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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 anthrax-killing virus from Africa is unusually large

From a zebra carcass on the plains of Namibia in Southern Africa, an international team of researchers has discovered a new, unusually large virus (or bacteriophage) that infects the bacterium that causes anthrax. The novel bacteriophage could eventually open up new ways to detect, treat or decontaminate the anthrax bacillus and its relatives that cause food poisoning. The work is published Jan. 27 in the journal PLOS One.

The virus was isolated from samples collected from carcasses of zebras that died of anthrax in Etosha National Park, Namibia. The anthrax bacterium, Bacillus anthracis, forms spores that survive in soil for long periods. Zebras are infected when they pick up the spores while grazing; the bacteria multiply and when the animal dies, they form spores that return to the soil as the carcass decomposes.

Photo: Vultures gather at a zebra carcass (Holly Ganz/UC Davis)
zebra_carcass

While anthrax is caused by a bacterium that invades and kills its animal host, bacteriophages, literally “bacteria eaters” are viruses that invade and kill bacterial hosts.

The first thing the team noticed was that the virus was a voracious predator of the anthrax bacterium, said Holly Ganz, a research scientist at the UC Davis Genome Center and first author on the paper.

Photo: The Tsamsa phage is unusually large (SEM by Jochen Klumpp/ETH Zurich) tsamsa_virus

They also noticed that the new virus, named Bacillus phage Tsamsa, is unusually large, with a giant head, a long tail and a large genome, placing it among the largest known bacteriophages.

Tsamsa infects not only B. anthracis but also some closely related bacteria, including strains of Bacillus cereus, which can cause food poisoning. Sequencing the genome allowed researchers to identify the gene for lysin, an enzyme that the virus uses to kill bacterial cells, that has potential use as an antibiotic or disinfecting agent.

Bacteriophages are often highly specific to a particular strain of bacteria, and when they were first discovered in the early 20th century there was strong interest in them as antimicrobial agents. But the discovery of penicillin and other antibiotics eclipsed phage treatments in the West, although research continued in the Soviet Union.

“With growing concerns about antibiotic resistance and superbugs, people are coming back to look at phages,” said Ganz said.

One advantage of bacteriophages is that because they tend to be very specific, they can potentially target only “bad” bacteria while leaving beneficial bacteria unharmed. Also, phages evolve with the host and have the potential to overcome bacterial resistance, said coauthor Jochen Klumpp of the Institute of Food, Nutrition and Health, ETH Zurich.

Ganz began the work as a postdoctoral scientist on a team led by Wayne Getz, Professor of Environmental Science, Policy and Management at UC Berkeley and at the University of KwaZulu-Natal, South Africa. Sequencing of the phage genome was conducted at UC Davis after Ganz joined the laboratory of Professor Jonathan Eisen.

Ganz said that she hoped the publication of the phage’s sequence information would enable other researchers to investigate further and potentially develop applications for the phage and its proteins.

“You might use it to detect the anthrax bacillus or B. cereus; use it as an alternative to antibiotics or as part of a decontaminant,” she said.

Other authors on the study in addition to Ganz, Getz and Klumpp are: Christina Law and Richard Calendar, UC Berkeley; Martina Schmuki, Fritz Eichenseher, and Martin Loessner, ETH Zurich, Switzerland; Jonas Korlach, Pacific Biosciences, Menlo Park, Calif.; and Wolfgang Beyer, University of Hohenheim, Stuttgart, Germany. The work was supported by the NIH.

Probing hydrogen catalyst assembly, part II

Biochemical reactions sometimes have to handle dangerous things in a safe way. New work from researchers at UC Davis and Stanford University shows how cyanide and carbon monoxide are safely bound to an iron atom to construct an enzyme that can generate hydrogen gas. The work is published Jan. 24 in the journal Science.

Producing hydrogen with catalysts based on abundant metals, such as iron, is key to hopes of using hydrogen to replace carbon-based fuels. But before you can make hydrogen, you have to make the catalyst that enables the reaction –something bacteria have been able to do for millennia.

Video: Dave Britt discusses the chemistry of forming hydrogen catalysts

Jon Kuchenreuther, a postdoctoral researcher working with Professor Dave Britt, project scientist Simon George and colleagues at the UC Davis Department of Chemistry, with James Swartz and colleagues at Stanford, used a variety of analysis techniques to study the chain of chemical reactions that assembles these catalysts based on clusters of iron and sulfur atoms adorned with cyanide (CN) and carbon monoxide (CO) molecules.

