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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.

Watching the structure of glass under pressure

Glass has many applications that call for different properties, such as resistance to thermal shock or to chemically harsh environments. Glassmakers commonly use additives such as boron oxide to tweak these properties by changing the atomic structure of glass. Now researchers at the University of California, Davis, have for the first time captured atoms in borosilicate glass flipping from one structure to another as it is placed under high pressure.

The findings may have implications for understanding how glasses and similar “amorphous” materials respond at the atomic scale under stress, said Sabyasachi Sen, professor of materials science at UC Davis. Sen is senior author on a paper describing the work published Aug. 29 in the journal Science.

Boron oxide is often added to glass to control a range of properties, including chemical durability, flow resistance, optical transparency and thermal expansion. Material scientists know that the structure around the boron atoms in borosilicate glass changes with pressure and temperature, switching from a flat triangular configuration with three oxygen atoms surrounding one boron atom to a four-sided tetrahedron, with four oxygen atoms surrounding one boron.

As borosilicate glass is put under pressure, the structure of boron oxide changes from triangular to tetrahedral through a pyramid-shaped intermediate.

As borosilicate glass is put under pressure, the structure of boron oxide changes from triangular to tetrahedral through a pyramid-shaped intermediate.

Until know, material scientists have only been able to study these structures in one state or the other, but not in transition. Sen and graduate student Trenton Edwards developed a probe that enabled them to make nuclear magnetic resonance (NMR) measurements of the environment of boron atoms in glass under pressures up to 2.5 Gigapascal.

They found that under pressure, the flat triangles of boron and three oxygen atoms first deform into a pyramid shape, with the boron atom pushed up. That may bring it close to another oxygen atom, and let the structure turn into a tetrahedron, with four oxygen atoms surrounding one boron.

Intriguingly, although glass is structurally isotropic and the stress on the glass is the same in all directions, the boron atoms respond by moving in one direction in relation to the rest of the structure.

“This is an unexpected finding that may have far-reaching implications for understanding a wide range of stress-induced phenomena in amorphous materials,” Sen said.

The work was done in collaboration with Jeffrey Walton, project scientist with the UC Davis NMR Facility. It was funded by the U.S. National Science Foundation.

More information: Perspective article from Randall Youngman of Corning, Inc.

Protein is key to forming short-term memories

Synapses from the brainstem.

Synapses from the brainstem.

Short-term memory is essential for everyday life — whether remembering a phone number while dialing, carrying on a conversation, or forming the basis of long-term memories. Neuroscientists think that short-term memory is based on changes in both the properties of brain cells and the connections, called synapses, between them.

Now Diasynou Fioravante, formerly of Harvard Medical School and now at the UC Davis Center for Neuroscience, and colleagues have identified a sensor that plays a key role in modifying neurons and synapses to create short-term memories. The work was published Aug. 5 in the journal eLife.

Brain function depends on signals jumping across synapses. When an electrical signal is generated by the cell before the synapse, calcium ions flow into the cell and trigger release of molecules called neurotransmitters which cross the synapse to the next cell, producing an electrical signal. The size of the signal is a measure of synaptic strength.

Synaptic strength can change over both the short-term (tens of seconds) and long-term. A short-term increase in strength called post-tetanic potentiation is thought to underlie formation of short-term memory. It amplifies the signal across the synapse by increasing the amount of neurotransmitter released in response to each electrical impulse, and it is triggered by an increase of calcium in the presynaptic cell.

Protein kinase C (green stain) on synapses (red). Yellow color shows PKC on synapses.

Protein kinase C (green stain) on synapses (red). Yellow color shows PKC on synapses.

Fioravante and colleagues now show that an enzyme called protein kinase C is responsible for this effect. They found that genetically modified mice that lack protein kinase C do not show this short-term potentiation, but that it could be restored by reintroducing the enzyme. A version of protein kinase C that lacks the ability to bind calcium was unable to trigger post-tetanic potentiation.

The work could provide tools to manipulate brain plasticity and study how memories are formed, Fioravante said. It could also eventually provide new ways to improve short-term memory function in patients with memory deficits.

The researchers think that protein kinase C is likely the first of a new class of sensors that make short-term, local modifications to how brain cells work and connect with each other.

Coauthors on the paper are: YunXiang Chu, Arthur de Jong, Pascal Kaeser and Wade Regehr at Harvard Medical School, and Michael Leitges at the University of Oslo. The work was funded by the National Institutes of Health.

