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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.

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


Algae “see” a wide spectrum of light

Aquatic algae can sense an unexpectedly wide range of color, allowing them to sense and adapt to changing light conditions in lakes and oceans. The study by researchers at UC Davis was published earlier this year in the journal Proceedings of the National Academy of Sciences.

Phytochromes are the eyes of a plant, allowing it to detect changes in the color, intensity, and quality of light so that the plant can react and adapt. “They control all aspects of a plant’s life,” said Professor Clark Lagarias, senior author on the study. Typically about 20 percent of a plant’s genes are regulated by phytochromes, he said. Phytochromes use bilin pigments that are structurally related to chlorophyll, the molecule that plants use to harvest light and use it to turn carbon dioxide and water into food.

Freshwater-dwelling Cyanophora algae like these are among those able to sense a surprisingly wide spectrum of light.

Freshwater-dwelling algae like these are among those able to sense a surprisingly wide spectrum of light.

Lagarias’ laboratory in the Department of Molecular and Cellular Biology at UC Davis studies these phytochromes and their properties. Phytochromes from land plants, Lagarias said, respond to red light — plants absorb red and reflect green light, which is why they look green. Red light does not penetrate far into water, and some marine and shore-dwelling algae lack phytochrome genes. But others do not, so Lagarias and colleagues looked at the properties of phytochromes from a variety of algae. They found that phytochromes from algae, unlike those of land plants, are able to perceive light across the visible spectrum — blue, green, yellow, orange, red and far-red.

Cyanophora paradoxa, one of the algae with newly discovered phytochromes.

Cyanophora paradoxa, one of the algae with newly discovered phytochromes.

This broad spectral coverage likely helps algae make use of whatever light they can in the ocean, Lagarias said — whether adjusting their light-harvesting chemistry for changing conditions, or rising and sinking in the water column as light levels at the surface change. Because different colors of light penetrate to different depths in water, algae face challenges in light harvesting that land plants do not. This work from the Lagarias lab shows one way that algae can rise to the occasion.

Phytochromes themselves have a long evolutionary history and likely arose from the interaction between oxygen and bilins, pigment molecules closely tied to chlorophyll and the oxygen-carrying heme pigment in hemoglobin, Lagarias said. The ancestral form appears to be sensitive to red light, similar to phytochromes of modern land plants. But between the origin and today, phytochromes went through a stage of massive diversity when they could detect a much wider range of wavelengths.

The broad color palette of algal bilin-based light sensors found in nature.

The broad color palette of algal bilin-based light sensors found in nature.

“It’s a molecule that has been there and back again,” Lagarias said.

The discoveries help researchers better understand the role of light and response to light in shaping ecology, as well as a model for how living cells react to light. They could also help in breeding of aquatic crops that could take advantage of different light conditions.

Coauthors on the paper are: at UC Davis, Nathan Rockwell, Deqiang Duanmu, and Shelley Martin; Alexandra Worden and Charles Bachy at the Monterey Bay Aquarium Research Institute and Canadian Institute for Advanced Research; Dana Price and Debashish Bhattacharya, Rutgers University. The work was supported by multiple agencies including the NIH, NSF, US Department of Agriculture, Department of Defense, the Packard Foundation and the Gordon and Betty Moore Foundation.

More information:

Clark Lagarias talks about phytochromes, algae and light detection

Commentary by Katrina Forest, University of Wisconsin-Madison.

African wildlife declines could set off rodent-borne disease

Removing large wildlife from the African savanna sets off a boom in rodents and increases the risk to humans from rodent-borne disease, according to research published today in the Proceedings of the National Academy of Sciences. The project was lead by Hillary Young, assistant professor at UC Santa Barbara, and took advantage of the Kenya Long-Term Exclosure Experiment (KLEE), lead by Professor Truman Young at UC Davis.

Begun in 1996, KLEE involves fencing off areas of savanna at Kenya’s Mpala Research Station to exclude large wild animals including elephants, giraffe and zebra, and/or grazing cattle. The experiment has given important insights into the effects of cattle and wild animals on each other and on rangeland ecology.

