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 Strategic Communications, and mostly edited by Andy Fell.

UC Davis Releases New Version C-STEM Studio for Teaching Math with Coding

The Center for Integrated Computing and STEM Education at the University of California, Davis, has released version 4 of its popular C-STEM Studio software suite. In addition to free breakthrough tools for teaching math, coding, robotics and making, this major update includes expanded support with textbooks and curriculum for Lego Mindstorms NXT and EV3 robots, Raspberry Pi computers and Arduino control boards as well as Barobo Linkbots. These hardware platforms and related curriculum are seamlessly integrated in C-STEM Studio for learning math with hands-on physical computing and real-world projects.

C-STEM Studio is compatible with robots widely used in school classrooms.

Video: Why Study Bird Brains?

Why study the brains of birds? Do birds even have brains worth talking about? In fact, birds can show complex behavior and mental function. We can learn a lot from studying the neuroscience of birds — knowledge that we can relate to how human brains function in health and disease. In this video, Rebecca Calisi Rodriguez, assistant professor of neurobiology, physiology and behavior in the UC Davis College of Biological Sciences, introduces her own work on bird brains and talks to some prominent neuroscientists about their work.

More information

Rebecca Calisi’s lab website 

Where Things Go Wrong: Perspective on Cascading Failures

By Aditi Risbud Bartl

Sometimes, one darn thing leads to another in a series of cascading failures. Understanding the weak points that lead to such cascades could help us make better investments in preventing them.

Professor Raissa D’Souza in the UC Davis College of Engineering studies complex systems and how they can go wrong.

In the Nov. 17 issue of Science, Raissa D’Souza, professor of computer science and mechanical and aerospace engineering at UC Davis, wrote a perspective article about cascading failures that arise from the reorganization of flows on a network, such as in electric power grids, supply chains and transportation networks.

Diet and the Brain: Exploring the Food-Brain Axis

by Greg Watry

Nearly 47 million people worldwide live with dementia, according to the Alzheimer’s Association. That number is expected to rise to 76 million by 2030. While there is no cure for dementia, scientists are investigating various drugs to help mitigate cognition loss associated with the condition.

UC Davis researchers propose that foods provide signals that influence the brain and other body systems.

When it comes to understanding and preventing age-related cognitive dysfunction, Professor Raymond Rodriguez, Department of Molecular and Cellular Biology in the College of Biological Sciences at UC Davis, looks to food for answers.

New X-ray Spectroscopy Explores Hydrogen-generating Catalyst

Using a newly developed technique, researchers from Japan, Germany and the U.S. have identified a key step in production of hydrogen gas by a bacterial enzyme. Understanding these reactions could be important in developing a clean-fuel economy powered by hydrogen.

The single-celled green alga Chlamydomonas reinhardtii has an iron-based enzyme that can generate hydrogen gas. (JGI)

The team studied hydrogenases – enzymes that catalyze production of hydrogen from two widely distributed organisms: Chlamydomonas reinhardtii, a single-cell algae and Desulfovibrio desulfuricans, a bacterium.

In both cases, their hydrogenase enzymes have an active site with two iron atoms.

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

For more podcast episodes, subscribe to Three Minute Egghead on iTunes or follow us on Soundcloud.

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.

Supercomputer Simulates Dynamic Magnetic Fields of Jupiter, Earth, Sun

By Becky Oskin

As the Juno space probe approached Jupiter in June last year, researchers with the Computational Infrastructure for Geodynamics’ Dynamo Working Group were starting to run simulations of the giant planet’s magnetic field on one of the world’s fastest computers. While the timing was coincidental, the supercomputer modeling should help scientists interpret the data from Juno, and vice versa.

Video: Simulation of Jupiter’s magnetic fields 

“Even with Juno, we’re not going to be able to get a great physical sampling of the turbulence occurring in Jupiter’s deep interior,” Jonathan Aurnou, a geophysics professor at UCLA who leads the geodynamo working group, said in an article for Argonne National Laboratory news. “Only a supercomputer can help get us under that lid.”