Tag Archives: DNA

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…)

Beacons Light up Stem Cell Transformation

By Guest PostSeptember 12, 2012Sciencealpl, bglap, biotechnology, bone cell, bone specific, brown university, chathuraka jayasuriya, differentiation, DNA, eric darling, fluorescence, gene, gene col1a1, gene expression, glowing, green spot, hetal desai, indu voruganti, medicine treatment, messenger rna, mg 63, milestone, molecular beacon, mrna, qian chen, regenerative, stem cell, tissue

In a new study, Brown University researchers demonstrate a new tool for visually tracking in real-time the transformation of a living population of stem cells into cells of a specific tissue. The “molecular beacons,” which could advance tissue engineering research, light up when certain genes are expressed and don’t interfere with the development or operation of the stem cells.

PROVIDENCE, R.I. [Brown University] — A novel set of custom-designed “molecular beacons” allows scientists to monitor gene expression in living populations of stem cells as they turn into a specific tissue in real-time. The technology, which Brown University researchers describe in a new study, provides tissue engineers with a potentially powerful tool to discover what it may take to make stem cells transform into desired tissue cells more often and more quickly. That’s a key goal in improving regenerative medicine treatments. (more…)

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…)

Researchers Share Surprising Discovery about Coral Reef Ecology

By Guest PostSeptember 4, 2012Environment, Natureacidification, algae, algal symbionts, american samoa, climate change, coastal development, coral reef, coral species, coral tissue, david garrison, DNA, ecology, endosymbionts, environment disturbance, environmental change, environmental stress, french polynesia, functional ecosystem, future, generalists, global stressors, hawaii, himb, hollie putnam, host, manoa, moorea, nsf, ocean acidification, photosynthesis, pollution, prediction, reef corals, ruth gates, skeletal growth, skeletons, soest, stresss, symbiodinium, taiwan, temperatures, theory, threat, tissue sample

Researchers at the UH Manoa School of Ocean and Earth Science and Technology (SOEST) made a discovery that challenges a major theory in the field of coral reef ecology.

The general assumption has been that the more flexible corals are, regarding which species of single-celled algae (Symbiodinium) they host in coral tissues, the greater ability corals will have to survive environmental stress. In their paper published August 29, 2012, however, scientists at the Hawaii Institute of Marine Biology (HIMB) at SOEST and colleagues documented that the more flexible corals are, the more sensitive to environment disturbances they are. (more…)

Microbes Help Hyenas Communicate via Scent

By Guest PostSeptember 2, 2012Natureage, animal, animal behavior, bacteria, beneficial relationship, chemical signature, communication, communication system, diversity, DNA, hyena, hyena clan, kay holekamp, kenyan plains, kevin theis, key controller, mammal, michigan state university, microbial community, reproductive status, scent gland, sex, symbiotic bacteria, trait

EAST LANSING, Mich. — Bacteria in hyenas’ scent glands may be the key controllers of communication.

The results, featured in the current issue of Scientific Reports, show a clear relationship between the diversity of hyena clans and the distinct microbial communities that reside in their scent glands, said Kevin Theis, the paper’s lead author and Michigan State University postdoctoral researcher.

“A critical component of every animal’s behavioral repertoire is an effective communication system,” said Theis, who co-authored the study with Kay Holekamp, MSU zoologist. “It is possible that without their bacteria, many animals couldn’t ‘say’ much at all.” (more…)

Two New Owls Discovered in the Philippines

By Guest PostAugust 22, 2012Natureasian ornithology, birdlife international, birdtour asia, camiguin hawk owl, camiguin sur, cebu, cebu hawk owl, deforestation, discovery, DNA, forest, forktail, island, mammalogy, michigan state university, mindanao, new owls, ninox hawk owls, oriental bird club, pam rasmussen, Philippines, species of owls, vocalization

EAST LANSING, Mich. — Two new species of owls have been discovered in the Philippines, and a Michigan State University researcher played a key role in confirming their existence.

The discovery, which is featured in the current issue of Forktail, the Journal of Asian Ornithology, took years to confirm, but it was well worth the effort, said the paper’s lead author Pam Rasmussen, MSU assistant professor of zoology and assistant curator of mammalogy and ornithology at the MSU Museum.

“More than 15 years ago, we realized that new subspecies of Ninox hawk-owls existed in the Philippines,” she said. “But it wasn’t until last year that we obtained enough recordings that we could confirm that they were not just subspecies, but two new species of owls.” (more…)

Diagnostic Technique Uses Immune Cell DNA

By Guest PostJuly 10, 2012Scienceafrican american, bladder cancer, blood samples, brock christensen, brown university, carmen marsit, cd4, cell carcinoma, cell membrane, chemical alteration, devin koestler, DNA, granulocyte leukocytes, immune cell, karl kelsey, leukocytes, methylation, ovarian cancer, t lymphocytes

By looking at signature chemical differences in the DNA of various immune cells called leukocytes, scientists have developed a way to determine their relative abundance in blood samples. The relative abundance turns out to correlate with specific cancers and other diseases, making the technique, described in two recent papers, potentially valuable not only for research but also for diagnostics and treatment monitoring.

PROVIDENCE, R.I. [Brown University] — When a person is sick, there is a tell-tale sign in their blood: a different mix of the various types of immune cells called leukocytes. A group of scientists at several institutions including Brown University has discovered a way to determine that mix from the DNA in archival or fresh blood samples, potentially providing a practical new technology not only for medical research but also for clinical diagnosis and treatment monitoring of ailments including some cancers. (more…)

A SMART(er) Way to Track Influenza

By Guest PostJune 12, 2012Scienceaartik sarma, amplification, andrew artenstein, anubhav tripathi, biological debris, brown assay, brown university, carmichael ong, DNA, first aid kit, flu detection test, genetic sequence, H1N1, hiv, influenza rna, influenza rna sequence, iPhone, magnetics, memorial hospital, microfluidics, nasba, nucleic acid sequence, pigs, polymerase chain reaction, prototype, rhode island, rna partners, rna probe, rna strand, smart, smart detector, stephanie mccalla, steven opal, swine flu, tb, tracking of influenza, tuberculosis, united states, virus in mexico

Brown University researchers have created a reliable and fast flu-detection test that can be carried in a first-aid kit. The novel prototype device isolates influenza RNA using a combination of magnetics and microfluidics, then amplifies and detects probes bound to the RNA. The technology could lead to real-time tracking of influenza. Results are published in the Journal of Molecular Diagnostics.

PROVIDENCE, R.I. [Brown University] — In April 2009, the world took notice as reports surfaced of a virus in Mexico that had mutated from pigs and was being passed from human to human. The H1N1 “swine flu,” as the virus was named, circulated worldwide, killing more than 18,000 people, according to the World Health Organization. The Centers for Disease Control and Prevention in the United States said it was the first global pandemic in more than four decades. (more…)