa, recently of Hokkaido University, Japan. “Bits and pieces that originated in the interior of other much larger parent bodies.”

Fragments of the Sutter's Mill meteorite (NASA photo).

Fragments of the Sutter’s Mill meteorite (NASA photo).

The Sutter’s Mill meteorite fell just 60 miles from the UC Davis main campus. Scientists from UC Davis, including Yin, immediately traveled to the site with students and colleagues looking for specimens and reaching out to the public to provide meteorite donation for science.

Yin confirmed that the main mass was carbonaceous chondrite – one of the rarest types to hit the Earth and containing cosmic dust and presolar materials that helped form the planets of the solar system. The meteorite’s main mass was X-rayed by CT scan at UC Davis, and the university acquired a portion of this mass.

Nobel winner headlines math/biology workshop

2013 Nobel laureate Michael Levitt of Stanford University will headline a one-day workshop on mathematics and biology to be held at UC Davis Nov. 22. Biology and Mathematics in the Bay Area aims at “creating a fairly informal atmosphere to explore the role of mathematics in biology,” according to the advance flyer. “Our goal is to encourage dialogue between researchers and students from different disciplines in an atmosphere that promotes the open exchange of ideas and viewpoints.”

Also speaking: Ileana Streinu at Smith College; Sean Mooney, Buck Institute; Sharon Aviran and Steve Kowalczykowski, UC Davis.

The meeting is free, but advance registration is required by Monday, Nov. 17. More information including registration is available at http://bambameeting.org/

Stress increases sociality in zebra finches

Stress in early life affects social behavior in adult zebra finches.

Stress in early life affects social behavior in adult zebra finches.

A new study shows that young birds raised under stressful conditions leave home earlier and develop a wider social network.

The paper co-authored by Damien Farine, now a post-doctoral researcher at the University of California, Davis, anthropology department, Neeltje Boogert, University of St Andrews, and Karen Spencer, Oxford University, was published in Biology Letters Wednesday, Oct. 29.

The researchers found that zebra finch chicks stressed during early development showed more independence from their parents, associated more randomly with other members of their flock and were less choosy about the birds they fed alongside.

“Stress is a possible mechanism to allow birds to try alternative strategies,” Farine said. “If you get a lot of this stress happening you may see them doing behaviors they have done before including widespread dispersals. When we see birds popping up in places they’ve not been before it might have something to do with stressful development. This could thus have major implications for maintaining locally-adapted behaviors and genetic structure across different sub-populations.”

Wild birds secrete a stress hormone when faced with food scarcity, predators or competition. The researchers artificially increased stress hormone levels in zebra finch chicks and tested how this affected their foraging behavior. The birds’ were monitored in aviaries where the stressed chicks and their families could visit bird feeders at any time and with any other birds. Each bird was fitted with a chip that recorded each time a bird visited one of the feeders over the course of five weeks.

For the full study go to http://rsbl.royalsocietypublishing.org/lookup/doi/10.1098/rsbl.2014.0561.

Follow Damien Farine on Twitter at @DamienFarine.

Contributed by Jeffrey Day.

UC Davis, Livermore announce graduate mentorship program awards

Contributed by AJ Cheline

Since 1963, UC Davis and Lawrence Livermore National Laboratory (LLNL) scientists and engineers have conducted joint interdisciplinary research that leverage the strengths of both institutions to address a variety of critical societal problems. Over the last year, leaders from LLNL and UC Davis have been working together to develop mechanisms that reinvigorate and deepen the partnerships between the institutions. Several joint faculty and lab researcher workshops have taken place over the last few months to identify and develop new topical areas of common interests. A number of joint grant proposals to federal funding agencies have been submitted and work is ongoing to identify funding mechanisms that facilitate additional collaborations.

As a component of this initiative, a Joint UCD-LLNL Graduate Mentorship Award program has been established. This program was created to provide a unique opportunity for graduate students to experience the complimentary research environment of both a leading university and a national laboratory during their PhD studies. The Mentorship Awards provide funding for up to three years of financial support for the graduate student. Graduate students will engage in research activities at both Livermore and Davis campuses under the joint supervision of the UC Davis faculty mentor and the LLNL staff scientist or engineer.

A Call for Proposals was issued through the UC Davis Office of Research, eliciting 25 submissions. Proposals were reviewed by independent peer review, following a process coordinated by LLNL and UC Davis. The quality of proposals was viewed as being uniformly high, with the following projects selected to receive funding in this first round:

Efficient Simulations for a Large-Scale Model of Cardiac Rhythms
UC Davis Co-Principal Investigator: Timothy Lewis, Professor of Mathematics
LLNL Co-Principal Investigator: David Richards

Engineered Nanostructure for Regulation of Cellular Signaling Cascades
UC Davis Co-Principal Investigator: Gang-yu Liu, Professor of Chemistry
LLNL Co-Principal Investigator: Ted Laurence

Ultralow Density Metal Foams for High Energy Density and Advanced Materials Research
UC Davis Co-Principal Investigator: Kai Liu, Professor of Physics
LLNL Co-Principal Investigator: Jeff Colvin

Rare Event Detection: Neutrinos and Dark Matter
UC Davis Co-Principal Investigator: Robert Svoboda, Professor of Physics
LLNL Co-Principal Investigator: Adam Bernstein

Funding for this program was provided by the University Relations and Science Education Group, LLNL, the UC Office of the President Laboratory Management Office, and UC Davis Office of Research.