Skip directly to: Main page content

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.

Chirp Microsystems waves on touch-free future

Within just a few years, we’ve got used to controlling devices by swiping, scrolling or tapping our fingers on a touch screen. But soon you might not even have to touch anything at all to check your email or play a video – just wave your hand in the air, thanks to ultrasonic technology from Chirp Microsystems, a startup company founded in 2013 by researchers from UC Davis and UC Berkeley.

Chirp’s technology is “disruptive” in the ultrasound area, said David Horsley, professor of electrical and computer engineering at UC Davis and co-founder of the company. Chirp’s ultrasound transducers are smaller and operate with much lower power needs than any currently available.

“Nobody is quite doing what we’re doing right now,” Horsley said.

[Horsley’s laboratory at UC Davis works on Micro-Electromechanical Systems (MEMS) and nanostructures that could be used for new sensors and other applications. In one project, they are developing a novel fingerprint reader based on ultrasound.]

Video demonstration of Chirp technology

Like sonar, but tiny

The principle behind Chirp is well-known: it’s basically sonar, giving off ultrasound waves and measuring how long they take to return after bouncing off surrounding objects. By using an array of multiple sensors, Chirp can measure hand movements and gestures and use them in a control interface.

What’s so disruptive about Chirp is that compared to current technology, its transducers are tiny, just millimeters across, can be built on a single microchip, and use very little power – as little as 10 microwatts, far less than a conventional ultrasound transducer or a digital camera.

The technology could be used in motion and gesture sensors, for object avoidance in drones and home robotics such as automated vacuum cleaners, and many other applications, Horsley said.

It’s part of a revolution in microsensors. At one time, gyroscopic motion sensors were bulky, expensive devices only found in aircraft or rockets. In the 1990s, microelectro- mechanical sensors, or MEMS, began to be incorporated in high-end cars as airbag sensors. Now, every smartphone, as well as personal activity monitors such as Fitbit, includes motion sensors.

“We think this could be very widely used within a few years,” Horsley said.

Chirp is currently located in downtown Berkeley and exhibited at this year’s Consumer Electronics Show in Las Vegas. The startup has received support from the National Science Foundation through a Small Business Innovation Research grant, and participated in UC Davis’ Engineering Translational Technology Center and the Skydeck incubator at UC Berkeley.

UC Davis entomologists on the trail of virus-carrying mosquito

Aedes aegypti, a daytime-biting mosquito that predominantly feeds on humans, has spread to at least seven counties since June 2013, according to UC Davis medical entomologist Anthony Cornel of the UC Kearney Agricultural Research and Extension Center, Parlier, and the UC Davis Department of Entomology and Nematology.

Aedes aegypti carries yellow fever, Zika and other viruses. (CDC photo)

Aedes aegypti carries yellow fever, Zika and other viruses. (CDC photo)

“It’s an issue of great concern, especially as current control methods do not appear to be working well,” said Cornel, who does research on the mosquito in Clovis, Fresno County, where it was discovered in June 2013. Simultaneously, the insect was found in the cities of Madera and San Mateo.

“This ongoing widespread invasion and establishment proves that this is no longer a regional issue and has affected many cities and towns in California,” he wrote Feb. 8 in F1000 Research.

But Cornel is optimistic that the pest management intervention strategies and surveillance and control tactics now underway will help control its spread. Aedes aegypti can transmit dengue, yellow fever, Zika and chikungunya viruses.

Zika virus vector

The Zika virus, now spreading throughout the Western hemisphere, was first identified in Uganda in 1947 in rhesus monkeys, according to the World Health Organization. It was subsequently identified in humans in 1952 in Uganda and the United Republic of Tanzania. Outbreaks of Zika virus disease have been recorded in Africa, the Americas, Asia and the Pacific.

Despite the mosquito’s invasion in parts of the United States, there are no reported cases of locally transmitted Zika virus in California or in the contiguous United States, according to the Centers for Disease Control and Prevention. U.S. cases have all involved travelers returning home from countries plagued with disease outbreaks.

Cornel works with the Consolidated Mosquito Abatement District, based in Fresno County, to tackle the spread of the mosquito there. The district covers 1,058 square miles, including part of Kings County.

