The genome of the cucumber has been sequenced by an international consortium lead by Chinese and U.S. institutions. The annotated genome was published online Nov. 1 by the journal Nature Genetics.

The cucumber genome will give insight into the genetics of the whole cucurbit family, which includes pumpkins and squash, melon and watermelon, and be a platform for research in plant biology, said William Lucas, professor and chair of the Department of Plant Biology at the University of California, Davis. Lucas helped with the development and management of the project.

“This is going to help a large community — we can now go ten times faster than we could before,” Lucas said.

Lucas studies the vascular transport systems, phloem and xylem, that plants use to move nutrients, minerals and signaling molecules throughout the body of the plant. Pumpkins and cucumber are model plants for studying vascular transport, because their vascular system is large and easy to access.

The Lucas research group has shown that plants use both proteins and RNA –  molecules copied or transcribed from DNA — as signaling molecules that are transported around the plant through the phloem. These signals can affect plant growth, coordinate activity through the plant and help it fight infection. For example, in 2007 they showed that “florigen,” the signal that tells the growing tips of plants to make flowers in response to seasonal changes, is a protein transmitted through the phloem.

The new study identified 800 phloem proteins in the cucumber genome. With the help of the genome data, researchers will be able to rapidly identify and characterize all the protein, RNA and other molecules in the phloem sap, Lucas said.

There are already indications that far more is going on in the phloem than anybody, “including me,” had previously expected, he said.

The study shows that five of the seven chromosomes in cucumber arose from ten ancestral chromosomes shared with melon, and gene-coding stretches of DNA share about 95 percent similarity to melon. Preliminary studies in the Lucas lab at UC Davis have established comparable similarity between cucumber and pumpkin.

The cucumber genome will also provide insights into traits such as disease and pest-resistance, the “fresh green” odor of the fruit, bitter flavors and sex expression.

The cucumber is the seventh plant to have its genome sequence published, following the well-studied model plant Arabidopsis thaliana, the poplar tree, grapevine, papaya, and the crops rice and sorghum.

The sequencing effort, begun earlier this year, was coordinated by Professor Sanwen Huang of the Chinese Academy of Agricultural Science and included the Genome Center at the Beijing Genome Institute-Shenzhen and UC Davis as well as several laboratories in China and others in the U.S., Denmark, the Netherlands, Australia and South Korea.

Part of the effort relied on new methods developed by the Beijing Genome Institute to assemble short pieces of DNA, about 50 base pairs, into the sequence. The Beijing Genome Institute-Shenzhen can now sequence and assemble genomes much faster, and at lower cost, than previously possible, Lucas said.

“This will be the forerunner for many genomes done at a cost-effective rate,” he said.

A proposal that butterfly caterpillars are descended from the mating of an ancient insect with a type of worm is comprehensively rejected by a new paper to be published this week in the journal Proceedings of the National Academy of Sciences.

The author of the original paper, Donald Williamson of the University of Liverpool, England, appealed to the scientific community to test his hypothesis. Rick Grosberg, professor in the Department of Evolution and Ecology and the Center for Population Biology at UC Davis, and Mike Hart of Simon Fraser University, British Columbia took up the challenge, showing that Williamson’s hypothesis can be disproven using data already published and readily available.

“There’s not a shred of genetic evidence supporting a hybridization event, which there absolutely should be,” Grosberg said. “All the predictions that you would make, beyond the most basic, do not hold up.”

Williamson proposed that caterpillars are descended from an onychophoran, an animal sometimes called a “velvet worm.” These worms have a segmented body and simple legs. In the distant past, he proposed, such a worm mated with an ancestral insect. The resulting hybrid had two genomes, one from each parent. The worm-like genome went on to form the modern caterpillar, while the insect genome formed the adult butterfly. The two genomes would have continued side-by-side to the present day, with each controlling different stages of the life cycle.

Among Williamson’s predictions are that modern butterflies and other insects with a caterpillar stage will have a larger genome than either modern onychophorans or insects that do not have a caterpillar.

