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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.

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).

Baby desert tortoises get a headstart in the Mojave

A baby desert tortoise lies on its back atop a scale inside a new building at Mojave National Preserve. It wriggles—slowly­—its arms and feet like an infant on a changing table.

The site, the Ivanpah Desert Tortoise Research Facility, is designed to give struggling desert tortoises like this one a headstart on survival. Located on the preserve itself, researchers from the University of California, Davis and the University of Georgia, will use the facility to research juvenile tortoise survival.

Desert tortoises are tough. They can flourish in places most species find inhospitable. Able to store water for use during a drought, they can go a year without water. Yet habitat loss and other disturbances have threatened their existence, and they are now federally listed as a threatened species.

“The Mojave desert tortoise population has been declining for decades due to loss of habitat, deaths on roadways, disease, and other factors,” said Brian Todd, an associate professor of wildlife biology at UC Davis. “We are excited that our partnership with the National Park Service’s Mojave National Preserve will allow us to study how these factors affect tortoises.”

The facility was built in 2012 by Chevron on Molycorp land and managed until recently by National Park Trust. A dedication ceremony in early September commemorated the transfer of the facility to Mojave National Preserve.

The Desert Tortoise Research Facility includes a LEED Silver-certified laboratory building, two acres of predator-proof tortoise enclosures containing native vegetation, and seven acres of high-quality tortoise habitat. This enables scientists to study them in a protected but natural environment.

Since the facility opened, 185 desert tortoise hatchlings have emerged within the protected facility and 46 have been released and are being monitored.

By raising juvenile tortoises to a larger size and releasing them in the preserve, the scientists expect they can both improve populations of the desert tortoise as well as study survival and behavior of young tortoises, something Todd said was otherwise not possible.

“This new facility provides scientists the opportunity to test methods for increasing the survival of juvenile tortoises to reproductive age,” said Stephanie Dubois, superintendent of Mojave National Preserve. “This research could lead to the development of proven methods for recovering this species that continues to decline.”

Contributed by Kat Kerlin

Psychologist’s research supports gay marriage decision

When a panel of the 7th Circuit Court of Appeals struck down gay marriage bans in Wisconsin and Indiana this week, the justices cited work by UC Davis professor of psychology Gregory Herek.

In the 40-page opinion, Judge Richard A. Posner wrote, “…there is little doubt that sexual orientation, the ground of the discrimination, is an immutable (and probably an innate, in the sense of in-born) characteristic rather than a choice.” Posner cited a paper published by Herek and colleagues in 2010, which found that 95 percent of gay men and 84 percent of lesbians perceived they had little or no choice about their sexual orientation.

About 20 federal courts have now ruled against state laws that ban gay marriage, or ban recognition of out-of-state same-sex marriages, while one U.S. district court has upheld a state ban, so it’s likely the issue will soon be heard by the Supreme Court.

 

Climate-smart agriculture requires three-pronged global research agenda

Faced with climate change and diminishing opportunities to expand productive agricultural acreage, the world needs to invest in a global research agenda addressing farm and food systems, landscape and regional issues and institutional and policy matters if it is to meet the growing worldwide demand for food, fiber and fuel, suggests an international team of researchers.

In a paper appearing online in the journal Agriculture and Food Security, the authors summarize the findings of the second international Climate Smart Agriculture conference held in March 2013 at UC Davis.

“Climate-smart agriculture has become a global policy initiative for economic development, poverty reduction and food security,” says lead author Kerri Steenwerth, a U.S. Department of Agriculture soil scientist and adjunct professor in the UC Davis Department of Viticulture and Enology.

“It makes sense for farmers, consumers and food businesses because it is focused on the long-term sustainability of supply chains, and applies both to farmers’ fields and to the natural landscape,” she said.

The objectives recommended in the new paper set the stage for a stronger emphasis on moving knowledge into action and involving researchers in helping communities and societies to change and adapt.

Steenwerth has posted a blog entry about the paper on the Biomed Central blog. The blog and the paper were supported by the UC Davis College of Agricultural and Environmental Sciences.

A third global science conference on Climate-Smart Agriculture is scheduled to be held March 16-18, 2015 in Montpellier, France.

The other authors on the paper from UC Davis were: Louise Jackson, Amanda Hodson, Arnold Bloom, Michael Carter, Jan Hopmans, William Horwath, Bryan Jenkins, Ermias Kebreab, Mark Lubell, Samuel Sandoval Solis, Michael Springborn, Stephen Wheeler, and Lovell Jarvis.

Authors representing other institutions were Andrea Cattaneo and Leslie Lipper, both of the Food and Agriculture Organization of the United Nations in Rome, Italy; Colin Chartres of the University of Canberra in Australia; Jerry Hatfield of the ARS/USDA National Laboratory for Agriculture and the Environment in Ames, Iowa; Kevin Henry of Colorado State University; Rik Leemans and Pablo Tittonell, both of Wageningen University, the Netherlands; Siwa Msangi of the International Food Policy Research Institute in Washington, D.C.; Ravi Prabhu of the World Agroforestry Center in Nairobi, Kenya; Matthew Reynolds of the Consultative Group on International Agricultural Research in Mexico; William Sischo of Washington State University; Sonja Vermeulen of the University of Copenhagen, Denmark; and Eva Wollenberg of the Consultative Group on International Agricultural Research (CGIAR).