How far north in California will the mosquito spread?

“I don’t want to exclude the possibility that it may spread as far north as Sacramento,” said Cornel, who collects, rears and researches mosquitoes from all over the world, including the U.S., Mali, Cameroon, Comoros, Tanzania, South Africa and Brazil. “We need to see if it overwinters as eggs or adults or both.”

Setting a mosquito trap

UC Davis medical entomologist Anthony Cornel setting a sentinel trap to capture Aedes aegypti mosquitoes. (Credit: Katherine Brisco)

It’s troubling that the mosquito is becoming more and more resistant to pesticides, Cornel said.

“We have found that the Aedes aegypti have insecticide resistance genes which likely explains why their ultra-low volume and barrier spray applications have not worked as well as expected,” he said.

At Clovis, Cornel and his colleagues trap mosquitoes in gravid or ovitraps; study overwintering and flight dispersal; and employ mark-release-capture trials to estimate dispersal and population size, needed to plan biological (Wolbachia) and chemical auto-dissemination control strategies.

Their document, “Surveillance and Control of Aedes aegypti Mosquito in Clovis, Calif.,” published in F1000 Research details their research with text and maps. It is work of Cornel and Yoosook Lee of UC Davis; Stephen Dobson of the University of Kentucky; Corey Bansfield of MosqMate Inc. and Jodi Holeman, Mark Amireno, Charles Smith and Stephen Mulligan III of the Consolidated Mosquito Control District. In the document, Mulligan, director of the Consolidated Mosquito Control District, describes Aedes aegypti as “the rat of the mosquitoes.”

The California team works with University of Kentucky scientists to develop novel control strategies. One trial involves coating male mosquitoes with insect growth regulators, which are passed on to the females. Males are also infested with a biopesticide or “a good bacteria-like organism,” Wolbachia. “The male transfers it to the female, which affects the ovaries and negatively affects immature development,” Cornel explained. “It’s not new, but it’s not been employed in large trials.”

Cornel has found that males can fly well over 200 meters in one night from their breeding site. Aedes aegypti fly mostly during cooler periods of the day and stick to the shade when it’s hot, they Cornel said. People get bitten while walking around at dusk.

New yard drains a breeding site

The researchers target mosquito breeding sites, primarily yard drains. These drains installed in new home developments empty into the gutter or street and are places mosquitoes can breed out of sight – perhaps even underground.

“These drains are not easily accessible and we can’t see the mosquitoes,” Cornel said. He suggests that cities everywhere address this public safety issue and redesign the yard drains.

It’s crucial for the public to become involved, Cornel said. “We have to focus on public education. We have to get the message across to eliminate mosquito breeding sites. We can’t go to every house. We must rely on the public to eliminate the breeding sites.”

More information

For a longer version of this post, see here

Hepatitis virus-like particles as potential cancer treatment

UC Davis researchers have developed a way to use the empty shell of a Hepatitis E virus to carry vaccines or drugs into the body. The technique has been tested in rodents as a way to target breast cancer, and is available for commercial licensing through UC Davis Office of Research.

Hepatitis E virus is feco-orally transmitted, so it can survive passing through the digestive system, said Marie Stark, a graduate student working with Professor Holland Cheng in the UC Davis Department of Molecular and Cell Biology.

Cheng, Stark and colleagues prepared virus-like particles based on Hepatitis E proteins. The particles do not contain any virus DNA, so they can’t multiply and spread and cause infections.

Hepatitis E virus-like particles can be modified so that molecules such as LXY30, which binds to cancer cells, can be attached to them. (Marie Stark/UC Davis)

Hepatitis E virus-like particles can be modified so that molecules such as LXY30, which binds to cancer cells, can be attached to them. (Marie Stark/UC Davis)

Such particles could be used as vaccines that are delivered through food or drink. The idea is that you would drink the vaccine, and after passing through the stomach the virus-like particles would get absorbed in the intestine and deliver vaccines to the body.

But the particles could also be used to attack cancer. Stark and Cheng did some tinkering with the proteins, so that they carry sticky cysteine amino acids on the outside. They could then chemically link other molecules to these cysteine groups.

