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Foodborne illnesses and the 100K Genome Project

Bart Weimer
An ambitious effort to sequence the genomes of 100,000 infectious microorganisms and speed diagnosis of foodborne illnesses has been launched by the University of California, Davis, Agilent Technologies, and the U.S. Food and Drug Administration.

Bart Weimer, professor in the UC Davis School of Veterinary Medicine, serves as director of the 100K Genome Project and co-director of the recently established BGI@UC Davis facility, where the sequencing will be done. Other collaborators include the U.S. Centers for Disease Control and Prevention and the U.S. Department of Agriculture.

The new five-year microbial pathogen project focuses on making the food supply safer for consumers. The group will build a free, public database including sequence information for each pathogen's genome — the complete collection of its hereditary information. The database will contain the genomes of important foodborne pathogens including Salmonella, Listeria, and E. coli, as well as the most common foodborne and waterborne viruses that sicken people and animals.

The project will provide a roadmap for developing tests to identify pathogens and help trace their origins more quickly. The new genome database also will enable scientists to make discoveries that can be used to develop new methods for controlling disease-causing bacteria in the food chain.

"This landmark project will revolutionize our basic understanding of these disease-causing microorganisms," said Harris Lewin, vice chancellor for research at UC Davis.

The sequencing project is critically important for tackling the continuing outbreaks of often-deadly foodborne diseases around the world. In the United States alone, foodborne diseases annually sicken 48 million people and kill 3,000, according to the CDC.

"The lack of information about food-related bacterial genomes is hindering the research community's ability to improve the safety and security of the world food supply," Weimer said.  "The data provided by the 100K Genome Project will make diagnostic tests quicker, more reliable, more accurate and more cost-effective."

"We see this project as a way to improve quality of life for a great many people, while minimizing a major business risk for food producers and distributors," said Mike McMullen, president of Agilent’s Chemical Analysis Group.

A consumer-focused article about the project is available on the FDA website.

(This article was condensed from a UC Davis news release. Read the full press release and watch a video of Bart Weimer giving an overview of the project.)

Posted on Thursday, July 26, 2012 at 9:20 AM

Adding variety: avocados and guacamole

anr avocado99 650x433
I have limited cooking skills, so I’m lucky that my wife is a great cook and an even better baker – lemon bars, anyone?

But there’s one dish she prefers that I prepare: guacamole. I was thinking about this when I was reviewing our recent photo shoot at UC ANR’s South Coast Research and Extension Center in Irvine, which included images of strawberries, citrus and avocados.

Avocados from South Coast Research and Extension Center (above and top images by Elena Zhukova)
UC’s nine research and extension centers support about 350 research projects, including avocado studies at South Coast. UC’s research is critical to keeping California’s $460 million avocado industry competitive. While California produces about 90 percent of the nation’s avocado crop, the market faces increasing global pressure from countries such as Mexico, Chile and Peru.

“Our whole goal is to make the industry in California more sustainable,” said UC Cooperative Extension specialist Mary Lu Arpaia, in the Department of Botany and Plant Sciences at UC Riverside.

Arpaia leads UC’s efforts to develop new avocado varieties. The dominant variety, Hass, started in 1926 in Southern California and has become so common globally that it could become generic, Arpaia said.

“My belief is the way we’re going to differentiate ourselves as a California industry and survive is by breeding something unique,” Arpaia said.

UC Riverside has developed several avocado varieties, signing a license agreement last year for its latest release, GEM. The great-granddaughter of the Hass avocado, GEM shares Hass’ desired characteristics such as a creamy, nutty flesh while offering growers additional benefits such as being a smaller tree that typically is more productive, Arpaia said.

Arpaia is evaluating more varieties. The next potential release is likely two to three years away, she said.

Meanwhile, Arpaia also is collaborating with the U.S. Department of Agriculture to improve the postharvest quality of avocados – how packing houses and distribution centers should handle the fruit, for how long and at what temperature.

