Tag Archives: berkeley lab

New Details on the Molecular Machinery of Cancer

By Guest PostFebruary 17, 2013Scienceactivation, adam smith, addition of phosphate, anton arkhipov, autophosphorylation, berkeley lab, cancer, cancer therapies, cancers, cell surface protein, cellular functions, computational modeling, egf ligand, egfr, epidermal growth factor, fluorescence spectroscopy, gene, immune system, jay groves, john kuriyan, ligand induced dimerization, living cells, molecular machinery, nicholas endres, nuclear magnetic resonance, photon, post translational process, protein activation, quantitative approach, quantitative biology techniques, rahul das, receptor, receptor tyrosine kinases, single compound molecule, specific proteins, t-cell receptors, time resolved, uc, university of california

Berkeley Lab Researchers Resolve EGFR Activation Mystery

Researchers with Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley have provided important new details into the activation of the epidermal growth factor receptor (EGFR), a cell surface protein that has been strongly linked to a large number of cancers and is a major target of cancer therapies.

“The more we understand about EGFR and the complex molecular machinery involved in the growth and proliferation of cells, the closer we will be to developing new and more effective ways to cure and treat the many different forms of cancer,” says chemist Jay Groves, one of the leaders of this research. “Through a tour-de-force of quantitative biology techniques that included cutting edge time-resolved fluorescence spectroscopy in living cells, Nuclear Magnetic Resonance, and computational modeling, we’ve determined definitively how EGFR becomes activated through to its epidermal growth factor (EGF) ligand.” (more…)

Genome-wide Atlas of Gene Enhancers in the Brain On-line

By Guest PostFebruary 6, 2013Scienceautism, axel visel, basal ganglia, berkeley lab, biological functions, brain on line, cerebral cortex, cerebrum, chip seq studies, chromatin immunoprecipitation, cognition, collection of data, dalit may, dna basepairs, dna elements, embryonic forebrain, emotion, epilepsy, evolution, gene, gene enhancers, gene regulating elements, gene regulatory functions, genetic mutations, genome wide atlas, gray matter, hani girgis, human brain, human diseases, junk dna, leila taher, molecular toolbox, motor functions, neurological disorders, non coding mutation, olga golonzhka, protein coding genes, schizophrenia, sequences of dna, telencephalon

Collaboration Led by Berkeley Lab Researchers Creates High-Resolution Map of Gene Regulatory Elements in the Brain

Future research into the underlying causes of neurological disorders such as autism, epilepsy and schizophrenia, should greatly benefit from a first-of-its-kind atlas of gene-enhancers in the cerebrum (telencephalon). This new atlas, developed by a team led by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) is a publicly accessible Web-based collection of data that identifies and locates thousands of gene-regulating elements in a region of the brain that is of critical importance for cognition, motor functions and emotion.

“Understanding how the brain develops and functions, and how it malfunctions in neurological disorders, remains one of the most daunting challenges in contemporary science,” says Axel Visel, a geneticist with Berkeley Lab’s Genomics Division. “We’ve created a genome-wide digital atlas of gene enhancers in the human brain – the switches that tell genes when and where they need to be switched on or off. This enhancer atlas will enable other scientists to study in more detail how individual genes are regulated during development of the brain, and how genetic mutations may impact human neurological disorders.” (more…)

New Research Will Help Shed Light on Role of Amazon Forests in Global Carbon Cycle

By Guest PostFebruary 1, 2013Environmentabsorbing, alan di vittorio, Amazon, amazon basin, amazon forest landscape, analytical method, annual carbon accumulation, atmosphere, berkeley lab, biogeochemical process, biogeochemistry, brazil, carbon cycle, carbon cycling, carbon dioxide pollution, carbon sequestration, central amazon, climate change, climatic warming, co2 concentration, CO2 emissions, daniel marra, dar roberts, earth, forest carbon budgets, forest mortality patterns, gabriel ribeiro, Germany, global climate system, global warming effect, human activities, hurricane katrina, impact, jeffrey chambers, joerg tews, manaus, max planck institute, mortality map, natural disturbances, old growth forests, pixel, planet, plot based analyses, positive feedback mechanism, robinson negron juarez, satellite images, simulation modeling, spatial scale, superstorm sandy, terrestrial ecosystems, tree mortality patterns, trends, tropical, tulane university

Berkeley Lab scientists devise new tools for detecting previously unknown tree mortality.