“How does biology make these complicated active sites?” Britt said. “You can’t release cyanide or carbon monoxide into the cell. It turns out that it’s formed and kept on iron throughout.”

In work published in Science last year, the researchers showed that the amino acid tyrosine first binds to the iron/sulfur cluster, and is then split by the enzyme HydG to create a radical. The new paper picks up the story from there, showing that carbon monoxide and cyanide derived from the splitting of tyrosine, remain bound to the same iron atom as the tyrosine radical is removed. This iron/cyanide/carbon monoxide structure becomes part of the final cluster.

The team principally used a technique called Fourier Transform Infra Red spectroscopy to follow the process. FTIR measures vibrations in bond length, and both cyanide and carbon monoxide show strong signals with this method.

Metal atoms in biological molecules are usually bound to large structures, like amino acids or heme groups, Britt said. For metals to be bound to small molecules, like carbon monoxide and cyanide, is “some unusual chemistry by itself,” he said.

Other authors on the paper are: at UC Davis, Professor Stephen Cramer, postdoctoral researchers Jon Kuchenreuther, William Myers, Daniel Suess and Troy Stich; Vladimir Pelmenschikov, Technical University of Berlin; and Stacey Shiigi, Stanford University. The work was supported by grants from the U.S. Department of Energy.

Previously: Unique chemistry in hydrogen catalysts (news release, Oct. 2013)

Probing the surface, and just below

Contributed by Lynn Yarris, Lawrence Berkeley National Lab

“The interface is the device,” Nobel laureate Herbert Kroemer famously observed, referring to the remarkable properties to be found at the junctures where layers of different materials meet. In today’s burgeoning world of nanotechnology, the interfaces between layers of metal oxides are becoming increasingly prominent, with applications in such high-tech favorites as spintronics, high-temperature superconductors, ferroelectrics and multiferroics. Realizing the vast potential of these metal oxide interfaces, especially those buried in subsurface layers, will require detailed knowledge of their electronic structure.

A new technique from an international team of researchers working at Berkeley Lab’s Advanced Light Source (ALS) promises to deliver the goods. In a study led by UC Davis physics professor Charles Fadley, who holds a joint appointments with Berkeley Lab’s Materials Sciences Division, the team combined two well-established techniques for studying electronic structure in crystalline materials into a new technique that is optimized for examining electronic properties at subsurface interfaces. They call this new technique SWARPES, for Standing Wave Angle-Resolved Photoemission Spectroscopy.

“SWARPES allows us for the first time to selectively study buried interfaces with either soft or hard x-rays,” Fadley says. “The technique can be applied to any multilayer prototype device structure in spintronics, strongly correlated/high-TC superconductors, or semiconductor electronics. The only limitations are that the sample has to have a high degree of crystalline order, and has to be grown on a nanoscale multilayer mirror suitable for generating an x-ray standing wave.”

As the name indicates, SWARPES combines the use of standing waves of x-rays with ARPES, the technique of choice for studying electronic structure. A standing wave is a vibrational pattern created when two waves of identical wavelength interfere with one another: one is the incident x-ray and the other is the x-ray reflected by a mirror. Interactions between standing waves and core-level electrons reveal much about the properties of each atomic species in a sample. ARPES from the outer valence levels is the long-standing spectroscopic workhorse for the study of electronic structure. X-rays striking a material surface or interface cause the photoemission of electrons at angles and kinetic energies that can be measured to obtain detailed electronic energy levels of the sample. While an extremely powerful tool, ARPES, a soft x-ray technique, is primarily limited to the study of near-surface atoms. It’s harder x-ray cousin, HARPES, makes use of more energetic x-rays to effectively probe subsurface interfaces, but the addition of the standing wave capability provides a much desired depth selectivity.

P

Experimental setup and basic principles of SWARPES shows (a) the experimental geometry and electron spectrometer; (b) the configuration of the multilayer SrTiO3/La0.7Sr0.3MnO3 (STO/LSMO) sample, and the type of ARPES data obtained from it; (c) SW-excited photoemission intensity rocking curves from Mn 3p and Ti 2p3/2 core levels; and (d) the theoretically-simulated intensity of the x-ray standing wave field as a function of depth and grazing x-ray incidence angle, indicating angles at which the interior of the LSMO layer (Line Cut 1) or the STO/LSMO interface (Line Cut 2) are preferentially emphasized.

