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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.

UC Davis partners in new photonics manufacturing institute

UC Davis is a partner in new $610 million institute for photonics manufacturing innovation announced July 27 by Vice President Joe Biden at an event in Greece, N.Y.

The Integrated Photonics Institute for Manufacturing Innovation (IP-IMI) aims to stimulate new investment and industrial growth based on photonics technology, which uses light, rather than electrons, to carry information. Integrated photonics has the potential to pack more processing power onto a single chip, opening new possibilities in computing, telecommunications and related fields.

Integrated photonics device designed and fabricated in Professor Yoo's lab at UC Davis. Credit: Binbin Guan

Integrated photonics device designed and fabricated in Professor Yoo’s lab at UC Davis. Credit: Binbin Guan

“I am very excited that our campus is part of this new national manufacturing institute,” said Professor S. J. Ben Yoo, Department of Electrical and Computer Engineering, who is leading the UC Davis team. “UC Davis is a strong partner in the Integrated Photonics Institute thanks to the very generous support of Chancellor Katehi and the campus, as well as the technology progress we have been making at UC Davis.”

The new institute is led by the Research Foundation of the State University of New York (RF SUNY) and headquartered in Rochester, N.Y. The consortium includes 55 companies and 20 universities, as well as community colleges and non-profit organizations. UC Davis and UC Santa Barbara are major partners on the West Coast.

The Center for Nano and Micro Manufacturing (CNM2) at the UC Davis College of Engineering will play a major role in the West Coast hub of the Institute. The Center includes a 10,000 square foot Class 100 clean room with tools for microscale manufacturing, as well as research space and microscope facilities. Chancellor Linda Katehi has directed that $6.5 million allocated to the Center be used to support UC Davis’ role in the manufacturing institute.

Total funding comprises $110 million in federal funds (Department of Defense) and $500 million in non-federal funds, including $250 million from the state of New York and $40 million from the California Governor’s Office of Economic Development (GO-Biz).

The Integrated Photonics Institute for Manufacturing Innovation is the sixth of nine such public-private partnerships established by the White House to boost advanced manufacturing and foster American innovation.

More information:

White House fact sheet

Ben Yoo’s laboratory website

Related: New device for ultrafast optical communications

Psychology researchers build mind map of memories evoked by music

Contributed by Alex Russell

A snatch of music can evoke powerful memories. Now a team led by UC Davis psychologist Petr Janata is working to building a map of brain regions that react to music that triggers particular memories. The results will expand our knowledge on how the brain encodes memories. It could also provide a way to improve quality of life for those suffering debilitating conditions including Alzheimer’s disease.

Map of music in the brain

Brain scans show how different regions light up in response to familiar (green), memory-evoking (red) or “pleasing” (blue) songs. (Janata lab, UC Davis)

“This technique is really at the fore of neuroimaging research right now,” says Janata, who won a Guggenheim Fellowship in 2010 for his work on music and autobiographical memory. “There are various types of experiments that show people large libraries of images and then try to reconstruct the images based on their brain activity. That’s similar to this idea but no one has done it with music.”

Their research uses a Web platform for crowdsourcing written memories. The website plays a 30-second clip of music and then asks questions like, “On a scale of one to five, how strong does a memory experience does it evoke?” The questions are all pre-programmed based on how a visitor responds. If a visitor reports that a music clip evokes a strong memory, they are prompted to write that memory out. Then they are asked to play another clip.

Interested in joining the study? Click here

A handful of visitors to the website have already submitted hundreds of these music-evoked memories. The team plans to invite some of these “super-users” to undergo a brain scan while they listen to those same clips. That way, the researchers may be able to identify overlaps between the language-based concepts in the written memories and areas in the brain that light up on the brain scan when they hear the music.

Janata is hoping to pinpoint areas throughout the brain that show more activity when a participant listens to a clip of music that sparks a powerful memory. By knowing beforehand the content of those memories, it might be possible to create a map — a “neurobiography” — with those memories.

“You get away from these overly rehearsed memories and instead you have a way of getting at these remote, forgotten events,” says Janata.

