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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.

Shale oil fracking, conventional crude drilling produce similar greenhouse gas emissions

By Kat Kerlin

It requires roughly the same level of greenhouse gas emissions to extract shale oil as it does to extract conventional crude oil, according to a pair of studies by UC Davis and Stanford University released this week by the U.S. Department of Energy’s Argonne National Laboratory.

The research analyzed the Eagle Ford shale play in Texas and the Bakken play in North Dakota. These plays are shale formations with low permeability that must be hydraulically fractured to produce oil and gas.

The Eagle Ford Shale in Texas is one of the largest oil and gas producing regions in the country.

The Eagle Ford Shale in Texas is one of the largest oil and gas producing regions in the country.

Eagle Ford and Bakken are the second and third largest oil-producing regions in the U.S., respectively, since 2012.  Together, Bakken and Eagle Ford accounted for 54 percent of oil production and 19 percent of gas production within seven major production regions in 2014.

Until now, there has been little information about how the production method impacts greenhouse gas levels.

Both studies showed that greenhouse gas emissions associated with shale oil production are similar to levels generated at conventional crude oil reserves, even after considering the flaring and venting of natural gas during the shale oil process. The emission intensity stays consistent during the lifespan of extraction at the oil play.

This contradicts an earlier estimate that the Bakken play might produce greenhouse gas emissions 20 percent higher than for crude oil production.

The Eagle Ford study was led by Sonia Yeh, a research scientist with the Institute of Transportation Studies at UC Davis. It looked at crude oil from different production zones for 2009–2013. Some zones produced more oil while others produced more gas. The study showed that wells in the gas-rich zone used roughly twice the amount of energy as wells in the oil-rich zone, which used an average of 1.2 percent of energy for production, extraction, and processing. Water use was also generally higher at the gas-rich wells.

“It was challenging to calculate the net energy use and net greenhouse gas emissions for Eagle Ford because of the wide range of products produced at these places, and there were no publicly available tools for horizontal drilling and hydraulic fracturing,” said Yeh. “The collaboration provided greater transparency and understanding of energy and climate impacts of oil production in these important regions.”

Sonia Yeh researchers greenhouse emissions at the UC Davis Institute of Transportation Studies.

Sonia Yeh researchers greenhouse emissions at the UC Davis Institute of Transportation Studies.

The studies calculate energy consumption and greenhouse gas emissions associated with the crude oil and natural gas extraction using the Oil Production Greenhouse Gas Emissions Estimator (OPGEE) model, with production data collected for shale oil well operations in both plays. This model estimates energy for the lifecycle—from the initial exploration to the refinery entrance gate—and includes production, processing and transport.

The research team incorporated the OPGEE results into the Greenhouse gases, Regulated Emissions, and Energy use in Transportation (GREET) model developed at Argonne National Laboratory to determine the full life-cycle energy and emissions impacts.

The research was funded by the Vehicle Technology Office and the Bioenergy Technology Office of the Energy Efficiency and Renewable Energy Office of the U.S. Department of Energy.

The full reports can be found online at

Follow Kat on Twitter at @UCDavis_Kerlin.

Magnetic skyrmions at room temperature: New digital memory?

An exotic, swirling object with the sci-fi name of a “magnetic skyrmion” could be the future of nanoelectronics and memory storage. Physicists at UC Davis and the National Institute of Standards and Technology (NIST) have now succeeded in making magnetic skyrmions, formerly found at temperatures close to absolute zero, at room temperature.

“This is a potentially new way to store information, and the energy costs are expected to be extremely low,” said Kai Liu, professor of physics at UC Davis and corresponding author of a paper on the work, published in the journal Nature Communications Oct. 8.

Skyrmions were originally described over 50 years ago as a type of hypothetical particle in nuclear physics. Actual magnetic skyrmions were discovered only in 2009, as chiral patterns of magnetic moments — think of a moment as a tiny compass needle — in materials close to absolute zero temperature, in the presence of a strong magnetic field.