“The standing wave can be moved up and down in a sample simply by rocking the angle of incidence around the Bragg angle of the mirror,” says Alexander Gray, a former member of Fadley’s UC Davis research group and affiliate with Berkeley Lab’s Materials Sciences Division, who is now a postdoctoral associate at Stanford/SLAC. “Observing an interface between a ferromagnetic conductor (lanthanum strontium manganite) and an insulator (strontium titanate), which constitute a magnetic tunnel junction used in spintronic logic circuits, we’ve shown that changes in the electronic structure can be reliably measured, and that these changes are semi-quantitatively predicted by theory at several levels. Our results point to a much wider use of SWARPES in the future for studying the electronic properties of buried interfaces of many different kinds.”

Fadley, Gray and their collaborators carried out their SWARPES tests at ALS Beamline 7.0.1. The Advanced Light Source is a U.S. Department of Energy (DOE) national user facility and Beamline 7.0.1 features a premier endstation for determining the electronic structure of metals, semiconductors and insulators. Additional corroborating measurements concerning the interface atomic structure were performed at the National Center for Electron Microscopy (NCEM), another DOE national user facility hosted at Berkeley Lab.

Results of this study have been published in Europhysics Letters (EPL). The paper is titled “Momentum-resolved electronic structure at a buried interface from soft X-ray standing-wave angle-resolved photoemission.” Gray was the lead author, Fadley the corresponding author. For a full list of co-authors and their host institutes download the paper here.

This research was supported primarily by the U.S. Department of Energy (DOE) Office of Science.

More information

For more about the research of Charles Fadley, go here
For more about Berkeley Lab’s Advanced Light Source go here
For more about NCEM go here

Review of California’s Low Carbon Fuel Standard shows shifts in fuel use

The latest progress report on California’s Low Carbon Fuel Standard (LCFS) shows a small increase in use of alternative transportation fuels, which include biofuels and electricity. Among alternative fuels, the report finds a decrease in ethanol made from corn and an increase in biodiesel made from waste materials.

“Status Review of California’s Low Carbon Fuel Standard, January 2014 Issue” finds that in 2013 the LCFS played a stronger role in incentivizing the use of biofuels from a variety of sources, including corn oil, canola, and biodiesel and renewable diesel from waste. It also finds slight increases in the use of electricity for transportation under the program, and that fuel suppliers in the program have generated excess credits.

Adopted by the California Air Resources Board (ARB) in 2009, the LCFS requires transportation fuel providers such as oil companies and refiners to gradually reduce the carbon intensity of their fuel by at least 10 percent by 2020. The state began implementing the rule in 2011.

The status review is authored by UC Davis Institute of Transportation Studies (ITS-Davis) research engineer Sonia Yeh and assistant project scientist Julie Witcover.

“One of the values of this periodic series of reports is that we can analyze trends over time,” says Yeh.

Among the findings in this status review are the following:

  • Fuel suppliers in the program generated excess LCFS credits, beyond what was required, in every quarter since the program was initiated.
  • While overall biofuel volume remained relatively constant since 2011, the contribution to LCFS credits of ethanol made primarily from corn or grain mixes decreased, while biodiesel and renewable diesel credits increased dramatically in 2013.
  • An increasing share and volume of biofuel LCFS credits came from the use of waste-based fuels, which garnered higher premiums from the LCFS than from the federal Renewable Fuel Standard (RFS2) in late 2013 due to their low LCFS carbon intensity ratings, higher LCFS credit prices and declining premiums from the RFS2.
  • Ethanol made from sugarcane or molasses contributed to a total of 5 percent of biofuel volume between 2011 and the first six months of 2013. In the same period, soy biodiesel contributed 0.3 percent of biofuel volume.
  • Reported electricity use for transportation increased almost four-fold from 2011 through the first half of 2013.
  • LCFS credit prices have increased since 2012, rising to about $80/credit in October and November 2013, and ending 2013 at about $50/credit in December.