Read the full paper online here.

Memory researcher wins Pentagon grant

Congratulations to Professor Charan Ranganath of the UC Davis Center for Neuroscience and Department of Psychology on his selection as a National Security Science and Engineering Faculty Fellow by the U.S. Department of Defense. The five-year, $2.6 million fellowship will support new work on learning and memory in Ranganath’s Dynamic Memory Laboratory at UC Davis.

Charan Ranganath is exploring the basis of memory.

Charan Ranganath is exploring the basis of memory.

The new project aims to connect neural oscillations, which are currently poorly understood, with activity in the cortex and hippocampus, brain regions that are known to be involved in forming and retrieving memories.

The studies could lead to better ways to assess memory function, methods to boost learning (for example in training situations), and to better rehabilitation of soldiers with brain injuries. The work could also contribute to development of brain-computer interfaces.

“NSSEFF grants are highly competitive, attracting the next generation of outstanding scientists and engineers to some of our most challenging scientific issues and opportunities,” said Dr. Robin Staffin, Director for Basic Research for the Department of Defense, in a news release. “The program provides grants to top-tier researchers from U.S. universities to conduct long-term, unclassified, basic research of strategic importance to the Department of Defense.”

Ranganath is one of just 10 Fellows selected for the program this year, and the only neuroscientist. He has previously received a UC Davis Chancellor’s Fellowship and a Guggenheim Fellowship.

More information: About the NSSEFF program

In this video, Ranganath and postdoc Frank Hsieh describe their recent discoveries on how memories are stored by when they occurred.

Stress-tolerant tomato relative sequenced

Domestic tomatoes (left) and three wild relatives. S. pennellii is on the far right.

Domestic tomatoes (left) and three wild relatives. S. pennellii is on the far right.

The genome of Solanum pennellii, a wild relative of the domestic tomato, has been published by an international group of researchers including the labs headed by Professors Neelima Sinha and Julin Maloof at the UC Davis Department of Plant Biology. The new genome information may help breeders produce tastier, more stress-tolerant tomatoes.

The work, published July 27 in the journal Nature Genetics, was lead by Björn Usadel and colleagues at Aachen University in Germany. The UC Davis labs carried out work on the transcriptome of S. pennellii — the RNA molecules that are transcribed from DNA and then translated into proteins — messages written from DNA and taken to other parts of the cell to tell it what to do. Analyzing the RNA transcriptome shows which genes are active under different circumstances. The UC Davis team published a paper last year comparing the RNA transcripts of domestic tomato and three wild relatives, including S. pennellii.

S. pennellii is inedible, but it can be interbred with domestic tomatoes to introduce useful traits, such as drought resistance.  Using the new genome data, the researchers found genes related to dehydration resistance, fruit development and fruit ripening. They also found genes that contribute to volatile compounds related to fruit scent and flavor.

The UC Davis portion of the work was supported by a grant from the National Science Foundation.

More information:

UC Davis Charles M. Rick Tomato Genetics Resource Center

The Tomato Anatomy Atlas



Reproducing deep-Earth chemistry

A new pressure cell invented by UC Davis researchers makes it possible to simulate chemical reactions deep in the Earth’s crust. The cell allows researchers to perform nuclear magnetic resonance (NMR) measurements on as little as 10 microliters of liquid at pressures up to 20 kiloBar.

“NMR is our window into the chemical world,” said Brent Pautler, a postdoctoral researcher in chemistry at UC Davis and first author on the paper published July 2 in the online edition of the journal Angewandte Chemie. “It lets us see chemical reactions as they are happening.”

The new device allows researchers for the first time to study chemical reactions in liquid water under pressure, without it freezing into a solid.

“We were able to get to the point where we could no longer ignore the compressibility of the water molecules,” Pautler said. “This is the first time this has ever been reported.”

Geochemists want to know what kind of chemistry is happening deep in the Earth’s crust, beyond the reach of boreholes. These chemical reactions could affect water and minerals that eventually migrate to the surface, or the behavior of carbon cycling between the Earth’s depths and the surface.

“Aqueous fluids deep in the Earth are the great unknown for geochemists,” said Chris Colla, a graduate student in Earth & Physical Sciences at UC Davis and co-author on the paper. “By doing NMR we can get an inside view of what is occurring deep in the Earth’s crust.”

