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Egghead is a blog about research by, with or related to UC Davis. Comments on posts are welcome, as are tips and suggestions for posts. General feedback may be sent to Andy Fell. This blog is created and maintained by UC Davis University Communications, and mostly edited by Andy Fell.

Brown pelicans released following Refugio oil spill

By Kat Kerlin

Rehabilitated pelicans once covered in oil from last month’s Refugio oil spill in Santa Barbara County were released today (June 12) at Goleta Beach.

Video: Rehabilitated pelicans returned into wild (LA Times)

Wildlife responders from the UC Davis Oiled Wildlife Care Network and California Department of Fish and Wildlife’s Office of Spill Prevention and Response (OSPR) placed satellite tracking devices on 12 brown pelicans affected by the spill.

Study to track rehabilitated birds’ survival

The devices will help researchers learn more about the survival rates of birds affected by oil spills and to see if they return to normal behaviors. Eight additional pelicans will be outfitted with the devices to serve as controls.

Twelve brown pelicans rehabilitated following the Refugio oil spill are being fitted with tracking backpacks before going back to the wild. Credit: Justin Cox/UC Davis

Twelve brown pelicans rehabilitated following the Refugio oil spill are being fitted with tracking backpacks before going back to the wild. Credit: Justin Cox/UC Davis

The solar-powered tracking devices each weigh 65 grams, about the weight of a “C” size battery, and are worn by the birds like a small backpack—with one loop in front of the wing, another behind the wing and two loops connected by Teflon ribbon under the bird’s body. The device allows pelicans to dive for fish with minimal disruption.

Track records

Researchers tracked oiled birds following the American Trader oil spill off Huntington Beach in 1990, but this study will use more advanced technology and newer rehabilitation methods. OWCN and OSPR are working with collaborators who have successfully tagged and tracked close to 100 brown pelicans after the Deepwater Horizon spill.

The oiled pelicans released today were recovered and cleaned after the spill in May and have been rehabilitating at the Los Angeles Oiled Bird Care and Education Center in the weeks since.

Other collaborators in the project include the U.S. Geological Survey, Clemson University, Humboldt State University’s Wildlife Department, U.S. Fish and Wildlife Service, and International Bird Rescue.

The study is being funded by the UC Davis Oiled Wildlife Care Network, which is based at the Karen C. Drayer Wildlife Health Center and the UC Davis School of Veterinary Medicine, and by OSPR.

More information

For updates on animals and birds rescued from the oil spill, follow the OWCN blog.

UC Davis Today: Wildlife experience the high price of oil (with video)

“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.

Chromothripsis involves slicing chromosomes into apparently random pieces, and reassembling it like a broken vase, often with pieces completely missing or in the wrong place. Generally speaking, this is not a good thing, although in one recently published case a woman was cured of a genetic disorder when the gene responsible was lost due to chromothripsis.

Han Tan, Professor Luca Comai and colleagues were studying centromeres, the handles by which chromosomes are moved and allocated to daughter cells during cell division. They discovered that when a variant of the model plant Arabidopsis with weakened centromeres is crossed to a plant with normal centromeres, the resulting embryos undergo chromothripsis, the cut-and-reassembly process leading to “shattered chromosomes.”

Other authors on the study were: At UC Davis, Isabelle Henry, Keith Bradnam, Mohan Marimuthu and Ian Korf; Martin Lysak and Terezie Mandakova, Masaryk University, Czech Republic; and Maruthachalam Ravi, formerly at UC Davis and now at the Indian Institute of Science Education and Research, Thiruvananthapuram, India. The work began under the guidance of the late Simon Chan at UC Davis and was supported by the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation.

Death in the tide pools: Rapid die-off of urchins and sea stars a grim warning of climate change

By Kat Kerlin

In August 2011, scientists at the UC Davis Bodega Marine Laboratory walked into their labs to a strange, disturbing sight: Thousands of purple sea urchins and other marine invertebrates were dead in their tanks, which are fed directly by seawater. Outside, the tea-colored ocean washed up carcasses of red abalone, large sea stars, and football-sized, snail-like chitons.

Less conspicuous—but even more heavily impacted as a population—were the millions of purple sea urchins and tiny sea stars that died along a 62-mile stretch of coast in Northern California, according to a UC Davis-led study published in the journal PLOS ONE that documents the die-off.

“We might not have known urchins and six-armed sea stars were affected if lab-held animals hadn’t died right in front of us,” said the study’s lead author Laura Jurgens, a graduate student at UC Davis Bodega Marine Laboratory who earned her doctorate in May.

