Tag Archives: prediction

Form, Function and Folding: In Collaboration with Berkeley Lab, a Team of Scientists Move Toward Rational Design of Artificial Proteins

By Guest PostAugust 26, 2012Scienceamino acid, barney yoo, berkeley lab, bioinspired nanomaterial, blind structure, function, glenn butterfoss, ilya chorny, jonathan jaworski, ken dill, kent kirshenbaum, modeling, molecular foundry, n alkyl, natural selection, new york university, peptoid molecule, peptoid trimers, prediction, protein, protein sequence, qm, qm calculation, remd, richard bonneau, ronald zuckermann, stony brook university, structure, synthetic cousin, temple university, vincent voelz, xray crystallography

In the world of proteins, form defines function. Based on interactions between their constituent amino acids, proteins form specific conformations, folding and twisting into distinct, chemically directed shapes. The resulting structure dictates the proteins’ actions; thus accurate modeling of structure is vital to understanding functionality.

Peptoids, the synthetic cousins of proteins, follow similar design rules. Less vulnerable to chemical or metabolic breakdown than proteins, peptoids are promising for diagnostics, pharmaceuticals, and as a platform to build bioinspired nanomaterials, as scientists can build and manipulate peptoids with great precision. But to design peptoids for a specific function, scientists need to first untangle the complex relationship between a peptoid’s composition and its function-defining folded structure. (more…)

Going with the Flow

By Guest PostJuly 29, 2012Environmentalgal blooms, bp settlement, bruce lipphardt, buoys, carthe, deepwater horizon, dennis kirwan, drifters, google earth, gps device, gulf of mexico, helga huntley, ocean current, oceanography, oil spill, plume movement, prediction, satellite gps, university of delaware

Scientists studying ocean currents and oil spills with large-scale experiment

Scientists are releasing hundreds of floating GPS devices into the Gulf of Mexico this week near the Deepwater Horizon site to study the role of ocean currents in oil spills. The experiment is the largest in scale of its kind, deploying 300 satellite-tracked, untethered buoys, called drifters, over the course of two and a half weeks.

“We’re trying to use the drifters as a simulation of an oil spill,” said Dennis Kirwan, Mary A.S. Lighthipe Professor of Marine Studies in the University of Delaware’s College of Earth, Ocean, and Environment. “This is a big event in oceanography.” (more…)

What’s Happening with the Higgs Boson

By Guest PostJune 28, 2012Scienceantibottom quark, atlas, beate heinemann, CERN, cms, dark matter, data reduction, electron volts, electrons, extra dimension, fermions, gamma rays, geneva, higgs, higgs boson, higgs field, ian hinchliffe, inner detector, Large Hadron Collider, lhc, miniature black holes, murdock gil gilchriese, nuclear research, particles of matter, photon channel, photons, prediction, quarks, Space, specific masses, standard model, supersymmetry, switzerland, tau particles, w bosons

Berkeley Lab scientists, major contributors to the ATLAS experiment at the Large Hadron Collider, explain what the excitement is about

CERN, the European Organization for Nuclear Research headquartered in Geneva, Switzerland, will hold a seminar early in the morning on July 4 to announce the latest results from ATLAS and CMS, two major experiments at the Large Hadron Collider (LHC) that are searching for the Higgs boson. Both experimental teams are working down to the wire to finish analyzing their data, and to determine exactly what can be said about what they’ve found.

“We do not yet know what will be shown on July 4th,” says Ian Hinchliffe, a theoretical physicist in the Physics Division at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), who heads the Lab’s participation in the ATLAS experiment. “I have seen many conjectures on the blogs about what will be shown: these are idle speculation. Things are moving very fast this week, and it’s an exciting time at CERN. Many years of hard work are coming to fruition.” (more…)

It’s in the Genes: Research Pinpoints How Plants Know When to Flower

By Guest PostMay 27, 2012Nature, Scienceandrew millar, arabidopsis, barley, benjamin to, biofuels, biology, circadian clock, factors, fkf1 protein, flowering locus t, flowering plants, know, mathematical model, molecular changes, molecular events, photoreceptor, plant, plants, prediction, protein, robert smith, sandra hines, scientists, sequence, shoot apex, sunlight, takato imaizumi, time keeping mechanism, university of edinburgh, university of washington, uw lab, wheat, when to flower, young hun song

Scientists believe they’ve pinpointed the last crucial piece of the 80-year-old puzzle of how plants “know” when to flower.

Determining the proper time to flower, important if a plant is to reproduce successfully, involves a sequence of molecular events, a plant’s circadian clock and sunlight.

