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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.

Three students win EPA fellowships

Three UC Davis graduate students are among 105 to receive Science To Achieve Results (STAR) fellowships from the Environmental Protection Agency. The STAR fellows will receive a maximum funding of $42,000 a year for up to two years for doctoral students.

The UC Davis recipients and their projects are: Rachel Wigginton, “Predicting Return of Ecosystem Services Based on Impacts of Invasive Ecosystem Engineers;” Matthew Whalen, “Biodiversity of native and invasive suspension feeders affects water quality and potential for harmful algal blooms” and Kelly Gravuer, “Maintaining ecosystem function under climate change: Understanding and managing plant-soil microbe community dynamics.” All three are doctoral students.

“These fellowships are helping our next generation of scientists and engineers earning advanced degrees in environmental sciences conduct cutting edge research,” said Lek Kadeli, Acting Assistant Administrator for EPA’s Office of Research and Development in a news release. “Through this support, EPA is ensuring that the United States will have the scientific knowledge to meet future environmental challenges, which will strengthen our nation’s economy and security, while better protecting our health and environment in addition to combating climate change.”

More information about the EPA STAR Fellowship program. Wigginton also blogs at Sweet Tea, Science and is on Twitter at @RachelWigginton. Whalen tweets as @killerwhalen13.

Icelandic volcano sits on massive magma hot spot

By Kat Kerlin

Spectacular eruptions at Bárðarbunga volcano in central Iceland have been spewing lava continuously since Aug. 31. Massive amounts of erupting lava are connected to the destruction of supercontinents and dramatic changes in climate and ecosystems.

New research from UC Davis and Aarhus University in Denmark shows that high mantle temperatures miles beneath the Earth’s surface are essential for generating such large amounts of magma. In fact, the scientists found that the Bárðarbunga volcano lies directly above the hottest portion of the North Atlantic mantle plume.

The study, published online Oct. 5 and appearing in the November issue of Nature Geoscience, comes from Charles Lesher, professor of Earth and Planetary Science at UC Davis and a visiting professor at Aarhus University, and his former PhD student, Eric Brown, now a post-doctoral scholar at Aarhus University.

“From time to time the Earth’s mantle belches out huge quantities of magma on a scale unlike anything witnessed in historic times,” Lesher said. “These events provide unique windows into the internal working of our planet.”

Such fiery events have produced large igneous provinces throughout Earth’s history. They are often attributed to upwelling of hot, deeply sourced mantle material, or “mantle plumes.”

Recent models have dismissed the role of mantle plumes in the formation of large igneous provinces, ascribing their origin instead to chemical anomalies in the shallow mantle.

Holuhraun fissure eruption on the flanks of the Bárðarbunga volcano in central Iceland on Oct. 4, 2014, showing the development of a lava lake in the foreground. Vapor clouds over the lava lake are caused by degassing of volatile-rich basaltic magma. (Photo: Morten S. Riishuus, Nordic Volcanological Institute)

Holuhraun fissure eruption on the flanks of the Bárðarbunga volcano in central Iceland on Oct. 4, 2014, showing the development of a lava lake in the foreground. Vapor clouds over the lava lake are caused by degassing of volatile-rich basaltic magma. (Photo: Morten S. Riishuus, Nordic Volcanological Institute)

Based on the volcanic record in and around Iceland over the last 56 million years and numerical modeling, Brown and Lesher show that high mantle temperatures are essential for generating the large magma volumes that gave rise to the North Atlantic large igneous provinces bordering Greenland and northern Europe.

Their findings further substantiate the critical role of mantle plumes in forming large igneous provinces.

“Our work offers new tools to constrain the physical and chemical conditions in the mantle responsible for large igneous provinces,” Brown said. “There’s little doubt that the mantle is composed of different types of chemical compounds, but this is not the dominant factor. Rather, locally high mantle temperatures are the key ingredient.”

The research was supported by grants from the US National Science Foundation and by the Niels Bohr Professorship funded by Danish National Research Foundation.