In January, Janata and his team won two years of seed funding from the Institute for Social Sciences to expand this work. The collaboration includes Associate Professor of Linguistics Raul Aranovich, Professor of Statistics and director of the Data Science Initiative Duncan Temple Lang and Associate Professor of Psychology Arne Ekstrom.

More information

Learn more about the project at the ISS website.

Video: Janata explaining how the brain processes music (World Science Festival)

 

 

 

 

Dairy products boost effectiveness of probiotics, new studies show

Probiotics, those living bacteria and yeasts that offer a variety of health benefits, especially for the digestive system, are now available to consumers in yogurt and a variety of other food products as well as in nonfood supplements. But little is known about how the products containing those probiotics might influence their effectiveness.

Could it really be important whether you consume a probiotic in yogurt or other fermented foods and beverages rather than in a supplement? And is there something about dairy products that makes them particularly well suited for probiotics?

Results from two recent mouse-based studies, led by UC Davis food microbiologist Maria Marco, suggest that the answer is a resounding “yes.”

“Taken together, our findings indicate that the manner in which a probiotic is delivered – whether in food or supplement form – could influence how effective that probiotic is in delivering the desired health benefits,” said Marco, an associate professor in the Department of Food Science and Technology at UC Davis.

In both of the preclinical studies, the researchers examined the performance in the intestine of Lactobacillus casei, one of the most common probiotics, frequently found in yogurt and other dairy foods. It has been shown to be helpful in preventing a host of digestive problems ranging from diarrhea and lactose intolerance to more severe, chronic disorders including inflammatory bowel disease, or IBD.

While dairy foods such as yogurt are often used to deliver probiotics commercially and in clinical research trials, it has been unclear exactly why dairy products are preferred over other foods and beverages or nonfood supplements, Marco said. She noted that two suspected benefits were the dairy carbohydrates that support the growth of the probiotics and the potential for dairy foods to buffer the probiotics from exposure to acidic conditions in the stomach.

In the first of the two UC Davis studies, published July 7 in the Journal of Proteome Research, the investigators tested whether the low temperatures at which dairy foods are stored might better prepare the probiotics to survive and function in the intestine. They compared how a particular strain of L. casei, allowed to incubate in refrigerated milk, persisted in the intestine compared to when that probiotic was delivered in milk without the cold-temperature incubation step. (The journal article is available at: http://bit.ly/1HQI2a3)

The researchers found that 205 L. casei proteins were produced either at higher levels or exclusively when the probiotic was allowed to incubate in refrigerated milk, and that these proteins, which were produced before the dairy product was even consumed, were key to survival of L. casei in the digestive tract.In the second study, published July 10 in the journal Applied and Environmental Microbiology, the researchers compared L. casei delivered in milk to milk alone and to L. casei delivered in a nonnutritive, buffered medium, in terms of the effectiveness in preventing symptoms of IBD in mice.

They discovered that mice fed L. casei in milk exhibited fewer symptoms of IBD than did mice fed milk alone or the same probiotic strain in a nonfood supplement format. They also demonstrated that mutant forms of L. casei, which were unable to produce certain milk-based proteins, were unable to prevent the disease, further underscoring the importance of the dairy-based delivery system for this probiotic. (The accepted manuscript is available, open access, at the journal’s website at http://bit.ly/1L2HZKN. It will be published in edited form in September .

“We are now beginning to understand the concise mechanisms by which probiotic bacteria benefit human health,” Marco said. “These findings are pivotal to understanding the conditions in both the food product and the digestive tract that influence the effectiveness of the probiotic, and they really point to the need now for similar studies with humans.”

Lead author on both of the papers was Bokyung Lee, a postdoctoral scholar in the School of Veterinary Medicine’s Comparative Pathology Laboratory. Also collaborating with Marco and Lee were other UC Davis researchers in the Department of Food Science and Technology, the Genome Center, and the School of Veterinary Medicine.

Maria Marco is best reached via e-mail at mmarco@ucdavis.edu.

IVAN network helps communities fight environmental hazards

A partnership that helps residents of underserved communities in California report environmental hazards to enforcement agencies should be enhanced and expanded, a University of California, Davis, report says.