A zebra tests the fence at the Kenya Longterm Exclosure Experiment. Credit: Duncan Kimuyu

A zebra tests the fence at the Kenya Longterm Exclosure Experiment. Credit: Duncan Kimuyu

In the current study, the researchers found that when large animals such as elephants, giraffe and zebra were excluded from an area with electric fencing, the rodent population doubled. The rodents carry fleas, and tests on the fleas showed significant numbers of bacteria that cause Bartonellosis, a disease that can damage the heart, spleen and liver and cause memory loss in humans.

“We were able to demonstrate that declines in large wildlife can cause an increase in the risk for diseases that are spread between animals and humans,” said Hillary Young, in a news release. “This spike in disease risk results from explosions in the number of rodents that benefit from the removal of the larger animals.”

Without large mammals, mice like these multiply rapidly. And so do their fleas and flea-borne diseases.

Without large mammals, mice like these multiply rapidly. And so do their fleas and flea-borne diseases. Credit: Hillary Young/UCSB.

Rodent-borne disease outbreaks are common in the study area. Declines in large wildlife have been linked to increases in small animals such as rodents elsewhere in the world, and may also be having an effect on rodent-borne disease.

Why does a decline in large animals like elephants and zebra affect rodents? The loss of large animals may mean more food and shelter for small ones. Small animals generally interact more closely with humans than large ones, Young noted.

“Elephants are an irreplaceable part of our global biodiversity portfolio,” Young said, “but they also appear to be circuitously protecting us from disease.”

Other authors on the study are: Douglas J. McCauley, UC Santa Barbara; Rodolfo Dirzo of Stanford University; Kristofer M. Helgen of the National Museum of Natural History, Smithsonian Institution; Sarah A. Billeter, Michael Y. Kosoy and Lynn M. Osikowicz of the Division of Vector-Borne Infectious Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention; Daniel J Salkeld of Colorado State University, Fort Collins, and the Woods Institute for the Environment at Stanford University; and Katharina Dittmar of the University at Buffalo, The State University of New York.

KLEE is a collaboration with the University of Nairobi, the National Museums of Kenya and the Kenya Wildlife service. The work was by the National Science Foundation, the James Smithson Fund of the Smithsonian Institution, the National Geographic
Society, the Natural Sciences and Engineering Council of Canada, the African Elephant Program of the US Fish and Wildlife Service, the Woods Institute for the Environment, and the Smithsonian Institution Women’s Committee.

More information: full news release from UC Santa Barbara

UC Davis-led team achieves first light for flying infrared instrument

As we blogged last week, the EXES (Echelon-Cross-Echelle Spectrograph) instrument, a collaboration involving UC Davis and NASA Ames scientists and engineers and led by research scientist Matthew J. Richter of the UC Davis Physics Department, successfully carried out its first two flights with the Stratospheric Observatory for Infrared Astronomy (SOFIA) on the nights of April 7 and 9.

EXES is a high-resolution astronomical spectrograph that operates at wavelengths from 4.5 to 28.3 microns. It is designed to provide unprecedented study of spectral features, particularly from molecules, at wavelengths unavailable or inherently difficult to observe from ground-based telescopes. SOFIA is a modified Boeing 747SP aircraft that carries a 2.5 meter telescope to altitudes of 39,000 to 43,000 feet, above 99 percent of Earth’s atmospheric water vapor, for over eight hours of observing time. The combination of EXES’s high spectral resolution and SOFIA’s ability to open new spectral regions will provide data that cannot be duplicated by any facility: past, current, or in development; ground-based or space!

EXES team members about the SOFIA flying observatory. Left to right, Curtis DeWitt, UC Davis postdoc; Matt Richter, UC Davis, EXES PI; Mark McKelvey, NASA Ames, EXES Co-PI. The telescope is on the other side of the pressure bulkhead at the back of the photo. The EXES instrument is the cylinder protruding from the bulkhead.

EXES team members about the SOFIA flying observatory. Left to right, Curtis DeWitt, UC Davis postdoc; Matt Richter, UC Davis, EXES PI; Mark McKelvey, NASA Ames, EXES Co-PI. The telescope is on the other side of the pressure bulkhead at the back of the photo. The EXES instrument is the cylinder protruding from the bulkhead.