They worked with a molecule called LXY-30, developed by researchers at the UC Davis Comprehensive Cancer Center, which is known to stick to breast cancer cells. By using a fluorescent marker, they could show that virus-like particles carrying LXY-30 could home in on breast cancer cells both in a laboratory dish and in a mouse model of breast cancer.

Results of the study are published in the journal Nanomedicine. Information about licensing the technology can be found here.

So perhaps one day, cancer patients might drink their medicine and UC Davis-designed virus-like particles carrying anticancer drugs will home in on their target.

More information

Description of Hepatitis E virus-like particles

Symposium honors DNA maintenance pioneer

Some of the world’s leading experts in how DNA is protected and repaired from damage will meet at UC Davis Feb. 12-13 for a symposium in honor of Stephen Kowalczykowski, distinguished professor of microbiology and molecular genetics at the UC Davis College of Biological Sciences. Registration information is available here.

“Genome maintenance” is essential to life, said Frederic Chedin, Professor of Molecular and Cellular Biology, who is co-organizer of the symposium with Professors Wolf-Dietrich Heyer and Neil Hunter, Department of Microbiology and Molecular Genetics. Every second of the day, our DNA sustains damage for example from chemicals, radiation or just natural processes inside the cell. Breaks and lesions in DNA can lead to cancer, disease and developmental defects. Living things, from bacteria to plants to people, have evolved a fundamentally similar set of tools and processes that constantly defend and repair DNA.

“Steve’s work has had an enormous influence on the field,” Chedin said. In hundreds of publications, his laboratory has analyzed the proteins involved in genome maintenance, Chedin said.

Of special significance, over the past 15 years Kowalczykowski’s lab, working with the late Ron Baskin at UC Davis, has pioneered a set of techniques that allowed them to watch the individual proteins that repair DNA at work on a single molecule in real time. This technique has provided a series of fundamental insights into how these “molecular machines” function.

Long-time followers of this blog will know that we’ve featured Kowalczykowski’s work numerous times, for example when his favorite enzyme was compared to a Bugatti supercar or in helping work out the cause of a rare but devastating birth defect. His was also one of two UC Davis labs that were first in the world to purify the protein associated with the breast cancer susceptibility gene, BRCA2.

Speakers at the two-day symposium include alumni of Kowalczykowski’s lab at UC Davis, including Piero Bianco (University of Buffalo, NY), who was first author on the 2001 Nature paper describing the single-molecule visualization experiment; Maria Spies, now a faculty member at the University of Iowa; and Daniel Anderson, a former graduate student now at the Massachusetts Institute of Technology.

Also speaking will be Peter von Hippel of the University of Oregon, Kowalczykowski’s own postdoctoral mentor.

Von Hippel, who still runs an active research lab, pioneered work on how proteins interact with DNA and RNA, Kowalczykowski said.

“My success has been a reflection of his training,” he said. “Pete is one of the most thought-provoking individuals in the world, and he’s trained dozens of people in this field.”

The symposium will be held at the Buehler Alumi and Visitors Center on the UC Davis campus. It is sponsored by the UC Davis Comprehensive Cancer Center, Office of Research, the College of Biological Sciences Tracy and Ruth Storer Lectureship in Life Sciences, and the Department of Microbiology and Molecular Genetics.

The symposium is free and open to the community. More information and registration can be found here.

Over-evolved: Specialist jaw doomed Lake Victoria’s cichlid fish

By Betsy Towner Levine

A UC Davis Evolution and Ecology team has discovered that cichlid fishes in Africa’s Lake Victoria have suffered a unique and unexpected effect of evolutionary adaptation: mass extinction.

While a graduate student in Interim Dean Peter Wainwright’s lab, Ph.D. student Matthew McGee studied the die-off of cichlid species in Lake Victoria that occurred after Nile perch were introduced into the lake in the 1950s.

Since then the perch, Lates niloticus, have decimated the lake’s fish-eating cichlids, once the most species-rich group of cichlids in Lake Victoria. The native fish have essentially been removed and replaced by the invader.

The Orange rock hunter, a predatory cichlid native to Lake Victoria. Fish like this have been almost wiped out by competition from invasive Nile perch.