The Earth’s forests perform a well-known service to the planet, absorbing a great deal of the carbon dioxide pollution emitted into the atmosphere from human activities. But when trees are killed by natural disturbances, such as fire, drought or wind, their decay also releases carbon back into the atmosphere, making it critical to quantify tree mortality in order to understand the role of forests in the global climate system. Tropical old-growth forests may play a large role in this absorption service, yet tree mortality patterns for these forests are not well understood.

Now scientist Jeffrey Chambers and colleagues at the U.S. Department of Energy’s (DOE) Lawrence Berkeley National Laboratory (Berkeley Lab) have devised an analytical method that combines satellite images, simulation modeling and painstaking fieldwork to help researchers detect forest mortality patterns and trends. This new tool will enhance understanding of the role of forests in carbon sequestration and the impact of climate change on such disturbances. (more…)

Synchrotron Infrared Unveils a Mysterious Microbial Community

By Guest PostJanuary 31, 2013Science16s rrna gene, acid mine runoff, advanced light source, alexander probst, als, ancient things, another amazing lifestyle, archaea, bacteria, barbs, berkeley lab, biochemistry, biofilm, black smokers, boiling hot springs, bsisb, carbon, christine moissl eichinger, common hydrocarbon, deep sea, deepwater horizon, dna microarray, extremophiles, fatty acids, fourier transform, functional groups, giovanni birarda, gulf of mexico, hami, hami protein, hoi-ying Holman, hooks, hydrogen atoms, infrared spectromicroscopy, inhospitable environments, jet propulsion laboratory, kasthuri venkateswaran, latin, long alkylic chains, lovers, membrane lipids, microbe samples, muehlbacher schwefelquelle, mysterious microbial community, NASA, oil plume, oil spill research, phylochip, protein strands, second genome, sippenauer moor, sm1 euryarchaeon, sm1 research team, southern germany, sr ftir, strings of pearls, sulfur springs, synchrotron ftir, synchrotron infrared, synchrotron radiation, syntrophic, todd desantis, university of regensburg

Berkeley Lab scientists join an international collaboration to understand how archaea and bacteria work together deep in a cold sulfur spring

In the fall of 2010, Hoi-Ying Holman of the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) was approached by an international team researching a mysterious microbial community discovered deep in cold sulfur springs in southern Germany.

“They told me what they were doing and said, ‘We know what you contributed to the oil-spill research,’” recalls Holman, who heads the Chemical Ecology group in Berkeley Lab’s Earth Sciences Division. “They wondered if I could help them determine the biochemistry of their microbe samples.” (more…)

New Path to More Efficient Organic Solar Cells Uncovered at Berkeley Lab’s Advanced Light Source

By Guest PostJanuary 12, 2013Environmentacceptor, advanced light source, affordable, als, als beamlines, amount, berkeley lab, brian collins, christopher mcneill, convert, crystallinity, donor, earth, efficient, electricity, eliot gann, energy use, exciton journey, fossil fuels, fullerene solar film, harald ade, john tumbleston, land mass, nanometers, north Carolina, organic cell, photovoltaic cells, photovoltaic devices, physicist, polymer, r soxs, research, resonant soft, silicon based, size matters, solar cell, solar energy, solvent diiodooctane, state university, stxm, sunlight, ultraviolet light beams, volume, x ray, x ray scattering, zhe li

Why are efficient and affordable solar cells so highly coveted? Volume. The amount of solar energy lighting up Earth’s land mass every year is nearly 3,000 times the total amount of annual human energy use. But to compete with energy from fossil fuels, photovoltaic devices must convert sunlight to electricity with a certain measure of efficiency. For polymer-based organic photovoltaic cells, which are far less expensive to manufacture than silicon-based solar cells, scientists have long believed that the key to high efficiencies rests in the purity of the polymer/organic cell’s two domains – acceptor and donor. Now, however, an alternate and possibly easier route forward has been shown.