Long-term consequences

The scientists documented almost 100 percent mortality of purple sea urchins and six-armed sea stars over the study area, which stretched from southern Mendocino County to Bodega Bay in Sonoma County. Intertidal zones that once looked like pools of purple held only burrows in the bedrock—telltale markers that purple sea urchins were once there. Only 10 purple urchins were found in an area once home to millions of them.

Tidepools before (left) and after (right) the 2011 die off. Only burrows in the rock remained. Laura Jurgens/UC Davis Bodega Marine Laboratory

Tidepools before (left) and after (right) the 2011 die off. Only burrows in the rock remained. Laura Jurgens/UC Davis Bodega Marine Laboratory

The disappearance of these species to the area suggests long-term population and ecosystem consequences, the study said.

“We’re expecting real ecological changes in how these tide pools operate,” Jurgens said.

The silver-dollar-sized, six-armed sea star is a key tide-pool predator, and purple sea urchins serve as cleanup crews and recyclers for kelp detritus that washes ashore, processing the kelp into nutrients. Purple sea urchins also provide food for shorebirds and some mammals living along the coast.

 Algal bloom likely culprit

Unlike sea star wasting syndrome, a disease that has progressed over years as sea stars literally waste away, this die-off was fast, wiping out these two species in as little as a few days. The die-off also occurred about two years before recent incidences of sea star wasting syndrome were observed along the West Coast.

Six-armed sea stars like this one experienced almost 100 percent mortality across a 62-mile stretch of coast in Northern California in 2011. Credit: Laura Jurgens/UC Davis Bodega Marine Laboratory

Six-armed sea stars like this one experienced almost 100 percent mortality across a 62-mile stretch of coast in Northern California in 2011. Credit: Laura Jurgens/UC Davis Bodega Marine Laboratory

Instead, the study said the mass mortality was likely caused by a harmful algal bloom. Such blooms are expected to occur more often due to the combination of global warming, ocean acidification, and land-use changes.

Jurgens said that is all the more reason why documenting such mass mortality events is important to better understand — and prepare for –trends happening to ocean ecosystems.

‘We might forget’

Purple sea urchins have begun to recolonize the area. But it might be decades before the more home-bodied six-armed sea stars return to the area, since their babies can only crawl small distances away from their mothers. Males and females would need to arrive on floating debris to begin to repopulate the species here, which Jurgens said is unlikely to happen very often.

“If someone were to come to this area, they wouldn’t know these six-armed sea stars existed here, even though this has been a main part of their species range,” Jurgens said. “If something disappears and we don’t document it, we might not ever know it was there, and we might forget.”

Study support

The study was primarily funded by the National Science Foundation. It also received financial support from the Monitoring Enterprise, California Ocean Sciences Trust, Partnership for Interdisciplinary Studies of Coastal Oceans, the David and Lucile Packard Foundation and the California Department of Fish and Wildlife.

Co-authors from UC Davis Bodega Marine Laboratory and the UC Davis Coastal Marine Sciences Institute include evolution and ecology professors Brian Gaylord and Rick Grosberg, as well as Laura Rogers-Bennett from BML, UC Davis Wildlife Health Center, and the California Department of Fish and Wildlife. Other co-authors include UC Santa Cruz professor Peter Raimondi, and graduate student Lauren Schiebelhut and associate professor Michael Dawson from UC Merced.

More information:

Read the study:

Understanding how cells follow electric fields

Many living things can respond to electric fields, either moving or using them to detect prey or enemies. Weak electric fields may be important growth and development, and in wound healing: it’s known that one of the signals that guides cells into a wound to repair it is a disturbance in the normal electric field between tissues. This ability to move in response to an electric field is called galvanotaxis or electrotaxis.

UC Davis dermatology professor Min Zhao, Peter Devroetes at Johns Hopkins University and colleagues hope to unravel how these responses work, studying both body cells and Dictyostelium discoideum, an amoeba that lives in soil. Dictyostelium is unusual because it spends part of its life crawling around as a single-cell amoeba, but occasionally multiple amoebae will come together to form a fruiting body.

In a paper just published in the journal Science Signaling, Zhao and colleagues screened Dictyostelium for genes that affect electrotaxis. They used special barcoded microplates developed by Tingrui Pan, professor of biomedical engineering at UC Davis to screen hundreds of amoeba strains.