Read the full study at

Video: Lava Fountains from Bardarbunga Volcano Holuhraun Fissure Eruption viewed by Helicopter

Bee/orchid evolution wins Packard Fellowship

Santiago Ramirez, an assistant professor in the Department of Evolution and Ecology at the UC Davis College of Biological Sciences, has been awarded a Packard Fellowship in Science and Engineering from the David and Lucille Packard Foundation. Ramirez is one of 18 scientists nationwide to receive the prestigious fellowship, worth $875,000 over five years, this year.

The fellowships are intended to give early-career scientists the freedom and flexibility to “think big” and explore new ideas and approaches.

Ramirez’ research focuses on how species adapt to each other as they evolve. Evolutionary biologists have long recognized that interactions between species play a central role in creating biological diversity. However, exactly how ecological pressures and genetics combine so that species co-evolve and adapt to each other is not well understood.

Ramirez’s research uses approaches from genetics, ecology and physiology to investigate bees and orchids have evolved together and adapted to each other. His research team is studying a group of bees called the orchid bees. This particular group of bees visits orchids — as well as other plant sources — to collect floral scents that the males present to females during courtship display. The orchids have evolved such degree of specialization to attract male bees that the plants exclusively depend on scent-seeking males for pollination.

Orchid bees and the plants they visit are highly dependent on each other.

Orchid bees and the plants they visit are highly dependent on each other.

Biologists have been puzzling over pollination for a long time: Charles Darwin and Alfred Russell Wallace worked on the problem, proposing that flowers and pollinators engaged in a race that resulted in deeper flowers and pollinators with longer noses. In fact, more than 80 percent of the world’s flowering plants depend on insects for pollination.

Previous recipients of Packard Fellowships at UC Davis are Professor Matthew Augustine, Department of Chemistry, and Professor Matthew Franklin, Department of Computer Science.

New sequencing reveals genetic history of tomatoes

By Roger Chetelat

This week, an international team of researchers, led by the Chinese Academy of Agricultural Sciences in Beijing, is publishing in the journal Nature Genetics a brief genomic history of tomato breeding, based on sequencing of 360 varieties of the tomato plant.

The C.M. Rick Tomato Genetics Resource Center here at UC Davis played an important role in this study by providing seed of both cultivated tomato varieties and related wild species.

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

Domestic tomatoes (left) and three wild relatives.

This study, which builds on the first tomato genome sequence completed just two years ago, shows in great detail how the processes of early domestication and modern breeding influenced the genetic makeup of cultivated tomatoes. (UC Davis researchers also took part in an effort to sequence the genome of a wild relative of the cultivated tomato.)

Analysis of the genome sequences of these 360 varieties and wild strains shows which regions of the genome were under selection during domestication and breeding. The study identified two independent sets of genes responsible for making the fruit of modern commercial tomatoes 100 times larger than their wild ancestors.

An important finding is that specific regions of the tomato genome were unintentionally depleted in genetic variation: for example, in DNA around genes conferring larger fruit size or genes for resistance to diseases afflicting tomato plants.

These stretches of genetic uniformity illustrate the need to increase overall genetic diversity in modern varieties and highlight the important role that the Rick Tomato Genetics Resource Center and similar collections play in housing much of the genetic variability that will be critical for future breeding and research on tomato.

Plant geneticist Roger Chetelat directs the C.M. Rick Tomato Genetics Resource Center at UC Davis.

Medicine Nobel: How the brain makes sense of place

The 2014 Nobel Prize in Physiology or Medicine has been awarded to three neuroscientists, John O’Keefe, May-Britt Moser and Edvard I. Moser, for their discoveries of brain cells that allow us to make sense of place and location and navigate our environment.

In 1971, O’Keefe, then working at University College London, identified “place cells” in an area of the brain called the hippocampus. In rats, specific place cells activated when a rat was in a specific location, making up a map of the room inside the rat’s brain.

