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About Egghead

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.

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


NSF funds NetSage to analyze, improve international data networks

Every day, thousands of researchers rely on robust data networks to share petabytes of data with their colleagues around the world. A new $5 million, five-year National Science Foundation grant, awarded to Indiana University, the University of California, Davis and the University of Hawaii at Mānoa, seeks to bolster these networks by enabling unprecedented measurement and analysis.

The grant will fund NetSage, a network measurement, analysis and visualization service designed to address the needs of today’s international networks. The principal investigators are: Jennifer Schopf at Indiana University; Sean Peisert, assistant professor of computer science at UC Davis; and Jason Leigh at the University of Hawaii.

“It’s about helping people to do better science,” said Peisert. Scientists increasingly rely on moving vast of data around the world, for example from the Large Hadron Collider in Switzerland, or from telescopes such as the planned Large Synoptic Survey Telescope located on mountain tops in Chile or Hawaii.

These international networks move data at an unprecedented scale. But there can be problems especially with “elephant flows,” when a large volume has to move across the pipe in a limited time, Peisert said. Even a small degradation in the network can have a big impact on performance.

The NetSage service will help network engineers gain a better understanding of current traffic patterns across the NSF’s international network links, where large data flows come from and where they go, and where loss of data is occurring, and whether it is caused by network congestion or other issues.

The award (#1540933) is part of the NSF’s International Research Network Connections (IRNC) program.

More information: Full story from Indiana University

New study analyzes “thinspiration” images of women on social media sites

By Jeffrey Day

Some of the most popular social media sites are filled with images of extremely thin women that might be harmful to those who view them — whether they are seeking them or not, according to research from the University of California, Davis. The images were often cropped to remove heads or focus on just a few body parts.

Doctoral candidate Jannath Ghaznavi and associate professor Laramie Taylor in the Department of Communication examined about 300 photographs from Twitter and Pinterest postings that used the terms “thinspiration” and/or “thinspo” to tag images and ideas promoting extreme thinness and often casting eating disorders in a positive light.

Their paper “Bones, body parts, and sex appeal: An analysis of #thinspiration images on popular social media” was recently published in Body Image: An International Journal of Research.

“Imagine a teenage girl or even a young woman looking for inspiration using terms such as ‘attractive,’ ‘fit,’ or ‘pretty,’” Ghaznavi said. “She will likely find images of headless, scantily clad, sexualized women and their body parts.”

Images from Twitter, popular among younger audiences, were most likely to be cropped to remove heads and focus on specific body parts compared to Pinterest, according to the study.

The content analysis cannot speak to the effects of viewing the images, the researchers concede, but they point to studies that have shown repeated exposure to such content can result in body dissatisfaction and disordered eating attitudes.

“A young woman looking at these image may think that’s what she should look like,” Ghaznavi said. “That could prompt these girls and women to resort to extreme dieting, excessive exercise or other harmful behaviors in order to achieve this thin ideal.”

Cosmic collisions wake up snoozing galaxies

Galaxies are often found grouped into clusters, which contain many ‘red and dead’ members that stopped forming stars in the distant past. Now astronomers have found that when galaxy clusters collide, the resulting shockwave can “wake up” these dormant galaxies and drive a new generation of star formation.

The international team that made the discovery is led by Andra Stroe of Leiden Observatory in the Netherlands and David Sobral of Leiden and the University of Lisbon, Portugal, and researchers Will Dawson and James Jee from UC Davis and the Lawrence Livermore National Laboratory, and David Wittman, associate professor of physics at UC Davis. The work is published April 24 in two papers in the journal Monthly Notices of the Royal Astronomical Society.

The astronomers observerd merging galaxy cluster CIZA J2242.8+5301, nicknamed the ‘Sausage’, through telescopes in La Palma and Hawaii.

A composite image of the ‘Sausage’ merging galaxy cluster. Yellow circles are cluster galaxies, where accelerated star formation is taking place. Green marks shock waves (regions of radio emission),  and purple marks hot gas between the galaxies that emits X-rays. The cluster is one of the most massive in the known Universe. Credit: Andra Stroe

A composite image of the ‘Sausage’ merging galaxy cluster. Yellow circles are cluster galaxies, where accelerated star formation is taking place. Green marks shock waves (regions of radio emission), and purple marks hot gas between the galaxies that emits X-rays. The cluster is one of the most massive in the known Universe. Credit: Andra Stroe

“We found that as shock waves associated with major cluster mergers pass through galaxies it actually causes enhanced star formation rates, somewhat of a baby boom of stars,” Dawson said. “This is a bit surprising because galaxy clusters are typically thought to be hostile environments which quench new star formation.”

The shock when two clusters merge cause turbulence in galactic gas, creating cold, dense clouds of gas that favor star formation, the researchers say.

However, Sobral said that this rapid star formation at this rate leads to a lot of massive, short-lived stars which explode as supernovae within a few million years, driving gas out of galaxies so that they run out of “star fuel” and lapse back into a dead state.

The next step is to see if the Sausage cluster is unique and that these bursts of star formation need very particular conditions. By studying a much bigger sample of galaxies, the team hope to find out exactly how they happen.

(Adapted from a news release issued by the Royal Astronomical Society)

More information:

The papers can be found here and here


When galaxy clusters collide

Puzzling galaxy cluster not so puzzling after all, maybe

Merging cluster cosmologists merge

Dark matter’s odd behavior baffles astronomers