The UC Davis Center for Regional Change released the report on the Identifying Violations Affecting Neighborhoods (IVAN) program July 13 in Sacramento. The “neighborhood watch” for environmental hazards has been used in the Wilmington area of Los Angeles, the Imperial Valley, Coachella Valley, Kern County, Fresno County and Kings County.

“Our research shows that the program has improved health and well-being in some of California’s most disadvantaged communities and facilitated collaboration between residents, environmental justice organizations and public agencies to solve environmental problems,” said Shrayas Jatkar, a master’s degree candidate in community development, who authored the report with Jonathan London, CRC director.

The CRC report examined four cases in which IVAN played a significant role: a cattle feed lot polluting a water source, improper disposal of fracking fluid, a hazardous waste disposal site and a gas leak. All where brought to the attention of enforcement agencies by community residents. Now in its fifth year, the program is a partnership among community groups and local, state and federal agencies. The report provides suggestions for improving IVAN including:

  • Ensure the sustainability of the program through diversified funding.
  • Train community members to enhance their skills as “civic scientists” involved in environmental monitoring.
  • Link the IVAN and California Environmental Protection Agency reporting systems.
  • Expand the program to additional communities.

More information: Link to information about the IVAN Summit in July 2015 and the livestream from the summit.

Full news release here.

Warm winters can help wildfire recovery, as long as there’s enough rain

By Kat Kerlin

Using more than a decade’s worth of daily satellite images, researchers have determined ecosystems of South Africa’s Cape Floristic Region bounce back from wildfires much more quickly in warmer winter weather.

However, there is an important caveat for other areas with Mediterranean climates at high risk of fires, such as drought-stricken California: The rate of recovery also depends on sufficient rainfall, especially in summer.

Data from South Africa shows how climate influences recovery from wildfire and could be generally applied to similar regions in California and Australia. (Andrew Latimer/UC Davis)

Data from South Africa shows how climate influences recovery from wildfire and could be generally applied to similar regions in California and Australia. (Andrew Latimer/UC Davis)

The model developed by Yale, UC Davis and University of Connecticut could help predict which ecosystems are most vulnerable to climate change, according to the study published the week of July 6 in the journal Proceedings of the National Academy of Sciences.

Findings could apply to California, Australia

The findings should also apply to the Mediterranean basin and places like California and Australia with similar climates.

“If you’re in an area where soil is poor or where there’s a drought, it slows down the regrowth of vegetation and makes it more vulnerable to fire that comes back,” said co-author Andrew Latimer, an associate professor in the UC Davis Department of Plant Sciences.

Lessons for coastal California

Latimer said that, for California, the study is most applicable to the state’s coastal and chaparral areas, such as Santa Barbara and Los Angeles. There, the coastal vegetation is similar to that seen in the South African shrubland, and some areas have been experiencing more fire because of accidental ignitions.

“This area of South Africa is rich in biodiversity, and we noticed that some areas recover more quickly from fires than others,” said lead author Adam Wilson, a postdoctoral researcher at Yale at the time of the study, and now an assistant professor at the University at Buffalo. “This model helps explain why that is.”

What’s ‘under the hood’

The NASA satellite captured images of the Cape Floristic Region on Africa’s southern tip with a resolution of 500 meters. Over more than a decade, the images showed that western areas of the region recovered more slowly from fires than those in the east. The model developed by Wilson and his team revealed the two most important variables for rates of recovery were average temperature in winter and rainfall in the summer.

“The study represents a methodological advance in our ability to infer what’s going on ‘under the hood’ in ecosystems using data collected from space,” Wilson said.

21st century linguistics: helping computer scientists write better code

By Jeffrey Day

Raúl Aranovich, an associate professor of linguistics at UC Davis, is using his knowledge of language structure and theory on a project to identify programmers most likely to write vulnerable code.

He is working with UC Davis computer scientists Prem Devanbu and Vladimir Filikov on a National Science Foundation funded project called “Language, Computation and Cybersecurity.

Q&A with Raúl Aranovich

“There’s this big debate whether an author leaves a quantitative fingerprint on his or her work. It could be from things like average sentence length or how many adverbs you include in your writing or your speech,” Aranovich said.

