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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.

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

SOFIA flying observatory passing over tonight

The SOFIA flying lab will make its second flight with the EXES experiment on board tonight. The EXES (Echelon-Cross-Echelle-Spectrograph) project is lead by UC Davis phyicist Matt Richter.

The flight plan should have SOFIA, which operates out of Palmdale, Calif., taking off about 7 p.m. Pacific Time and flying over the Sacramento area before heading out over the ocean west of Oregon and Washington for a series of observing legs.

Richter and his team will be aboard and expect to get in about eight hours of observations during the 10-hour flight.

Modeling of silicon nanoparticles for solar energy

Silicon nanoparticles embedded in a zinc sulfide matrix are a promising material for new types of solar cell. Computational modeling by Stefan Wipperman, Gergely Zimanyi, Francois Gygi and Giulia Galli at UC Davis and colleagues shows how such a material might work.

“Designing materials with desired properties for renewable energy application is a topic of great current interest in physics, chemistry, and materials science, and one of the goals of the Materials Genome initiative, launched in the US in 2011. Our paper focuses on the search for design rules to predict Earth abundant materials for the efficient conversion of solar energy into electricity,” Zimanyi said in an email.

Their work is published March 14 in the journal Physics Review Letters and featured on the journal’s cover.

A silicon nanoparticle (grey rods) in a zinc sulfide matrix is coated with sulfur atoms (yellow). Blue blobs represent electron orbitals. Modeling suggests these nanoparticles would efficiently separate light-induced negative and positive charges in solar cell.

A silicon nanoparticle (grey rods) in a zinc sulfide matrix is coated with sulfur atoms (yellow). Blue blobs represent electron orbitals. Modeling suggests these nanoparticles would efficiently separate light-induced negative and positive charges in solar cell.

The image shows a silicon nanoparticle (grey rods), coated in sulfur atoms (yellow spheres) from the surrounding matrix. The blue blobs represent electron orbitals. This model was produced by ab initio molecular dynamics modeling and electron structure calculations, Zimanyi said.

Incoming photons create electron/hole pairs. A solar cell generates current by separating negatively-charged electrons and positive holes to different electrodes. In this structure, the models predict that the junction between nanoparticle and the zinc sulfur matrix will allow efficient separation of charges.

Coauthors on the paper are Márton Vörös, UC Davis and Adam Gali, Budapest University of Technology and Economics and Hungarian Academy of Sciences.

Hubble weighs the “El Gordo” colliding galaxy cluster

NASA’s Hubble Space Telescope has weighed the largest known galaxy cluster in the distant universe and found that it definitely lives up to its nickname: El Gordo, Spanish for “the fat one.”

By precisely measuring how much the gravity from the cluster’s mass warps images of far more distant background galaxies, a team of astronomers lead by James Jee of the UC Davis physics department has calculated the cluster’s mass to be as much as 3 million billion times the mass of our Sun. The Hubble data show that the cluster is roughly 43 percent more massive than earlier estimates based on X-ray and dynamical studies of the unusual cluster.

“It’s given us an even stronger probability that this is really an amazing system very early in the universe,” Jee said.

Weighing El Gordo posed a challenge, because the cluster as we see it from Earth is in fact two colliding clusters, complicating the techniques used for mass estimates.

A fraction of the cluster’s mass is locked up in several hundred galaxies, and a larger fraction is in hot gas that fills the entire volume of the cluster. The rest is tied up in dark matter, an invisible form of matter that makes up the bulk of the mass of the universe.

The El Gordo galaxy cluster is the largest observed from a time when the universe was half its current age. A new estimate puts its mass at a million times that of our Milky Way galaxy. (NASA photo)

The El Gordo galaxy cluster is the largest observed from a time when the universe was half its current age. A new estimate puts its mass at three million billion Suns. (NASA photo)

The immense size of El Gordo was first reported in January 2012. Astronomers estimated its huge mass based on observations from NASA’s Chandra X-ray Observatory and galaxy velocities measured by the European Southern Observatory’s Very Large Telescope array in Paranal, Chile. They were able to put together estimates of the cluster’s mass based on the motions of the galaxies moving inside the cluster and the very high temperatures of the hot gas between the cluster galaxies.

But they noticed that the cluster (catalogued as ACT-CL J0102-4915) looked as if it might have been the result of a titanic collision between a pair of galaxy clusters, an event the researchers describe as “seeing two cannonballs hit each other.”