More than 30 years later, the Mosers discovered “grid cells,” that allow our brains to create coordinates and navigate between points.

Arne Ekstrom, associate professor at the UC Davis Center for Neuroscience, is building on the work of O’Keefe and the Mosers to understand how the brain can navigate a real or virtual environment.

“It is incredibly exciting that the Nobel committee has chosen to recognize and honor the seminal work of John O’Keefe and Edvard and May-Brit Moser,” Ekstrom said in an email.  “Their work has completely changed our perspective on the interface between brain and behavior, providing a critical and previously non-existent link between the activity of individual neurons and higher order cognition.”

Their work demonstrates that changes in the activity of neurons in the hippocampus and entorhinal cortex underlie the ability to spatially navigate and remember information regarding where we are, Ekstrom said.  Dr. O’Keefe’s groundbreaking work in the 70s  ushered in decades of high-impact work elucidating how these cells change their firing pattern due to changes in spatial geometry, vestibular cues, and visual cues.  In this way, place cells provide not just a code for navigation but for memory more generally. His work has also influenced our understanding of the human brain, where the existence of place cells have been confirmed in rare neurosurgical patients who explore virtual reality while undergoing brain recordings, by suggesting that place cells may be one of many different cellular mechanisms for coding the details of memories.

The Mosers’ work has similarly been highly influential in our understanding of navigation by suggesting that neurons in the entorhinal cortex code for spatial environments by firing in a regular, grid-like fashion as a rat explores a spatial environment.  These cells differ, though, in several important ways from the place cells described by O’Keefe, in that they are less sensitive to changes in spatial geometry and provide a more detailed “metric” of space than place cells do.  Recent work has also confirmed the existence of grid-cells in human neurosurgical patients; their integration into a larger memory system in humans is just beginning to be explored, including by work here at UC-Davis.

More information:

– Arne Ekstrom’s Human Spatial Cognition Lab

New York Times profile of the winners

Could Western China repeat California’s success in agriculture?

By Colin Carter

Recently I joined a large delegation from UC Davis, led by Chancellor Linda P.B. Katehi, at the 80th anniversary celebration of China’s Northwest Agricultural and Forestry University in Shaanxi province, including an international forum on the development of western China cosponsored by UC Davis. For all of us, the forum was a powerful reminder that western China is key to the future prosperity of that nation — much like California, which rose from obscurity to become the richest and most agriculturally productive state in the U.S.

Xi’an, the capital of Shaanxi province, was the beginning of the Silk Road, which opened up political and economic linkages between China and other civilizations. Western China has vast land area and undeveloped resources that will be critical for the future economic development of the country.

In terms of economic development over the past 30 years, eastern China is far ahead of western China, which now is home to 400 million people, including most of China’s poor communities. Seventy percent of those people are engaged in agriculture and have farm incomes less than one-third that of urban incomes. Solving these looming problems of the west will be key to China’s future.

This may seem a daunting task, but remember that just over 110 years ago California was considered a poor, desert region and yet it has since grown to become the richest state and number one agricultural producer in the nation. California and much of the American West prospered as infrastructure, market incentives and water were made available, and its agricultural development was accelerated by research, teaching and extension services provided by the University of California.

UC Davis and Northwest Agriculture and Forestry University recently agreed to work together to establish a joint research center on food safety. Through this and other initiatives, many of us at UC Davis are eager to partner with China and the Northwest Agriculture and Forestry University to help solve the agricultural, environmental and ecological challenges associated with the economic development of Western China.

Professor Colin Carter is an agricultural economist at UC Davis with roughly 30 years of research experience in China.

Making oxygen before life

About one-fifth of the Earth’s atmosphere is oxygen, pumped out by green plants as a result of photosynthesis and used by most living things on the planet to keep our metabolisms running. But before the first photosynthesizing organisms appeared about 2.4 billion years ago, the atmosphere likely contained mostly carbon dioxide, as is the case today on Mars and Venus.