Nanodots induce magnetic skyrmions (arrows) in the film below. Skyrmions are stable magnetic structures and could be a new way to store data at low energy cost. (Kai Liu/UC Davis)

Nanodots induce magnetic skyrmions (arrows) in the film below. Skyrmions are stable magnetic structures and could be a new way to store data at low energy cost. (Dustin Gilbert and Kai Liu/UC Davis)

Magnetic skyrmions fall into two types, Liu said: “Bloch skyrmions,” with a hurricane-like spiral pattern of magnetic moments around a perpendicular center, surrounded by magnetic moments oriented in the opposite direction to the center; and “hedgehogs,” where the magnetic moments orient like spikes on a  hedgehog or sea urchin.

The interesting thing about magnetic skyrmions, Liu said, is that they are “topologically protected:” they can be continuously deformed, in the same way that a coffee mug shape can be deformed into a bagel shape, but they do not readily go back into a state where all the magnetic moments are aligned. That means they can potentially store information at an energy cost much lower than current technology, Liu said.

Together with graduate student Dustin Gilbert, now a postdoctoral fellow at NIST, Liu and colleagues designed a nanosynthesis approach to achieve artificial “Bloch” magnetic skyrmions at room temperature. They created a pattern of magnetic nanodots, each about half a micron across, on a multilayered film where the magnetic moments are aligned normal to the plane. They used ion beam irradiation to modify the interface between the dots and the film to allow “imprinting” of the magnetic moments of the dots into the film.

Using neutron-scattering at NIST Center for Neutron Research, they were able to resolve the magnetic profiles along the depth of the hybrid structure. Combined with magnetic imaging studies at NIST and Lawrence Berkeley Laboratory, they were able to find the first direct evidence of arrays of stable spiral magnetic skyrmions beneath the nanodots at room temperature, even without an external magnetic field.

The availability of stable magnetic skyrmions at room temperature opens up new studies on their properties and potential development in electronic devices, such as nonvolatile magnetic memory storage.

Coauthors on the paper are Brian Maranville, Andrew Balk, Brian Kirby, Daniel Pierce, John Unguris and Julie Borchers at NIST, and Peter Fischer, LBL and UC Santa Cruz. Nanofabrication work and other characterizations were carried out in Liu’s laboratory and at the Center for Nano and Micro Manufacturing at UC Davis. The work was funded by the National Science Foundation.

More information

NIST, UC Davis scientists float new approach to creating computer memory (NIST)

UC Davis experts praise Nobel Chemistry prize for DNA repair

“Terrific,” “Amazing news,” “Excellent choice,” were some of the terms two UC Davis experts in DNA repair used to describe the award of the 2015 Nobel Prize for Chemistry to three pioneers of the field this morning. The recipients are:  Tomas Lindal, Francis Crick Institute, London; Paul Modrich, Howard Hughes Medical Institute and Duke University; and Aziz Sancar of the University of North Carolina Chapel Hill.

“They discovered that DNA in your body, which suffers from millions of DNA damaging events from every day due to normal chemical processes, is repaired efficiently by remarkably complex and disparate sets of repair machineries and mechanisms,” said Stephen Kowalczykowski, distinguished professor of microbiology and molecular genetics in the UC Davis College of Biological Sciences.

Damage to DNA can lead to cancer and birth or developmental defects. Several genes identified as linked to cancer, for example the “breast cancer gene” BRCA2, have turned out to be involved in maintenance or repair of DNA.

“This is a wonderful recognition of the DNA repair field and underlines its importance for general biology and human disease,” said Wolf-Dietrich Heyer, professor and chair of microbiology and molecular genetics, who studies how DNA is repaired during recombination, the process of copying DNA.

Heyer noted connections to work at UC Davis. For example, Professor Sheila David at the Department of Chemistry works on MUTY, a protein that carries out base excision repair, the process discovered by Paul Modrich. David’s laboratory showed how one form of colorectal cancer is caused by a defect in MUTY, Heyer said.

“The approaches taken by all three awardees are the same that Stephen Kowalczykowski and I use to analyze recombinational DNA repair, biochemical reconstitution supported by genetic insights,” Heyer said. Kowalczykowski in particular has pioneered methods to study single molecules at work in DNA repair, allowing insights beyond conventional biochemistry, and has published work in collaboration with Modrich.

The pioneering work by Lindal, Modrich and Sancar brought order and understanding to the field, Kowalczykowski said.

“This understanding allowed the next generation of scientists to probe these biological processes with increasing sophistication. Finally, many, many decades later, we’ve come to learn and understand how defects in these very important repair pathways contribute to cancer development in humans,” Kowalczykowski said.