The Orange rock hunter, a predatory cichlid native to Lake Victoria. Fish like this have been almost wiped out by competition from invasive Nile perch.

The going theory had been that the perch ate the cichlids. In reality, they out-ate them.

Now a postdoctoral researcher at the University of Bern in Switzerland, McGee discovered that Nile perch were able to monopolize fish-eating cichlids’ food source, identifying the primary culprit as the cichlids’ specialized pharyngeal jaws. The findings were published in the November 27 edition of the journal Science.

A specialized trait in several fish groups, pharyngognathy involves multiple modifications of the jaw apparatus in the back of the throat that allow a fish to generate high bite force. This makes it good at feeding on tough and hard prey items.

The innovation is thought to have played an important role in cichlids’ spectacular diversification throughout marine and freshwater ecosystems. But pharyngeal jaws don’t open widely enough to efficiently swallow large prey items such as fish. Instead, fish-eating cichlids must awkwardly chop large prey into pieces.

“This is like trying to cut a steak with a meat tenderizer,” McGee said. “It’ll work eventually, but there are better tools for the job.”

When fast-eating Nile perch invaded the cichlids’ habitat in Lake Victoria, the indigenous species were at a distinct disadvantage.

“We did not anticipate that predatory cichlids would take hours to swallow a fish when Nile perch took seconds,” McGee said. The cichlids were so slow, in fact, that McGee bought a portable desk for use in his lab, so he could do other work while watching his study subjects chew.

The findings illustrate an important side effect of evolution: Innovative adaptations come with liabilities as well as benefits.

“This work overturns the long-held belief that the primary cause of the extinctions was that the Nile perch ate the cichlids,” said Wainwright, who co-authored the study. “It shows that this major evolutionary innovation carries some crucial trade-offs, so that it is not always beneficial.”

For nearly 50 years, the robust pharyngeal jaws of cichlids, wrasses and other pharyngognathous fishes have been considered a classic example of evolutionary innovation that opened up new niches through increased trophic flexibility. Although this is almost certainly correct, McGee’s results suggest that the innovation involves a major trade-off that severely limits the size of prey that can be eaten.

This leads to competitive inferiority in predatory niches and extinction in the presence of a predatory invader lacking the innovation.

McGee added that such trade-offs merit further study, as researchers often assume that major innovations are mostly beneficial without carefully considering their downsides.

“Biologists study trade-offs and specializations all the time, but for some reason major evolutionary innovations often get a free pass,” he said. “Our study shows that competition from invasive species is a bigger deal than we previously thought, which shakes everything up.”

McGee also hopes the discovery will increase efforts to conserve fish-eating Victorian cichlids.

“Endangered fish get a lot less attention than tigers and rhinos, but I think our work shows that it is critically important to dedicate resources towards preserving these species as well, not just for conservation but for increasing our understanding of biodiversity and the processes that sustain it,” he said.

The research was done with funding by the National Science Foundation and Sloan Foundation, and with assistance from the Lake Victoria Species Survival Program, the Tanzania Fisheries Research Institute and the American Cichlid Association.

More information: Here’s the paper in Science

Betsy Towner Levine is senior writer in the UC Davis College of Biological Sciences. 

UC Davis/Chile research targets muscle disease

Keith Baar’s laboratory in the Department of Neurobiology, Physiology and Behavior is beginning a collaboration on inherited muscle disease with at team at the University of Finis Terrae in Santiago, Chile supported by an anonymous donation to the Chilean university.

The project will focus on disorders related to desmin, a protein within muscle that transmits force, said Baar, associate professor in the College of Biological Sciences.

Keith Baar studies how muscle and connective tissue grow and function.

Keith Baar studies how muscle and connective tissue grow and function.

Muscles that lack desmin due to a genetic defect are unable to transmit force and as a result get injured more easily and over time get more connective tissue, he said.

Muscle strength and size is closely related both to longevity and quality of life as we age, Baar said. Conditions that weaken the muscles – including inherited disorders (like desminopathies and dystrophy), cancer and aging – all share common properties, he said.

“If we can find ways to build or retain muscle, we can help people lead longer, happier and more productive lives,” he said.