“We are looking at open-source software communities where developers collaborate online. Because all collaboration is online there’s a lot of language involved, and also a lot of code that’s being exchanged. We’re trying to see what the social dynamics of programmers are around their style for coding and their linguistic style. Once we identify these linguistic profiles within the group and we understand the group dynamics then we can find which programmers are more prone to writing vulnerable code.”

Read a full Q and A with Aranovich at the UC Davis Institute for Social Sciences.

Network of tubes plays a key role in plants’ immune defense

Chloroplasts, better known for taking care of photosynthesis in plant cells, play an unexpected role in responding to infections in plants, researchers at UC Davis and the University of Delaware have found.

Infection causes tubes called stromules (blue) to grow from chloroplasts (purple) to the nucleus of a plant cell (yellow) carrying signals that boost immune defenses.

Infection causes tubes called stromules (blue) to grow from chloroplasts (purple) to the nucleus of a plant cell (yellow) carrying signals that boost immune defenses.

When plant cells are infected with pathogens, networks of tiny tubes called stromules extend from the chloroplasts and make contact with the cell’s nucleus, the team discovered. The tubes likely deliver signals from the chloroplast to the nucleus that induce programmed cell death of infected cells and prepare other cells to resist infection. The work is published online June 25 in the journal Developmental Cell.

“This opens a new area of understanding how the chloroplast communicates with the nucleus, and likely with other organelles within the cell,” said Savithramma Dinesh-Kumar, professor of plant biology at UC Davis and senior author on the paper.

Chloroplasts in neighboring uninfected cells also produce stromules, apparently signaling the nucleus to switch on genes that make cells more resistant to infection. The overall effect is to wall off and contain an infection, Dinesh-Kumar said.

Stromules were first described more than 50 years ago, but until now their role in a specific biological process has remained a mystery.

Mammalian cells lack chloroplasts but do have mitochondria, which play a role in cellular suicide. Exactly what chloroplasts, do other than photosynthesis, has been largely ignored, Dinesh-Kumar said. But it’s clear that they are “powerhouses” producing molecules for the rest of the cell.

The work was supported by the NIH. Other authors on the paper are Jeffrey Caplan, Amutha Sampath Kumar, Kyle Hoban, Shannon Modla and Kirk Czymmek at the University of Delaware and Eunsook Park and Meenu S. Padmanabhan at the UC Davis Department of Plant Biology and Genome Center.

Engineering new routes to biochemicals

Living cells can make a vast range of products for us, but they don’t always do it in the most straightforward or efficient way. Shota Atsumi, a chemistry professor at UC Davis, aims to address that through “synthetic biology:” designing and building new biochemical pathways within living cells, based on existing pathways from other living things.

Engineered bacteria use both glucose and acetate, instead of just glucose, as raw material to make isobutyl acetate, which can be used in chemical manufacturing and as fuel.

Engineered bacteria use both glucose and acetate, instead of just glucose, as raw material to make isobutyl acetate, which can be used in chemical manufacturing and as fuel.

In a new paper published by Nature Communications June 25th, Atsumi and colleagues Yohei Tashiro and Shuchi Desai describe building a new pathway that lets the bacterium, E. coli, feed on both sugar (glucose) and acetate, a common waste material from biomass, to make isobutyl acetate. This product can be used as the basis for flavoring agents, solvents and fuels.

The original pathway starts with glucose, which is converted into both isobutanol (via a pyruvate intermediate) and into acetyl-coenzyme A, a common building block in biochemistry used for making biochemicals such as proteins, fats and alcohols, among other things.  The theoretical maximum carbon yield from this pathway is 67 percent, which is lower than chemists would like to see.

Atsumi’s team engineered E. coli so that they could scavenge acetate to make acetyl-CoA while using glucose to make isobutanol. The new pathway raises the theoretical maximum carbon yield of isobutyl acetate to 75 percent.

The process might be further improved by using an acetate-assimilation pathway from other soil bacteria that are better at living off acetate than E. coli, the authors note. Because acetyl-CoA is such an important material for making other biological molecules, direct acetate assimilation could have wide application in biotechnology.

