Tag Archives: function

Berkeley Lab Scientists Create First 3-D Model of a Protein Critical to Embryo Development

By Guest PostSeptember 21, 2012Science3d model, aebp2, alessio maiolica, angstroms, arm1, arm2, berkeley lab, birth defect, cancer, chromatin environment, claudio ciferri, complex, complex 2, crystal structure, DNA, electron microscopy, eva nogales, franz herzog, function, gabriel lander, human, mass spectrometry, mechanism, model, molecular architecture, nucleosome, polycomb, prc2, progression, protein, protein biochemistry, repressive, ruedi aebersold, therapeutic drug

The first detailed and complete picture of a protein complex that is tied to human birth defects as well as the progression of many forms of cancer has been obtained by an international team of researchers led by scientists with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab). Knowing the architecture of this protein, PRC2, for Polycomb Repressive Complex 2, should be a boon to its future use in the development of new and improved therapeutic drugs.

“We present a complete molecular organization of human PRC2 that offers an invaluable structural context for understanding all of the previous biochemical and functional data that has been collected on this complex,” says Berkeley Lab biophysicist Eva Nogales, an electron microscopy expert who led this research. “Our model should also be an invaluable tool for the design of new experiments aimed at asking detailed questions about the mechanisms that enable PRC2 to function and how those mechanisms might be exploited.” (more…)

Evolution is as Complicated as 1-2-3

By Guest PostSeptember 20, 2012Scienceanalysis, bacteria, bacterial evolution, biological function, citrate, citrate molecule, DNA, e coli, evolution, function, genomics, glucose, jeff barrick, michigan, module, mutation, mutational piece, organism, oxygen, potentiation, puzzle, richard lenski, state university, traditional diet, zachary blount

EAST LANSING, Mich. — A team of researchers at Michigan State University has documented the step-by-step process in which organisms evolve new functions.

The results, published in the current issue of Nature, are revealed through an in-depth, genomics-based analysis that decodes how E. coli bacteria figured out how to supplement a traditional diet of glucose with an extra course of citrate. (more…)

Gardener’s Delight Offers Glimpse into the Evolution of Flowering Plants

By Guest PostSeptember 5, 2012Nature, Sciencealessandra sullivan, ancient lineage, anemonella thalictroides, antirrhinum majus, arabidopsis thaliana, blossoms, carpels, darwin, di stilio lab, double dandy peony, double peppermint petunia, doubled strawberry, eudicots, family ranunculaceae, flower, flower diversification, flowering species, function, gene, genetic interruption, geologic time, gunter theissen, kelsey galimba, mutant, mutation, northeastern us, period, petal, pink, plant, plant model, rainer melzer, rose, rue anemone, seed production, sexual organ, sexual reproduction, snapdragon, thalictrum, theadora tolkin, vanilla lily, veronica di stilio

The Pink Double Dandy peony, the Double Peppermint petunia, the Doubled Strawberry Vanilla lily and nearly all roses are varieties cultivated for their double flowers.

The blossoms of these and other such plants are lush with extra petals in place of the parts of the flower needed for sexual reproduction and seed production, meaning double flowers – though beautiful – are mutants and usually sterile.

The genetic interruption that causes that mutation helped scientists in the 1990s pinpoint the genes responsible for normal development of sexual organs stamens and carpels in the plant Arabidopsis thaliana, long used as a plant model by biologists. (more…)

More Sophisticated Wiring, Not Just a Bigger Brain, Helped Humans Evolve Beyond Chimps

By Guest PostAugust 26, 2012Scienceamino acids, autism, bipolar syndrome, brain disease, brain region, brain tissue, cellular protein, chimp, chimp brain, chimpanzee, circadian rhythm, clock, daniel geschwind, DNA, expression, foxp1, foxp2, frontal cortex, frontal lobe, function, gene manufacture, genevieve konopka, genome, hippocampus, human, human brain, human evolution, human gene, hypothesis, jeremy davis turak, kellen winden, plasticity, schizophrenia, striatum, tara friedrich, ucla

Human and chimp brains look anatomically similar because both evolved from the same ancestor millions of years ago. But where does the chimp brain end and the human brain begin?

