UC Davis scientists explore the microbiome

Today’s White House announcement of the National Microbiome Initiative will bring new funding and attention to better understand the billions of microbes that swarm around in and around us and probably play an important role in our health, food and environment. At UC Davis, many scientists are already exploring this hidden world. Here are a few of them.

Jonathan Eisen is one of the pioneers of studying microbe communities through genetic sequencing. His lab is involved in understanding the complete “Tree of Life,” and projects on microbial communities associated with buildings, as well as communities on different plants and animals, including people, dogs and cats. A prolific blogger, Eisen regularly calls out examples of excessive microbiome hype.

Microbe studies zoom in on effects of HIV in the gut

By Pat Bailey

The curtain cloaking how AIDS and HIV (human immunodeficiency virus) impact the human digestive and immune systems has been drawn back a bit further, thanks to a team of researchers from UC Davis’ departments of Food Science and Technology and Medical Microbiology and Immunology.

The small intestine­ is extremely difficult to study because of its location in the body but plays a critical role in human health. Its inner lining offers both a portal for absorbing nutrients and a barrier against toxins or invasive microbes.

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.

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.

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.

KVIE documentary highlights the latest in genomics, precision medicine

On Wednesday, June 24 KVIE public television will air “A Path to Healing: Genomics and Disease Prevention,” examining how California doctors and patients are using the new science of genomics and DNA sequencing to treat cancer, muscular dystrophy and other diseases. It airs at 7 p.m. on KVIE channel 6.

The documentary features a number of experts from UC Davis including Ralph deVere White, director UC Davis Comprehensive Cancer Center, and Richard Michelmore, director of the UC Davis Genome Center, as well as the stories of patients offered hope by new treatments.

“Chromosome shattering” seen in plants, cancer

Plants can undergo the same extreme “chromosome shattering” seen in some human cancers and developmental syndromes, UC Davis researchers have found. Chromosome shattering, or “chromothripsis,” has until now only been seen in animal cells. A paper on the work is published in the online journal eLife.

The process could be applied in plant breeding as a way to create haploid plants with genetic material from only one parent, said Ek Han Tan, a postdoctoral researcher in the UC Davis Department of Plant Biology and first author on the paper. Although plants don’t get cancer, it might also allow cancer researchers to use the laboratory plant Arabidopsis as a model to study chromosome behavior in cancer.

UC Davis/Mars Inc. team advances to finals of FDA Food Safety Challenge

A team from the UC Davis School of Veterinary Medicine and scientists from Mars, Inc. has been selected as a finalist for the Food and Drug Administration Food Safety Challenge competition. UC Davis and four other finalists will travel to Washington D.C. this summer to participate in a technology “demo day” where the final winner will be selected.

The finalists were selected for potential breakthrough ideas on how to find disease-causing organisms in food – especially Salmonella in fresh, minimally processed produce. The FDA is also looking for solutions that can test for other microbial pathogens in other foods.

Rice can “borrow” stronger immunity from other plant species, study shows

Like most other plants, rice is well equipped with an effective immune system that enables it to detect and fend off disease-causing microbes. But that built-in immunity can be further boosted when the rice plant receives a receptor protein from a completely different plant species, suggests a new study led by UC Davis plant-disease experts.

The study findings, which may help increase health and productivity of rice, the staple food for half of the world’s population, are reported online in the journal PLOS Pathogens.

UC Davis leads new effort in livestock genomics

By Pat Bailey

Scientists and breeders working with poultry and livestock species will get a new set of tools from an international project that includes the University of California, Davis.

The UC Davis team is led by functional genomicist Huaijun Zhou, an associate professor and Chancellor’s Fellow in the Department of Animal Science. The researchers will focus on the genomes of the chicken, cow and pig, which make up the largest meat-producing industries in the United States.

Functional genomics can reveal how DNA controls genes that improve livestock species.

Functional genomics can reveal how DNA controls genes that improve livestock species.