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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.

UC Davis reactor gets a role in Mars mission

By Jocelyn Anderson

As NASA prepares for manned missions into deep space, UC Davis’ McClellan Nuclear Research Center is playing an integral role in the groundwork.

The center recently helped develop a technique for performing neutron radiography on a breakable ring used in rocket stage separation. After the launch sequence, different modules will separate from each other when an explosive core in the ring detonates. Such rings will eventually be used on Orion, the spacecraft intended to bring humans to Mars in the 2030s, and likely also will be tested at MNRC.

Because of its vital role in the mission, the ring must be flawless.

“These are flight critical parts,” said David Kametz, manager of project engineering-separation systems for Simsbury, Connecticut-based Ensign-Bickford Aerospace & Defense, which is building parts for NASA. “In other words, they have to work. So we do everything we can to put all the requirements in place to make sure that any possibility of a flaw gets detected.”

The neutron beams from the center’s nuclear reactor are able to uncover much more than an X-ray. Neutron radiography is capable of imaging light elements (like water and carbon) and heavy elements (lead, titanium), giving it a wide range of applications.

Rocket parts being prepared for neutron radiography at UC Davis' McClellan Nuclear Radiation Center. The reactor can find tiny flaws inside solid components. (UC Davis photo)

Rocket parts being prepared for neutron radiography at UC Davis’ McClellan Nuclear Radiation Center. The reactor can find tiny flaws inside solid components. (UC Davis photo)

“It can be very precise,” said Hal Bollman, senior reactor operator and facility manager of the MNRC, which is owned and operated by UC Davis. “Our imaging screens are capable of — and standardized for — about 100 micron resolution, about 4 thousandths [.004] of an inch.”

That is just how pinpointed NASA needs its testing, added Kametz, noting that for a part to be deemed unusable, the flaw would have to be within 50 thousandths of an inch (.05).

The frangible ring that was tested is 18 feet in diameter, separated into quadrants. Orion’s ring will be the same size, but divided in three. Because the facility was created for planes on the former Air Force base, the size of the space gives it the added benefit of being able to test large-scale parts.

And though each part was previously individually tested, NASA is requesting proof nothing harmful happened when the stainless steel tube with rubber bladder and explosive core was assembled within the ring.

“They need to have full confidence that the part is ready to go,” said Kametz. “These guys are the only ones we’ve found who are able to shoot these parts.”

UC Davis lands three new USDA food safety grants

By Pat Bailey

UC Davis scientists are leading three new research projects on food safety, recently funded with more than $5 million in grants from the U.S. Department of Agriculture’s National Institute of Food and Agriculture.

These grants are part of USDA’s $19 million effort to ensure the availability of a safe, nutritious and economically competitive food supply.

Preventing cross-contamination in produce processing

One project will focus on preventing foodborne illnesses by developing and eventually commercializing new fresh-produce processing technologies and methods. The new systems will minimize the risk of bacterial cross-contamination while the produce is washed, handled and packaged.

This more than $4.7 million project, conducted in partnership with Drexel and Rutgers universities, will be led by Nitin Nitin, an associate professor in the departments of food science and technology and biological and agricultural engineering. The research team will include food microbiologists, engineers, food chemists and process modelers, working to develop new procedures and technologies

The grant includes $3 million for UC Davis-based research. For more details, visit the Biological and Agricultural Engineering web site.

Blocking bacterial spoilage in fruits and veggies

Another newly funded project will be led by Maria Marco, associate professor in the Department of Food Science and Technology. Marco and colleagues intend to identify the genetic basis of traits of lactic acid bacteria found on fruits and vegetables. These bacteria are important for preventing food spoilage and for producing fermented foods and beverages, such as sauerkraut, kimchi, chocolate, sourdough bread and table olives.

The researchers expect their investigations will lead to fruits and vegetables with significantly better flavor, texture and nutritional quality. The USDA-NIFA grant for this project totals more than $498,000.

