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.

How antibiotics open door to “bad” gut bacteria: more oxygen

By Carole Gan

Antibiotics are essential for fighting bacterial infection, but they can also make the body more prone to infection and diarrhea. Exactly how do antibiotics foster growth of disease-causing microbes – and how can resident “good” microbes in the gut protect against pathogens, such as Salmonella?

Now research led by Andreas Bäumler, professor of medical immunology and microbiology at UC Davis Health System, has identified the chain of events that occur within the gut lumen of mice after antibiotic treatment that allow “bad” bugs to flourish.

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.

Discovery links Brucella infection, inflammation, chronic diseases

By Carole Gan

Researchers at UC Davis have discovered an unexpected link between how the immune system sounds an alarm when its cells are taken over by pathogens during an infection and how an inflammatory response is triggered.

The finding of this novel link, published in the journal Nature on March 23, is important because it helps researchers understand how a cell senses bacterial or viral infection, and how these pathways are linked to inflammatory diseases, such as inflammatory bowel disease, diabetes and atherosclerosis.

UC Davis entomologists on the trail of virus-carrying mosquito

Aedes aegypti, a daytime-biting mosquito that predominantly feeds on humans, has spread to at least seven counties since June 2013, according to UC Davis medical entomologist Anthony Cornel of the UC Kearney Agricultural Research and Extension Center, Parlier, and the UC Davis Department of Entomology and Nematology.

Aedes aegypti carries yellow fever, Zika and other viruses. (CDC photo)

Aedes aegypti carries yellow fever, Zika and other viruses. (CDC photo)

“It’s an issue of great concern, especially as current control methods do not appear to be working well,” said Cornel, who does research on the mosquito in Clovis, Fresno County, where it was discovered in June 2013. Simultaneously, the insect was found in the cities of Madera and San Mateo.

Hepatitis virus-like particles as potential cancer treatment

UC Davis researchers have developed a way to use the empty shell of a Hepatitis E virus to carry vaccines or drugs into the body. The technique has been tested in rodents as a way to target breast cancer, and is available for commercial licensing through UC Davis Office of Research.

Hepatitis E virus is feco-orally transmitted, so it can survive passing through the digestive system, said Marie Stark, a graduate student working with Professor Holland Cheng in the UC Davis Department of Molecular and Cell Biology.

Symposium honors DNA maintenance pioneer

Some of the world’s leading experts in how DNA is protected and repaired from damage will meet at UC Davis Feb. 12-13 for a symposium in honor of Stephen Kowalczykowski, distinguished professor of microbiology and molecular genetics at the UC Davis College of Biological Sciences. Registration information is available here.

“Genome maintenance” is essential to life, said Frederic Chedin, Professor of Molecular and Cellular Biology, who is co-organizer of the symposium with Professors Wolf-Dietrich Heyer and Neil Hunter, Department of Microbiology and Molecular Genetics. Every second of the day, our DNA sustains damage for example from chemicals, radiation or just natural processes inside the cell. Breaks and lesions in DNA can lead to cancer, disease and developmental defects. Living things, from bacteria to plants to people, have evolved a fundamentally similar set of tools and processes that constantly defend and repair DNA.

UC Davis/Chile research targets muscle disease

Keith Baar’s laboratory in the Department of Neurobiology, Physiology and Behavior is beginning a collaboration on inherited muscle disease with at team at the University of Finis Terrae in Santiago, Chile supported by an anonymous donation to the Chilean university.

The project will focus on disorders related to desmin, a protein within muscle that transmits force, said Baar, associate professor in the College of Biological Sciences.

Keith Baar studies how muscle and connective tissue grow and function.

Keith Baar studies how muscle and connective tissue grow and function.

Muscles that lack desmin due to a genetic defect are unable to transmit force and as a result get injured more easily and over time get more connective tissue, he said.

How antiviral from Hepatitis C could damage other viruses

A new virus-killing peptide springs from an unexpected source: another virus, Hepatitis C.

Now biomedical engineers at UC Davis and Nanyang Technological University, Singapore show how the HCV alpha-helical (AH) peptide can make holes in the types of membranes that surround viruses. The work is published Jan. 5 in Biophysical Journal.

HCV-AH is known to be active against a wide range of viruses including West Nile, dengue, measles and HIV.

The HCV-AH peptide appears to target an Achilles’ heel common to many viruses, most likely a property of the lipid coating or envelope, said study author Atul Parikh, professor of biomedical engineering at UC Davis. That means that it’s less likely that viruses can readily evolve to become resistant to the peptide.

Guided ultrasound plus nanoparticle chemotherapy cures tumors in mice

By Holly Ober

Thermal ablation with magnetic resonance–guided focused ultrasound surgery (MRgFUS)  is a noninvasive technique for treating fibroids and cancer. New research from UC Davis shows that combining the technique with chemotherapy can allow complete destruction of tumors in mice.

MRgFUS combines an ultrasound beam that heats and destroys tissue with a magnetic resonance imaging to guide the beam and monitor the effects of treatment. The effectiveness of the treatment can be limited by the need to spare normal tissue or critical structures on the tumor margins, as well as the need to eliminate micrometastases.