A new UCLA study pinpoints uniquely human patterns of gene activity in the brain that could shed light on how we evolved differently than our closest relative. The identification of these genes could improve understanding of human brain diseases like autism and schizophrenia, as well as learning disorders and addictions.

The research appears Aug. 22 in the advance online edition of the journal Neuron. (more…)

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…)

Jekyll and Hyde Bacteria Aids or Kills, Depending on Chance

By Guest PostJuly 10, 2012Sciencealex martin, alexander martin, anthony heidt, bacteria, chronic infection, deadly killer, DNA, function, jekyll and hyde, kwi suk kim, michigan state university, microbe, microbiome, microorganism, molecular genetics, pathogen, reproduction, rudolph sloup, todd ciche

EAST LANSING, Mich. — Living in the guts of worms are seemingly innocuous bacteria that contribute to their survival. With a flip of a switch, however, these same bacteria transform from harmless microbes into deadly insecticides.

In the current issue of Science, Michigan State University researchers led a study that revealed how a bacteria flips a DNA switch to go from an upstanding community member in the gut microbiome to deadly killer in insect blood.

Todd Ciche, assistant professor of microbiology and molecular genetics, has seen variants like this emerge sometimes by chance resulting in drastically different properties, such as being lethal to the host or existing in a state of mutual harmony. Even though human guts are more complex and these interactions are harder to detect, the revelation certainly offers new insight that could lead to medical breakthroughs, he said. (more…)

Neurons that Control Overeating also Drive Appetite for Cocaine

By Guest PostJune 25, 2012Scienceappetite, behavior, body, brain, brain function, cocaine, cognitive behavior, diabetes, diphtheria toxin, drug addiction, Environment, function, hypothalamus, jeremy bober, jozelia g ferreira, marcelo o dietrich, metabolic disorder, neurons, obesity, overeating, tamas l horvath, transgenic mice

Researchers at Yale School of Medicine have zeroed in on a set of neurons in the part of the brain that controls hunger, and found that these neurons are not only associated with overeating, but also linked to non-food associated behaviors, like novelty-seeking and drug addiction.

Published in the June 24 online issue of Nature Neuroscience, the study was led by Marcelo O. Dietrich, postdoctoral associate, and Tamas L. Horvath, the Jean and David W. Wallace Professor of Biomedical Research and chair of comparative medicine at Yale School of Medicine.

In attempts to develop treatments for metabolic disorders such as obesity and diabetes, researchers have paid increasing attention to the brain’s reward circuits located in the midbrain, with the notion that in these patients, food may become a type of “drug of abuse” similar to cocaine. Dietrich notes, however, that this study flips the common wisdom on its head. (more…)

Homing in on Higgs: Michigan Researchers Predict Summer Discovery

By Guest PostJune 4, 2012Scienceaaron armbruster, algorithms, atlas, atoms, bing zhou, CERN, Chicago, electromagnetic radiation, electrons, fermilab, forces, function, geneva, gordon kane, higgs, higgs boson, higgs field particles, homer neal, jianming qian, junjie zhu, Large Hadron Collider, laws, laws of nature, lhc, missing piece, Nature, neutrons, newton, particle physics, physics theory, protons, quarks, rudolf thun, standard model, stephen hawking, summer, switzerland, tevatron particle accelerator, university of michigan, vacuum like state

ANN ARBOR, Mich.— Whether the Higgs boson exists could be settled by the end of summer, say University of Michigan physicists involved in the search for the missing piece of particle physics’ Standard Model.

“We’re zooming in,” said Jianming Qian, physics professor in the College of Literature, Science & the Arts. “We are increasing the data set and improving our search algorithms. With certain luck, we may be able to discover it this summer, but it depends on nature.”

Qian is one of the 28 U-M researchers involved in experiments at CERN’s Large Hadron Collider (LHC) in Switzerland. He’ll spend most of his time through August in Geneva, where more than 1,000 scientists from around the world have been looking for Higgs since the collider turned on about four years ago. (more…)