Working at Berkeley Lab’s Advanced Light Source (ALS), a premier source of X-ray and ultraviolet light beams for research, an international team of scientists found that for highly efficient polymer/organic photovoltaic cells, size matters. (more…)

How Computers Push on the Molecules They Simulate

By Guest PostJanuary 9, 2013Scienceacceleration, albert einstein, algorithm, analytical results, artifacts, atoms and molecules, behavior, Berkeley, berkeley lab, calculation, california, california institute, chemical fuel, collide, computer method, conserve energy, david sivak, digital representation, digitize time, dna repair, driving force, effective friction, energy dense, equation, error, finite time steps, fluid, french physicist, gavin crooks, john chodera, langevin dynamics, model brownian motion, modeling molecular system, modern computer, molecular machines, molecular scale motion, molecule, momentum, natural system, nonequilibrium driving force, nonequilibrium statistical mechanics, particle, passage of time, paul langevin, photosynthesis, pollen grain, qb3, quantitative biosciences, quantum mechanics, real world, simulation, source, tenacious errors, theoretical method, thermal energy, toy models, university, velocity, water, water molecules

Berkeley Lab bioscientists and their colleagues decipher a far-reaching problem in computer simulations

Because modern computers have to depict the real world with digital representations of numbers instead of physical analogues, to simulate the continuous passage of time they have to digitize time into small slices. This kind of simulation is essential in disciplines from medical and biological research, to new materials, to fundamental considerations of quantum mechanics, and the fact that it inevitably introduces errors is an ongoing problem for scientists.

Scientists at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have now identified and characterized the source of tenacious errors and come up with a way to separate the realistic aspects of a simulation from the artifacts of the computer method. The research was done by David Sivak and his advisor Gavin Crooks in Berkeley Lab’s Physical Biosciences Division and John Chodera, a colleague at the California Institute of Quantitative Biosciences (QB3) at the University of California at Berkeley. The three report their results in Physical Review X. (more…)

A New Way to Study Permafrost Soil, Above and Below Ground

By Guest PostJanuary 6, 2013Environmentarctic landscape, arctic tundra, atmosphere, barrow region, berkeley lab, carbon dioxide, cessna aircraft, climate change, electrical resistance tomography, electromagnetic data, geophysical measurements, greenhouse gasses, ground penetrating radar, large spatial scales, lidar, lidar airborne measurements, methane, microtopography, ngee arctic project, permafrost layer, permafrost soils, polygons, remote sensing device, remote sensing tools, surface topography, susan hubbard, terrestrial ecosystem, trapped carbon

Berkeley Lab research could lead to a better understanding of the Arctic ecosystem’s impact on the planet’s climate

What does pulling a radar-equipped sled across the Arctic tundra have to do with improving our understanding of climate change? It’s part of a new way to explore the little-known world of permafrost soils, which store almost as much carbon as the rest of the world’s soils and about twice as much as is in the atmosphere.

The new approach combines several remote-sensing tools to study the Arctic landscape—above and below ground—in high resolution and over large spatial scales. It was developed by a group of researchers that includes scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). (more…)

Boosting Galactan Sugars Could Boost Biofuel Production

By Guest PostDecember 23, 2012Environmentai oikawa, april liwanag, arabidopsis thaliana, atmosphere, berit ebert, berkeley lab, bioenergy fuel crops, biofuels, carbon neutral, carsten rautengarten, cellulosic biomass, denmark, diesel, emilie rennie, enzyme, ethanol, ferment, fuels, galactan, galactan synthase, galactose, gals1, gals2, gals3, gasoline, gt92 enzyme, gt92 proteins, henrik scheller, jet fuels, mads clausen, mathias andersen, mechanical stress, miscanthus, overexpressors, pentoses, plant cell walls, polymer, six carbon sugar, snowfall, switchgrass, technical university, wind, yeast, yves verhertbruggen, β galactan synthase

Collaboration at JBEI Identifies the First Enzyme Linked to Galactan Synthesis

Galactan is a polymer of galactose, a six-carbon sugar that can be readily fermented by yeast into ethanol and is a target of interest for researchers in advanced biofuels produced from cellulosic biomass. Now an international collaboration led by scientists at the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) has identified the first enzyme capable of substantially boosting the amount of galactan in plant cell walls.

Unlike ethanol, advanced biofuels synthesized from the sugars in plant cells walls could replace gasoline, diesel and jet fuels on a gallon-for-gallon basis and be dropped into today’s engines and infrastructures with no modifications required. Also, adanced biofuels have the potential to be carbon-neutral, meaning they could be burned without adding excess carbon to the atmosphere. Among the key challenges to making advanced biofuels cost competitive is finding ways to maximize the amount of plant cell wall sugars that can be fermented into fuels. (more…)