The team identified a number of genes, including one called PiaA, which encodes a critical component of a pathway controlling motility. Other genes associated with electrotaxis in Dictyostelium were also linked to the same pathway.

Video: Amoeba crawling in an electric field

Right now, no one nows how cells detect these very weak electric fields, Zhao said. The screening technique could be used to identify more genes linked to electrotaxis and help researchers piece together exactly how electrical signals are detected and turned into action.

Audio: Min Zhao and Peter Devroetes talk about the work in this Science podcast

Coauthors on the paper include biologists, engineers and mathematicians. They are: at UC Davis, Runchi Gao, Siwei Zhao, Yaohui Sun, Sanjun Zhao, Jing Gao, and Alex Mogilner; Jane Borleis, Stacey Willard, Ming Tang, Huaqing Cai, and Yoichiro Kamimura at Johns Hopkins University; Yuesheng Huang, Jianxin Jiang, Xupin Jiangat the State Key Laboratory of Trauma, Burns and Combined Injury, Third Military Medical University, Chongqing, China; and Zunxi Huang, Yunnan Normal University, Kunming, China.

The work was supported by the National Science Foundation (U.S.), the California Institute for Regenerative Medicine, National Institutes of Health, the National Science Foundation of China and the Wellcome Trust.

Previously: Cells and cell fragments move oppositely in electric fields


Help fund koala microbiome study

The koala might be the world’s cutest animal. It also has a strange and toxic diet, and koalas are threatened by chlamydia, a sexually transmitted disease. How are these things related?

Koalas live on eucalyptus leaves, which are so full of tannins that they are toxic to most animals. Koalas deal with this by having a special brew of bacteria in their gut that can digest the tannins in eucalyptus leaves. Baby koalas (joeys) acquire these microbes from their mothers by eating a special form of nutrient-rich feces, called “pap,” for the first two months after they wean from breast milk.

Could antibiotic treatment, given to cure koalas of chlamydia, affect their gut microbes? UC Davis graduate student Katie Dahlhausen plans to find out, working with Jonathan Eisen at the UC Davis Genome Center and Adam Polkinghorne at the University of the Sunshine Coast, Australia.

Dahlhausen is currently fundraising for the project through Indiegogo. Check out her project page and video.

Bugs and slugs ideal houseguests for seagrass health

By Kat Kerlin

Marine “bugs and slugs” make ideal houseguests for valuable seagrass ecosystems. They gobble up algae that could smother the seagrass, keeping the habitat clean and healthy. That’s according to results from an unprecedented experiment spanning the Northern Hemisphere and led by an international team of scientists, including marine biologists from UC Davis.

The study, led by the Virginia Institute of Marine Science, was conducted simultaneously at 15 sites across seven countries through a project called the Zostera Experimental Network, or ZEN, after the seagrass species Zostera marina.

“Our results show that small marine invertebrates are really important,” said Pamela Reynolds, a postdoctoral scholar at UC Davis and VIMS and the ZEN project coordinator.

Invertebrates like this isopod keep seagrass clean and healthy. (Pamela Reynolds)

Invertebrates like this isopod keep seagrass clean and healthy. (Pamela Reynolds)

“They graze down seaweeds that might otherwise smother the seagrass. It’s a really neat partnership — the animals get a home, and the seagrass stays clean. We found that the more diverse communities of these little algae-eating animals do a better job of keeping the seagrass clean and healthy.”

Reynolds said the results support that comprehensive coastal management should consider how to maintain robust populations of animals in addition to managing for the more conspicuous effects of pollution and disturbance.

Seagrasses declining

Seagrass meadows provide valuable fish nurseries and feeding grounds for birds, sea turtles and manatees. They sequester carbon, and their root systems help bind and protect coastlines. Yet, they are declining worldwide due to host of factors.

The researchers explored which of two known threats to seagrass has the greater impact on seagrass ecosystems: pollution from fertilizers or the loss of invertebrate species due, in part, to fishing.

The importance of biodiversity

To simulate nutrient pollution, the team members fertilized the seagrass similarly to how one would a lawn. Then they drove away small crustacean grazers by applying a chemical deterrent, simulating changes in the food web from fishing. On average, removing the grazers produced more algae than adding the fertilizer. Researchers at work in North Carolina.

“Our results provide rare large-scale confirmation of the importance of biodiversity to healthy ecosystems,” said Emmett Duffy, the study’s lead author and director of the Smithsonian’s Tennenbaum Marine Observatories Network. “It’s widely understood that controlling algal overgrowth of seagrasses requires reducing fertilizer runoff, but it turns out that maintaining diverse populations of the bugs and slugs that clean these underwater plants is just as important.”