Data readily available online show that this is not true, Hart and Grosberg point out. In fact, butterflies have a smaller genome than either onychophorans or other insects.

Several insect genomes have been sequenced, although the genome of the onychophoran Priapulus is not yet complete. But a published study of 149 genes from insects, onychophorans, scorpions, crustaceans and other arthropods does not show that onychophorans are particularly closely related to the butterflies, or that butterflies have a mix of insect and velvet worm genes.

The original paper, published in the same journal earlier this year, was met with widespread incredulity. Many scientists questioned how the paper came to be published. One researcher quoted by the media compared the journal to a supermarket tabloid.

PNAS has two routes for accepting scientific papers. Most follow a similar route to other scientific journals. They are submitted to the editorial office, which assigns other scientists to carry out an independent, confidential peer review. But in the case of PNAS, members of the National Academies can also “communicate” a limited number of papers per year to the journal and manage the peer review process themselves.

The Williamson paper was submitted by this latter route, communicated by Lynn Margulis, professor at the University of Massachussetts, Amherst.

Grosberg and Hart opted not to address the issue of how the paper came to be published.

“We wanted to point out that the data and tests exist, and deal with it on scientific grounds,” Grosberg said.

Grosberg noted that Williamson has been advocating similar ideas since 1989, claiming that sea squirts in his laboratory could interbreed with sea urchins, a different phylum of marine animal. Other scientists, including Hart, have not been able to reproduce that work, and shown that the actual larvae that Williamson raised contained only sea urchin DNA

“The good side of this is that this idea might have lain around and resurfaced in minor journals for decades. Now it’s been front and center,” Grosberg said.

“The scientific process worked in the end, but a bunch of people went to a lot of trouble to refute an extremely implausible idea.”

From Phyllis Brown, UC Davis Health System Public Affairs

When you rationalize driving your SUV with the world growing ever warmer or smoking with the threat of lung cancer looming, a distinct area in the middle of the frontal lobes of your brain allows you to adjust your attitudes to justify your behavior, research conducted at UC Davis has found.

In a study published in the journal Nature Neuroscience, UC Davis researchers report that a portion of the brain that sits on top and in front of the connection of the brain’s two hemispheres is the place where we wrestle with our inner conflicts. The place is called the anterior cingulate cortex. Psychologists call the process cognitive dissonance.

“Psychologists have studied cognitive dissonance for decades and this research has had many applications from marketing to politics, but we have never known exactly how it works before,” said senior study author Cameron Carter, a professor of psychiatry and behavioral sciences and director of the UC Davis Imaging Research Center.

For the study, research subjects were placed inside an MRI and asked questions that would create cognitive dissonance while scientists obtained fMRI images that detected minute increases in blood flow to activated areas of the brain. The subjects were asked to answer questions about the MRI experience but give answers that minimized their discomfort at being inside the cramped, claustrophobic machine. They were asked to prevaricate because other, waiting subjects were watching. The researchers also obtained fMRI images of control subjects who were not asked to minimize their discomfort for the benefit of other participants.

The study found that two distinct areas of the brain showed activity in the prevaricating subjects that did not become active in the study controls. The areas were the anterior cingulate cortex and, to a slightly lesser extent, the anterior insula. The anterior cingulate cortex is thought to be a strictly cognitive area, while the insula is considered to be a region that processes more emotions.  Both have previously been shown to be active during various kinds of psychological conflicts, and in this case they were engaged by the conflict between the stated beliefs and the participants’ true feelings. Strikingly, the more these areas were activated by the conflict between real and stated attitudes, the more the person later changed their attitude outside of the scanner and experienced it as more pleasant.

The study advances brain science and our understanding of how attitudes change and begin to provide insights into how attitudes get manipulated by marketers or politicians, said van Veen, who is now a post-doctoral fellow at the Helen Wills Neuroscience Institute at UC Berkeley. It may also help us advance why some people are more susceptible to induced attitude change than others, noted Carter.