“We wondered what happens when you catch a cluster in the midst of a major merger and how the merger process influences both the X-ray gas and the motion of the galaxies,” explained John Hughes of Rutgers University. “So the bottom line is that because of the complicated merger state, it left some questions about the reliability of the mass estimates we were making.”

“That’s where the Hubble data came in,” said Felipe Menanteau of the University of Illinois at Urbana-Champaign. “We were in dire need for an independent and more robust mass estimate given how extreme this cluster is and how rare its existence is in the current cosmological model. There was all this kinematic energy that could be unaccounted for and could potentially suggest that we were actually underestimating the mass.”

The expectation of “unaccounted energy” comes from the fact that the merger is occurring tangentially to the observers’ line-of-sight. This means they are potentially missing a good fraction of the kinetic energy of the merger because their spectroscopic measurements only track the radial speeds of the galaxies.

The team used Hubble to measure how strongly the mass of the cluster warped space. Hubble’s high resolution allowed measurements of so-called “weak lensing,” where the cluster’s immense gravity subtly distorts space like a funhouse mirror and warps images of background galaxies. The greater the warping, the more mass is locked up in the cluster. “What I did is basically look at the shapes of the background galaxies that are farther away than the cluster itself,” explained Jee.

Though galaxy clusters as massive as El Gordo are found in the nearby universe, such as the so-called Bullet cluster, nothing like this has ever been seen to exist so far back in time, when the universe was roughly half of its current age of 13.8 billion years. The team suspects such monsters are rare in the early universe, based on current cosmological models.

The team’s next step with Hubble will be to try to get a large mosaic image of the cluster. It doesn’t fit into Hubble’s field of view. It’s like looking at a giant’s head and shoulders from the side, say researchers. “We can tell it’s a pretty big El Gordo, but we don’t know what kind of legs he has, so we need to have a larger field of view to get the complete picture of the giant,” said Menanteau.

(Adapted from a NASA news release)

First peanut genomes sequenced

The genome of the peanut, a staple food for millions in the developing world as well as an important cash crop, has been sequenced by a multinational consortium including researchers at the UC Davis Genome Center.

The new peanut genome sequence will be available to researchers and plant breeders across the globe to aid in the breeding of more productive, more resilient peanut varieties. Sequence data will be online at from April 2.

An international consortium has produced genome sequences for the two ancestors of cultivated peanuts.

An international consortium has produced genome sequences for the two ancestors of cultivated peanuts.

Peanut (Arachis hypogaea), also called groundnut, is an important crop both commercially and nutritionally. Globally, farmers tend about 24 million hectares of peanut each year, producing about 40 million metric tons. While the oil and protein rich legume is seen as a cash crop in the developed world, it remains an important sustenance crop in developing nations.

The peanut grown in fields today is the result of a natural cross between two wild species, Arachis duranensis and Arachis ipaensis, that occurred in the north of Argentina between 4,000 and 6,000 years ago. Because its ancestors were two different species, today’s peanut is a tetraploid, meaning the species carries two separate genomes which are designated A and B sub-genomes.

IPGI researchers sequenced the DNA of both ancestors, covering more than 96 percent of peanut genes. Professor Richard Michelmore’s laboratory at the UC Davis Genome Center generated ultra-high density genome maps for the two peanut genomes. These maps provided the frameworks for ordering the sequence fragments and joining them together into chromosome-scale pieces. UC Davis researchers also sequenced the genes that are actually expressed in each ancestor (the transcriptome).

By comparing the ancestral sequences with that of cultivated peanuts, geneticists and breeders will be able to look for genetic changes involved in domestication and make it easier to introduce traits from wild peanut that can improve crops such as disease resistance and drought tolerance, said UC Davis research scientist Lutz Froenicke.

The two ancestor species were collected from nature decades ago. One of the ancestral species, A. duranensis, is widespread but the other, A. ipaensis, has only ever been collected from one location, and indeed may now be extinct in the wild. Fortunately because of the long-sighted efforts of germplasm collection and preservation, both species were available for study and use by the IPGI.