Like the previous status reviews, published in Spring 2013 and November 2012, this data-rich report on LCFS compliance, fuel use, and credit markets includes a special topic. This issue’s special topic summarizes the results of an October 2013 UC Davis paper that examines ARB’s LCFS cost-containment proposals. It finds that cost-containment mechanisms, such as a cap on credit prices, may play an important role in limiting high credit prices and program costs, thereby safeguarding the LCFS credit market and the LCFS program itself.

The status report is funded through a research contract with ARB and the ITS-Davis NextSTEPS research program.

Read the full paper at: http://www.its.ucdavis.edu/research/publications/publication-detail/?pub_id=2008

Contributed by ITS-Davis.

Under pressure: new insights in superconductors

Recent work on a superconducting material first discovered at UC Davis is helping reveal the behavior of “unconventional” superconductors, and that physical pressure has a different type of effect on these materials than chemical doping.

The material, cerium cobalt indium-5 or CeCoIn5, belongs to the class of “unconventional” superconductors, said Nicholas Curro, a physics professor at UC Davis and coauthor on the work. CeCoIn5 was initially discovered in the laboratory of Professor Zachary Fisk when he was a faculty member at UC Davis; Fisk is now at UC Irvine.

Superconductors, which carry electrical current without resistance, are already used in devices such as magnetic resonance imaging machines, but these are usually based on liquid helium cooled close to absolute zero. Inexpensive superconductors that work at room temperature would have enormous potential for power transmission and new technology.

The best bet for such a material, Curro said, would be an unconventional superconductor. However, physicists do not yet have a comprehensive theory to describe how these materials work.

While CeCoIn5 works only at very low temperatures, it can help physicists develop and test their theories, Curro said.

“It’s an experimental system we can use to learn about magnetic superconductivity, just like a fruit fly can teach us about genetics,” he said.

CeCoIn5 is in a “quantum critical state,” meaning that it is close to a transition point between superconductivity and showing magnetic properties, or antiferromagnetism. It can be nudged between these states in two ways: chemical doping, or replacing some of the indium atoms with cadmium pushes it towards antiferromagnetism; atmospheric pressure moves it the other way, into superconductivity.

In the new study, published in December in Nature Physics, an international team including researchers in South Korea, China, Brazil, Russia as well as Curro at UC Davis and Fisk and Long Pham at UC Irvine studied what happens inside CeCoIn5 as it moves between these states.

“The most common approach to add dopants, but we show that this does not have the effect you expect,” Curro said. “It turns out that the effect of doping is a different process from the effect of pressure.”

The researchers found that when the material was chemically doped, blob-like areas of antiferromagnetism formed around the flaws in the structure created by replacing indium with cadmium. If these blobs were large enough, the material became antiferromagnetic on a large scale and superconductivity disappeared.

In CeCoIn5, antiferromagnetic droplets nucleate at dopant sites and extend outwards to a finite distance. Under pressure, the extent of the droplets decreases and the droplets no longer interact. Credit: Curro lab
Image: As pressure increases to the right, blobs of antiferromagnetic properties (colored) shrink. (Curro lab)

But if the material was put under pressure, these antiferromagnetic areas shrank and superconductivity took over again.

The doped atoms acted as “seeds” for antiferromagnetism, much like crystals can seed a saturated rain cloud, Curro said. The results show the need for caution in interpreting findings from chemically doping compared to other methods for tweaking superconductivity properties, he said.

More information: Nick Curro’s lab website

Full paper: www.nature.com/nphys/journal/vaop/ncurrent/full/nphys2820.html

UC Davis work leads to FDA action on antibacterial soaps

On Dec. 16, the U.S. Food and Drug Administration called on manufacturers of antibacterial soaps to demonstrate that the anti-microbial agents have added benefit over  washing with soap and water, and that these additives do not pose unacceptable risks.

This is a major step for the regulatory agency, and there were many academic contributors to the decision. However, the NIEHS Superfund Research Program at UC Davis can be credited with having made a major contribution to raising awareness of the problem.

“This environmental and human health issue illustrates the best traits of UC Davis in facilitating the collaboration that led to a rapid appreciation of an environmental and human health problem,” said Professor Bruce Hammock, the program’s director. The NIEHS Superfund Program brought together researchers in four major colleges and served as a focus for national and international collaboration on the issue. It also brought together a variety of groups with interest in the problem, Hammock said.