This work has contributed to human health through new therapies and drugs, a tribute to the value of basic science funded by the public sector and private charities in the U.S. and United Kingdom, he said.

We are only just beginning to appreciate the full impact of DNA repair on the origins and treatment of cancer, Heyer said. Kowalczykowski and Heyer are both members of the UC Davis Comprehensive Cancer Center. The Center’s Molecular Oncology Program is working on both basic mechanisms of DNA repair and translational studies that bring these fundamental insights to the clinic.

Related information

Nobel Prize announcement

Two UC Davis labs purify BRCA2 breast cancer gene protein

New pathway for repairing DNA damaged by oxygen radicals

Collaborating for the cure

Does hunting explain why zebras are not domesticated?

By Kathleen Holder

Why do people ride horses but not their striped African cousins?

A few zebras have accepted a rider or pulled a cart, but zebras have never been truly domesticated — and for good reason: They can be aggressive, panicky and unpredictable, making them difficult to halter and saddle train. While smaller than horses, they have powerful legs that can carry them at speeds up to 35 mph, and with a kick, can break the jaw of a predator. Those Chuck Norris-like skills are useful when you have lions, cheetahs and hyenas chasing you down for lunch.

Long experience of humans as predators might explain why zebras cannot be domesticated, unlike feral horses, UC Davis researchers propose. (Photo by Tim Caro/UC Davis).

Long experience of humans as predators might explain why zebras cannot be domesticated, unlike feral horses, UC Davis researchers propose. (Photo by Tim Caro/UC Davis).

But a new study by UC Davis researchers suggests that fear of four-legged carnivores may not be the sole explanation of why zebras are hard for humans to tame. Their enduring wildness may be the evolutionary legacy of a long relationship with predators on two legs —humans themselves.

Alexali Brubaker, who earned her Ph.D. in psychology from UC Davis in 2103 and is now research coordinator for the Third Millennium Alliance, and psychology professor emeritus Richard Coss compared the flight behavior of plains zebras in Africa with that of feral horses in Nevada and California when a human approached on foot.

In areas frequented by people, feral horses allowed a researcher to approach much closer than did zebras — waiting until they got about 54 yards away before going into alert mode and an average 18 yards before running away, compared with the zebras’ 68 yards alert distance and 40 yards before fleeing.

Brubaker and Coss say zebras’ wariness may be an evolutionary adaptation that allowed the species to survive hundreds of thousands of years of hunting by humans in Africa. Their 40-yard no-human zone is just outside the effective range of poisoned arrows used by African hunters for at least 24,000 years.

In Central Asia, early horses were hunted initially by archaic humans. Even then, Ice Age weather conditions provided long periods where horses, better adapted to cold climates, saw few human hunters. However, modern humans who replaced them after migrating to Asia from Africa 40,000 to 50,000 years ago were capable hunters of horses. Coss said that timeframe was not long enough to evolve an instinctual fear of humans.

The researchers were surprised to find, on the other hand, that in remote areas where people are rarely seen, modern feral horses exhibited as much or more wariness as zebras. Horses showed alert behavior (raising their heads, stopping grazing), on average, when a person got within 218 yards and then moved away when the human was 160 yards away. For the zebras in unpopulated areas, the average distances were 167 yards for an alert response and 115 yards for flight.

“This finding indicates,” Coss said, “that despite domestication, horses have not lost their keen awareness that an upright, approaching shape viewed from a distance could constitute a predatory threat.”

Their study, reported online Sept. 7 in the Journal of Comparative Psychology, also sheds new light on the question about where horses were first domesticated through selective breeding.

Coss said the findings point to Central Asia where, “their initial wariness of humans was likely assuaged by frequent exposure to humans as it is today when wild horses are rounded up and find homes under private care.”

Kathleen Holder writes about social sciences for the UC Davis College of Letters and Science. Follow Kathleen at @kmholder


Scientists solve the riddle of zebras’ stripes

Why zebras have stripes: The debate goes on 

Grant for natural hazards research at UC Davis centrifuge

The National Science Foundation will award almost $5 million over five years to UC Davis to include the large earthquake-simulating centrifuge at the Center for Geotechnical Modeling as part of the new Natural Hazards Engineering Research Infrastructure program.