About the peanut
In the U.S. peanuts are a major row crop throughout the South and Southeast. While they are an economic driver for the U.S. economy, the legume is also crucial to the diets and livelihood of millions of small farmers in Asia and Africa, many of whom are women. Apart from being a rich source of oil (44–55 percent), protein (20–50 percent) and carbohydrates (10–20 percent), peanut seeds are an important nutritional source for niacin, folate, calcium, phosphorus, magnesium, zinc, iron, riboflavin, thiamine and vitamin E.

About the International Peanut Genome Initiative
The International Peanut Genome Initiative brings together scientists from the United States, China, Brazil, India and Israel to delineate peanut genome sequences, characterize the genetic and phenotypic variation in cultivated and wild peanuts and develop genomic tools for peanut breeding. The initial sequencing was carried out by the BGI, Shenzen, China. Assembly was done at BGI; USDA-ARS, Ames, Iowa; and UC Davis. The project was made possible by funding provided by the peanut industry through the Peanut Foundation, by MARS Inc., and three Chinese Academies (Henan Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences, Shandong Academy of Agricultural Sciences). A complete list of the institutions involved with the project and the other funding sources is available at

Infrared observatory to take flight

On March 31, a team from UC Davis and NASA Ames installed the EXES Science Instrument aboard SOFIA, the Stratospheric Observatory for Infrared Astronomy. EXES (Echelon-Cross-Echelle Spectrograph) is designed to observe light in the mid-infrared at high resolution. It operates from 4.5 to 28.3 microns, a region of the spectrum with many molecular transitions, according to UC Davis researcher Matt Richter, lead investigator on the EXES project.

Richter and colleagues hope to use to observe molecules such as water, methane and hydrogen both in our solar system and in nearby galaxies. Proposed projects include observing water and methane around forming stars, and mapping hydrogen, methane and water in the atmospheres of Jupiter and Mars.

EXES team members in front of the instrument installed on the SOFIA flying laboratory, March 2014. Pictured from left are Matt Richter (UCD - PI), Mark McKelvey (Ames - Co-I), Mike Case (UCD - Software Engineer), Curtis DeWitt (UCD - Postdoc), and Jeff Huang (Ames - Systems Engineer). SOFIA is a NASA/German Space Agency project -- a converted 747 that carries an infrared telescope high into the atmosphere.

EXES team members in front of the EXES instrument installed on the SOFIA flying laboratory, March 2014. Pictured from left are Matt Richter (UC Davis – PI), Mark McKelvey (Ames), Mike Case (UC Davis), Curtis DeWitt (UC Davis), and Jeff Huang (Ames). SOFIA is a NASA/German Space Agency project — a converted 747 that carries an infrared telescope high into the atmosphere.

Water in the Earth’s atmosphere blocks much of the infrared light from the sky. SOFIA, a joint project involving NASA and the German Space Agency, is a Boeing 747SP aircraft modified to take a 2.5 meter telescope to the stratosphere and above 99 percent of the Earth’s atmospheric water vapor for 8-9 hour observing sessions. At that altitude, large portions of the infrared spectrum, blocked at even the best ground-based sites, become available for astronomical observations.

The combination of EXES’s high spectral resolution and SOFIA’s access to new wavelengths will provide data that cannot be duplicated by any facility: past, current, or in development; ground-based or space. Of particular interest will be studies of water, methane and molecular hydrogen, basic molecules that are difficult to study from the ground.

EXES is the sixth instrument of the seven initial instruments for SOFIA and will have its first two flights April 7 and April 9.

Physicists reflect on gravity wave discovery

Sky maps from the BICEP-2 telescope reveal evidence of gravity waves.

Sky maps from the BICEP-2 telescope reveal evidence of gravitational waves.

Contributed by Lloyd Knox, Department of Physics

On March 17, the scientific world was shaken by a dramatic announcement: Astronomers reported what many consider to be the “smoking gun” of a theorized stage in the very early evolution of the universe called inflation, revealed in data they gathered using the BICEP-2 telescope at the South Pole.

While many believed this signal was out there, it was unclear if it would be strong enough to be seen in our lifetimes, or even ever. This announcement was a very exciting one for cosmologists around the world, and of particular significance to Professor Andreas Albrecht, chair of the UC Davis physics department.

In 1982 Albrecht and Paul Steinhardt of Princeton University invented “slow-roll inflation,” a mechanism operating in the earliest fractions of a second of the Big Bang that appeared to explain key features of our universe: principally, why the universe is big and smooth and old.

