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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.

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.

Neutrinos leave mark on early universe

Much of the time, popular stories about science emphasize the broader impact, the implications for the field, what it might mean for our lives. But in reality, science is often about finding that some detail of the universe works the way we had already predicted, and for scientists that’s pretty cool too.

In one such discovery, UC Davis physicists have for the first time seen the signature of neutrinos spreading through the hot plasma of the early universe, at a time when light itself was still trapped in the plasma. The work is published in the journal Physical Review Letters.


The Planck sky map shows how neutrinos influenced the structure of the early universe. (ESA)

The Planck sky map shows how neutrinos influenced the structure of the early universe. (ESA)

The result, noted Professor Lloyd Knox, who lead the research team, was completely expected. Nonetheless, Knox said: “I feel really privileged that I got to lead the team that first detected this. It’s like we’ve reached out and touched the Big Bang.”

The only surprise was that the effect was detectable at all, Knox said.

Tens to hundreds of thousands of years after the Big Bang, before there were stars or galaxies, the universe was filled with super-hot plasma, hotter than the surface of the sun. Light particles (photons) could not make their way through the plasma, because they kept bumping off other particles.

But neutrinos could start flowing much earlier than light, because neutrinos interact very weakly with other particles.

Very small density variations led to acoustic waves in the plasma. Looking back today, we see those variations as ripples in the cosmic microwave background. Eventually, those variations – or anisotropies – would allow galaxies to form, giving structure to the universe.

Using data from the Planck space telescope, Knox and graduate students Brent Follin, Marius Millea and Zhen Pan looked for the gravitational influence of the neutrinos on these plasma waves. It had been predicted that the neutrinos would cause a very slight shift in the phase of the waves, and that is what they found: that the waves are just a little bit further along than they would be without the effect of neutrinos.

“It’s one thing to predict it and talk about it, but then you look and it’s there!” Knox said. “It’s astounding.”

The Planck Space Observatory

The Planck Space Observatory

Launched in 2009 by the European Space Agency with NASA participation, the Planck telescope is positioned about a million miles from Earth to collect light from the beginnings of the universe. Knox leads the U.S. team analyzing Planck data to determine the basic parameters of the cosmos. The satellite has now stopped observations, but a final set of sky maps will be released next year, Knox said.

Read the paper: First detection of the acoustic oscillation phase shift expected from the cosmic neutrino background

What’s a neutrino, anyways? (via the IceCube experiment, University of Wisconsin-Madison)


Planck’s new map brings universe into focus

UC Davis solution for better nitrogen climate modeling adopted by IPCC

By Kat Kerlin

Lawrence Berkeley National Laboratory researchers who provide global climate models to the Intergovernmental Panel on Climate Change have publicly thanked UC Davis associate professor Ben Houlton and his colleagues for creating a new solution to more accurately forecast nitrogen’s effects on global warming.

In an opinion piece in Nature Climate Change, the authors discuss how they have modified their model equations so that they now provide realistic predictions  anchored in Houlton’s benchmarking technique, published in that journal in April.

“We agree that terrestrial models must represent these losses accurately if they are to credibly estimate emissions of nitrogen- and carbon-containing greenhouse gases important in climate change predictions,” wrote authors Qing Zhu and William Riley of the Lawrence Berkeley National Laboratory. “We believe the … estimates produced by Houlton, et. al., are valuable benchmarks for Earth system models.”

Nitrogen is a critical component of climate change. It determines how much carbon dioxide emissions natural ecosystems can absorb, and it directly warms the climate as nitrous oxide in the atmosphere. It occurs naturally in the air and water and also enters the environment through man-made agricultural fertilizers. Recent analyses suggest that excess nitrogen in the air from human actions causes $400 billion dollars of economic and human welfare damages worldwide.

“Nitrogen has so many different effects on climate change, and is a centerpiece in people’s health and our global food economy,” Houlton said. “It’s really exciting to see how our new nitrogen tracking scheme is being used to substantially improve how the world’s leaders will confront the most pressing issues of our time”.

Follow Kat on Twitter at @UCDavis_Kerlin

Molecular machine, not assembly line, assembles microtubules

When they think about how cells put together the molecules that make life work, biologists have tended to think of assembly lines: Add A to B, tack on C, and so on. But the reality might be more like a molecular version of a 3-D printer, where a single mechanism assembles the molecule in one go.

Take, for example, tubulin. Building from two subunits, alpha and beta tubulin, this protein assembles into microtubules that play a vital role inside cells – giving structure, pushing or pulling other things around, or providing a track on which other molecules can pull themselves along.

Perhaps most crucially, when cells divide, microtubules form the spindle structure that first aligns the chromosomes in the middle of the cell then pulls them apart, so that each new cell gets one chromosome from each pair. This process often goes wrong in cancer cells, resulting in chromosomal instability.

Jawdat Al-Bassam at the UC Davis Department of Molecular and Cellular Biology and colleagues have now taken a close look at the proteins that assemble tubulin, and found that they comprise a single machine, not a stepped pathway as previously thought. The work is published online in the journal eLife.

The basic unit of tubulin is a dimer of alpha- and beta- tubulin. This dimer gives microtubules directionality, which is key to many of their other properties, such as being able to assemble or disassemble from either end, and allowing motor proteins to walk along them in a specific direction.  This unique organization of tubulin is preserved among all living plant and animal cells, because it is essential for way in which microtubules assemble, Al-Bassam said.

Assembling alpha-beta tubulin dimers involves six known genes, Al-Bassam said. The conventional model arranged these proteins as an assembly line starting with alpha and beta subunits and ending with the finished alpha-beta dimer.

Four proteins come together to make the machine that assembles tubulin, the building block of microtubules.

Four proteins come together to make the machine that assembles tubulin, the building block of microtubules.

“What we showed instead is that largest four of these six genes form a machine that functions as a single entity,” Al-Bassam said. They also discovered that a newly discovered subunit, a GTP-ase enzyme of a type usually thought to act as a switch, in fact powers the whole machine using chemical energy.  The energy maybe required to build stable alpha and beta tubulin assembly.

“We didn’t expect it ourselves,” Al-Bassam said.

The researchers worked with the tubulin system from yeast, but the human genes are very similar.

They first tried to reconstitute the system by working with one or two genes at a time, but this “assembly line” approach just didn’t work. Then they put all six genes into a single piece of DNA, so that they would all be transcribed together – and found that they could reconstitute the “3-D printer” that assemble tubulin dimers.

Even small defects in the genes that assemble tubulin are associated with serious developmental disorders, such as Kenny-Caffey syndrome and Giant Axonal Neuropathy. Cancer cells often show an inability to separate chromosomes properly during cell division, due to problems with microtubules.

Al-Bassam said the results open up new ways of thinking about tubulin, tubulin-related disorders and molecular biology in general.  Understanding this system may provide a new strategy to control microtubules, particularly in cells that are dividing out of control such as in certain cancers.

“It turns out there are lots of things we can think about as these kinds of machines,” he said. “Most important functions in cells are carried by molecules that work in groups.”

More information: Tubulin cofactors and Arl2 are cage-like chaperones that regulate the soluble αβ-tubulin pool for microtubule dynamics (eLife)