The geotechnical centrifuge at UC Davis is the largest of its kind in the world. It is used for scale model experiments of the effect of earthquakes on soils and buildings.

The geotechnical centrifuge at UC Davis is the largest of its kind in the world. It is used for scale model experiments on the effect of earthquakes on soils and buildings.

The Center operates a nine-meter (30-foot) radius centrifuge with a shake table, the largest of its kind in the world. Researchers can build complex models of soils and structures on the shake table, fit them with instruments and sensors, and shake them while they rotate on this massive machine. This allows accurate scale-model studies of soils and soil-structure systems such as buildings and foundations, near-shore and off-shore energy infrastructure foundations, underground structures, pipelines, ground improvement technologies, wharves, embankment dams, and levee systems.

The grant will support research operations at the Center over the next five years, making it available to NSF-funded researchers nationwide as well as at UC Davis. The research performed will enable major advances in the ability of engineers to predict and improve the performance of soil and soil-structure systems affected by earthquake, wave, wind, and storm surge loadings.

The Center for Geotechnical Modeling, housed in the UC Davis Department of Civil and Environmental Engineering, has operated the large centrifuge as a unique, shared national resource for more than 30 years. The facilities have been used by researchers from the Universities of California (Davis, Berkeley, Los Angeles, San Diego, and Irvine), Colorado, Texas, and Washington; Oklahoma State; Arizona State; Oregon State; Virginia Tech; and Tokyo Institute of Technology, among others.

About NSF’s Natural Hazards Engineering Research Infrastructure program

The NHERI program includes various shared-use research facilities that will replace the George E. Brown Jr. Network for Earthquake Engineering Simulation. From 2015 through 2019, NHERI will be a distributed, multiuser, national facility created to provide the natural hazards engineering community with access to research infrastructure (earthquake and wind engineering experimental facilities, cyberinfrastructure, computational modeling and simulation tools, and research data), coupled with education and community outreach activities.

Other facilities funded under the program include a “Wall of Wind” hurricane simulator at Florida International University, the tsunami wave flume at Oregon State University, and the large outdoor shake table at UC San Diego.

More information

NSF news release

Center for Geotechnical Modeling website


Cold rush: Bird diversity higher in winter than summer in Central Valley

By Kat Kerlin

During the warmer months, the air surrounding California’s rivers and streams is alive with the flapping of wings and chirping of birds. But once the buzz and breeding of spring and summer are over, these riparian areas grow quiet. Sometimes it seems as though there are hardly any birds there at all.

Not so, according to a study from the UC Davis Department of Wildlife, Fish and Conservation Biology.

The fox sparrow commonly winters in the Central Valley. A UC Davis study found bird diversity in the area is actually higher in the winter than in summer, highlighting the importance of protecting habitat for birds year-round. Credit: Andrew Engilis/UC Davis

The fox sparrow commonly winters in the Central Valley. A UC Davis study found bird diversity in the area is actually higher in the winter than in summer, highlighting the importance of protecting habitat for birds year-round. Credit: Andrew Engilis/UC Davis

Researchers examined bird diversity in the lower Cosumnes River and lower Putah Creek watersheds in the Central Valley between 2004 and 2012. They found that just as many bird species used the riparian habitats in the winter as in the summer, and genetic diversity was actually higher in the winter than during summer months.

It turns out that while many birds headed south for the winter to tropical habitats, birds that breed in the boreal forest of Canada flew in to take their place. These “neotemperate migrants,” as the researchers call them, include birds such as the yellow-rumped warbler, white-crowned sparrow, fox sparrow, cedar waxwing, and varied thrush.

“You might have to look harder, but there are just as many species there,” said lead author Kristen Dybala, a UC Davis postdoctoral student at the time of the study and currently a research ecologist with Point Blue Conservation Science. “We found strong evidence that Central Valley ecosystems are very important in supporting bird populations throughout the year.”

Cold comfort

This study highlights the need to protect and restore riparian habitats to support birds throughout their annual life cycle—not just during the breeding times of spring and summer.  Often neglected in conservation planning, wintering habitat can be key to a songbird’s survival, affecting its reproductive success, migration timing, and overall health.

