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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.

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

Baboons don’t just follow the leader

By Jeffrey Day

Baboons live in a strongly hierarchical society, but the big guys don’t make all the decisions.

A new study from the University of California, Davis, and the Smithsonian Tropical Research Institute reveals that animals living in complex, stratified societies make some decisions democratically. The study also breaks ground in how animal behavior data is collected.

The study is being published Friday (June 19) in Science.

GPS collaring of baboons shows that troops have a democratic process for deciding where to go.

GPS collaring of baboons shows that troops have a democratic process for deciding where to go.

“It’s not necessarily the biggest alpha males that influence where groups go,” said co-author Meg Crofoot, assistant professor of anthropology at UC Davis. “Our results illustrate an important distinction between social status and leadership, and show that democratic decision-making takes place even in highly stratified societies.”

This study was the first to use GPS tracking with a large group of primates. Researchers fitted 25 olive baboons in Kenya with GPS tracking collars.

“We can closely examine how they are responding to one another,” Crofoot said. “These technological advances are giving us unprecedented windows into the lives of group-living of animals.”

Patterns of collective movement in baboons are remarkably similar to models that can predict the movements of fish, birds, and insects.

“Decision making in complex societies may not be all that that different than that in animals with a more simple societal structures,” Crofoot said.  “They may all be playing by the same rules.”

More information:

See full press release

Read the full paper at Science

Video from Untamed Science

Wild bees pollinate crops, but that’s not why they should be conserved

By Kathy Keatley Garvey

Wild bee diversity is declining worldwide at unprecedented rates, and steps must be taken to conserve them — and not just those that are the main pollinators of agricultural crops, declare 58 bee researchers in a study published June 16 in the journal Nature Communications.

“This study provides important support for the role of wild bees to crop pollination,” said co-author and pollination ecologist Neal Williams, associate professor in the UC Davis

Wild pollinators such as bumblebees contribute to crop production. (Credit: Kathy Keatley Garvey/UC Davis).

Wild pollinators such as bumblebees contribute to crop production. (Credit: Kathy Keatley Garvey/UC Davis).

Department of Entomology and Nematology. “At the same time, we found that in any one region, much of the pollination services from wild bees to a given crop come from just a few species, thus we need to be careful about using a simplistic economic ecosystem-services argument for biodiversity conservation and maintain actions that target biodiversity as specific goal.”

Wild, or non-managed bees, include bumble bees (genus Bombus), sweat bees (genus Lasioglossum) and small carpenter bees (genus Cerantina).

The study, led by David Kleijn of Wageningen University, The Netherlands, found that wild bees contribute about $3,251 per hectare ($1300 per acre) in “crop pollination services,” about the same as the economic contribution from “managed” bee colonies. However, they also found that 80 percent of the crop pollination from wild bees was provided by just two percent of wild bee species.

That means that the economic benefit of crop pollination might not be a good argument for conserving wild bee species, according to the authors. Measures taken to protect top pollinators might not benefit wild bee species as a whole.

The paper, “Delivery of Crop Pollination Services is an Insufficient Argument for Wild Pollinator Conservation,” is online at http://www.nature.com/naturecommunications. Among the co-authors are Robbin Thorp, distinguished emeritus professor of entomology at UC Davis, and conservation biologist Claire Kremen of UC Berkeley.

More:

UC Davis Bee Biology (Harry H. Laidlaw Jr. Honeybee Research Facility)

UC Davis Häagen-Dazs Honeybee Haven 

Engineering student builds machines for battlebots

Travis Smith has always been interested in building things. This summer, the UC Davis graduate student will be on national television building robots and then watching his creations stand up to spikes, chainsaws and flamethrowers as a team member in the sixth series of “Battlebots” on the ABC network.

Travis Smith, a Ph.D. student in engineering, is taking part in the sixth season of the TV show "Battlebots."

Travis Smith, a Ph.D. student in engineering, is taking part in the sixth season of the TV show “Battlebots.”

In the show, teams build armed robots that fight it out in an arena full of hazards. Think FIRST Robotics, but with chainsaws.

Smith was a chemical engineering major at UC Berkeley during Battlebots’ original TV run from 2000 to 2002. After graduating, he worked for Lockheed Martin, earning a Master’s degree from the University of New Orleans along the way. He is currently working towards a Ph.D. in mechanical and aerospace engineering with Professor Jae Wan Park, studying design of fuel cells.

“Battlebots is why I switched from chemical to mechanical engineering,” Smith said. He has also volunteered as a mentor for high school students taking part in the FIRST Robotics Competition in the New Orleans region.

As part of the “Machine Corps” team for Battlebots, Smith specializes in machining and analysis.

“There are some interesting engineering problems, it’s very cool,” he said.

Filming began May 17 and the first of six episodes will air June 21 at 9 p.m. on ABC.