During the two flights, the EXES team conducted commissioning observations to investigate and characterize instrumental performance so astronomers from around the world can propose for future EXES observations. These observations included looking at well-known, bright standard stars such as Aldebaran and Arcturus, mapping the planets Mars and Jupiter at settings tuned for selected molecular transitions, and demonstrating performance on a massive young star still so embedded in surrounding dust and gas that the star is optically invisible. All the main goals of the commissioning observations were successful, although further commissioning flights, scheduled for November, will be required to understand EXES more precisely. While these observations are primarily intended for instrument commissioning, the unique capabilities of EXES on SOFIA make it likely that scientific publications will result from these first two flights. The work to understand the data has already begun.

Contributed by Matt Richter.

How brain structures grow as memory develops

Our ability to store memories improves during childhood, associated with structural changes in the hippocampus and its connections with prefrontal and parietal cortices. New research from UC Davis is exploring how these brain regions develop at this crucial time. Eventually, that could give insights into disorders that typically emerge in the transition into and during adolescence and affect memory, such as schizophrenia and depression.

Located deep in the middle of the brain, the hippocampus plays a key role in forming memories. It looks something like two curving fingers branching forward from a common root. Each branch is a folded-over structure, with distinct areas in the upper and lower fold.

The hippocampus plays a key role in creating memories. Credit: Life Sciences Database (Japan), via Wikipedia.

The hippocampus (red) plays a key role in creating memories. Credit: Life Sciences Database (Japan), via Wikipedia.

“For a long time it was assumed that the hippocampus didn’t develop at all after the first couple of years of life,” said Joshua Lee, a graduate student at the UC Davis Department of Psychology and Center for Mind and Brain. Improvements in memory were thought to be due entirely to changes in the brain’s outer layers, or cortex, that manage attention and stretagies. But that picture has begun to change in the past five years.

Recently, Lee, Professor Simona Ghetti at the Center for Mind and Brain and Arne Ekstrom, assistant professor in the UC Davis Center for Neuroscience, used magnetic resonance imaging to map the hippocampus in 39 children aged eight to 14 years.

While subfields of the hippocampus have been mapped in adult humans and animal studies, it’s the first time that they have been measured in children, Ghetti said.

“This is really important to us, because it allows us to understand the heterogeneity along the hippocampus, which has been examined in human adults and other species” Ghetti said.

Looking at three subregions — the cornu ammonis (CA) 1, CA3/dentate gyrus and subiculum — they found that the first two expanded with age, with the most pronounced growth in the right hippocampus. Only in the oldest 25 percent of the children, within a few months either side of 14, did the sizes of all three regions decrease.

MRI slices through the hippocampus of an 8-year-old. Colors show different regions that were studied.

MRI slices through the hippocampus of an 8-year-old. Colors show different regions that were studied.

When they tested the children for memory performance, children with a larger CA3/dentate gyrus tended to perform better, they found. The work was published online March 15 by the journal Neuroimage.

In a related study in collaboration with the laboratory of Professor Silvia Bunge at UC Berkeley, published March 27 in Cerebral Cortex, the researchers also demonstrated how white matter connections projecting from the hippocampus to the brain cortex are related to memory function in children.

The cerebral cortex manages attention. Areas are connected by white matter tracts. Credit: Mammalian Brain Collection, University of Wisconsin-Madison, funded by NSF/NIH; via

The cerebral cortex manages attention. Areas are connected by white matter tracts. Credit: Mammalian Brain Collection, University of Wisconsin-Madison, funded by NSF/NIH; via

“White matter” tracts connect the prefrontal and parietal regions of the brain cortex, which control how we pay attention to things and engage in memory strategies, with the media-temporal lobe, the area that includes the hippocampus.

In the study, children performed a memory test that prompted them either to actively memorize an item — and therefore engage the prefrontal and parietal cortices — or to view an image passively. The ability to successfully modulate attention was linked to development of white matter tracts linking the prefrontal and parietal cortex tothe mediatemporal lobe, Ghetti said, but not to fronto-parietal connections.