“Habitat conservation and restoration doesn’t just benefit breeding birds, but also supports continental populations of boreal breeding songbirds that require winter habitat for the half of their life spent not on breeding grounds,” said co-author Andrew Engilis, a scientist and curator of the UC Davis Museum of Wildlife and Fish Biology. “We are sure that if similar analyses were done in other regions of the U.S., there would be similar results.”

The study is published in the journal The Condor: Ornithological Applications. Melanie Truan, an ecologist with the UC Davis Museum of Wildlife and Fish Biology, was also a co-author.

The study was funded by the Solano County Water Agency, Putah Creek Council, CALFED Bay-Delta Program, U.S. Environmental Protection Agency, California Department of Water Resources, UC Davis Department of Wildlife, Fish and Conservation Biology and the cities of Davis and Winters, California.

Follow Kat on Twitter: @UCDavis_Kerlin

Atmospheric carbon dioxide can change how coffee trees grow

Plants use nitrogen from the atmosphere in unexpected ways. writes Kat Kerlin

Trees need nitrogen to grow, and they would prefer to get it from the soil. But in a pinch, when soils are poor, they will look to the atmosphere as sort of a nitrogen “food pantry,” grabbing it from the sky, according to a UC Davis study. However, amid rising levels of carbon dioxide, that back-up source of nitrogen is harder for the trees to access, limiting their growth.

The study, published in the journal Nature Scientific Reports, helps explain why rising CO2 levels are not accompanied by a boom in tree growth, as scientists formerly expected.

“If we were to include the effect of soils and nitrogen from the air, it would radically change the predictions of how plants respond to elevated CO2,” said lead author Lucas Silva, a researcher in the Department of Land, Air and Water Resources at UC Davis.

UC Davis researcher Lucas Silva takes carbon dioxide measurements from a coffee tree leaf. Credit: Courtesy Lucas Silva/UC Davis

UC Davis researcher Lucas Silva takes carbon dioxide measurements from a coffee tree leaf. Credit: Courtesy Lucas Silva/UC Davis

Silva’s colleague, UC Davis Plant Sciences professor Arnold Bloom, showed in a 2010 Science study and a 2014 Nature study how rising CO2 threatens human nutrition in grain crops. Inspired by that work, Silva wanted to understand how elevated CO2 would influence how trees use nutrients from the soil and the air.

He and his research team grew coffee trees at the UC Davis Controlled Environment Facility, exposing the trees to different levels of CO2 and nitrogen.

The team found that, when exposed to increased levels of CO2, trees growing in soils with readily available nitrogen grew bigger and took up less nitrogen from the atmosphere. Trees growing in poorer soils were smaller, and take more of their nitrogen from the air. But increasing the amount of CO2 in the air decreased the ability of the plants to take up nitrogen from the air through their leaves.

This showed Silva that plants use nitrogen from the atmosphere in ways previous studies hadn’t anticipated.

On the one hand, this could be a good thing: Trees are able to take up through their canopies nitrogen that would otherwise have been lost from terrestrial ecosystems.

“The bad news is, in a world where we have rising CO2 levels, we will likely see less and less nitrogen uptake from the air,” Silva said. “And, if soils are limiting, we could see a widespread decrease in tree growth.”

This work was developed in collaboration with the National Center for Coffee Research, Manizales, Colombia and supported by the Fulbright Exchange Program and by LAWR professor William Horwath’s J.G. Boswell Endowed Chair in Soil Science.

Follow Kat Kerlin on Twitter at @UCDavis_Kerlin.

Nanoporous gold sponge makes pathogen detector

By Jocelyn Anderson

Sponge-like nanoporous gold could be key to new devices to detect disease-causing agents in humans and plants, according to UC Davis researchers.

In two recent papers in Analytical Chemistry (here & here), a group from the UC Davis Department of Electrical and Computer Engineering demonstrated that they could detect nucleic acids  using nanoporous gold, a novel sensor coating material, in mixtures of other biomolecules that would gum up most detectors. This method enables sensitive detection of DNA in complex biological samples, such as serum from whole blood.

Nanoporous gold is like a sponge of tiny pores. It could be used to make new devices to detect pathogens. (Erkin Şeker, UC Davis).