UC Davis graduate student to attend Lindau Nobel Laureate meeting

By Derrick Bang

Christopher Chapman, a Ph.D. student in the UC Davis Department of Biomedical Engineering, has been selected to attend the 65th annual Lindau Nobel Laureate Meeting, taking place June 28-July 3 in Lindau, Germany. Chapman will join a U.S. delegation of roughly 55 “young researchers,” as they’re designated by the Lindau committee.

Christopher Chapman, a PhD student in the UC Davis Department of Biomedical Engineering

The U.S. delegation will be among the Lindau Meeting’s approximately 650 global student and postdoctoral researchers from all three natural science Nobel Prize disciplines: medicine and physiology, physics, and chemistry. They’ll meet and confer with the 65 Nobel Laureates who will gather to interact with this next generation of leading scientists and researchers.

“I’m happily surprised,” Chapman admits. “The selection process began back in September 2014, and has taken awhile, so I’ve tried not to think about it too much. But now that I’ve been chosen, and the reality has sunk in, I’ve started talking to people, and now I’m getting quite excited.

“I’m already planning how to use this meeting for networking, because being able to build one’s network on an international scale doesn’t happen frequently. And, of course, I’m excited by the chance to interact and learn directly from Nobel Laureates. Since my work focuses on a wide range of areas within these three natural science disciplines, this is an incredible opportunity.”

Chapman is a member of the Multifunctional Nanoporous Metals Research Group headed by Erkin Şeker, a professor in the UC Davis Department of Electrical and Computer Engineering. Chapman earned twin undergraduate degrees in biomedical engineering and mechanical engineering in 2012, at North Carolina State University; he expects to complete his doctorate at UC Davis in 2016.

His research has focused on nanoporous gold. He is engineering a microchip-based testing platform to rapidly screen for materials and surface chemistries with the long-term goal of developing a next-generation neural electrode coating for making recordings from single brain cells.

Two other UC Davis scientists, Aimee Bryan and Pablo Zamora, attended the Lindau Nobel meeting in 2013.

The first Lindau Nobel Laureate Meeting took place in 1951. Today, the annual meetings provide a globally recognized forum for the transfer of knowledge between generations of scientists, while inspiring and motivating both Nobel Laureates and international “best talents.”

“Crosstalk” gives clues to diabetes

Sometimes, listening in on a conversation can tell you a lot. For Mark Huising, an assistant professor in the Department of Neurobiology, Physiology and Behavior at the UC Davis College of Biological Sciences, that crosstalk is between the cells that control your body’s response to sugar, and understanding the conversation can help us understand, and perhaps ultimately treat, diabetes.

Huising’s lab has now identified a key part of the conversation going on between cells in the pancreas. A hormone called urocortin 3, they found, is released at the same time as insulin and acts to damp down insulin production. A paper describing the work appears online on June 15 in the journal Nature Medicine.

“It’s a beautiful system,” Huising said. “It turns out that there is a lot of crosstalk going on in the islets to balance insulin and glucagon secretion. The negative feedback that urocortin 3 provides is necessary to tightly control blood sugar levels at all times.”

Diabetes affects millions of Americans every year. Both forms of the disease — type 1, “juvenile” or “insulin-dependent” diabetes, and type 2 or “adult-onset” diabetes — occur when the body fails to regulate the level of sugar properly.

Diabetes is tied to structures called the Islets of Langerhans in the pancreas. Within the islets, beta cells make insulin. Increasing blood sugar stimulates insulin production, which causes the body’s cells to pull sugar out of circulation.

The islets also house alpha cells, which make another hormone, glucagon, which acts on the liver to release more glucose into the bloodstream.

An islet of Langerhans with urocortin stained green in beta cells. Glucagon-making cells are stained red. Credit: Mark Huising.

An islet of Langerhans with urocortin stained green in beta cells. Glucagon-making cells are stained red. Credit: Mark Huising.

Urocortin 3 was originally identified as a hormone that is related to the signal in our brain that kick-starts our stress response. Instead, urocortin 3 is produced by islet beta cells and stored and released alongside insulin. In a series of experiments, Huising’s group showed that urocortin 3 causes another cell type in the islets, delta cells, to release somatostatin, which turns down insulin production and acts as a natural brake on the release of insulin.

Urocortin 3 is reduced in laboratory animal models of diabetes and in beta cells from diabetic patients. Without urocortin 3, islets produce more insulin, but at the same time lose control over how much insulin they release.

By understanding how different cells and systems communicate to regulate blood sugar, Huising hopes to get a better understanding of what happens when this regulation goes wrong, leading to the different forms diabetes. Eventually this approach could lead to new ways to treat or prevent the disease.

Coauthors on the study were, at UC Davis: Talitha van der Meulen, Anna Hunter and Christopher CowingZitron; Cynthia Donaldson, Elena Cáceres, Michael Adams and Andreas Zembrzycki at the Salk Institute, La Jolla; and Lynley Pound and Kevin Grove at Oregon Health Sciences University. The work was funded by the Juvenile Diabetes Research Foundation, the Clayton Medical Research Foundation Inc., and the National Institutes of Health.

More:

Link to the full paper

Hartwell Foundation awards grant for work on juvenile diabetes