Reducing harmful bacteria in leafy vegetables

The third UC Davis project, funded with a new $499,812 grant from USDA-NIFA, will focus on two important strains of E. coli (O157:H7) and salmonella (SL1344) bacteria. Theses bacteria can invade fresh produce in the field or during processing and, when consumed, cause serious foodborne illnesses in people.

The research team, led by Maeli Melotto, assistant professor in the Department of Plant Sciences, will investigate how these bacteria enter and thrive inside leafy vegetables, especially lettuce and spinach. Findings from the study will help guide development of innovative procedures for reducing the presence of these disease-causing bacteria in leafy vegetables.

All of these grants were provided by USDA-NIFA through the Agriculture and Food Research Initiative, authorized by the 2014 Farm Bill.

Math links ecological flash mobs and magnet physics

By Kat Kerlin

How does an acorn know to fall when the other acorns do? What triggers insects, or disease, to suddenly break out over large areas? Why do fruit trees have boom and bust years?

The question of what generates such synchronous, ecological “flash mobs” over long distances has long perplexed population ecologists. Part of the answer has to do with something seemingly unrelated: what makes a magnet a magnet.

A study by scientists at the University of California, Davis, found that the same mathematical model that’s been used to study how magnets work – a well-known concept in physics called the Ising model– can be applied to understanding what causes events to occur at the same time over long distances, despite the absence of an external, disruptive force.

A simulated eco-flash mob: population density near a critical transition in the synchrony of an ecological system. Credit: UC Davis

A simulated eco-flash mob: population density near a critical transition in the synchrony of an ecological system. Credit: UC Davis

The work, published online April 8 in the journal Nature Communications, provides new ways of measuring synchrony in ecology, which has broader implications for things like extinction and disease.

Animal (and fruit tree) magnetism

What does all of this have to do with the magnet holding up the to-do list on your refrigerator?

Consider the vole. (voleI know, cute.)

“They get kicked out of the nest and have a typical distance they travel,” said co-leading author Alan Hastings, a professor in the Department of Environmental Science and Policy. “But the populations are rising and falling over much longer distances. The effect on the voles is happening much farther than that individual vole travels in his lifetime.”

That effect can be explained by the Ising model of ferromagnetism, according to the study. The authors show how long-range synchronization can arise directly from short-range, local interactions — just as atoms in magnetic materials can align to produce a magnetic field.

“Our paper forges an unexpectedly strong connection between physics and population biology,” said co-leading author Andrew Noble, a UC Davis project scientist. “It’s the discovery of a common framework for understanding seemingly unrelated scientific questions.”

Take, for example, fruit trees. Every few years certain trees bear exceptional amounts of fruit or nuts in between years when they produce almost none in a poorly understood process called masting.peaches

“All the fruit trees have their big year on the same year because of the same model that has to do with getting little magnets lined up at once to create a big-scale magnet,” Hastings explained. “Improving our understanding of models that describe how things go into synchrony over long distances is very important for understanding population dynamics.”

Science mashups

The work was funded by the National Science Foundation’s INSPIRE program, which supports interdisciplinary collaborations between scientific fields that don’t often work together. Coauthor on the paper is Jonathan Machta of the University of Massachussetts- Amherst and the Santa Fe Institute.

Rice can “borrow” stronger immunity from other plant species, study shows

Like most other plants, rice is well equipped with an effective immune system that enables it to detect and fend off disease-causing microbes. But that built-in immunity can be further boosted when the rice plant receives a receptor protein from a completely different plant species, suggests a new study led by UC Davis plant-disease experts.

The study findings, which may help increase health and productivity of rice, the staple food for half of the world’s population, are reported online in the journal PLOS Pathogens.

“Our results demonstrate that disease resistance in rice — and possibly related crop species — could very likely be enhanced by transferring genes responsible for specific immune receptors from dicotyledonous plants into rice, which is a monocotyledonous crop,” said lead author Benjamin Schwessinger, a postdoctoral scholar in the UC Davis Department of Plant Pathology.

Immune receptors vary between plant groups

Receptors are specialized proteins that can recognize molecular patterns associated with disease-causing microbes, including bacteria and fungi, at the beginning of an infection. These receptors are found on the surface of plant cells, where they play a key role in the plant’s early warning system.

