Volume 30 · Number 4 · Summer 2013
News & Notes
Cracking the code of food poisoning
UC Davis, Agilent Technologies and the U.S. Food and Drug Administration are leading an ambitious effort to sequence the genomes of 100,000 infectious microorganisms and speed diagnosis of foodborne illnesses. In this video, Professor Bart Weimer of the UC Davis School of Veterinary Medicine discusses the project. Weimer serves as director of the 100K Genome Project and co-director of the recently established BGI@UC Davis facility.
Striking a blow at foodborne diseases, the 100K Pathogen Genome Project at UC Davis has sequenced the genomes of its first 10 infectious microorganisms, including strains of Salmonella and Listeria — providing the compete collection of their hereditary information.
“We are creating a free, online encyclopedia or reference database of genomes so that during a foodborne disease outbreak, scientists and public health professionals can quickly identify the responsible microorganism and track its source in the food supply using automated information-handling methods,” said Professor Bart Weimer, director of the 100K Genome Project and co-director of BGI@UC Davis, the Sacramento facility where the sequencing is carried out.
Weimer estimates that the availability of this genomic information will cut in half the time necessary to diagnose and treat foodborne illnesses, and will enable scientists to make discoveries that can be used to develop new methods for controlling disease-causing microorganisms in the food chain.
The project is dedicated to sequencing the genomes of 100,000 bacteria and viruses that cause serious foodborne illnesses in people around the world.
In the United States alone, foodborne diseases annually sicken 48 million people and kill 3,000, according to the Centers for Disease Control and Prevention.
The initial 10 genome sequences mark the first in a series that the project will enter into a publicly available database at the National Center for Biotechnology Information of the National Institutes of Health.
“This initial release validates the entire process, from start to finish, of acquiring the bacterium, producing the genome sequence and making automated public releases,” Weimer said.
Weimer said the 100K Genome Project currently is now sequencing a second set of 1,500 microbial genomes, with an anticipated release this fall.
About the 100K Genome Project
The 100K Genome Project was launched in March 2012 as a collaborative effort among UC Davis, Agilent Technologies, and the U.S. Food and Drug Administration. Since then, the U.S. Centers for Disease Control and Prevention, Department of Agriculture, and National Institutes of Health, as well as seven corporate partners, have joined the worldwide effort.
SmartPhones not so smart?
Popular texting, messaging and microblog apps developed for the Android smartphone have security flaws that could expose private information or allow forged fraudulent messages to be posted, according to UC Davis researchers.
Zhendong Su, professor of computer science, said his team has notified the app developers of the problems.
The security flaws were identified by graduate student Dennis (Liang) Xu, who collected about 120,000 free apps from the Android marketplace. The researchers focused initially on the Android platform, which has about a half-billion users worldwide. Android is quite different from Apple’s iOS platform, but there may well be similar problems with iPhone apps, Xu said.
The victim would first have to download a piece of malicious code onto his or her phone. This could be hidden in a useful app, or attached to a “phishing” email or Web link. The malicious code would then invade the vulnerable programs.
The programs were left vulnerable because their developers inadvertently left parts of the code public that should have been locked up, Xu said. “It’s a developer error. This code was intended to be private but they left it public.”
Stilling the adverse effects of stress
Focusing on the present rather than letting the mind drift may help to lower levels of the stress hormone cortisol, suggests new research from the Shamatha Project at UC Davis.
The ability to focus mental resources on the immediate or “here and now” experience is an aspect of mindfulness, which can be improved by meditation training.
“This is the first study to show a direct relation between resting cortisol and scores on any type of mindfulness scale,” said Tonya Jacobs, a postdoctoral researcher at the UC Davis Center for Mind and Brain and first author of a paper describing the work.
High levels of cortisol, a hormone produced by the adrenal gland, are associated with physical or emotional stress. Prolonged release of the hormone contributes to wide-ranging, adverse effects on a number of physiological systems.
The new findings are the latest to come from the Shamatha Project, a comprehensive long-term, control-group study of the effects of meditation training on mind and body.
Led by Clifford Saron, associate research scientist at the Center for Mind and Brain, the Shamatha Project has drawn the attention of both scientists and Buddhist scholars including the Dalai Lama, who has endorsed the project.
A Rockin‘ Teacher
Christopher Reynolds was surprised with a cake shaped like Jimi Hendrix’s classic guitar when it was announced that he had won the 2013 UC Davis Prize for Undergraduate Teaching and Scholarly Achievement.
Peek inside the office of music professor Christopher Reynolds, and you’ll see the expected — rows and rows of books, stacks of sheet music and a sketch of Beethoven on the wall.
But take a few more steps inside and you bump into a life-size cardboard cutout of Elvis clad in a shimmering gold suit, a gift from a co-worker. To talk to Reynolds for a few minutes is to learn his favorite musician of all time is the late, great guitarist Jimi Hendrix, with the band Led Zeppelin coming in a close second. “I could do a whole quarter on Zeppelin,” said the musicologist, who has taught on campus since 1985.