Everything ZEN

The ZEN project is now in its second generation and has expanded to 25 institutions and more than 50 research sites from the Russian Arctic to Mexico and South Korea. Ongoing work by this collaborative team of more than 200 scientists and students seeks to understand how the diversity of seagrass animals and plants contributes to fish production, carbon storage and other ecosystem services.

“Honestly, its a new way of doing science for many of us,” said Jay Stachowicz, professor of Evolution and Ecology at UC Davis. “Ceding control of our experiments and data collection is hard for many of us who were trained to be fiercely independent. But the payoff is this kind of surprising result that none of us could have obtained on our own and a built-in consensus because we were all involved in each phase of the project.”

The study was published in Ecology Letters and supported by grants from the National Science Foundation and local support from the 15 partner institutions.

Wave machine links microbes and sea spray to clouds and climate

How do you catch a wave upon the sand? Put it in a machine.

By Kat Kerlin

In a wooden building overlooking the Pacific Ocean, 3,800 gallons of seawater are emptied into a long, clear, covered tank — a wave machine. On one side of the 33-meter-long flume is a mechanical paddle, working like a kid in a bathtub to push water forward. The water builds into a wave that breaks on the machine’s “beach,” a board representing the coastline. As the broken wave falls, bubbles burst, producing sea spray particles that are sucked up into sampling tubes.

Analyzing these particles has allowed a team of scientists led by UC San Diego and including UC Davis to gain insights into how microbes in ocean water control the ability of sea spray droplets to serve as “seeds” for clouds.

The wave machine at the Scripps Institute of Oceanography is being used to study how ocean microbes influence climate. Credit: Christina McCluskey

The wave machine at the Scripps Institute of Oceanography is being used to study how ocean microbes influence climate. Credit: Christina McCluskey

The work, described in the journal ACS Central Science, also demonstrates how changes in the ocean can influence changes in the sky. The research is expected to help researchers build better climate models.

Sea spray is composed of bubbles of ocean water carrying sea salt, bacteria, viruses, and complex organics like proteins, fats, and sugars.

“When you change that composition, you start to change the ability of these particles to take up water and grow into cloud droplets,” said Chris Cappa, an associate professor in the UC Davis Department of Civil and Environmental Engineering, who was among the group of scientists collaborating on this work, a project of the Center for Aerosol Impacts on Climate and the Environment.


Microbes and sea spray

The research team used the wave machine at UCSD’s Scripps Institution of Oceanography to recreate a phytoplankton bloom on a large experimental scale. What does phytoplankton have to do with sea spray? Lots.

The phytoplankton itself does not end up in sea spray. However, as it grows and dies, it produces molecules that can become part of the sea spray droplets when waves break, a process that was previously poorly understood. The study found that a critical factor that controls the concentration of these molecules in sea water is their destruction by ocean microbes, This in turn affects the chemical composition of sea spray particles and helps determine how and if the particles can act as cloud seeds.

“It’s this combination of production and destruction of these key molecules that ultimately determines the influence of sea spray particles on clouds and global climate,” Cappa said.

Lead author and CAICE director Kimberly Prather, a UC San Diego chemistry professor, said the study has provided a new understanding of the importance of how microbes in seawater control the cloud-forming ability of sea spray aerosol. (Watch a related webinar by Prather discussing aerosol chemistry and climate).

The study received funding from the National Science Foundation through the Centers for Chemical Innovation program.

Milk contributes $21 billion to California’s economy

Milk is California’s top agricultural commodity, and California is the biggest dairy state with an astonishing $9.4 billion of milk sold last year, according to a new report from the California Milk Advisory Board. The dairy industry contributed approximately $21 billion in value added to California’s gross state product in 2014, according to the study conducted by the University of California Agricultural Issues Center (AIC) at UC Davis. Including sales of inputs to dairy farms and milk processors along with raw milk and wholesale milk product sales, the dairy industry contributed $65 billion in total sales to the California economy in 2014. The growing demand for dairy products like cheese and yogurt as well as strong dairy exports accounted for 189,000 jobs that are dependent on the state’s milk production and processing.

News release from UC Division of Agriculture and Natural Resources

Download the full report

California's dairy industry, by the numbers

California’s dairy industry, by the numbers

UC Davis plans joint research with Brazil

FAPESP, the São Paulo Research Foundation and UC Davis announced May 12 the launch of a new program to strengthen collaborative research in physical sciences, engineering, biomedical sciences and agriculture within the framework of the cooperation agreement signed by the two institutions in 2012.