The major antimicrobial compounds used in liquid soap are triclosan, about 85 percent of the market and triclocarban, which makes up most of the rest.  The compounds were originally used in surgical scrubs, but they were added originally to liquid soaps as “value-added” ingredients. They evolved to the point where manufacturers almost had to put the antimicrobials in liquid soaps to enter the market, Hammock said.

UC Davis researchers have made many contributions to the study of these compounds. The original paper on the surprisingly high biological activity of triclocarban was published by the UC Davis Superfund Program in 1999, and the Davis Superfund program has targeted these materials for subsequent study for the last 10 years in a truly  interdisciplinary and collaborative effort.

Professor Tom Young’s group in the Department of Civil and Environmental Engineering found that the materials were at quite high levels in biosolids and sewage effluent and tended to build up in the environment. In a collaboration with Professor Kate Scow (Department of Land, Air and Water Resources) they found that the materials could be delivered to agricultural fields as biosolids, and the Scow – Young team studied their effects on soil microbes.

Young’s group and the Superfund analytical core developed excellent mass spectrometry methods for analysis of the materials and Shirley Gee’s program on biosensors developed rapid, field portable bioassays. These methods were used not only for environmental monitoring but actually for monitoring human blood levels after showering with anti-microbial containing soaps.

In 2008 a collaborative paper put compiled by Ki Chang Ahn working with several Superfund laboratories including those of Michael Denison, Bruce Hammock, Dietmar Kultz, Bill Lasley and Isaac Pessah published a screen of a number of environmental contaminants and their activity on biological assays developed in the Superfund Program. This was followed by a second paper in Environmental Health Perspectives by Christophe Morriseau titled “Toxicology in the Fast Lane” which demonstrated that triclosan bound to the ryanodine receptor. Among other things this study and the work of Young and colleagues stimulated Swee Teh of the veterinary school to examine the effect of these materials on fish, raising further environmental concerns.

Based in part on this work and in part on a collaborative Superfund Grant among U.C. Davis, Arizona State, and UC San Diego, a collaborative study with Robert Tukey’s laboratory at UC San Diego reported in 2012 biological activity and mechanism of action of triclocarban and a second study in PNAS involving Dr. Nipavan Chiamvimonvat from the medical school, Hammock from the agricultural college and led by Pessah from the veterinary school investigated the mechanism of action of triclosan on the ryanodine receptor and reported that high doses of the compound in mice could lead to atrial fibrillation and cardiac arrest. This later paper in PNAS had almost 40,000 views in the year since its publication and likely was the single most important supporter of the recent FDA action.

The UC Davis – NIEHS Superfund Program did much more than publish papers — it has held scientific meetings, forums, and community programs in the area. For example the UC Davis Superfund Program hosted a symposium on the topic at Asilomar and arranged an open forum at UC Davis to further discussion among stake holders including the public, producers and distributors of the antimicrobials in hand soap and the state and federal regulatory agencies involved in their regulation.

The scientists at UC Davis have also publicly urged careful evaluation of the benefits and risks of these antimicrobials, urging State and Federal agencies to take action on high volume uses that offer little benefit quickly while making a more careful study of low-volume uses that clearly have benefits.

Contributed by Bruce Hammock.

Humboldt research award for synchrotron expert

Professor Stephen P. Cramer of the UC Davis Department of Chemistry, an expert in synchrotron spectroscopy, has received a Humboldt Research Award from the Alexander von Humboldt Foundation and may now spend up to one year cooperating closely with a team at Helmholtz-Zentrum Berlin (HZB) and Freie Universität Berlin. Cramer was nominated by Professor Emad Aziz, who heads a Joint Lab for “Ultrafast Dynamics in Solution and at Interfaces” at HZB and Freie Universität. Cramer is Advanced Light Source Professor at UC Davis and at the Lawrence Berkeley National Laboratory.

“If one walks around a synchrotron facility, one will invariably see essential equipment developed in the Cramer group,”Aziz said. “For more than three decades, Steve Cramer has played a major role in developing and popularizing synchrotron radiation spectroscopy tools for chemical analysis.”

Aziz and his team are now looking forward to work with Cramer, especially on using and developing further X-ray absorption-, X-ray emission and RIXS-experiments in the soft X-ray region at the BESSY II synchrotron in Berlin, as well as in the hard X-ray regime at PETRA III at DESY in Hamburg.