Lead author on the paper is UC Berkeley researcher Carter Wendelken, with coauthors Lee, Bunge and Ghetti as well as Jacqueline Pospisil, Marcos Sastre and Julia Ross, all at UC Davis. It’s part of a large collaborative study of memory function and brain growth in children, lead by Ghetti and Bunge, and funded by the National Institutes of Health. The study will look at the development of in a cohort of children from age eight to 14 years.

More information: Simona Ghetti’s Memory and Development Lab at UC Davis

Plants, worms, people and cancer

What do plants and worms and humans have in common, and how can they help humans?

To address that deceptively simple question, Professors Anne Britt of Plant Biology and JoAnne Engebrecht of Molecular and Cellular Biology are collaborating through the first-ever College of Biological Sciences Kingdom-Crossing grant to identify genes shared by plants and worms that are involved in DNA metabolism.Caenorhabditis elegans

Their work may ultimately pinpoint new genes that are key to genome stability and that, when malfunctioning, cause disease.

“Understanding how our genomes are maintained, whether in plants or worms or humans, is critical in diseases like cancer,” Engebrecht said. “Everyone has someone who has been affected by cancer in their lives and the disease is clearly a consequence of genome instability.”

She added that they are trying to understand how that process works with the ultimate goal of providing either diagnostics or chemotherapy agents.

“Anne and JoAnne’s collaboration exemplifies the spirit of our Kingdom-Crossing grants,” Dean James E. K. Hildreth said. “They are reaching beyond their own areas of expertise to find the commonalities between life forms. This type of research will hopefully contribute to real-world solutions for major problems in the areas of health, food and the environment.”

ArabidopsisThe project idea took seed in Britt’s lab.

“I work in Arabidopsis and what we found is that when expose the plant to ionizing radiation, Arabidopsis switches on hundreds of genes in response,” Britt said.

The Britt lab found that plants, unlike animals, strongly upregulate hundreds of genes in response to DNA damage. The most overrepresented category of those genes were ones involved in DNA metabolism, which includes repair, recombination and synthesis. And, in fact, at the top of the list was the breast cancer gene, BRCA1.

Britt began looking for a way to find out whether those same genes would be conserved in all eukaryotes or if they are plant-specific.

“Given the importance of BRCA1, there might be other transcripts in the group that are incredibly important for genome stability and maybe even cancer biology. In which case it would be great to look for them in animal systems,” Britt said.

So Britt approached Engebrecht, who works with the worm Caenorhabditis elegans, thinking the worms might be an ideal intermediary between her plant gene list and the animal kingdom.

Through the Kingdom-Crossing grant, which fosters collaboration between experts in different life systems, the professors were able to hire researcher Kayla Aung to bridge the work between their labs.

Aung spearheaded the project, setting to work with Britt’s Arabidopsis gene list and generating a new one of orthologous genes in C. elegans. She then developed an assay to explore whether, when she inactivates these orthologous genes in worms and then exposes them to radiation, the worms show sensitivity to the radiation.

Sensitive genes go on a short list of good candidates for those involved in genome stability of both plant and animal systems.

“I’ve found some interesting candidates for further investigation,” Aung says, “And there are still many more to assay.”

Britt added that the technique is a novel one, and that Arabidopsis and C. elegans are actually ideal organisms for the hunt for genes involved in disease.

“People did look for upregulated genes in animals and fungi but they found that the effects were small and therefore hard to observe reproducibly,” she said.

She added that looking for cancer genes by knocking out various genes and then looking for sensitivity to radiation would kill the cell line in those systems, whereas both plants and worms are perfectly fine. They mature into viable organisms despite the gene inactivation and radiation.

The researchers said the project is a good proof-of-concept endeavor for this method of gene-function discovery, adding that their collaboration has enriched their own research.

“It’s been fun to interact with Anne and think a little bit outside of what my normal sphere of science is,” Engebrecht said. “We try to think in larger terms when we’re discussing and I learn things I wouldn’t with specialists from my own lab.”

“For every scientist on campus you chat with regularly, they chat with other scientists, and it creates new connections not just with two people, but dozens,” Britt added.

Contributed by Betsy Towner Levine, College of Biological Sciences