Some of the receptors, however, occur only in certain groups of plant species.

For example, the monocotyledon plant group, including rice and other grasses that sprout with a single seed leaf, contains different receptor proteins than does the dicotyledon group, including plants like beans, which germinate with two seed leaves.

Borrowed receptors launch stronger immune response

In this study, Schwessinger and colleagues successfully transferred the gene for an immune receptor from the model plant Arabidopsis, a member of the mustard family, into rice.

The rice plants that subsequently expressed this gene and produced the related immune receptor proteins were able to sense Xanthomonas oryzae pv. oryzae, an important bacterial disease of rice.

This demonstrated that receptors introduced to rice from the Arabidopsis plants via genetic engineering were able to make use of the rice plants’ built-in immune signaling mechanisms and cause the rice plants to launch a stronger defensive immune response against the invading bacteria.

Other researchers on the study include Pamela Ronald in the UC Davis Department of Plant Pathology; Ofir Bahar, formerly of UC Davis and now at the Agricultural Research Organization’s Volcani Center in Israel; and Cyril Zipfil from the Sainsbury Laboratory in the UK.

Funding for the study was provided by the European Molecular Biology Organization, headquartered in Germany; the Human Frontier Science Program Organization of France; the Gatsby Charitable Foundation, headquartered in London; the U.S. Department of Energy and the National Institutes of Health.

More information

To hear Schwessinger briefly describe his research on plant immunity, visit The Academic Minute.

Similar studies involving the transfer of immune receptors between species are reported in the journals New Phytologist, PLOS Pathogens, and the Journal of Integrative Plant Biology.

Cosmic lens splits supernova into four images

Astronomers using NASA’s Hubble Space Telescope have for the first time spotted four images of the same distant exploding star, arranged in an “Einstein’s Cross,” a cross-shape pattern created by the powerful gravity of a foreground galaxy embedded in a massive cluster of galaxies.

Distant supernova split into four images by massive galaxy cluster in the four ground. Because light is taking different paths through the cluster, other images of the supernova may appear later.

Distant supernova split into four images by massive galaxy cluster in the four ground. Because light is taking different paths through the cluster, other images of the supernova may appear later.

First predicted by Albert Einstein, gravitational lensing is similar to a glass lens bending light to magnify and distort the image of an object behind it.

Although astronomers have discovered dozens of multiply imaged galaxies and quasars, they have never seen a stellar explosion resolved into several images.

The lensed supernova was found by the Grism Lens Amplified Survey from Space (GLASS) collaboration. The GLASS group is working with the FrontierSN team to analyze the supernova. A paper describing the discovery appeared March 6 in a special issue of the journal Science celebrating the centenary of Albert Einstein’s Theory of General Relativity.

“Until now, we’ve only been able to study galaxies that are multiply lensed,” said Marusa Bradac, an astronomer in the UC Davis Department of Physics and coauthor on the paper. “For the first time we now see a supernova in this role and this is extremely exciting.”

This unique observation will help astronomers refine their estimates of the amount and distribution of dark matter in the lensing galaxy and cluster. Dark matter cannot be seen directly but is believed to make up most of the universe’s mass.

“These kinds of systems are pure gold, because they allow us to study the supernova and the dark matter in the galaxy, as well as determine the history of the entire Universe,” Bradac said.

A supernova is a short-lived event, but when the four images fade away astronomers will have a rare chance to catch a rerun because the current four-image pattern is only one component of the lensing display. The clumps of dark matter in the galaxy cluster are bending images of the supernova through multiple different routes, like train tracks through a mountain range. The supernova may have appeared in a single image some 20 years ago, and it is expected to reappear once more in the next one to five years.

The prediction of a future appearance is based on computer models of the cluster, which describe the various paths the divided light is taking through the maze of clumpy dark matter in the galactic grouping. The supernova images do not arrive at Earth at the same time because some of the light is delayed as it travels around bends created by the gravity of dense dark matter in the intervening galaxy cluster.