That the universe might have gone through a period of inflation (accelerated expansion) had been realized a few years earlier, but the variety proposed by Albrecht and Steinhardt, and separately by Andrei Linde, was the first one that actually worked. Based on the BICEP-2 data, it now appears slow-roll inflation is actually what nature has chosen to do!

Albrecht was thrilled with the announcement and said his head has been “spinning all week.”

“Back in the 80′s, it was thrilling to work with such adventurous new ideas, but the ideas were so new and exotic it seemed a stretch to think that nature might have actually chosen to work that way. A few decades later, it is even more thrilling to contemplate the huge amount of evidence that nature really does seem to have chosen to inflate!” Albrecht wrote. (Read more of Albrecht’s thoughts on the discovery here.)

Albrecht noted that although inflationists long believed the gravity wave signal would be there, they had no way of knowing how strong the signal would be, or if they would be able to detect it even with future technology.

“It is amazing to learn that nature has been incredibly generous with us, and chosen a path where the gravitational wave signal is about as strong as it could be,” he said. The strength of the signal opens up a whole new field of gravitational wave astronomy, he said.

UC Davis physics professor Nemanja Kaloper has been another leading thinker about many aspects of inflation and he commented on a number of aspects of the discovery.

Regarding our quest for the fundamental laws of nature: “The fact that the [energy] scale of inflation is so close to the so called unification scale, where the observed matter forces may be united into the so called Grand Unified Theory (or GUT), is uncanny. Does it mean that such a GUT really exists? Is it an accident? Or are all hints of such dynamics in actual fact really indications of something else, pointing to some special corners of quantum gravity, string theory or some yet undiscovered grander scheme? We don’t know yet, but the promise of discovery is real.”

Regarding implications for models of inflation: “[This result] cuts like a hot knife through the proverbial butter of hundreds, if not thousands, of different scenarios, and tweaks of scenarios, of inflationary dynamics (and non-inflationary alternatives). The non-inflationary alternatives are now de facto ruled out. Perhaps we will still see some claims of tweaks to them, attempting to salvage what’s left, but they will be ugly, complicated and unappealing. Furthermore, most of the many inflationary models are also ruled out, being relegated to the dustbins of history of cosmology.”

Professor Lloyd Knox is an expert on the observational signatures of inflation working with data from the South Pole Telescope (SPT) and from the Planck satellite. Just last July we wrote about a step towards discovering gravitational waves, using data from the SPT. Knox praised the BICEP-2 team saying, “This measurement requires sensitivity to temperature differences on the sky of about 10 billionths of a Celsius degree, which means controlling all sources of spurious signal at this level. It’s a beautiful experiment.”

Even so, Knox said he is particularly concerned about contamination from interstellar dust.

“Fortunately we should be able to get a definitive answer on this question with the Planck data we will be releasing later this year,” he said.

“If this holds up, I just can’t believe how lucky I am to be alive now and to be a cosmologist,” Knox said. “The next 10 to 20 years will be VERY interesting! Cosmologists 100 years from now may very well be filled with envy.”

Honda Smart Home Open House is March 25

There will be a community open house at the Honda Smart Home in West Village on campus next Tuesday afternoon, March 25, noon to 4 p.m.. If you’ve been wondering what this zero-net energy smart home is all about, this is your chance to tour the home, talk to project leaders and learn more about it.

The house is on N. Sage Street in West Village, a block north of the village square.

The event is free and open to the public.

HSH_community announcement_FINAL[1]


Upcoming: Friday talks on science of elite sports

If you’re interested in a scientific approach to athletic performance or coaching, an upcoming series of visiting lectures at UC Davis is for you. Beginning on April 4, the first three speakers are: Stuart Kim, Stanford University, on using genetics to improve performance of elite athletes; Asker Jeukendrup, global head of the Gatorade Sports Science Institute, on fueling elite performance; and Chip Schaefer, director of athletic performance for the Sacramento Kings, on screening to decrease injury and improved performance.

A full program is available at

Seminars will be held at 1 p.m. on Fridays in room 126, Wellman Hall and are open to the public. The series is part of a new course in the Exercise Biology major, “The Changing Face of Science in Elite Sports,” organized by Keith Baar, associate professor in the Department of Neurobiology, Physiology and Behavior, College of Biological Sciences.