“The study contributes a lot to our knowledge about cognitive dissonance, and how and why people change their attitudes,” van Veen said. “It shows that the phenomenon of cognitive dissonance is real and is not just a figment of the imagination of social psychologists — there really is something going on in people’s brains when they make an argument that goes counter to what they actually think. Furthermore, it shows that the degree to which people’s opinions are subsequently changed depends on how active their anterior cingulate cortex was making a new link between the known cognitive functions of this region and the processes of changing people’s attitudes.”

Other study authors include Marie K. Krug of UC Davis and Jonathan W. Schooler of UC Santa Barbara.

The study was funded by the National Institute of Mental Health and the Burroughs-Wellcome Foundation.

The 2009 Nobel Prize for Physics is split between Charles Kao, for developing fiber optics, and Willard Boyle and George Smith, who invented the Charge Coupled Device or CCD at Bell Laboratories in 1969. CCDs are now the ubiquitous heart of digital cameras.

UC Davis physics professor Tony Tyson joined Bell Labs around the same time as Boyle and Smith invented the CCD, and has worked on the development of these light-sensing chips and ever more powerful digital cameras throughout his career.

“The invention of the CCD at Bell Labs by Boyle and Smith has transformed our view of the universe and of ourselves.  The ubiquitous CCD imager inside our cameras enables us all to snap digital photos of the universe around us.  And it lets astronomers view the distant universe in increasingly wide and faint detail,” Tyson said.

Tyson’s first scientific use of a digital camera was to take pictures of red-blood cells in sickle cell anemia. In the 1990s, he built the Big Throughput Camera or BTC, which was used to make the discovery that the universe is not only expanding, but that the expansion is speeding up. Now, he is leading the effort to build the Large Synoptic Survey Telescope or LSST, which will have a 3-billion-pixel camera and will survey the night sky in exquisite detail.

As Tyson tells the story, Boyle and Smith’s boss at Bell Labs asked them to find a solution to the problem of echo on telephone lines. The phone company was using a delayed tape to replay signals and cancel out the echo, but the tapes kept breaking. They wanted a solid-state device that could slightly delay the audio signal in a predictable way.

“After their boss left they scribbled on the blackboard and came up with a scheme in about half an hour,” Tyson said. Boyle and Smith built their device with nine silicon electrodes in about a month and got it to work, but found a problem.

“They realised it worked better when someone was standing over it, so they tried turning out the room lights, and it worked perfectly,” Tyson said.

Within moments, Boyle and Smith realised that they had just made a nine-pixel imaging device.

Bell Labs tried to use the new technology for their Picturephone, replacing vacuum tubes with solid-state circuits. (Tyson has what may be the only surviving Picturephone in his office). But the Picturephone never took off commercially, and the company killed the project. Among other problems, the phones required so much bandwidth on the old, copper wiring as to be prohibitively expensive — a problem that would be solved with the development of fiber-optic cables.

Tyson says he initially regarded cameras based on charge-coupled devices as “an amusement” and built an early 100 by 100 pixel camera in his garage. At the time, astronomers were using 10″ by 10″ photographic plates for their observations.

But Tyson said that as he tinkered with CCDs, he realized that if they could be made in a mosaic, they could indeed be used for astronomy. Since then, he has designed and built cameras for telescopes including the BTC and the LSST.

“It’s enabled all sorts of very nice science from biomedicine to astronomy,” Tyson said.

Additonal UC Davis connection: Charles Kao is second cousin of Winston Ko, dean of mathematical and physical sciences.

Today’s award of the Nobel Prize for Physiology and Medicine to Elizabeth Blackburn of UCSF, Carol Greider of Johns Hopkins University and Jack Szostak at Harvard, “for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase,” is a “Nobel no-brainer,” said Stephen Kowalczykowski, distinguished professor of microbiology and of molecular and cellular biology at UC Davis.

“It was a most appropriate and well deserved award. The discovery had broad implications; from understanding a fundamental aspect of chromosome biology to providing a basis for treating cancer and limiting aging,” Kowalczykowski said in an email.