“Our model for the dark matter in the cluster gives us the prediction of when the next image will appear because it tells us how long each train track is, which correlates with time,” said Steve Rodney of Johns Hopkins University, leader of the FrontierSN team. “We already missed one that we think appeared about 20 years ago, and we found these four images after they had already appeared. The prediction of this future image is the one that is most exciting because we might be able to catch it. We hope to come back to this field with Hubble, and we’ll keep looking to see when that expected next image appears.”

Measuring the time delays between images will help the astronomers fine-tune the models that map out the cluster’s mass.

Patrick Kelly of UC Berkeley spotted the four images of the exploding star on Nov. 11, 2014, in the galaxy cluster MACS J1149.6+2223, located more than 5 billion light-years away. The FrontierSN and GLASS teams teams spent a week analyzing the object’s light, confirming it was the signature of a supernova. They then turned to the W. M. Keck Observatory on Mauna Kea, in Hawaii, to measure the distance to the supernova’s host galaxy, which is 9.3 billion light-years from Earth.

The supernova appears about 20 times brighter than its natural brightness, because it is being magnified by both the lens of the galaxy cluster and by a massive elliptical galaxy within the cluster.

The astronomers nicknamed the supernova Refsdal in honor of Norwegian astronomer Sjur Refsdal, who, in 1964, first proposed using time-delayed images from a lensed supernova to study the expansion of the universe.

Image credits: NASA, ESA, and S. Rodney (JHU) and the FrontierSN team; T. Treu (UCLA), P. Kelly (UC Berkeley) and the GLASS team; J. Lotz (STScI) and the Frontier Fields Team; M. Postman (STScI) and the CLASH team; and Z. Levay (STScI)

Adapted from a NASA news release.

So-called mute cicadas are not so silent

By Kathy Keatley Garvey

Are “mute” cicadas really mute? If so, how do they communicate and attract mates?

A team of scientists including Christian Nansen, agricultural entomologist at UC Davis, answers these questions in a new paper, “How Do ‘Mute’ Cicadas Produce their Calling Songs?” in the Feb. 25th edition of PLOS ONE.

Cicadas in the genus Karenia lack the specialized sound-producing structures, called tymbals, that characterize most cicadas, according to Nansen and colleagues Changquing Luo and Cong Wei, both of Northwest A & F University, Shaanxi, China.

But the word mute is misleading, says Nansen. “They do indeed produce sounds.”

The researchers found that Karenia caelatata produces impact sounds by banging the leading edge, or costa of the forewing against the operculum, a lid covering the insect’s equivalent of an ear. The operculum of K. caelatata is larger than in other cicadas and extends past the edge of the body.

When the male mute cicadas are at rest, the wings are held back over the body with the trailing edge of the wing is locked into a groove on the animals back. When the male wants to make some noise, he lifts his abdomen from the tree branch and rapidly opens and closes his wings. With the back edge of the wing locked in place, the leading edge beats against the hard operculum to make a clicking sound. It’s somewhat like beating a drum while other cicada species with tymbal mechanisms play an orchestra of diverse and loud sounds.

“The new sound-production mechanism expands our knowledge on the diversity of acoustic signaling behavior in cicadas and further underscores the need for more bioacoustic studies on cicadas which lack tymbal mechanism,” Nansen and colleagues concluded in their abstract.

Video: How the mute cicada sings (ScienceNews)

Cicadas, also known as “tree crickets” (from Latin cicada), are among the most widely recognized of insects due to their large size, usually 2 to 5 centimeters or more, and loud sounds, sometime as high as 120 decibels. Theirs is among the loudest of all insect-produced sounds. Cicadas live in warm climates, from temperate to tropical. Immature cicadas spend most of their lives sucking juice from tree roots. The adults suck plant juices from stems.

The best-known North American genus, Magicicada, has a long life cycle of 13 or 17 years and emerges in great numbers.

Cicadas damage cultivated crops, shrubs, and trees, mainly from females scarring tree branches where they lay their eggs. In many cultures, cicadas are a delicacy on the menu.

Core work: Iron vapor gives clues to formation of Earth and Moon

By Kat Kerlin

Recreating the violent conditions of Earth’s formation, scientists are learning more about how iron vaporizes and how this iron rain affected the formation of the Earth and Moon. The study is published March 2 in Nature Geoscience.