Baar’s partner in the project is Professor Herman Zbinden of the University of Finis Terrae, a private university in Chile with a focus on exercise and muscle physiology.

The two-year project will support a postdoctoral researcher, who will divide their time equally between Santiago and Davis. It will also enable Chilean researchers to spend time at UC Davis learning techniques and conducting experiments in Baar’s laboratory.

Baar’s Functional Molecular Biology Lab works on the molecular biology of muscles and skeletal tissues, including growing new tissues in the lab.

More information: Story from University of Finis Terrae (in Spanish)

How antiviral from Hepatitis C could damage other viruses

A new virus-killing peptide springs from an unexpected source: another virus, Hepatitis C.

Now biomedical engineers at UC Davis and Nanyang Technological University, Singapore show how the HCV alpha-helical (AH) peptide can make holes in the types of membranes that surround viruses. The work is published Jan. 5 in Biophysical Journal.

HCV-AH is known to be active against a wide range of viruses including West Nile, dengue, measles and HIV.

The HCV-AH peptide appears to target an Achilles’ heel common to many viruses, most likely a property of the lipid coating or envelope, said study author Atul Parikh, professor of biomedical engineering at UC Davis. That means that it’s less likely that viruses can readily evolve to become resistant to the peptide.

Parikh, Nam-Joon Cho of Nanyang Technological University and colleagues tested the properties of HCV-AH with simplified model lipid membranes. Essentially, these are tiny “soap bubbles” made up of a layer of lipids, just like living cells and viruses, but without the cellular contents.

The HCV-AH peptide had different effects depending on the composition of the membrane. When the membranes were rich in cholesterol, like those of many viruses, the peptide caused the membrane lipids to clump together forming bright spots under the microscope. But cholesterol-free membranes did not show the same effect.

Video: “Bubbling” shows membranes failing as a result of exposure to AH peptide

Additional experiments showed that the peptide also had different effects depending on the size of the vesicle.

There are currently no antiviral drugs that work by destabilizing the virus membrane, Cho said, although some have been proposed.

The researchers now plan to move to study the effects of the peptide on more complex membranes and then live human cells and viruses. If the mechanism still seems promising, it could eventually move into preclinical testing.

“Understanding how the drug candidate interacts with these biologically important lipids, we reason, should open the door to deciphering the rich and complex biology of these systems and lead to new opportunities for antiviral strategies,” Parikh said.

The work was supported by the U.S. Department of Energy, the National Research Foundation and the National Medical Research Council of Singapore, and Nanyang Technological University.

Vesicles exposed to HCV-AH peptide show damage as membranes are reorganized. (JM Hanson).

Vesicles exposed to HCV-AH peptide show damage as membranes are reorganized. (JM Hanson).

More information: Read the original paper

Related: Emergent behavior lets bubbles sense environment












UC Davis joins UC Water effort to improve state’s water security

By Kat Kerlin

It’s hard to manage what you don’t measure.

UC Davis is playing a major role in solving California’s biggest water woes by joining forces across the UC system. The UC Water Security and Sustainability Research Initiative aims to account for all of California’s water, better understand how and where it flows, and help demonstrate how water can be managed differently to allow for greater water security.

“Our goal is to learn more about our entire water system so we can concretely begin to restructure it, especially with regard to smarter management of groundwater and surface water,” said Graham Fogg, a UC Davis hydrogeology professor and co-principal investigator of UC Water for the Davis campus. “We’ve gotten by pretty well in the past because we had enough groundwater storage to absorb our mistakes. But in this new age of scarcity, that’s less and less true.”

To better manage California's water, we need to measure where it goes.

To better manage California’s water, we need to measure where it goes. (Gregory Urquiaga/UC Davis)

UC Water plans to tie together UC Merced’s snow and surface water sensor system, which tracks how much water is entering streams and reservoirs from the Sierra Nevada mountains, with the groundwater expertise of UC Davis and UC Santa Cruz to see the groundwater impacts downstream. UC Berkeley is addressing how science can be implemented with policy. As a multi-campus research initiative, UC Water is expanding to include more water researchers throughout the UC.