Over the past 40 years, researchers have thought that there must have been a small amount of oxygen in the early atmosphere. Where did this abiotic (“non-life”) oxygen come from? Oxygen reacts quite aggressively with other compounds, so it would not persist for long without some continuous source.

Now UC Davis graduate student Zhou Lu, working with professors in the Departments of Chemistry and of Earth and Planetary Sciences, has shown that oxygen can be formed in one step by using a high energy vacuum ultraviolet laser to excite carbon dioxide. (The work is published Oct. 3 in the journal Science).

“Previously, people believed that the abiotic (no green plants involved) source of molecular oxygen is by CO2 + solar light — > CO + O, then O + O + M — > O2 + M (where M represents a third body carrying off the energy released in forming the oxygen bond),” Zhou said in an email. “Our results indicate that O2 can be formed by carbon dioxide dissociation in a one step process. The same process can be applied in other carbon dioxide dominated atmospheres such as Mars and Venus.”

UC Davis chemists have shown how ultraviolet light can split carbon dioxide to form oxygen in one step. Credit: Zhou Lu

UC Davis chemists have shown how ultraviolet light can split carbon dioxide to form oxygen in one step. Credit: Zhou Lu

Zhou used a vacuum ultraviolet laser to irradiate CO2 in the laboratory. Vacuum ultraviolet light is so-called because it has a wavelength below 200 nanometers and is typically absorbed by air. The experiments were performed by using a unique ion imaging apparatus developed at UC Davis.

Such one-step oxygen formation could be happening now as carbon dioxide increases in the region of the upper atmosphere, where high energy vacuum ultraviolet light from the Sun hits Earth or other planets. It is the first time that such a reaction has been shown in the laboratory. According to one of the scientists who reviewed the paper for Science, Zhou’s work means that models of the evolution of planetary atmospheres will now have to be adjusted to take this into account.

Coauthors on the paper are, in the UC Davis Department of Chemistry, postdoctoral researcher Yih Chung Chang, Distinguished Professor Cheuk-Yiu Ng and Distinguished Professor emeritus William M. Jackson; and Professor Qing-Zhu Yin, Department of Earth and Planetary Sciences. The work was principally funded by NASA, NSF, and the U.S. Department of Energy.

Curiosity helps learning and memory

Curiosity helps us learn about a topic, and being in a curious state also helps the brain memorize unrelated information, according to researchers at the UC Davis Center for Neuroscience. Work published Oct. 2 in the journal Neuron provides insight into how piquing our curiosity changes our brains, and could help scientists find ways to enhance overall learning and memory in both healthy individuals and those with neurological conditions.

“Our findings potentially have far-reaching implications for the public because they reveal insights into how a form of intrinsic motivation — curiosity — affects memory. These findings suggest ways to enhance learning in the classroom and other settings,” says first author Matthias Gruber, a postdoctoral researcher at the center.

Video: How curiosity changes the brain and enhances learning

Participants in the study first rated their curiosity about the answers to a series of trivia questions. Later, they had their brains scanned via functional magnetic resonance imaging while they learned the answers to these questions. First, they were presented with a selected trivia question and while they waited for the answer to pop up on the screen, they were shown a picture of a neutral, unrelated face.

Afterwards, participants performed a surprise recognition memory test for the presented faces, followed by a memory test for the answers to the trivia questions.

As might be expected, people were better at learning the trivia information when they were highly curious about it. More surprisingly, they also showed better learning of the unrelated faces that were shown while their curiosity was aroused. Information learned during a curious state was better retained over a 24-hour delay.

“Curiosity may put the brain in a state that allows it to learn and retain any kind of information, like a vortex that sucks in what you are motivated to learn, and also everything around it,” Gruber said.

Secondly, the investigators found that when curiosity is stimulated, there is increased activity in the brain circuit related to reward.

“We showed that intrinsic motivation actually recruits some of the same brain areas that are heavily involved in tangible, extrinsic motivation,” Gruber said. This reward circuit relies on dopamine, a chemical that relays messages between neurons.