“Awarding a Nobel Prize for understanding telomere structure and replication was a given (and to my mind, overdue),” said Neil Hunter, professor and Howard Hughes Fellow in microbiology and molecular and cellular biology. “And I couldn’t think of a more deserving trio of scientists.”

The impact of the discoveries for biology and medicine has been very high, sustained and of fundamental importance, Hunter said.

Lifeng Xu joined UC Davis as assistant professor of microbiology earlier this year after 8 years as a postdoc in Blackburn’s lab at UCSF.

“I’m really happy for her to get it,” Xu said of the award news. “She’s a great scientist, and such a humble person.”

Telomeres, Xu said, are structures on the ends of chromosomes. Normally, a loose end of DNA is regarded by the cell as a sign of damage that needs to be repaired, and telomeres stop this from happening. They also allow cells to continue dividing, which can be beneficial (in stem cells) or harmful (in cancer).

Every time a cell divides into two new cells, it copies its DNA. The enzyme that copies DNA cannot reach the end of the chromosome, so normally the telomeres become slightly shorter every time the cell divides. That puts a limit on how many divisions a cell can go through.

The telomerase enzyme restores the telomere after each division, so that the cell can continue to divide without limit, as in cancer.

Xu’s lab at UC Davis is interested in proteins that bind to telomeres and that help to protect telomeres, and that also help recruit the telomerase enzyme to the site. If we can better understand these structures, we might be able to exploit them to interfere with telomerase activity in cancer cells, Xu said.

Another UC Davis and UC link: co-recipient Carol Greider’s father, Kenneth Greider, was a physics professor at UC Davis, and she grew up in Davis. Carol Greider has a bachelor’s degree from UC Santa Barbara and a Ph.D. from UC Berkeley, where she worked with Blackburn.

Seven weeks camping by a frozen lake in one of the most inhospitable places on Earth might not be everyone’s idea of a good time, but geology professor Dawn Sumner is excited to be on her way to Antarctica this week. That’s because Lake Joyce, in the dry valleys of Antarctica, contains microbes that are slowly fossilizing right now and look tantalizingly similar to rocks from 3 billion years ago. Understanding just how microbes lived in those rocks can help us understand the first appearance of life on Earth, and might give some hints about what traces of life would look like elsewhere in the universe.

Sumner will be blogging the trip at dawninantarctica.blogspot.com.

The team members are Sumner and UC Davis postdoc Bekah Shepard; Dale Andersen, Darlene Lim and Alfonso Davila of the Carl Sagan Center for the Study of Life in the Universe; Ian Hawes, Aquatic Research Solutions Ltd.; Christopher McKay of NASA’s Ames Research Center; Wayne Pollard, McGill University; and Bernard Laval, University of British Columbia. After staging at McMurdo base, they will take a helicopter to Lake Joyce in the dry valleys. The 40-meter deep lake is permanently covered with 6 meters of ice. Some of the team will be diving in the lake to study microbial life.

More information about Lake Joyce is available on Dale Andersen’s website.

Last year, Bekah Shepard (then a graduate student in Sumner’s lab) took part in a diving expedition in Pavilion Lake, BC studying similar rock/microbe formations called microbialites. Watch our video report here.

Sumner is also interested in the search for life on Mars. In 2006, Sumner and Greg Chavdarian published work comparing features seen in the White Sands desert in New Mexico to features seen by the Mars rover Opportunity, suggesting that liquid water might be present near the surface of Mars.

Several other UC Davis scientists have visited Antarctica. Geology professor Ken Verosub, who made several trips to the continent in the late 1990s, called it “awe-inspiring.” Geophysicist Gary Acton was there in 2007-8 working on the ANDRILL drilling project. And a mountain in the Queen Maude range is named after Robert Feeney, a protein chemist who made several visits in the 1960s and wrote a book on Antarctic exploration.

There are news reports today of the first positive results from a clinical trial of an HIV vaccine. The trial was conducted in Thailand using two shots with different vaccines, neither of which had been shown to be effective on their own, in over 16,000 Thai men and women at risk of infection with HIV.