“It’s not so much that we’re out of water,” said UC Water program coordinator Leigh Bernacchi. “It’s that we’re not tracking it well. We don’t really know where it goes or how it’s used. Information is the key bottleneck.”

Making water clear

Fogg said that while water levels in reservoirs are well-known, it’s less clear for groundwater. He’s working to develop a tool, using Yolo County as a prototype, that can calculate the change in groundwater storage on a monthly or weekly basis. With a better understanding of how water moves in the system, UC Davis will also work to develop a water accounting tool that can determine how groundwater recharging today is expected to improve future water storage.

“Increasing groundwater recharge is key, but it must be done many years in advance to effect water security and sustainability. We will never convince people to massively increase recharge water today, decades before it’s ultimate use, unless we can demonstrate the long-term future benefits,” Fogg said. “If people are supposed to manage water differently, how can they if they don’t know the state of the system at any given time? A lot of this has to do with making the water system more transparent and managing for the long term.”

‘I think of us as the water campus’

UCOP has provided $4 million in funding for the UC Water over four years. In the first year, UC Water additionally awarded $120,000 in grants to several UC Davis scientists:

  • Professor Jay Lund, director of the Center for Watershed Sciences, is lead investigator on a grant shared with UC Merced professor Mark Beutel and UC Berkeley’s Stephanie Carlson to optimize water flows and temperature of reservoirs for fish during drought.
  • Senior researcher Josué Medellín-Azuara is using drones to study evapotranspiration in the Sacramento-San Joaquin Delta.
  • Professor Kate Scow and Cooperative Extension specialist Daniele Zaccaria, both of UC Davis, will study the application of technologies for estimating water use in row crops at the Russell Ranch Sustainable Agricultural Facility

“UC Davis is itself impressive in water,” Fogg said. “I think of us as the water campus. But there are these critical strengths in water at other UCs. Leveraging those produces not only stronger research, but potentially could be game-changing for California water management.”

Follow Kat on Twitter at @UCDavis_Kerlin.

iGEM competition stretches student researchers

By Pat Bailey

As 2015 draws to a close, a team of UC Davis undergraduates can look back with pride and a sigh of relief on one of the most grueling but rewarding experiences of their college career.

Students Gabriel Freund, Muntaha Samad, Andrew Shepherd, Logan Vinson and Joanne Wu, were selected last spring as members of UC Davis’ 2015 iGEM (International Genetically Engineered Machines) team. They were joined by Andrew Michelmore, who is from Davis but attends Santa Clara University.

Gabriel Freund in the lab

Gabriel Freund in the lab

The team members, with majors ranging from biology to engineering, participated with some 280 teams from 30 countries in the final Jamboree competition in Boston, just as fall quarter kicked off here on campus. Throughout the summer they had designed and tested a small device capable of detecting the presence of the chemical triclosan in water, a project they chose for iGEM.

They were advised by faculty members Justin Siegel, Ilias Tagkopoulos and Mark Facciotti as well as graduate students Alex Carlin, Aaron Cohen and Russell Neches, and staff researcher Andrew Yao.

Detecting antimicrobial contamination

Triclosan is an antimicrobial compound used in hand sanitizers, soaps and other household products. It’s effective in slowing or stopping the growth of bacteria, fungi and mildew, but there is concern that triclosan may contribute to bacterial resistance and endanger human health by disrupting normal hormone development.

Research elsewhere also has shown that triclosan is passing through some municipal water treatment plants rather than being removed.

So the iGEM team set out to develop a small device that could be used in research labs and wastewater treatment plants to efficiently and economically identify triclosan in water. They envisioned it as an analytical alternative to gas chromatography-mass spectrometry and ELISA (enzyme-linked immunosorbent assay.)

Their experimental device was designed to work by electronically monitoring the activity of certain enzymes in water samples.  In a normal water sample, there is a predictable pace to enzyme activity, which slows significantly if triclosan is present.

Success at dawn

The summer months flew by as the team members in their various roles scrambled to carry out lab work, interview researchers and consult with experts on the environmental health issues related to triclosan.

Despite the rush to complete the project, things were grinding slowly in the lab. Just one day before the team members were to fly out to Boston, they had yet to succeed in detecting triclosan in water samples.