Understanding how flowering works in the simple plant used in this study – Arabidopsis – should lead to a better understanding of how the same genes work in more complex plants grown as crops such as rice, wheat and barley, according to Takato Imaizumi, a University of Washington assistant professor of biology and corresponding author of a paper in the May 25 issue of the journal Science. (more…)

Hacking Code of Leaf Vein Architecture Solves Mysteries, Allows Predictions of Past Climate

By Guest PostMay 27, 2012Environment, Natureancient greeks, carbon dioxide, christine scoffoni, climate, conifers, cycads, Environment, ferns, flowering plants, fossil record, global ecology, hacking code, images of leaves, lawren sack, leaf fossils, leaf sizes, leaf vein architecture, leaf vein systems, mathematical equation, mathematical linkages, michael rawls, past climate, photosynthesis, photosynthetic rate, plants, prediction, respiration, scaling patterns, superhighways, theophrastus of lesbos, tropical forest tree, ucla life scientists, vein network, water transport, xylem pipes

UCLA life scientists have discovered new laws that determine the construction of leaf vein systems as leaves grow and evolve. These easy-to-apply mathematical rules can now be used to better predict the climates of the past using the fossil record.

The research, published May 15 in the journal Nature Communications, has a range of fundamental implications for global ecology and allows researchers to estimate original leaf sizes from just a fragment of a leaf. This will improve scientists’ prediction and interpretation of climate in the deep past from leaf fossils.

Leaf veins are of tremendous importance in a plant’s life, providing the nutrients and water that leaves need to conduct photosynthesis and supporting them in capturing sunlight. Leaf size is also of great importance for plants’ adaptation to their environment, with smaller leaves being found in drier, sunnier places. (more…)

One Year Later: Japan Quake, Tsunami a Cautionary Tale for Pacific Northwest

By Guest PostMarch 8, 2012Environment, Generalalki, british columbia, cascadia subduction zone, earthquakes, hokkaido university, Japan, jody bourgeois, john vidale, long beach peninsula, magnitude 9, northern california, ocean shores, one year anniversary, oregon, pacific northwest, prediction, puget sound, sapporo, seattle fault, seismometer readings, sunday, tohoku earthquake, tsunami, tsunami evacuation, united states, university of washington, Washington

Sunday marks the one-year anniversary of the great Tohoku earthquake and tsunami that devastated Japan, killing more than 16,000 people and causing billions of dollars in damage.

University of Washington scientists say the event has some important lessons for the Pacific Northwest – most notably, not that a similar event can happen here but that it WILL happen here, and that this region is still much less prepared than Japan was a year ago. (more…)

Evolution of Earliest Horses Driven by Climate Change

By Guest PostFebruary 24, 2012Environment, Nature, Scienceaaron wood, atmosphere, bighorn basin, body size, cabin fork area, carbon, carbon dioxide, cause and effect, climate model, clydesdale, concentration, doug boyer, dwarfing phenomenon, earliest horse, evolution, florida museum of natural history, fossil, geochemical analysis, global temperature, h richard lane, horse teeth, industrial revolution, jonathan bloch, mammal, national science foundation, natural selection, North America, nsf, ocean, ornithologist, oxygen levels, paleocene-eocene thermal maximum, petm, prediction, ross secord, sifrhippus sandae, stephen chester, temperature, university of florida, university of nebraska lincoln, worland, yale

*The hotter it gets, the smaller the animal?*

When Sifrhippus sandae, the earliest known horse, first appeared in the forests of North America more than 50 million years ago, it would not have been mistaken for a Clydesdale.

It weighed in at around 12 pounds–and it was destined to get much smaller over the ensuing millennia.

Sifrhippus lived during the Paleocene-Eocene Thermal Maximum (PETM), a 175,000-year interval of time some 56 million years ago in which average global temperatures rose by about 10 degrees Fahrenheit. (more…)

New U-M Computer Model Predicts Cholera Outbreaks Up To 11 Months in Advance

By Guest PostJanuary 23, 2012Environment, Scienceaaron king, annual monsoon flooding, attack rates, bacterium, Bangladesh, capital city, cholera cases, cholera outbreaks, climate change, climate factors, climate sensitive urban core, climate variability, computer model, cycles of cholera, dhaka, diarrheal disease, disease transmission, ecology, el niño southern oscillation, enso episode, fecal oral diseases, mercedes pascual, michael emch, mohammad yunus, pathogen, post monsoon, prediction, risk factors, robert reiner, sanitary conditions, space and time, spatial location, university of michigan, urban periphery, vaccination, vibrio cholera, warning system

ANN ARBOR, Mich.— A new University of Michigan computer model of disease transmission in space and time can predict cholera outbreaks in Bangladesh up to 11 months in advance, providing an early warning system that could help public health officials there.

The new forecast model applies specifically to the capital city of Dhaka and incorporates data on both year-to-year climate variability and the spatial location of cholera cases at the district level. This allowed the researchers to study both local variation in disease transmission and response to climate factors within the megacity of 14 million people. (more…)