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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 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

Fanconi anemia gene poisons DNA repair

Fanconi anemia is a rare, inherited disorder that affects about one in 350,000 births. It affects the blood and bone marrow and many other organs, can cause physical abnormalities and vulnerability to cancer. Recently, the case of a child with serious Fanconi-like symptoms has helped researchers at The Rockefeller University in New York and UC Davis better understand the causes of the disease, and discover a new role for a protein already known to be involved in DNA repair and protection from cancer. The work was published recently in the journal Molecular Cell.

Rockefeller University maintains an international registry of people with Fanconi anemia or similar conditions, with the goal of helping researchers understand what causes the disease. Some 18 genes have been linked to Fanconi anemia, all involved in repair of “interstrand crosslinks” where two strands of DNA get stuck together. These crosslinks can be caused by chemicals generated during normal cell metabolism, by anticancer drugs and alcohol metabolism, and they can cause serious damage to DNA if not quickly removed.

Agata Smogorzewska and colleagues at the Rockefeller looked at the case of a child born with Fanconi anemia-like symptoms, identified through the registry. Sequencing of the child’s genome showed that she did not have any of the known genetic mutations linked to the condition. She did have just one unusual mutation in one of two copies of the gene for

Researchers treated patient cells with an agent that caused DNA cross links. The cells failed to repair them, producing broken chromosomes that fused with one another (red arrows). Laboratory of Genome Maintenance at The Rockefeller University/Molecular Cell

Researchers treated patient cells with an agent that caused DNA cross links. The cells failed to repair them, producing broken chromosomes that fused with one another (red arrows). Laboratory of Genome Maintenance at The Rockefeller University/Molecular Cell

RAD51, a protein involved in a different DNA repair process. This was something of a puzzle, because generally one “good” copy of a gene is sufficient for normal cellular functions. Neither of the girl’s parents had the mutation or symptoms.

Working in cell lines, Smogorzewska’s group was able to show that introducing this mutation made cells vulnerable to DNA damage from interstrand crosslinks, and cutting it out of the patient’s cell lines “cured” the problem in those cells.

They then turned to Professor Stephen Kowalczykowski at UC Davis, whose laboratory has extensively studied RAD51 and other related proteins involved in DNA repair. Kowalczykowski’s lab has shown, for example, how RAD51 plays a crucial role in homologous recombination, in which missing DNA is repaired by using the matching DNA strand as a template. RAD51 forms a filament with single-stranded DNA to line up with its sister DNA molecule and begin the copying process.

Taeho Kim, a postdoctoral researcher in Kowalczykowski’s lab, purified the protein made by the mutated gene and carried out biochemical studies to see how it functioned both in repairing interstrand crosslinks and in homologous recombination.

“It was evident right away that it was altered, and altered in a very unique way,” he said.

Not only does the mutant RAD51 protein not work properly, but it poisons the ability of the healthy protein made by the normal copy of the gene to deal with crosslinks, Kowalczykowski said.

The patient is only alive at all, although with severe disabilities, because she has one good copy of the gene, Kowalczykowski said, and her cells contain higher levels of the normal than the mutant protein.

“In this patient, DNA repair is normal, but protection from crosslinks is not, and we don’t completely understand why,” he said.

The discovery could open up new studies of interstrand crosslink repair, Kowalczykowski said. This is an important type of DNA damage whose repair is still not well understood.

The new mutant gene, designated FANCR, is the first example of a “co-dominant” DNA repair gene in homologous recombination in humans. While, for simplicity, genetic counselors often think of genes as being completely “dominant” or “recessive,” real mutations are more subtle, Kowalczykowski noted. In this case, the FANCR mutation partially poisons RAD51’s function, but not completely. Kowalczykowski’s lab has previously discovered co-dominant mutations in bacterial genes – notably in the protein RecA, which is the equivalent of RAD51 in E. coli bacteria.

Kowalczykowski predicted that many more such co-dominant mutations would be found in human DNA repair, potentially making it harder to unravel the causes of disease and making genetic counseling more difficult.

In addition to UC Davis and the Rockefeller, the authors include researchers at the University of Minnesota, the Broad Institute and the New York Genome Center.

Read the original paper here

News article from The Rockefeller University





Galaxy cluster collision revives “radio phoenix”

The collision of two massive galaxy clusters 1.6 billion light years from Earth revived a radio source in a fading cloud of electrons, creating a “radio phoenix.” The phenomenon was recorded by a team of astronomers including William Dawson of the UC Davis physics department and Lawrence Livermore National Laboratory.

Composite image of colliding galaxy cluster Abell 1033 combines X-ray data from Chandra (pink) along with radio data (green) and optical data that reveals the density of the galaxies (blue). (NASA)

Composite image of colliding galaxy cluster Abell 1033 combines X-ray data from Chandra (pink) along with radio data (green) and optical data that reveals the density of the galaxies (blue). (Chandra X-ray Observatory)

According to a news release from the Chandra X-ray observatory,

Astronomers think that the supermassive black hole close to the center of Abell 1033 erupted in the past. Streams of high-energy electrons filled a region hundreds of thousands of light years across and produced a cloud of bright radio emission. This cloud faded over a period of millions of years as the electrons lost energy and the cloud expanded.

The radio phoenix emerged when another cluster of galaxies slammed into the original cluster, sending shock waves through the system. These shock waves, similar to sonic booms produced by supersonic jets, passed through the dormant cloud of electrons. The shock waves compressed the cloud and re-energized the electrons, which caused the cloud to once again shine at radio frequencies.

The “phoenix” can be seen as the bright white splotch in the center of this image. X-rays are shown in pink and dark matter in blue.

Galaxy clusters are the most massive objects in the universe held together by gravity. Understanding how they grow is important for understanding how the universe has evolved over time.

Previously, Dawson and colleagues observed how the collision of another pair of galaxy clusters caused a new burst of star formation in a dormant area.