Nanoporous gold is like a sponge of tiny pores. It could be used to make new devices to detect pathogens. (Erkin Şeker , UC Davis)

“Nanoporous gold can be imagined as a porous metal sponge with pore sizes that are a thousand times smaller than the diameter of a human hair,” said Erkin Şeker, assistant professor of electrical and computer engineering at UC Davis and the senior author on the papers. “What happens is the debris in biological samples, such as proteins, is too large to go through those pores, but the fiber-like nucleic acids that we want to detect can actually fit through them. It’s almost like a natural sieve.”

Rapid and sensitive detection of nucleic acids plays a crucial role in early identification of pathogenic microbes and disease biomarkers. Current sensor approaches usually require nucleic acid purification that relies on multiple steps and specialized laboratory equipment, which limit the sensors’ use in the field. The researchers’ method reduces the need for purification.

“So now we hope to have largely eliminated the need for extensive sample clean-up, which makes the process conducive to use in the field,” Şeker said.

The result is a faster and more efficient process that can be applied in many settings.

The researchers hope the technology can be translated into the development of miniature point-of-care diagnostic platforms for agricultural and clinical applications.

“The applications of the sensor are quite broad ranging from detection of plant pathogens to disease biomarkers,” said Şeker.

For example, in agriculture, scientists could detect whether a certain pathogen exists on a plant without seeing any symptoms. And in sepsis cases in humans, doctors might determine bacterial contamination much more quickly than at present, preventing any unnecessary treatments.

Other authors of the studies were Pallavi Daggumati, Zimple Matharu, and Ling Wang in the Department of Electrical and Computer Engineering at UC Davis.

This work is funded by the UC Davis Research Investments in the Sciences and Engineering (RISE) program, which encourages interdisciplinary work to solve problems facing the world today, as well as the UC Lab Fees Research Program and the National Science Foundation.


Effect of Nanoporous Gold Thin Film Morphology on Electrochemical DNA Sensing

Biofouling-Resilient Nanoporous Gold Electrodes for DNA Sensing

Follow UC Davis research on Twitter @ucdavisresearch

Oxygen oasis in Antarctic lake reflects distant past

At the bottom of a frigid Antarctic lake, a thin layer of green slime is generating a little oasis of oxygen, a team including UC Davis researchers has found. It’s the first modern replica discovered of conditions on Earth two and a half billion years ago, before oxygen became common in the atmosphere. The discovery is reported in a paper in the journal Geology.

The switch from a planet with very little available oxygen to one with an atmosphere much like today’s was one of the major events in Earth’s history, and it was all because some bacteria evolved the ability to photosynthesize. By about 2.4 billion years ago, geochemical records show that oxygen was present all the way to the upper atmosphere, as ozone.

What is not clear is what happened in between, or how long the transition – called the Great Oxidation Event – lasted, said Dawn Sumner, professor and chair of earth and planetary sciences at UC Davis and an author on the paper. Scientists have speculated that here may have been “oxygen oases,” local areas where was abundant before it became widespread around the planet.

The new discovery in Lake Fryxell in the McMurdo Dry Valleys could be a modern example of such an ancient oxygen oasis, and help geochemists figure out what to look for in ancient rocks, Sumner said.

Diving in Lake Fryxell, Antarctica, researchers found an oasis of oxygen mimicking conditions on Earth two and a half billion years ago. (Tyler Mackey/UC Davis)

Diving in Lake Fryxell, Antarctica, researchers found an oasis of oxygen mimicking conditions on Earth two and a half billion years ago. (Tyler Mackey/UC Davis)

Sumner and collaborators including Ian Hawes of the University of Canterbury, New Zealand have been studying life in these ice-covered lakes for several years. The microbes that survive in these remote and harsh environments are likely similar to the first forms of life to appear on Earth, and perhaps on other planets.

The discovery occurred “a little by accident,” Sumner said. Hawes and Tyler Mackey, a UC Davis graduate student working with Sumner, were helping out another research team by diving in Lake Fryxell. The lakes of the Dry Valleys typically contain oxygen in their upper layers, but are usually anoxic further down, Sumner said. Lake Fryxell is unusual because it becomes anoxic at a depth where light can  still penetrate.

During their dives below the oxygen zone, Hawes and Mackey noticed some bright green bacteria that looked like they could be photosynthesizing. They took measurements and found a thin layer of oxygen, just one or two millimeters thick, being generated by the bacteria.