The work was supported by a Hellman Fellowship.

More about this work: Atsumi’s laboratory is also working on engineering cyanobacteria (blue-green algae) to make fuels from sunlight, and on getting bacteria to make scents and flavorings.

California’s wildflowers losing diversity in face of warmer, drier winters

By Kat Kerlin

Native wildflowers in California are losing species diversity after multiple years of drier winters, according to a study from the University of California, Davis, which provides the first direct evidence of climate change impacts in the state’s grassland communities.

The study, published in the journal Proceedings of the National Academy of Sciences, is based on 15 years of monitoring about 80 sampling plots at McLaughlin Reserve, part of UC Davis’ Natural Reserve System.

Drought and climate changes are reducing the diversity of California's grassland wildflowers. (Susan Harrison)

Drought and climate changes are reducing the diversity of California’s grassland wildflowers. (Catherine E. Koehler/UC McLaughlin Reserve)

“Our study shows that 15 years of warmer and drier winters are creating a direct loss of native wildflowers in some of California’s grasslands,” said lead author Susan Harrison, a professor in the Department of Environmental Science and Policy. “Such diversity losses may foreshadow larger-scale extinctions, especially in regions that are becoming increasingly dry.”

The researchers confirmed that drought-intolerant species suffered the worst declines.

Global trend

Similar trends have been found in other Mediterranean environments, such as those of southern Europe, bolstering the case for increased climate change awareness in the world’s semi-arid regions.

Taken together with climate change predictions, the future grassland communities of California are expected to be less productive, provide less nutrition to herbivores, and become more vulnerable to invasion by exotic species, the study said.

The researchers expect these negative to cascade up through the food web—affecting insects, seed-eating rodents, birds, deer and​ ​domesticated species like cattle, all of which rely on grasslands for food.

Rescue effect may be too late

Grasses and wildflowers may be able to withstand the current drying period through their extensive seed banks, which can lie dormant for decades waiting for the right conditions to germinate. However, California’s drought is expected to intensify in the coming decades, so this rescue effect may end up being too late for some species.

The study’s co-authors include Elise Gornish, a UC Cooperative Extension specialist in the UC Davis Department of Plant Sciences, and Stella Copeland, a doctoral student in the Department of Environmental Science and Policy.

The research was supported by the National Science Foundation.

Reserve system

The study reflects the UC Reserve System’s recently created Institute for the Study of the Ecological Effects of Climate Impacts. UC Davis manages five reserves representing a wide variety of habitats. They include:

  • Bodega Marine Reserve, which surrounds the Bodega Marine Laboratory;
  • Jepson Prairie Reserve, remnant natural prairie in the Sacramento Valley;
  • Donald and Sylvia McLaughlin Reserve, which protects unusual serpentine habitats near a mine site in Lower Lake;
  • Quail Ridge Reserve, which helps protect native habitats and wildlife near Lake Berryessa; and
  • Stebbins Cold Canyon Reserve, which has a mix of habitats, including grasslands, blue oak woodland, chaparral shrublands, riparian woodland and a seasonal stream.

More information:

Read the study

Related: UC Davis to help UC effort to study effects of climate change on ecosystems

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.

One patient, Gale Kilgore, shared her story with the Sacramento Bee this weekend. Kilgore is being treated at UC Davis for bladder cancer. In a new twist, mice grafted with pieces of Kilgore’s tumor are being used to test which treatment combinations will work best on her personal cancer.

Earlier this year, President Obama announced the Precision Medicine Initiative, directing investments in research on medicine tailored to an individual patient’s genetic makeup.

In addition to the Genome Center on the UC Davis campus, UC Davis has also partnered with BGI, the world’s largest genomics organization, to establish the BGI@UC Davis facility on the Sacramento campus.

Video preview: A Path to Healing

A Path to Healing talks to doctors, patients and scientists about genomics and precision medicine.

A Path to Healing talks to doctors, patients and scientists about genomics and precision medicine.

More information

UC Davis Magazine feature: Enter the genomics matrix

UC Davis and BGI announce partnership to establish start of the art genome center in Sacramento