“People definitely like fruit that is creamy, smooth, nutty and buttery. They like fruit that has a pleasant aftertaste,” said Arpaia, who conducts monthly avocado tasting panels at UC Riverside.

Packed with nearly 20 nutrients including potassium, avocados are an appetizing addition to salads and sandwiches. Arpaia likes them sliced, eaten alone, in a salad or on a warm corn tortilla. Some like them sweet in cheesecake or milkshakes. Of course, they’re best known as the base ingredient in guacamole.

I keep my guacamole simple: avocados (three), white onion (one-third), Roma tomatoes (three), lime (one), cilantro and salt. I start by scooping out the avocado pulp, slicing it into medium chunks and putting it in a bowl, mixing in lime juice. Then I dice the onion and tomatoes (seeded) into fine pieces and toss them in the bowl, followed by chopped cilantro. Next, I mash it up with a spoon, sprinkling on some salt and more lime juice. Test it and then serve.

For a spicier version, add garlic, jalapeños or serranos. The possibilities are plentiful. Just make sure you start with ripe avocados. What’s your favorite guacamole recipe?

Posted on Tuesday, July 24, 2012 at 8:22 AM
  • Author: Alec Rosenberg

Students play key role in building community around sustainable food systems

On an unusually cool July morning at the UC Davis Student Farm, students are harvesting tomatoes and other produce for the farm’s Community Supported Agriculture (CSA) membership program. The CSA baskets are pre-sold to members of the campus community and are among the ways students participate in the campus food system.

“It’s more than a way to sell food. It builds community, and that’s a powerful thing for students to learn,” said Raoul Adamchak, who coordinates the CSA and the Market Garden where the produce is grown.

Over the years, those involved in UC campuses’ food systems have garnered powerful lessons from students as well, resulting in organic gardens, student farms and increasingly sustainable food options at dining halls. These student-initiated components of campus food systems continue to nurture student opportunities to learn and get involved.

While the Student Farm has run its CSA for 16 years, the farm has been a part of the campus food system for 30 years by selling fresh organic produce to the UC Davis Coffee House, which is run by Associated Students, UC Davis. Most recently, it began selling produce to Sodexo-run UC Davis Dining Services – further diversifying its customer base.

“When Dining Services initially wanted to buy from us, we were hesitant,” said Mark Van Horn, director of the Student Farm. “Our CSA was well established and is still our highest grossing market. We’re at the upper limits of production and didn’t think we could grow more without negatively effecting education – the primary purpose of the farm. What changed our minds is that we realized our relationship with them is about education as well as production. We’re collaborating with Dining Services to educate students – more students than ever – about the entire food system.”

Dining Services also serves a key audience – incoming undergraduates and potential interns for the Student Farm, Russell Ranch at UC Davis and other programs that contribute to the campus food system.

“We’re trying to engage students in the food system so they can learn about where their food comes from and what’s in it,” said Dani Lee, UC Davis University Dining Services’ sustainability manager.

Dining Services labels the origin of campus-produced food. It regularly hosts outreach events, features displays about and organizes tours of the Student Farm, Russell Ranch and other campus-based partners. It has also established internships for students interested in waste reduction, gardening and sourcing food more locally.

Lee and Van Horn hope these efforts will help inspire students to learn more.

“We’re seeing more interest from students today than ever before,” Van Horn said. “I attribute it to a bigger cultural awakening catalyzed by folks like Michael Pollan and Eric Schlosser. They figured out that if you talk about agriculture, the environment and the whole food system just as ‘food,’ it’s more interesting. Students are coming in with more knowledge and commitment to these issues than ever before. Encouraging them to get actively involved in the food system is a great way to nurture what students years ago began when they founded the Student Farm, started the Coffee House, and got University of California administrators to commit to meeting a list of sustainability criteria by 2020.”