Cramer’s current research focuses on similar conundrums as Aziz’ research interests: they want to understand how enzymes in the cells of bacteria fix nitrogen or produce hydrogen, and thus perform processes that are essential for life on earth. These enzymes contain active iron-sulfur clusters that bind small molecules such as nitrogen, carbon monoxide and hydrogen. Given the excellent x-ray sources at BESSY II and PETRA III, a natural target for collaborative research will be a better understanding of the electronic structure of the active sites in these enzymes. The long-term goal for such studies is the development of synthetic catalysts that rival the capabilities of natural enzymes.

Since joining UC Davis and LBNL in 1990, Cramer’s group has emphasized development of EXAFS and other synchrotron-based X-ray spectroscopies to study metals in biological systems. The other methods have included soft X-ray absorption, X-ray absorption magnetic circular dichroism (XMCD), high-resolution X-ray fluorescence, resonant inelastic X-ray scattering (RIXS), and most recently, nuclear resonance vibrational spectroscopy (NRVS). Cramer and his team were the first to apply these techniques to metal-containing enzymes. The information from these spectroscopic results provides extra details that are often beyond the reach of X-ray diffraction methods.

The Humboldt research award is granted in recognition of a researcher’s entire achievements to date. The Humboldt Foundation grants up to 100 Humboldt Research Awards annually. Nominations may be submitted by established academics in Germany. The award is valued at 60,000 EUR.

More information about Humboldt research awards at http://www.humboldt-foundation.de/web/humboldt-award.html

New natural mosquito repellent discovered

A southern house mosquito, Culex quinquefasciatus, after lunch.

A southern house mosquito, Culex quinquefasciatus, after lunch.

Two recent papers by Professor Walter Leal, Dept. of Molecular and Cell Biology could have far-reaching consequences for both mosquito and moth control. But perhaps the most exciting outcome of the work is his serendipitous discovery of a naturally occurring chemical that repels mosquitoes and could lead to effective, non-toxic protection from their disease-carrying bites.

The first paper, published Oct. 28 in Proceedings of the National Academy of Sciences, focuses on the southern house mosquito’s sense of smell. Leal’s team identifies a large repertoire of olfactory genes through next-generation genetic sequencing.

About 10 years ago, Leal’s lab at UC Davis found the first olfactory protein from all mosquito species by a labor-intensive process of isolating proteins, cloning genes and generating recombinant proteins for tests. Now, with the state-of-the-art technology available at the UC Davis Genome Center, Leal says they did almost the same amount of work to get the entire repertoire of olfactory proteins: hundreds of receptors and binding proteins.

A surprise amid all the data was that one of the newly discovered receptors responded very well to ethyl 2-phenylacetate.

“Initially we thought this is an attractant, because it is derived from plants, but when we tested it turned out that this is a repellent. This was great news because better repellents, particularly from natural sources, are needed to protect people from bites,” Leal said.

Ethyl 2-phenylacetate has high potential as a repellent because it has low toxicity and is FDA-approved as a food flavoring.

Leal says that understanding the mosquito’s sense of smell is scientifically important because the insects use their acute olfactory sense to locate hosts and egg-laying sites. He hopes that this work will lead to opportunities to disrupt mosquitos’ communication without harming the environment.

“When researchers understand how mosquitos perceive the environment through small chemical molecules like attractants from plants, humans, and places for them to lay eggs, we can mimic these signals and distract them without affecting other species, especially beneficial insects such as the honey bee,” Leal said.

The southern house mosquito, a carrier of the West Nile Virus, lays about 200 eggs at a time in a single place.

“If we can lure them to the wrong place and trap them, we can in principle take out potentially 200 mosquitoes–about 100 females–from the environment,” Leal said. “Also, we can use chemicals to minimize mosquito bites and, consequently, reduce transmission of diseases.”

One of Leal’s primary research goals is to find receptors that the southern house mosquito utilizes to find water pools for laying eggs and from there identify chemicals that may help researchers lure them. He says they have had some success, but still need better lures.

In the second paper, published by PNAS Oct. 24 in collaboration with Nobel laureate Kurt Wuethrich, the researchers demonstrate evidence that pheromone-binding proteins in moths can be blocked, which may lead to the development of a new way to control their populations.

“Moth damage to U.S. agriculture alone exceeds $1 billion annually, thus the critical need for environmentally safe methods to control moth populations. This interruption of male-female communication could lead to reduced crop damage without toxic compound applications,” Leal said.

