Podcast: Knots, Math and Reconnection in DNA

If you’ve ever tried to untangle a pair of earbuds, you’ll understand how loops and cords can get twisted up. DNA can get tangled in the same way. In this episode of Three Minute Egghead, UC Davis biomathematician Mariel Vazquez talks about her work on the math of how DNA can be cut and reconnected. The math involved turns out to be involved in other fields as well — from fluid dynamics to solar flares.

https://soundcloud.com/andy-fell/knots-math-and-reconnection-in-dna

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Humans Gathered Grapes Long Before They Cultivated Them

By Diane Nelson

About 22,000 years ago, as the ice sheets that consumed much of North America and Europe began retreating, humans started to eat a fruit that today brings joy to millions of wine drinkers around the world: grapes.

People have been making wine from grapes for at least 8,000 years, but genetic evidence shows that humans influenced grape vines long before that (Gregory Urquiaga/UC Davis).

Protein Synthesis Machinery from Bacterial Consortia in One Shot

By Holly Ober

A new technique developed at UC Davis may have broken the barrier to rapid assembly of pure protein synthesis machinery outside of living cells.

Colored bacteria

E. coli bacteria tagged with different colors produced different mixtures of proteins. Together, the bacterial consortium makes all the proteins needed for mRNA translation/protein synthesis (Fernando Villarreal, UC Davis)

In order to reconstitute cellular reactions outside of biological systems, scientists need to produce the proteins involved. Rapid yet high purity reconstitution of the cellular reactions is critical for the high-throughput study of cellular pathways and cell-free diagnostic tests for various diseases. Reconstituting cellular reactions outside cells, however, requires the separate expression and purification of each protein required to execute the reactions. This process is expensive and time consuming, making the production of more than several proteins at once extremely challenging.

Exploring Role of Fish Oil Derivatives in Kidney Injury

By Kathy Keatley Garvey

Newly published research by an international team of scientists, headed by the Jun-Yan Liu lab of Tongji University, Shanghai, China, and Bruce Hammock’s lab at UC Davis gives insight into how fish oils may be protective or harmful in animal models of acute kidney injury. This knowledge may provide promising therapeutic strategies for those suffering from acute kidney injury, formerly called acute renal failure.

Jun-Yan Liu is exploring how metabolites from oils influence kidney disease.

For Seagrass, Biodiversity Is Both a Goal and A Means For Restoration

By Kat Kerlin

Coral reefs, seagrass meadows and mangrove forests work together to make the Coral Triangle of Indonesia a hotspot for marine biodiversity. The system supports valuable fisheries and endangered species and helps protect shorelines. But it is in global decline due to threats from coastal development, destructive fishing practices and climate change.

From left, Jordan Hollarsmith of Hasanuddin University and UC Davis, and Susan Williams and Katie DuBois of UC Davis look at seabed plots in Indonesia. Photo by Christine Sur, UC Davis

UC Davis Genome Researchers Facilitating NIH Data Commons Pilot

Researchers at the UC Davis School of Veterinary Medicine and Genome Center are taking part in an ambitious NIH initiative to make it easier for scientists to share research data and scientific tools online.

C. Titus Brown is associate professor in the UC Davis School of Veterinary Medicine and Genome Center.

“Harvesting the wealth of information in biomedical data will advance our understanding of human health and disease,” said NIH Director Francis S. Collins in a news release. “However, poor data accessibility is a major barrier to translating data into understanding. The NIH Data Commons Pilot Phase is an important effort to remove that barrier.”

See-through Zebrafish May Hold Clues to Ovarian Cancer

by Greg Watry

For thousands of years, animals have helped humans advance biomedical research. Early Greeks, such as Aristotle and Galen, studied animals to gain insights into anatomy, physiology and pathology. Today, model organisms, like mice, help researchers understand human diseases, opening the door to potential defenses and new therapies.

Postdoc Dena Leerberg, and Bruce Draper, associate professor of molecular and cellular biology in the UC Davis College of Biological Sciences, study reproductive development in zebrafish. David Slipher/UC Davis

Genome Project Aims to Restore Health of Redwood and Giant Sequoia Forests

By Ann Filmer

Some trees are better at surviving drought, fire, pests, and diseases than others. By identifying the genes responsible for these adaptations, scientists can compile a scalable database that will aid resource managers as they plan long-term conservation strategies, particularly as the climate changes.

UC Davis, Johns Hopkins University and Save the Redwoods League are working together to protect this iconic tree.

Professor David Neale, UC Davis Department of Plant Sciences, showed in preliminary research that it is feasible to sequence the redwood, which has a genome 10 times larger than ours. Redwoods are “hexaploid” with  six copies of each chromosome compared to humans’ two copies.

Live Fast Die Young: Updating Signal Detection Theory

Signal Detection Theory is a popular and well-established idea that has influenced behavioral science for around 50 years. Essentially, the theory holds that in a predator-prey relationship, prey animals will show more wariness and be more prone to flee as predators become more common. Danger signals are ambiguous, so in what appears to be a threatening situation, animals are better off running than hanging around to see if a predator really does strike.

Now Pete Trimmer, a postdoctoral research at UC Davis, has taken a fresh look at signal detection theory and come up with what at first look like counterintuitive results. In many cases, he says, animals should actually become less cautious as the risk of predation rises.

Crowdsourced Game Aims to Find Solutions to Aflatoxin

Mars, Inc., UC Davis and partners have launched a crowdsourcing initiative to solve the problem of aflatoxin contamination of crops. A series of aflatoxin puzzles will go online on Foldit, a platform that allows gamers to explore how amino acids are folded together to create proteins. The puzzles provide gamers with a starting enzyme that has the potential to degrade aflatoxin. Gamers from around the world then battle it out to redesign and improve the enzyme so that it can neutralize aflatoxin. Successful candidates from the computer game will be tested in the laboratory of Justin Siegel, assistant professor of chemistry, biochemistry and molecular medicine at UC Davis.