Video: Mimicking chemical reactions in the Earth’s crust

For example, Pautler, Colla and colleagues have already looked at calcium ions in solution. Dissolved calcium ions can be surrounded by four, six or eight water molecules. High pressure forces dissolved calcium into an eight-water state, they found.

The high-pressure measurements could also shed light on chemical processes involved in hydraulic fracturing, or “fracking,” and the behavior of buried nuclear waste over long periods of time. Fracking is the process of extracting oil and gas by injecting liquids under high pressure into rocks.

The high-pressure NMR cell was built in the machine shop at the Crocker Nuclear Laboratory with the help of Peter Klavins, research specialist in the Department of Physics, and Steve Harley, a former UC Davis graduate student now at the Lawrence Livermore National Laboratory.

Other coauthors on the paper are, at UC Davis: Prof. William Casey and Rene Johnson, Department of Chemistry; Jeffrey Walton, NMR Facility; André Ohlin, at Monash University, Australia and Dimitri Sverjensky at Johns Hopkins University and the Carnegie Institution of New York. The work was supported by the U.S. Department of Energy.

More information: Introduction to NMR spectroscopy (Chemwiki)

Honda releases plans for energy-efficient smart home

The Honda Smart Home at UC Davis’ West Village has got lots of attention since it was opened earlier this year. (For the latest, see this photospread in Dwell magazine).

Now Honda is making detailed plans and information about fixtures and fittings in the energy-efficient home available for anyone to download. In a blog post, Honda project manager Michael Koenig writes:

In the three months following our launch, the response to Honda Smart Home has been truly amazing. We’ve hosted over a thousand visitors in Davis including architects, builders, researchers, academics, media, policymakers and enthusiastic members of the public. And we’ve received inquiries and proposals from businesses all across the world looking to get involved in green building.

Many of the people and companies we’ve met with wanted to know how they could incorporate what we’ve demonstrated into their own projects, or build upon what we’ve learned in their own research. We want nothing more than to facilitate this effort, so today, we’re releasing a batch of files the get the process rolling.

Simply go to and click on the “downloads” tab at the top of the page to download the plans and files.


Obituary: Peter Marler FRS, birdsong expert

Saddened to hear of the death on Saturday of Peter Marler, a pioneer of research on birdsong and animal communication and professor emeritus at the UC Davis Department of Neurobiology, Physiology and Behavior and Center for Neuroscience.

According to the Sacramento Bee, Marler, who was in poor health, had to be evacuated from his home in Winters, CA early on July 5 due to a wildfire. He died later the same day.

I interviewed Marler in 2008 when he was elected as a Fellow of the Royal Society, equivalent to the U.S. National Academy of Sciences.

Marler had a lifelong interest in science and biology, starting his own natural history club as a school boy in England. He earned two doctoral degrees, in botany and in zoology, and worked at Cambridge University where he began his work studying birdsong. In 1957 he emigrated to the U.S.. He was at UC Berkeley from 1957 to 1966 then moved to Rockefeller University, where he worked on both bird and primate communication.

In 1989 he retired from Rockefeller and joined the new Center for Neuroscience at UC Davis.

Among Marler’s many achievements, he was the first to show that birds learn songs from other birds during a crucial phase of development. He also worked with Jane Goodall to study communication in chimpanzees, and studied how monkeys use different alarm calls in different situations.

For a full scientific biography in his own words, look here.


With climate changing, Southern plants do better than Northern locals

Can plants and animals evolve to keep pace with climate change? A study published May 19 in the journal Proceedings of the National Academy of Sciences shows that for at least one widely-studied plant, the European climate is changing fast enough that strains from Southern Europe already grow better in the north than established local varieties.

Small and fast-growing, Arabidopsis thaliana is widely used as the “lab mouse” of plant biology. The plant grows in Europe from Spain to Scandinavia and because Arabidopsis is so well-studied, there is a reference collection of seeds derived from wild stocks across its native range. Originally collected from 20 to 50 years ago, these plants have since been maintained under controlled conditions in the seed bank.

Johanna Schmitt, formerly at Brown University and now a distinguished professor in the UC Davis Department of Evolution and Ecology, and colleagues took banked seed samples originally from Spain, England, Germany and Finland and raised all the plants in gardens in all four locations.

Arabidopsis thaliana (Source: Wikipedia)

Arabidopsis thaliana (Source: Wikipedia)

“The southern imports do better across the range than locals,” Schmitt said.