Leal intends to launch new research into the repellent potential of ethyl 2-phenylacetate.

“The beauty of science is not to finding the answers to the questions we ask, but finding answers for question we did not have in mind.”

Leal’s mosquito research was funded by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health. For the full paper, see:

http://www.pnas.org/content/early/2013/10/23/1316059110.full.pdf

His moth research work was funded by the U.S. Department of Agriculture-National Institute of Food and Agriculture. For the full paper, see:

http://www.pnas.org/content/early/2013/10/23/1317706110.full.pdf

Contributed by Betsy Towner, College of Biological Sciences

A new look at heat transfer: Entransy

Is there a different way to think about heat transfer? For about 150 years, scientists and engineers have used the concept of entropy to understand transfer of heat into mechanical work or between materials systems. Now a UC Davis professor and colleagues in China are putting forward an alternative, at least for some applications.

“To me, entropy is just a tool,” said Ning Pan, a materials scientist and professor of textiles and clothing, and biological engineering at UC Davis. “It does not work well in all cases, for example in understanding heating and cooling of materials.”

Pan and Qun Chen, a former postdoctoral student at UC Davis and now a professor at Tsinghua University in China, have described their ideas in a series of papers. So far, they have carried out theoretical and computer modeling studies, which support their ideas, but have yet to test them in precise experimental systems.

Video: Prof. Ning Pan discusses entropy and entransy

Entropy is the measure of the universe running downhill. Most systems that involve energy generate some amount of heat, which is usually lost and cannot be recovered. In a closed system, entropy never decreases.

“It is interesting to note that many other physical energies (mechanical, electric, acoustic, etc.) turn into heat as the final form”, Pan said.

Entropy is sometimes also thought of as the increase in disorder in a system: disorder always increases. Cups break into fragments, but do not spontaneously reassemble; cream stirs into coffee, and does not separate out again with more stirring.

But Pan says that some experts have been dissatisfied with entropy as a measure for all heat transfer. His work with Chen shows that while entropy works well for describing heat transfer from mechanical systems, a new measure, which they call entransy, is better fit for explaining heating and cooling of materials, he said.

“As a materials scientist, I’m often thinking about the thermal properties of materials, and entransy is more useful for studying these properties. We have proved in our analysis that the extreme entransy dissipation, in place of the minimum entropy generation, is a more valid optimization criterion in heat transfer processes,” Pan said.

Pan hasn’t had much luck so far in converting his colleagues to the new measure. He’d like to find collaborators to carry out the precision temperature measurements necessary to prove their theory.

“It’s just another way to analyze and solve problems,” he said. “We’re not changing the fundamental physics, just how we understand them.”

More: “An alternative criterion in heat transfer optimization,” Proc. Roy. Soc. A, 2011, vol. 467 pp. 1012-1028.

Name that pupfish!

Getting to name new species must be one of the small pleasures of being a biologist. And if you’ve spent much of your Ph.D. painstakingly breeding thousands of hybrids of tiny fish, then flown with them to the Bahamas, you might as well have some fun with the naming, too.

Chris Martin, a graduate student working with Peter Wainwright in the Department of Evolution and Ecology, has been studying species of pupfish in some small lakes on the island of San Salvador in the Bahamas. There are about 50 species of pupfish across the Americas, and they are all pretty much the same — except in these lakes, where Martin found some oddities including a pupfish that crushes snails in its jaws and a fish that eats scales off other fish.

The rate of evolution among these fish is much higher than in other pupfish environments,

A shell-crushing pupfish from the Bahamas.

Martin found. In a follow up paper published in Science this year, he mapped the ‘adaptive landscape’ by breeding hybrids, releasing them into the lake and measuring which adaptations fared best.

Martin has now named two of his new fish species. Both are in the genus Cyprinodon: The scale-eater is C. desquamator, from the Latin for “one who peels off scales,” and the shell-feeder is C. brontotheroides, for its protuberant nose.

A brontothere

Martin named C. brontotheroides after a brontothere, an extinct Pleistocene mammal with a bony protuberance on its nose (unlike the modern rhino, whose horn is made of keratin).

It might be the first time a fish has been named after a giant, extinct mammal, Martin acknowledges.

Chris Martin is now pursuing postdoctoral research at UC Berkeley. Follow him on Twitter at @fishspeciation.