Freund spent a marathon 16-hour stint in the lab, and sometime just before dawn experienced the “eureka” moment, when the team’s “Fab I” enzyme accurately signaled the presence of triclosan.

“I got it,” Freund said, recalling that moment when exhilaration mixed with exhaustion and he knew that the team would have a functional device to present in Boston.

Competing in Boston

The UC Davis team members were all undergraduate students but because some were a bit older than the undergrad age limit, the team was placed in iGEM’s “overgraduate” division.

The weekend competition included a pre-designed team Wiki page, a 20-minute oral presentation and two poster sessions.

The 2015 UC Davis iGEM team was nominated for, but did not win, first place in the environmental track but was beaten out by the Delft University of Technology in the Netherlands in the overgraduate division.

Now recruiting 2016 iGEM team members

Recruitment is now underway for UC Davis’ 2016 iGEM team members, with applications due by Feb. 1.

Freund cautions that while iGEM is rewarding, the rigorous experience is not for the faint of heart.

“It was a huge challenge; it might have been the hardest thing I’ve ever done,” he said. “I found that it required me to really stretch my intellectual muscle, and at times I felt levels of stress I had never experienced before.”

But he also found that the concentrated summer of lab work, which advisors said was the equivalent of a master’s degree research project, immersed him in science in a way not possible in the classroom.

What advice would Freund give to the 2016-iGEM team members?

“Put your dog in the kennel and kiss your loved ones goodbye,“ he said, smiling.


Students take home trophy in synthetic biology competition (2011)

Olive oil sensor wins international competition for student inventors (2014)

Pat Bailey writes about agricultural and veterinary sciences for UC Davis Strategic Communications. Follow her on Twitter @UCDavis_Bailey.

New results from LUX dark matter detector

Contributed by the LUX Collaboration

The Large Underground Xenon (LUX) dark matter experiment, which operates nearly a mile underground at the Sanford Underground Research Facility (SURF) in the Black Hills of South Dakota, has already proven itself to be the most sensitive dark matter detector in the world. Now, a new set of calibration techniques employed by LUX scientists has again dramatically improved its sensitivity.

Researchers with LUX are looking for WIMPs, weakly interacting massive particles, which are among the leading candidates for dark matter.

“The nature of dark matter is one of the most important questions facing physics today, and this effort by the LUX collaboration is the most sensitive experiment for direct detection of WIMPs,” said Mani Tripathi, professor of physics at UC Davis and one of the founding principal investigators of LUX.

The LUX team at UC Davis consists of postdoctoral researchers Aaron Manalaysay and Scott Stephenson, and graduate students Sergey Uvarov, Brian Lenardo, James Morad, and Jacob Cutter.  Several undergraduate students are involved in this research, including Eric Emdee, Thomas Kurty, Nathaniel Nunez, Jack Zilinkas, and Megha Jain.

The new research is described in a paper submitted to Physical Review Letters and posted to ArXiv. The work re-examines data collected during LUX’s first three-month run in 2013, and helps to rule out the possibility of dark matter detections at low-mass ranges where other experiments had previously reported potential detections.

Dark matter is thought to be the dominant form of matter in the universe. Scientists are confident in its existence because the effects of its gravity can be seen in the rotation of galaxies and in the way light bends as it travels through the universe. Because WIMPs are thought to interact with other matter only on very rare occasions, they have yet to be detected directly.

Video: 4850 feet below: The hunt for dark matter (Science Friday)

Giant tank of liquid xenon

LUX consists of a third-of-a-ton of liquid xenon surrounded with sensitive light detectors. It is designed to identify the very rare occasions when a dark matter particle collides with a xenon atom inside the detector. When a collision happens, the xenon atom will recoil and emit a tiny flash of light, which is detected by LUX’s light sensors. The detector’s location at Sanford Lab beneath a mile of rock helps to shield it from cosmic rays and other radiation that would interfere with a dark matter signal.

So far, LUX hasn’t detected a dark matter signal, but its exquisite sensitivity has allowed scientists to all but rule out vast mass ranges where dark matter particles might exist. These new calibrations increase that sensitivity even further.