The team also discovered that when learning was motivated by curiosity, there was increased activity in the hippocampus, a brain region that is important for forming new memories, as well as increased interactions between the hippocampus and the dopamine reward circuit.

Charan Ranganath is exploring the basis of memory.

Charan Ranganath is exploring the basis of memory.

“So curiosity recruits the reward system, and interactions between the reward system and the hippocampus seem to put the brain in a state in which you are more likely to learn and retain information, even if that information is not of particular interest or importance,” said Charan Ranganath, senior author, and Professor at the UC Davis Center for Neuroscience and Department of Psychology.

Brain circuits that rely on dopamine tend to decline in function with aging, or sooner in people with neurological or psychiatric disorders. Understanding the relationship between motivation and memory could stimulate new efforts to improve memory in the healthy elderly and new approaches for treating patients with memory disorders. And in the classroom or workplace, learning could be enhanced if teachers or managers can engage students’ and workers’ curiosity about something they are naturally motivated to learn.

Coauthors on the study were Gruber, Ranganath and research scientist Bernard Gelman. The work was supported by the National Institutes of Health, the Simon J. Guggenheim Foundation, and the Leverhulme Trust.

Dust to dust: BICEP2 result on gravitational waves may not be so strong

Earlier this year, physicists celebrated results from the BICEP2 experiment which reported evidence of gravitational waves, a signature of cosmic inflation immediately after the Big Bang.

But earlier this week, results from the Planck space telescope cast doubt on the BICEP2 findings. Instead of showing gravitational waves at the beginning of time, BICEP2 might actually have picked up interstellar dust within our own galaxy.

Andy Albrecht, a UC Davis physics professor and well-known theorist on cosmic inflation, wrote this blog post reflecting on the “emotional roller coaster” of the BICEP2 and Planck findings. The lack of a gravitational signal at the level detectable by BICEP2 does not rule out cosmic inflation, because there are models that include a weaker signal, he wrote. But the story “has given people a wonderful window on the emotional energy that goes into doing science,” he wrote.

This is certainly a story about the passion that goes into doing science, but it is also a success story for science. While I do feel the BICEP2 team should have been more careful about how they presented their results, their over-optimistic beliefs about the limited impact of galactic dust on their data reflected a (mistaken) perspective that was widely held in our community regarding the overall strength of the dust emissions. The relentless march of progress is clearing up these misconceptions, and progress was in fact stimulated by the excitement surrounding the original announcement.

Interestingly, UC Davis physicist Lloyd Knox noted in a blog post at the time of the original result that he was concerned about contamination from interstellar dust.

Grant to help commercialize silicon surgical blades

A UC Davis engineering professor has received a grant of $200,000 from the National Science Foundation “Partnerships for Innovation: Accelerating Innovation Research- Technology Translation” program to move his silicon-based blades towards commercial development as surgical and shaving tools.

Silicon or ceramic blades are extremely sharp and hard, keeping an edge longer than metal blades, but they are expensive to manufacture. The technique recently invented by Saif Islam, professor of electrical and computer engineering at UC Davis, allows thin silicon blades to be mass-produced at much lower cost.

Islam and his team stumbled on the technique while making silicon wafers for research on solar panels. They produced some very thin vertical walls of silicon, which turned out to be extremely sharp.

Islam has formed a company, Atocera (formerly Nano-Sharp) to license the patented technology from UC Davis and take it into commercial development. The grant will support development of a plan for scaling up the process for making silicon surgical blades.

Using silicon opens possibilities for “smart” blades, Islam said.

“Potentially, we could incorporate electrical and optical technologies, taking advantage of the semiconductor platform, to facilitate an enhanced hair removal process,” he said.

Atocera is currently housed in the Engineering Translational Technology Center, the business incubator in the UC Davis College of Engineering. The company’s Interim CEO is Jim Olson, the center’s business specialist and co-founder. The work has previously been supported by a Proof of Concept grant from the University of California Office of the President (UCOP).