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 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)
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.
“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.
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 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.
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.
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.
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.
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).
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. (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.”
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
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.
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. ”
LUX improvementscoupled 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 science.energy.gov.
A team of researchers from the University of California, Davis and the University of Washington have demonstrated that the conductance of DNA can be modulated by controlling its structure, thus opening up the possibility of DNA’s future use as an electromechanical switch for nanoscale computing. Although DNA is commonly known for its biological role as the molecule of life, it has recently garnered significant interest for use as a nanoscale material for a wide-variety of applications.
In their paper published in Nature Communications, the team demonstrated that changing the structure of the DNA double helix by modifying its environment allows the conductance (the ease with which an electric current passes) to be reversibly controlled. This ability to structurally modulate the charge transport properties may enable the design of unique nanodevices based on DNA. These devices would operate using a completely different paradigm than today’s conventional electronics.
The A-form of DNA between two electrodes.
“As electronics get smaller they are becoming more difficult and expensive to manufacture, but DNA-based devices could be designed from the bottom-up using directed self-assembly techniques such as ‘DNA origami’,” said Josh Hihath, assistant professor of electrical and computer engineering at UC Davis and senior author on the paper. DNA origami is the folding of DNA to create two- and three-dimensional shapes at the nanoscale level.
“Considerable progress has been made in understanding DNA’s mechanical, structural, and self-assembly properties and the use of these properties to design structures at the nanoscale. The electrical properties, however, have generally been difficult to control,” said Hihath.
New Twist on DNA? Possible Paradigms for Computing
In addition to potential advantages in fabrication at the nanoscale level, such DNA-based devices may also improve the energy efficiency of electronic circuits. The size of devices has been significantly reduced over the last 40 years, but as the size has decreased, the power density on-chip has increased. Scientists and engineers have been exploring novel solutions to improve the efficiency.
“There’s no reason that computation must be done with traditional transistors. Early computers were fully mechanical and later worked on relays and vacuum tubes,” said Hihath. “Moving to an electromechanical platform may eventually allow us to improve the energy efficiency of electronic devices at the nanoscale.”
This work demonstrates that DNA is capable of operating as an electromechanical switch and could lead to new paradigms for computing.
To develop DNA into a reversible switch, the scientists focused on switching between two stable conformations of DNA, known as the A-form and the B-form. In DNA, the B-form is the conventional DNA duplex that is commonly associated with these molecules. The A-form is a more compact version with different spacing and tilting between the base pairs. Exposure to ethanol forces the DNA into the A-form conformation resulting in an increased conductance. Similarly, by removing the ethanol, the DNA can switch back to the B-form and return to its original reduced conductance value.
One Step Toward Molecular Computing
In order to develop this finding into a technologically viable platform for electronics, the authors also noted that there is still a great deal of work to be done. Although this discovery provides a proof-of-principle demonstration of electromechanical switching in DNA, there are generally two major hurdles yet to be overcome in the field of molecular electronics. First, billions of active molecular devices must be integrated into the same circuit as is done currently in conventional electronics. Next, scientists must be able to gate specific devices individually in such a large system.
“Eventually, the environmental gating aspect of this work will have to be replaced with a mechanical or electrical signal in order to locally address a single device,” noted Hihath.
The UC Davis members of the team included Juan Manuel Artés and Yuanhui Li of the Department of Electrical and Computer Engineering, and the University of Washington members included M.P. Anantram and Jianqing Qi from the Electrical Engineering Department.
This work is funded by the UC Davis Grant Research Investments in the Sciences and Engineering (RISE), which encourages interdisciplinary work to solve problems facing the world today, as well as the National Science Foundation (Grants 1231915 and 102781).
College students in the STEM fields could see sizable savings thanks to a $600,000 grant awarded to an open source textbook project developed at the University of California, Davis.
The ChemWiki project recently received $600,000 from the National Science Foundation to support further expansion of its open source textbooks into fields including statistics, math, geology, physics, biology and solar energy.