“We care about when iron vaporizes because it is critical to learning how Earth’s core grew,” said co-author Sarah Stewart, UC Davis professor of Earth and Planetary Sciences.

Shock and release

Scientists from Lawrence Livermore National Laboratory, Sandia National Laboratory, Harvard University and UC Davis used one of the world’s most powerful radiation sources, the Sandia National Laboratories Z-machine, to recreate conditions that led to Earth’s formation. They subjected iron samples to high shock pressures in the machine, slamming aluminum plates into iron samples at extremely high speeds. They developed a new shock-wave technique to determine the critical impact conditions needed to vaporize the iron.

The Z Machine at Sandia Lab is one of the most powerful accelerators in the nation.

The Z Machine at Sandia Lab is one of the most powerful radiation sources in the nation.

The researchers found that the shock pressure required to vaporize iron is much lower than expected, which means more iron was vaporized during Earth’s formation than previously thought.

Iron rain

Lead author Richard Kraus, formerly a graduate student under Stewart at Harvard, is now a research scientist at Lawrence Livermore National Laboratory. He said the results may shift how planetary scientists think about the processes and timing of Earth’s core formation.

“Rather than the iron in the colliding objects sinking down directly to the Earth’s growing core, the iron is vaporized and spread over the surface within a vapor plume,” said Kraus. “This means that the iron can mix much more easily with Earth’s mantle.”

After cooling, the vapor would have condensed into an iron rain that mixed into the Earth’s still-molten mantle.

To the moon

This process may also explain why the Moon, which is thought to have formed by this time, lacks iron-rich material despite being exposed to similarly violent collisions. The authors suggest the Moon’s reduced gravity could have prevented it from retaining most of the vaporized iron.

The work was conducted under the Sandia Z Fundamental Science Program and supported by the U.S. Department of Energy National Nuclear Security Administration.

UC Davis leads new effort in livestock genomics

By Pat Bailey

Scientists and breeders working with poultry and livestock species will get a new set of tools from an international project that includes the University of California, Davis.

The UC Davis team is led by functional genomicist Huaijun Zhou, an associate professor and Chancellor’s Fellow in the Department of Animal Science. The researchers will focus on the genomes of the chicken, cow and pig, which make up the largest meat-producing industries in the United States.

Functional genomics can reveal how DNA controls genes that improve livestock species.

Functional genomics can reveal how DNA controls genes that improve livestock species.

The UC Davis project is part of a comprehensive international effort, known as the Functional Annotation of Animal Genomes (FAANG) Initiative. The international initiative includes research scientists in France, the Netherlands, Australia, Canada and China. It mirrors earlier efforts, called ENCODE (Encyclopedia of DNA Elements), which assembled the functional elements in the human, mouse and model-organism genomes

“Initial sequences of the chicken, bovine and swine genomes were published during the last decade, identifying the genes that actually translate genetic material into proteins,” Zhou said.

“Those sequences represent the beginning of an exciting path to understanding the underlying digital code for the biology of these important agricultural species,” he said. “But it has become increasingly apparent that we also need to determine the function of surrounding regions of the genes in the genome, sometimes referred to as ‘functional elements.’ ”

Functional elements

These functional elements – once thought to be “junk DNA” because they don’t encode proteins – are now known to play a critical role in regulating how genes are expressed and how the genetic material is manifested in an animal’s traits.

“The functional elements and the molecular processes they influence, are key to controlling development and complex traits such as production, immune response, reproduction and behavior,” Zhou said.

Information gleaned by the new effort will aid breeders in developing healthier and more productive and sustainable farm animals.

Data produced by the UC Davis team and their collaborators on the FAANG Initiative will be freely distributed through the UCSC Genome Browser, a biological database hosted by UC Santa Cruz, and through Ensembl, a genome browser of the European Bioinformatics Institute (EBI).