The announcement was made during the opening of FAPESP Week UC Davis in Brazil, a two-day event attended by 26 scientists from UC Davis and institutions in São Paulo State to present research findings in a range of knowledge areas. The event is a follow-up to FAPESP Week California, held in November 2014 at UC Davis and UC Berkeley in the United States.

“We already collaborate strongly with FAPESP in social sciences and the humanities. Thanks to this success, we’ve decided to expand our partnership to other areas,” said Harris Lewin, vice chancellor for research, UC Davis.

Harris Lewin, VC for Research UC Davis

Harris Lewin

According to Lewin, ten projects each lasting two years will be jointly funded. The first call for proposals will be issued by end-2015.

Lewin stressed the highly interdisciplinary nature of the research done at UC Davis, where “the walls between disciplines are easily broken down.”

“Our main areas of interest for the years ahead are food security, water security, society, health, energy, the environment, transportation, and material science. Our disciplines intersect so much that research projects impact all these areas, which are linked to global challenges and to many of the themes addressed by the centers FAPESP supports in São Paulo. There’s a natural affinity between what goes on at UC Davis and what goes in here in São Paulo,” Lewin said.

For Carlos Henrique de Brito Cruz, FAPESP’s Scientific Director, UC Davis’s collaborative interdisciplinary research model is inspiring and has several important academic features that are consistent with the search for greater impact by universities in São Paulo State.

“The focus on problem solving at UC Davis’s research centers is especially interesting,” he said. “This is really positive and São Paulo’s scientists have a great new opportunity to collaborate with colleagues at UC Davis.”

Paul Dodd, associate vice chancellor for interdisciplinary research & strategic initiatives at UC Davis, also attended the session. He praised “the incredible work FAPESP has done to put the science done in São Paulo on the world map.”

“We interact with many research funding agencies worldwide, but I don’t know of a single one that has done more than FAPESP to project its research into other regions,” Dodd said.

FAPESP Vice President Eduardo Moacyr Krieger said FAPESP Week – an event already held several times in the United States, as well as other countries such as Argentina, Canada, China, Germany, Japan, Spain and the United Kingdom – has been an important mechanism for strengthening collaboration by researchers in São Paulo with colleagues all over the world. This is first time a FAPESP Week event has taken place in Brazil itself. Appropriately, the event was formally opened on the evening of May 11 with a visit to the Soccer Museum (Museu do Futebol), located at Pacaembu Stadium.

Related: Brazilian agreement boosts humanities, social science links

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.

Food poisoning affects one in six Americans every year, according to the FDA. Salmonella alone causes over a million illnesses, thousands of hospitalizations and some 450 deaths a year. Yet identifying a small amount of harmful bacteria on produce, among many more that are harmless or even potentialy beneficial, is difficult.

Team members are: from the School of Veterinary Medicine, Professor Bart Weimer, graduate student Azarene Foutouhi and postdoc Dylan Storey; and Bob Baker and Peter Markwell, both senior scientists at Mars, Inc.

The UC Davis-Mars Inc. team entry features patented “high throughput captured concentration” technology invented by Weimer and further demonstrated through a research partnership with Mars Inc. for use in many foods. The test uses fluidized bed technology and beads that grab the bacteria from the food, and can recognize, detect and verify bacteria in less than four hours without the need for growing the microbes. This will provide the food industry with a test that reduces the time from about one week to less than one day.

“Our technology is sensitive, fast and accurate and allows us to test large sample volumes, which is needed by large food processing operations and has been lacking in the past,” said Weimer. “It doesn’t require the growing of bacteria which is time consuming.”

This first-ever FDA Food Safety Challenge was developed under the America Competes Reauthorization Act of 2010, which grants all federal agencies broad authority to conduct prize competitions to spur innovation, solve tough problems, and advance their core missions. A panel of food safety and pathogen detection experts from the FDA, the Centers for Disease Control and Prevention, and the U.S. Department of Agriculture judged the submissions, determined finalists, and will select a winner. The UC Davis-Mars Inc. team was awarded $20,000 from a total prize pool of $500,000, with the remaining pot to be distributed to the winner.

More information

FDA Food Safety Challenge

100k Genome project takes aim at foodborne disease

100k Foodborne Pathogen Genome Project

Video: UC Davis researchers take aim at foodborne disease