UC Davis Dining Services already exceeds the UC goal of 20 percent sustainably produced food by 2020, but it isn’t stopping there.

“We’re constantly working on sourcing more products locally,” Lee said.

Lauren Cockrell, a fourth-year UC Davis student majoring in Sustainable Agriculture and Food Systems is pleased with the trajectory and believes ensuring student involvement in the effort to build a more sustainable food system is key.

“I’d like the next step to be an independent, entirely student-run food retail business that, at its core, values sustainability,” she said.

Posted on Friday, July 20, 2012 at 9:02 AM
  • Author: Eve Hightower

Looking to Darwin to understand soy

Soy is now everywhere in the American diet. Tofu has become a more mainstream ingredient, soy milk crowds dairy cases, and soy fillers and additives can be found in processed foods from soups to meat and vegi-burgers to flavorings like cheese powders. The ubiquitous bean’s high levels of estrogen-mimicking compounds, called phytoestrogens, have long been a topic of scientific study and the nation’s ongoing conversation about nutrition and health. Does eating soy impact our sexual development? Harm women’s reproductive health? Minimize the symptoms of menopause? In a confusing matrix of news reports over the past decade, it’s been reported to both encourage some cancers and protect against others.

Red colobus monkey eating the bark of a eucalyptus tree, a non-native estrogenic species that was planted as a source of fuel wood in Kibale National Park. Photo: Julie Kearney Wasserman
A recent study looks to our biological cousins, non-human primates, for answers.

“Despite great interest in the effects of phytoestrogens on humans and livestock, very little is known about how often estrogenic plants are consumed by our closest-living relatives, so I decided to begin screening the important plant foods of various wild primate species for estrogenic activity,” said Michael Wasserman, a postdoctoral scholar in the Department of Anthropology at McGill University and lead author of the study, who conducted the research while completing his Ph.D. in UC Berkeley’s Department of Environmental Science, Policy, and Management.

Working in lab of Dale Leitman, an adjunct professor in UC Berkeley’s Department of Nutritional Sciences and Toxicology, Wasserman measured the presence of phytoestrogens in the diets of two leaf-eating primate species from Uganda and found that both species routinely consumed estrogenic plants as part of the staple foods in their diets. The red colobus monkey of Kibale National Park consumed more than 10 percent of its diet in estrogenic plants, and in mountain gorilla of Bwindi Impenetrable National Park, studied by his co-author Jessica Rothman, an assistant professor of primate ecology at Hunter College, estrogenic plants comprised nearly 9 percent of the animals’ total diet.

Wasserman is now looking into how these plants affect the red colobus’s endocrine system, which, like ours, regulates many physiological processes and behaviors. He is also measuring the presence of phytoestrogens in the diets of fruit-eating primates, like the chimpanzee, which should yield more information about the relationship between these animals and plants.

As his findings grow, Wasserman hopes the research will shed light on how long humans have been eating estrogenic plant foods over our evolutionary history.

“Throughout most of human history we have lived as hunter-gatherers, consuming large amounts of wild plant foods, especially fruits, and our biology has changed little since these pre-agricultural times,” he said.

By studying chimpanzees, gorillas, and other wild primates that also depend on wild plant foods to meet their nutritional needs, Wasserman hopes to help clarify the importance of dietary niche (fruit- vs. leaf-eater) and phylogeny (ape vs. monkey) to phytoestrogen exposure.

“If it is only the leaf-eaters consuming these plants, then eating foods like soy may be a relatively new trend for us," Wasserman said. "If fruit-eating apes consume estrogenic plants, we have probably been consuming phytoestrogens for millions of years.”

The study is published in the May issue of the American Journal of Physical Anthropology.

Posted on Tuesday, July 17, 2012 at 9:21 AM
  • Author: Ann Brody Guy

Could you please pass me the bug kabobs?