Something similar could have been happening billions of years ago, Sumner said.

“The thought is, that the lakes and rivers were anoxic, but there was light available, and little bits of oxygen could accumulate in the mats,” she said.

The researchers now want to know more about the chemical reactions between the “oxygen oasis” and the anoxic water immediately above it and sediments below. Is the oxygen absorbed? What reactions occur with minerals in the water?

Understanding how this oxygen oasis reacts with the environment around it could help identify chemical signatures preserved in rocks. Researchers could then go looking for similar signatures in rocks from ancient lake beds to find “whiffs of oxygen” prior to the Great Oxidation Event.

The work was supported by the National Science Foundation and NASA.


Dawn Sumner’s Antarctic blog

Tyler Mackey’s Antarctic blog

Follow Dawn Sumner on Twitter: @sumnerd.


Fourth wheat gene is key to flowering and climate adaptation

By Pat Bailey

In the game of wheat genetics, Jorge Dubcovsky’s laboratory at UC Davis has hit a grand slam, unveiling for the fourth time in a dozen years a gene that governs wheat vernalization, the biological process requiring cold temperatures to trigger flower formation.

Identification of the newly characterized VRN-D4 gene and its three counterpart genes is crucial for understanding the vernalization process and developing improved varieties of wheat, which provides about one-fifth of the calories and proteins that we humans consume globally.

The new study, reported Aug. 31 online in the Proceedings of the National Academy of Sciences, also shows how the spring growth habit in some wheat varieties traces back to ancient wheat that grew in what is now Pakistan and India.

Different wheat for different climates

Wheat first appeared about 8,000 years ago in the coastal area of the Caspian Sea, where Europe and Asia converge. It quickly spread through both continents and now grows worldwide. Scientists attribute its adaptability to its rapidly changing genome and the fact that most types of wheat have two or three sets of chromosomes.

In cold climates, the vernalization process ensures that the cold-sensitive flowering parts of the wheat plant develop only after winter’s harshest months have passed and just in time for the warmer weeks of spring.  Such “winter wheat” is planted in the fall and harvested in early summer.

In contrast, “spring wheat” varieties don’t have a vernalization requirement and can be planted in spring and harvested in fall. This is essential for regions where winters are so severe that wheat cannot be sown in fall and grown through the winter months.

Vernalization key to wheat’s adaptability

“We’re extremely interested in understanding the adaptive changes, especially vernalization, which occurred in wheat during the early expansion of agriculture, said study first-author Nestor Kippes, a doctoral candidate in the Dubcovsky lab.

UC Davis research Nestor Kippes has discovered a fourth gene that controls response to cold winters in wheat.

UC Davis research Nestor Kippes has discovered a fourth gene that controls response to cold winters in wheat.

Because vernalization governs flowering time, it’s important to a plant’s reproductive success and key to maximizing grain production in wheat, barley and other cereal crops, Kippes said.

Although the world produces more than 700 million tons of wheat annually, the rapidly growing global human population continues to press for even greater production of wheat and other staple crops. And long-term global climate change promises to make that task even more challenging.

“The VRN-D4 gene and the other three vernalization genes can be used by plant breeders to modify vernalization requirements as they work to develop wheat varieties that are better adapted to different regions or changing environments,” Kippes said.

The Dubcovsky lab collaborated on this study with colleagues at Sabanci University in Turkey; Okayama University in Japan; the U.S. Department of Agriculture (USDA) Biosciences Research Lab in Fargo, North Dakota; Kansas State University in Manhattan, Kansas; and the Howard Hughes Medical Institute in Maryland.

The study was funded by the USDA, Howard Hughes Medical Institute, Gordon and Betty Moore Foundation, and the International Human Frontier Science Program Organization of France.

More about the Dubcovsky lab’s earlier research on wheat vernalization genes can be found at:

Newly Cloned Gene Key to More Adaptable Wheat Varieties (2006)

Newly Cloned Gene Key to Global Adaptation of Wheat (2004)

Wheat Gene Controlling Cold-Weather Requirement Cloned (2003)


Wheat geneticist Jorge Dubcovsky receives Wolf Prize in Agriculture

Follow Pat on Twitter: @UCDavis_Bailey