In fact, he plans to teach “a whole quarter” next year on a different British import — the Beatles.
His teaching abilities, punctuated with enthusiasm for all his subject matter — a vast breadth of music from Renaissance to rock — were recognized in March when he was chosen for the 2013 UC Davis Prize for Undergraduate Teaching and Scholarly Achievement.
Established in 1986, the prize was created to honor faculty who are both exceptional teachers and scholars. The $45,000 prize is believed to be the largest of its kind in the country and is funded through philanthropic gifts managed by the UC Davis Foundation. The winner is selected based on the nominations of other professors, research peers, representatives from the UC Davis Foundation Board of Trustees, and students.
Reynolds said teaching rock ‘n’ roll to 150 students, most of them nonmusicians, poses unique challenges.
“When I’m teaching Beethoven, I’m the expert. It’s new to them. In rock ‘n’ roll, every group of students that I teach is going to have some knowledge of what I’m teaching. I’m teaching fans, some of them really knowledgeable fans.”
Kabang returns home
Thronged by the news media and well-wishers, Kabang, the hero dog from the Philippines, was officially released from the UC Davis Veterinary Medical Teaching Hospital in June and cleared to return to her family.
The diminutive shepherd-mix is credited with saving two young girls from an oncoming motorcycle in the Philippines. Struck by the motorcycle in December 2011, Kabang lost her snout and upper jaw and was left with a horrendous gaping wound on her face.
Her remarkable survival captured the attention of the news media in the Philippines and eventually the hearts of hundreds of people around the world, who provided funds through the private organization Care for Kabang for her nearly eight months of treatments.
The dog was brought to UC Davis in October 2012, but university veterinarians discovered that she also had heartworm disease and a type of infectious cancer, known as a transmissible venereal tumor. Treatment for both of these health problems was necessary before dental and surgical procedures could be performed to deal with her facial wound.
A team of UC Davis veterinarians — specialists in oncology, infectious diseases, dental, oral and soft-tissue surgery, internal medicine and outpatient care — was quickly formed to coordinate Kabang’s multitreatment care. Because of the nature of Kabang’s health problems, each treatment had to be successfully completed before the next began.
On the scent of Dog evolution
Part of the ancient mystery behind the modern Western dog’s genetic makeup has been solved by researchers at the School of Veterinary Medicine.
Several thousand years after dogs originated in the Middle East and Europe, some of them moved south with ancient farmers, distancing themselves from native wolf populations and developing a distinct genetic profile that is now reflected in today’s canines.
These findings, based on the rate of genetic marker mutations in the dog’s Y chromosome, supply the missing piece to the puzzle of when ancient dogs expanded from Southeast Asia.
“Our findings reconcile more than a decade of apparently contradictory archaeological and genetic findings on the geographic origins of the dogs,” said Ben Sacks, lead study author and director of the Canid Diversity and Conservation Group in the Veterinary Genetics Laboratory at the School of Veterinary Medicine.
Considerable archaeological evidence indicates that the first dogs appeared about 14,000 years ago in Europe and the Middle East, while dogs did not appear in Southeast Asia until about 7,000 years later. Scientists have been puzzled, though, because growing genetic evidence suggests that modern Western dogs, including modern European dogs, are derived from a Southeast Asian population of dogs that spread throughout the world.
The problem: If dogs originated in Europe, why does genetic evidence suggest that modern European dogs are originally from Southeast Asia? Sacks and his team think they’ve found the answer.
“While dogs in other parts of Eurasia continued to readily interbreed with wolves, the dogs that moved into Southeast Asia no longer lived near wolves, and so they developed a totally different evolutionary trajectory, influenced by the agriculture of Southeast Asia,” he said.
“Those ancient dogs apparently underwent a significant evolutionary transformation in southern China that enabled them to demographically dominate and largely replace earlier Western forms.”
Native fish dwindling
Salmon and other native freshwater fish in California are likely to become extinct within the next century due to climate change if current trends continue, ceding their habitats to nonnative fish, according to scientists from the UC Davis Center for Watershed Sciences.
The study, published online in May in the online journal PLOS ONE, assessed how vulnerable each freshwater species in California is to climate change and estimated the likelihood that those species would become extinct in 100 years.
The researchers found that, of 121 native fish species, 82 percent are likely to be driven to extinction or very low numbers as climate change speeds the decline of already depleted populations. In contrast, only 19 percent of the 50 nonnative fish species in the state face a similar risk of extinction.
“If present trends continue, much of the unique California fish fauna will disappear and be replaced by alien fishes, such as carp, largemouth bass, fathead minnows and green sunfish,” said Peter Moyle, a professor of fish biology who has been documenting the biology and status of California fish for the past 40 years.