Possibly, people could be divided into the following two groups: those who knowingly eat insects, and those who think they have never eaten them. Since I am still assailed by the odd nightmare in which I am bringing to my lips a well-cooked bug that suddenly springs to life, I decided to tackle my bug-food phobia by visiting entomologist Douglas Yanega of UC Riverside last week.

Yanega has eaten insects, even relished them. With no difficulty whatsoever he has ingested honey bees, termites, mealworms, crickets, grasshoppers, ants, June beetles, silkworms and even scorpions.

Douglas Yanega is the senior museum scientist in the Entomology Research Museum at UC Riverside. He is seen here holding a water bug, an edible insect.
“These admittedly were not very tasty,” said Yanega, who is the senior museum scientist in the Entomology Research Museum, where he studies, identifies and catalogs insects. “In Thailand, however, I had queen weaver ants — a gourmet food there that tastes like either peanut butter or lemon, depending on which body part you’ve sunk your teeth into — and deep-fried mole crickets. Both were delicious!”

Eating insects is not unusual in Thailand, Yanega explained.  Insects, a good source of highly digestible protein, are part of the diet in Korea, China and Mexico as well. 

“You get more bang for the buck when you eat insects, where protein is concerned,” Yanega said. “True, the outer hardened shell is often not digestible, but the softer, internal tissues are. Of course, you want to avoid toxic insects. There are some that could kill you if you ate them.”

How does one know if an insect is toxic? In general, herbivorous insects tend to be more edible. Moreover, insects have evolved to alert other critters — and us! — that they are not suitable for consumption. Bright colors like red, orange or yellow juxtaposed with black on insect bodies are a sure warning from insects that you’d better stay away.

Photo shows monarch butterflies in the Entomology Research Museum at UC Riverside. It is not safe to eat monarch butterflies.
“Think of monarch butterflies, ladybird beetles, tiger moths. You never want to eat them,” Yanega said. “Some tiger moths will even make a noise to warn you to stay away. Other bugs will defensively ooze nasty secretions in your mouth, the moment you bite, to force you to spit them out and free them.”

Because few people experiment with eating insects, identifying those that are both edible and delicious can be a big challenge.

“You have, in the middle of the bell curve of insects, a whole lot that are edible but taste awful,” Yanega said. “And there are those at one end of the curve that are just toxic. But at the other end of this curve lie the prized ones: these are edible and tasty.”

In the United States, most people are culturally still averse to eating insects. If you travel to Mexico, however, you might eat stinkbugs, sometimes used to flavor food. Farther off, in Japan, you could enjoy wasp grubs and silkworm larvae. In the mainland parts of Southeast Asia, you can savor giant water bugs and mole crickets. 

Photo shows water bugs stored in the Entomology Research Museum at UC Riverside. Water bugs are edible.
“In Laos, they eat just about any available insect,” Yanega said. “Some insects are eaten raw, sometimes with small parts removed. Other insects are served deep fried or grilled.”

According to Yanega, one way to get introduced to an entomological diet is to first dry out insects, and then grind them up to a powder.

“You can use this powder as a supplement,” he said. “It’s the easiest way to go about eating insects as food. You can mix the powder into, say, wheat flour to get 'insect-enriched flour.'

If you’re cringing, rest assured that most of us already eat insects unknowingly. Much of food coloring uses insects. The waxy coloring that coats candies is oftentimes insect-based. And a lot of fresh produce has a built-in level of “insect contamination.”

“As long as you are not allergic to an edible insect, you’re safe eating it,” Yanega said. “If you can get past your phobia or stigma of putting bugs in your mouth, you should have no difficulty in adding insects to your diet.” 

Which is what most of us would have to do if we found ourselves stranded on an island and famished.

“Should that happen, never mind the brightly colored bugs,” Yanega said. “Instead, go after the ones that are cryptically colored, the ones that look as though they are hiding from something. They would be a much better bet.”

Posted on Thursday, July 12, 2012 at 8:45 AM

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