Collaborators at UC Davis include Pablo J. Ross, an animal scientist; Ian Korf, a molecular biologist in the Genome Center; Mary Delany, an avian geneticist; Juan Medrano, an animal geneticist; and Alison Van Eenennaam, a Cooperative Extension animal genomics and biotechnology specialist.

Other collaborators are Hans Cheng, a research geneticist at the USDA-ARS Avian Disease and Oncology Laboratory at Michigan State University; Chris Tuggle, an animal scientist at Iowa State University; Cathy Ernst, an animal scientist at Michigan State University; Vicki Leesburg an agricultural statistician with the USDA-ARS; Bing Ren, a molecular geneticist at the Institute of Genomics Institute, UC San Diego; Jim Kent, a bioinformatist at the UCSC Genome Browser; and Paul Flicek, a research scientist at EMBL-EBI.

The UC Davis project is provided by a $500,000 grant from the U.S. Department of Agriculture – National Institute of Food and Agriculture, and is also supported by the U.S. Poultry, Cattle, and Swine Genomes Coordination Funds; the National Pork Board; and Aviagen LTD.

Better measures of single molecule circuits

A hexane (six-carbon) molecule between two gold electrodes. A new UC Davis technique gives better measurements of these circuits. (Josh Hihath/UC Davis)

A hexane (six-carbon) molecule between two gold electrodes. A new UC Davis technique gives better measurements of these circuits. (Josh Hihath/UC Davis)

It’s nearly 50 years since Gordon Moore predicted that the density of transistors on an integrated circuit would double every two years. “Moore’s Law” has turned out to be a self-fulfilling prophecy that technologists pushed to meet, but to continue into the future, engineers will have to make radical changes to the structure or composition of circuits. One potential way to achieve this is to develop devices based on single-molecule connections.

New work by Josh Hihath’s group at the UC Davis Department of Electrical and Computer Engineering, published Feb. 16 in the journal Nature Materials, could help technologists make that jump. Hihath’s laboratory has developed a method to measure the conformation of single molecule “wiring,” resolving a clash between theoretical predictions and experiments.

“We’re trying to make transistors and diodes out of single molecules, and unfortunately you can’t currently control exactly how the molecule contacts the electrode or what the exact configuration is,” Hihath said. “This new technique gives us a better measurement of the configuration, which will provide important information for theoretical modeling.”

Until now, there has been a wide gap between the predicted electrical behavior of single molecules and experimental measurements, with results being off by as much as ten-fold, Hihath said.

Hihath’s experiment uses a layer of alkanes (short chains of carbon atoms, such as hexane, octane or decane) with either sulfur or nitrogen atoms on each end that allow them to bind to a gold substrate that acts as one electrode. The researchers then bring the gold tip of a Scanning Tunneling Microscope towards the surface to form a connection with the molecules. As the tip is then pulled away, the connection will eventually consist of a single-molecule junction that contains six to ten carbon atoms (depending on the molecule studied at the time).

By vibrating the tip of the STM while measuring electrical current across the junction, Hihath and colleagues were able to extract information about the configuration of the molecules.

“This technique gives us information about both the electrical and mechanical properties of the system and tells us what the most probable configuration is, something that was not possible before,” Hihath said.

The researchers hope the technique can be used to make better predictions of how molecule-scale circuits behave and design better experiments.

Coauthors on the paper are graduate students Habid Rascón-Ramos and Yuanhui Li and postdoctoral researcher Juan Manuel Artés, all at UC Davis. The work was supported by the National Science Foundation and the RISE program of the UC Davis Office of Research.

More information: Nature Materials News & Views article

Video from UC Davis/Mars symposium on innovation in food and health

Video streams from the Jan. 14 symposium on innovation in food, agriculture and health are now available online. The morning session can be found here and the afternoon, here.

The complete program is available here.

The morning session included a keynote address by Prof. Elizabeth Blackburn of UCSF and a panel discussion on “Scientific discovery and innovation: What can the future look like at the nexus of food, agriculture and health?”

The afternoon included a presentation on the African Orphan Crops Consortium by Howard Yana Shapiro and Allen Van Deynze, and panel discussions on solving agriculture’s greatest challenges and the role of venture capital in innovation.