Plants by the Numbers: Math, Computation and the Future of Plant Biology

by Greg Watry

What does the future of plant biology education and research look like? That’s the question on the mind of Siobhan Brady, associate professor of plant biology at UC Davis.

Big data approaches will be key to advances in plant biology, so students need to be trained in these areas. Unknown author/Wikipedia (CC BY 2.5)

In a Plant Physiology commentary paper, Brady, along with 37 other plant biologists from around the world, call for universities to integrate more quantitative and computational techniques into biology-oriented academic curricula. Introducing these skills early, the group advises, will help prepare tomorrow’s plant biologists for the next era of genomics research.

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.

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.

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.”

Swirling Quark-Gluon Plasma is the Swirliest Fluid Ever

STAR detector at Brookhaven

The Solenoidal Tracker at RHIC (STAR) detector is used to search for signatures of the quark-gluon plasma, a form of matter that filled the early universe. (Brookhaven National Laboratory)

The soup of fundamental particles called the quark-gluon plasma can swirl far faster than any known fluid – faster than the mightiest tornado or the superstorm that is Jupiter’s Great Red Spot.

The results, published Aug. 3 in the journal Nature, come from a new analysis of data from the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory.

Deep Underground Neutrino Experiment Breaks Ground

A special groundbreaking was held today (July 21) deep underground in South Dakota. Scientists, engineers and guests turned the first shovelfuls of the 800,000 tons of rock that will be excavated to build the Long Baseline Neutrino Facility (LBNF) at the Sanford Underground Research Facility. The cavern will house a giant detector for the Deep Underground Neutrino Experiment (DUNE).

The goal of DUNE is to better understand neutrinos and their role in the evolution of the universe, including why our universe is made of matter and not antimatter. DUNE will also be able to detect neutrinos from deep space, emitted by supernovae or black holes.

Microbes Could Bring Tea to California

Key to Tea’s Benefits May Be in the Soil

By Becky Oskin

Tea has long been linked to human health benefits like preventing cancer and heart disease. But with hundreds of chemical compounds hidden in tea leaves, it is unclear which substances have the strongest effects.

The slew of “healthy” chemicals in tea varies with the variety of plant, how and where it is grown, and how the leaves are processed. Even soil bacteria contribute to a plant’s chemical profile, including its color, taste and aroma.

Podcast: Melting Ice and the Quasi Liquid Layer

Water ice is peculiar stuff: Even below freezing, when it should be solid, it has a quasi-liquid layer on the outside. That’s what makes ice slippery. In this month’s Three Minute Egghead podcast, UC Davis chemist Davide Donadio describes his recent research looking at the surface of ice and what it has to do with clouds and air pollution.

https://soundcloud.com/andy-fell/melting-ice

Computer simulation of ice

Computer simulation of the surface of ice shows how layers melt in steps (Credit: Davide Donadio)

More information

Hear more Three Minute Egghead on Soundcloud or iTunes

Related news story: Ice Surface Melts One Step at a Time

Podcast: Synestia, a New Type of Planetary Object

In this month’s Three-Minute Egghead, Sarah Stewart and Simon Lock talk about synestias. A synestia is a new type of planetary object, they proposed, formed when a giant collision between planet-size objects creates a mass of hot, vaporized rock spinning with high angular momentum. Synestias could be an important stage in planet formation, and we might be able to find them in other solar systems.

https://soundcloud.com/user-570302262/three-minute-egghead-synestia-a-new-planetary-object?in=user-570302262/sets/three-minute-egghead-a-podcast

More information

News release: Synestia, A New Type of Planetary Object

New Theory Explains How the Moon Got There

Simon Lock’s Synestia Page