Digital course materials are steadily climbing in use in response to textbook cost concerns, according to an annual survey released in July by the National Association of College Stores. In August, the University of Maryland announced plans to completely eliminate print textbooks this academic year.
The ChemWiki is one of seven wikis that provide free, peer-reviewed textbooks and course materials, such as homework sets, online under an open license. Students can download the texts for free and professors can customize the materials for their courses, such as by rearranging the sequence of information. The seven wikis focus on STEM (science, technology, engineering and mathematics) topics such as biology, math, geology and physics.
“We’re trying to make a central database to completely supplant STEM textbooks,” said ChemWiki founder Delmar Larsen, a UC Davis chemistry professor. “This grant will give us three times the resources than we have had before. Our goal is to expand our reach to 300 million students annually, and a half-billion page views,” Larsen said.
Half of the grant will fund the ChemWiki and half will fund expanding the textbook network, Larsen said. The ChemWiki grant also supports faculty at Sonoma State University, Diablo Valley College, Contra Costa Community College, Hope College in Holland, Michigan, University of Arkansas at Little Rock, Howard University and College of Saint Benedict & Saint John’s University.
Battle of the books
Since March 2014, ChemWiki textbooks have been used in more than 30 different classes at campuses in the United States, Canada and the United Arab Emirates. These courses have saved students more than $1 million, Larsen said.
Some critics of open source textbooks complain that the texts can be rife with errors and therefore lower educational quality for students. However, Larsen said, ChemWiki course materials are peer-reviewed, like traditional print textbooks. “I get about four to five correction requests a week and once fixed they are never a problem, in contrast to traditional textbooks,” Larsen said.
Larsen and his colleagues also pitted the ChemWiki against traditional print textbooks in a recent study funded by a 2013 NSF grant. The study results were published Sep. 17, 2015, in the journal Chemistry Education and Research Practice.
In spring quarter 2014, Larsen taught half of a UC Davis general chemistry class, more than 475 students, using a standard print textbook. A similar number of students heard the same lectures from Larsen and his teaching assistants and studied the same material using the ChemWiki.
The results showed the learning gains for both classes were not statistically different when accounting for student demographics. There was no statistical difference in either class’s performance, Larsen said. Furthermore, high ChemWiki-using students (more than 400 total page views) showed about an eight percent increase in course performance. The results were evaluated by researchers from the Center for Education and Evaluation Services at the UC Davis School of Education.
Millions of visitors
The online textbooks are called wikis because faculty and student volunteers write them. About 5,000 students and 100 faculty have edited the ChemWiki or donated content since 2008. A small group of volunteers is currently translating the organic chemistry textbooks into Spanish and French.
“We need a lot of help to move the project forward,” Larsen said.
The ChemWiki website now has 8 million page views monthly, primarily from students. ChemWiki is the most visited chemistry website in the world and most visited UC Davis website, Larsen said. Currently, about 30 percent of Internet visitors to “ucdavis.edu” head to the ChemWiki.
Larsen said he launched the ChemWiki in 2008 because he was concerned about the high cost of textbooks. “I thought $200 was atrocious for a physical chemistry textbook,” Larsen said. “My response was, ‘I can do better, I should do better.’” Today, a single textbook for health or science majors can cost more than $350, Larsen said.
Open source textbooks are one of several digital options available to college instructors who are concerned about student costs.
UC Davis is also a leader in providing low-cost digital textbooks to students. Through its content licensing program, students (and faculty, who ultimately choose the textbooks) can use digital textbooks provided through UC Davis Stores. The lower digital prices saved students more than $1 million in the program’s first year.
UC Davis was also the first university to offer textbook price comparisons online and the first university to partner with Amazon. UC Davis provides the largest textbook rental program per capita in the United States.
UC Davis will host the National Association of College Stores’ 2016 Textbook Affordability Conference in April 2016.