“This shows that the adaptive optimum has moved really fast.”

Seed stocks banked decades ago may no longer be the best for their locations of origin, she said, although they still may be critical for preserving genetic diversity, especially from warmer parts of the species range that may facilitate adaptation to future climates.

Whether wild Arabidopsis can evolve fast enough to thrive in warming conditions, or southern varieties move north fast enough to replace northern strains, remains an open question, Schmitt said.

Arabidopsis is a fast-growing, short-lived species. For forest managers, there is another question: can trees that sprouted 30 or 40 years ago adapt in place to a rapidly changing climate?

“This is a concern for foresters — trees live a long time, but will they die if the climate rug is pulled out from under them?” Schmitt said.

Coauthors on the study are Amity Wilczek, Martha Cooper and Tonia Korves, all at Brown University. The study was supported by the National Science Foundation.

Rising carbon dioxide, less nutritious food?

This week’s report that the Antarctic ice sheets are in irreversible retreat grabbed headlines, but another report last week warned that rising carbon dioxide levels threaten the quality of the world’s food supply, as well.

Increased malnutrition and loss of life — due to declining levels of dietary zinc, iron, and protein in important food crops — will occur around the world as elevated atmospheric CO2 climbs to levels that are anticipated by 2050, reports an international team led by researchers at Harvard University and including UC Davis plant scientist Arnold Bloom. The study appeared online May 7 in the journal Nature.

Confirmation of this link between rising CO2 and declining crop nutrient content is particularly sobering for developing nations, where an estimated two billion people already suffer from zinc and iron deficiencies.

“This study indicates that the reduction of these nutrients in important grain and legume crops is one of the most significant health threats that has ever been shown to be associated with climate change,” Bloom said.

The researchers analyzed data from 41 cultivated varieties of grains and legumes grown in seven locations in Japan, Australia and the United States. The test crops were grown in open fields, rather than in greenhouses or growth chambers. In these experimental fields, CO2 levels were monitored and pure CO2 added, using a technology called “free air carbon dioxide enrichment.” This process maintained the CO2 levels in the range of 546-586 parts per million across all seven sites. Today CO2 levels are normally around 400 parts per million.

At harvest, the researchers tested the nutrient concentration of the edible portions of wheat and rice, maize and sorghum, and soybeans and field peas. The results showed significant decreases in the concentrations of zinc, iron and protein in wheat grains grown at the test sites — 9.3 percent, 5.1 percent and 6.3 percent respectively — compared to wheat grown at naturally occurring CO2 levels. In the experimental legume plots, zinc and iron also decreased significantly but protein did not.

Earlier this year, Bloom and another team of researchers demonstrated that elevated levels of carbon dioxide inhibit plants’ assimilation of nitrate into proteins. Those findings, published in the journal Nature Climate Change in April, also provide evidence that the nutritional quality of food crops is at risk as climate change intensifies.

More: News story from Harvard University.

Contributed by Pat Bailey

Animal scientist receives Borlaug communications award

The Council for Agricultural Science and Technology (CAST) has announced that Alison Van Eenennaam, a geneticist and Cooperative Extension specialist in animal genomics and biotechnology at UC Davis, is the recipient of its 2014 Borlaug CAST Communication Award.

Announcement of the award, which will be presented to Van Eenennaam on Oct. 15 along with the World Food Prize Symposium in Iowa, was made today at the World Bank in Washington, D.C..Alison van Eenennaam

Established in 1986 and named after Nobel laureate Norman Borlaug, the award is presented to a food or agricultural scientist who is actively engaged in research; has made significant contributions to science; and communicates the importance of food and agricultural science to the public, policymakers and the news media

Van Eenennaam’s research and extension program in UC Davis’ Department of Animal Science is focused on developing science-based educational materials about the uses of animal genomics and biotechnology in livestock production systems.

She has served on advisory committees in the U.S. Department of Agriculture and the U.S. Food and Drug Administration to provide expert counsel on animal biotechnology.

Van Eenennaam is a passionate advocate for science and frequently speaks about agricultural technology to the public and policymakers, both nationally and internationally. She frequently provides science-based commentary to the media on sometimes-controversial topics, including genetic engineering and cloning. She also works to increase public understanding of agricultural biotechnology, using a variety of media, including YouTube videos.

More: Alison Van Eenennaam’s Animal Biotechnology and Genomics page