Calibrating with neutrons

One calibration technique used neutrons as stand-ins for dark matter particles. Bouncing neutrons off the xenon atoms allows scientists to quantify how the LUX detector responds to the recoiling process.  Understanding this process in depth is aided by the Noble Element Simulation Technique (NEST), which is a software package developed primarily at UC Davis.

“Calibration of the LUX detector with neutrons has helped to inform our physics models describing the response that liquid xenon will have to WIMPs,” said Brian Lenardo, who led the effort to build these physics models that are used in NEST, and which are integral to the dark-matter results of LUX.

The neutron experiments help to calibrate the detector for interactions with the xenon nucleus. But LUX scientists have also calibrated the detector’s response to the deposition of small amounts of energy by struck atomic electrons. That’s done by injecting tritiated methane—a radioactive gas—into the detector.

“In a typical science run, most of what LUX sees are background electron recoil events”, said Professor Carter Hall of the University of Maryland. “Tritiated methane is a convenient source of similar events, and we’ve now studied hundreds of thousands of its decays in LUX. This give us confidence that we won’t mistake these garden-variety events for dark matter.”

Another radioactive gas, krypton, was injected to help scientists distinguish between signals produced by ambient radioactivity and a potential dark matter signal.

“The krypton mixes uniformly in the liquid xenon and emits radiation with a known, specific energy, but then quickly decays away to a stable, non-radioactive isotope. ” said Dan McKinsey, a UC Berkeley physics professor and co-spokesperson for LUX who is also an affiliate with Lawrence Berkeley National Laboratory. “By measuring the light and charge produced by these krypton events throughout the liquid xenon, we can flat-field the detector’s response, allowing better separation of dark matter events from natural radioactivity. ”

Computer simulations

LUX improvements coupled to the advanced computer simulations at Lawrence Berkeley National Laboratory’s National Energy Research Scientific Computing Center (NERSC) and Brown University’s Center for Computation and Visualization (CCV) have allowed scientists to test additional particle models of dark matter that now can be excluded from the search.

The LUX group at UC Davis operates the on-site computing cluster, which is a powerful supercomputer at the lab in South Dakota, and contributes to the processing of data arriving from the LUX detector.  LUX generates enormous amounts of data each second, which has to be shared among various computer clusters around the world and processed to extract meaningful dark-matter results.  “The challenging data-processing process involves code written by numerous people run on computing clusters at various institutions,” said James Morad, who served as LUX’s data processing manager.

Searching and new experiments

LUX is once again in search mode at Sanford Lab. The latest run began in late 2014 and is expected to continue until June 2016. This run will represent an increase in exposure of more than four times compared to our previous 2013 run.

The Sanford Lab is a South Dakota-owned facility. Homestake Mining Co. donated its gold mine in Lead to the South Dakota Science and Technology Authority (SDSTA), which reopened the mine in 2007 with $40 million in funding from the South Dakota State Legislature and a $70 million donation from philanthropist T. Denny Sanford. The U.S. Department of Energy (DOE) supports Sanford Lab’s operations.

The LUX scientific collaboration, which is supported by the DOE and National Science Foundation (NSF), includes 19 research universities and national laboratories in the United States, the United Kingdom, and Portugal.

Planning for the next-generation dark matter experiment at Sanford Lab is already under way. In late 2016 LUX will be decommissioned to make way for a new, much larger xenon detector, known as the LUX-ZEPLIN (LZ) experiment. Compared to LUX’s ⅓ of a ton of liquid xenon, LZ would have a 10-ton  liquid xenon target, which will fit inside the same 72,000-gallon tank of pure water used by LUX.

“The innovations of the LUX experiment form the foundation for the LZ experiment, which is planned to achieve over 100 times the sensitivity of LUX. The LZ experiment is so sensitive that it should begin to detect a type of neutrino originating in the Sun that even Ray Davis’ Nobel Prize winning experiment at the Homestake mine was unable to detect,” according to Harry Nelson from the University of California  Santa Barbara, spokesperson for LZ.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit the Office of Science website at

For more information, please visit the Sanford Lab website at

More information:

LUX Experiment Web Site:

Photos of LUX Experiment: