Tag Archives: protein

Yale Team Finds Order Amidst the Chaos Within the Human Genome; Mom and Dad’s Contributions Counted and Fossil DNA Not Dead After All

By Guest PostSeptember 6, 2012Sciencebiochemically, bottleneck, chao cheng, data mining, DNA, ekta khurana, elements, encode, encyclopedia, evolutionary remnant, fossil dna, gender specific, gene expression, genome, genome dynamic, human genome, joel rozowsky, junk, key function, koon kiu yan, mark gerstein, marker, middle manager, military, model organism, molecular interaction, non coding, protein, pseudogenes, regulation, rnas, social network, statistical model, worm, yale, yale researcher

The Encyclopedia of DNA Elements (ENCODE) project is the effort of hundreds of scientists to describe the workings of the human genome. Their research, outlined in 30 papers published in multiple journals Sept. 5, has confirmed our genome is far more complex than originally thought. Regions that contain instructions for making proteins, which carry out life’s functions, account for only about 1 percent of our genome. ENCODE has shed light on the other 99%. Almost 80 percent of the genome is biochemically active, much of it involved in some sort of regulation of genes. Vast regions of our DNA once considered “junk” contain some 400,000 regulators called enhancers, which play a key role activating or silencing genes despite residing far away from the gene itself. Yale University researchers played a key role ENCODE, helping to author 9 of the 30 papers published in four journals on Sept. 5. Some of their work is described below.

The massive Encyclopedia of DNA Elements (ENCODE) unveiled Sept. 5 reveals a human genome vastly more rich and complex than envisioned even a decade ago. In a key supporting paper published in the journal Nature, the lab of Yale’s Mark Gerstein, the Albert L. Williams Professor of Biomedical Informatics, has found order amidst the seeming chaos of trillions of potential molecular interactions. (more…)

To Cap or Not to Cap: Scientists Find New RNA Phenomenon That Challenges Dogma

By Guest PostSeptember 2, 2012Sciencebaskar bakthavachalu, brian kennedy, cancer, cell, cell life, chandrama mukherjee, cytoplasm, daniel schoenberg, deepak patil, embryonic development, gene, hibernation, messenger rna, mitotic cell cycle, molecule, mrna, neurological activity, ohio state university, protein, rna

COLUMBUS, Ohio – Some RNA molecules spend time in a restful state akin to hibernation rather than automatically carrying out their established job of delivering protein-building instructions in cells, new research suggests.

And instead of being a fluke or a mistake, the research suggests that this restful period appears to be a programmed step for RNA produced by certain types of genes, including some that control cell division and decide where proteins will work in a cell to sustain the cell’s life.

This could mean that protein production in cells is not as clear-cut as biology textbooks suggest, scientists say. (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…)

Some Harmful Effects of Light at Night Can Be Reversed, Study Finds

By Guest PostJuly 27, 2012Sciencebrain, chronic exposure, depression, depressive disorder, depressive symptom, drug, hamster, harmful effects, hippocampus, light, light cycle, light dark cycle, night, protein, randy nelson, rodent, siberian hamsters, tnf, tnf inhibitor, tracy bedrosian, tumor necrosis factor, xpro1595, zachary weil

COLUMBUS, Ohio – Chronic exposure to dim light at night can lead to depressive symptoms in rodents – but these negative effects can be reversed simply by returning to a standard light-dark cycle, a new study suggests.

While hamsters exposed to light at night for four weeks showed evidence of depressive symptoms, those symptoms essentially disappeared after about two weeks if they returned to normal lighting conditions.

Even changes in the brain that occurred after hamsters lived with chronic light at night reversed themselves after returning to a more normal light cycle. (more…)

Powerful New Approach to Attack Flu Virus

By Guest PostMay 29, 2012Scienceadaptable virus, avian flu, biopharmaceutical industry, dna deep sequencing, flu epidemics, flu virus, H1N1, H5N1, Israel, kurt stepnitz, la jolla, michigan state university, mutations, nature biotechnology, new approach, pandemic influenza viruses, protein, rehovot, san diego, Science, scripps research institute, smallpox, subtypes, swine flu, therapeutic proteins, tim whitehead, university of washington, weizmann institute

EAST LANSING, Mich. — An international research team has manufactured a new protein that can combat deadly flu epidemics.

The paper, featured on the cover of the current issue of Nature Biotechnology, demonstrates ways to use manufactured genes as antivirals, which disable key functions of the flu virus, said Tim Whitehead, assistant professor of chemical engineering and materials science at Michigan State University.

“Our most potent design has proven effective on the vulnerable sites on many pandemic influenza viruses, including several H1N1 (Spanish flu, Swine flu) and H5N1 (Avian flu) subtypes,” said Whitehead, the paper’s co-lead author. “These new therapeutics are urgently needed, so we were especially pleased to see that it neutralizes H1N1 viruses with potency.” (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…)

Study: Heart Damage after Chemo Linked to Stress in Cardiac Cells

By Guest PostMay 22, 2012Healthblocking, breast cancer, cancer cell, cardiac damage, cardiomyocytes, cellular level, chemotherapy, doxorubicin, drug, gene, govindasamy ilangovan, heart, heart muscle cells, heat shock factor 1, hsf 1, karthikeyan krishnamurthy, kaushik vedam, mdr1, multidrug resistance 1, nf kb, ohio state university, protein, ragu kanagasabai

COLUMBUS, Ohio – Blocking a protein in the heart that is produced under stressful conditions could be a strategy to prevent cardiac damage that results from chemotherapy, a new study suggests.

Previous research has suggested that up to a quarter of patients who receive the common chemotherapy drug doxorubicin are at risk of developing heart failure later in life. Exactly how that heart damage is done remains unclear.

In this study, scientists identified a protein called heat shock factor-1 (HSF-1) as a likely source of chemotherapy-related heart damage in mice and cell cultures. Heat shock factor-1 is known to be induced by stress – in this case, the chemotherapy treatment itself. (more…)

New Twist on Ancient Math Problem Could Improve Medicine, Microelectronics

By Guest PostMay 15, 2012Scienceancient math problem, carolyn phillips, filling problem, hidden facet, medicine, microelectronics, microprocessor, Nanotechnology, pentagon, protein, radiation beam, sanskrit manuscript, sharon glotzer, silicon chip, solution, starfish, three dimensions, traps, treating tumor, two dimensions, university of connecticut, university of michigan

ANN ARBOR, Mich.— A hidden facet of a math problem that goes back to timeworn Sanskrit manuscripts has just been exposed by nanotechnology researchers at the University of Michigan and the University of Connecticut.

It turns out we’ve been missing a version of the famous “packing problem,” and its new guise could have implications for cancer treatment, secure wireless networks, microelectronics and demolitions, the researchers say.

Called the “filling problem,” it seeks the best way to cover the inside of an object with a particular shape, such as filling a triangle with discs of varying sizes. Unlike the traditional packing problem, the discs can overlap. It also differs from the “covering problem” because the discs can’t extend beyond the triangle’s boundaries. (more…)