Participants volunteered for the study and were told about the potential risks associated with receiving the experimental vaccine before agreeing to participate.

All were given condoms, counseling and treatment for any sexually transmitted infections, and were tested every six months for HIV. Any who became infected were given free treatment with antiviral medicines. All participants continued to receive an HIV test every six months for three years after vaccinations ended.

The results: New infections occurred in 51 of the 8,197 given vaccine and in 74 of the 8,198 who received dummy shots. That worked out to a 31 percent lower risk of infection for the vaccine group. Two of the infected participants who received the placebo died.

Tomorrow (Sept. 25) the UC Davis Center for Comparative Medicine will host a public symposium marking a quarter-century of California’s response to the AIDS crisis. Speakers will include Nobel laureate Francoise Barré-Sinoussi and Willie Brown, former speaker of the California Assembly and mayor of San Francisco.

One of the symposium organizers, virologist Paul Luciw, said in an e-mail that the results of the new trial were promising and showed that an effective vaccine may eventually be developed.

“This vaccine trial establishes the basis for researchers to use novel immunological methods to enhance on the current combination vaccine and to test other anti-HIV vaccine combinations. Importantly, the individuals in this trial will be very valuable for studies aimed at defining immunological mechanisms of vaccine protection.  There may also be a genetic component to protection that could emerge from further studies on these participants. The promising results of this trial will reinforce the commitment for developing a truly effective and safe anti-HIV by the scientific community, foundations, governments, and commercial enterprises,” Luciw said.

More information about the Sept. 25 event can be found here.

The Planck space telescope has returned its first images of the sky. The mission, run by the European Space Agency with participation from NASA, will map tiny differences in microwave radiation left over from the Big Bang, allowing scientists to get a better picture of the structure of the universe when it was about 400,000 years old.

Lloyd Knox, a physics professor in the UC Davis cosmology group, says that Planck will provide improved data over previous microwave sky surveys such as WMAP. It will have a higher angular resolution, allowing structures to be mapped in finer detail; lower “noise” level and better data on polarization; and better frequency coverage, allowing astronomers to filter out other objects that emit microwaves from the cosmic microwave background.

As part of the overall data analysis effort, Knox is leading the U.S. team that will use data from Planck to draw conclusions about cosmology.

“The primary science driver is understanding cosmic inflation, the very early period when the seeds of the structure of the Universe were created,” Knox says. Planck will allow cosmologists to get a glimpse of the Universe when it was much simpler than it is today, allowing them to test theories about the origins of the universe and develop new ideas.

The probe was launched on a European Ariane rocket on May 14, and is now placed in one of the LaGrange points, a gravitational stable point about 930,000 miles from Earth where it can look out into deep space.

With Planck in position, the astronomers will build up their understanding of the telescope and its capabilities and what they can get from it, Knox said.

More information:

JPL press release

ESA Planck mission home page

JPL Planck mission page

Yesterday’s NY Times has a long, elegant science feature by Carl Zimmer on the evolution of flowers. Prominently quoted is UC Davis botanist James Doyle, who has appointments in both the Department of Evolution and Ecology and the Department of Geology.

UC Davis physicists, biomedical engineers and radiologists have developed a machine that combines two types of body scans to image breast cancer in 3-D. The new machine could be used to develop treatments for breast tumors tailored to the specific patient, by getting a better idea of where tumors lie within the breast tissue.

The scanner combines computed tomography (CT) which uses X-rays to get a 3-D image of body structure, and positron emission tomography, which images physiological process — including distinguishing benign from malignant tumors and what effect chemotherapy is having on tumors.

Initial results with the new machine are published in the Journal of Nuclear Medicine. The researchers now plan to begin clinical trials to test the machine in larger groups of patients.

Press release from UC Davis Health System.

Simon Cherry, a professor of biomedical engineering and one of the team on the new PET/CT machine, has previously developed scanners that can work on laboratory animals, including a combined PET/MRI scanner for use in research.