Biosingularity

Archive for February 2009

The stimulus bill was conceived as a way to jumpstart the economy with ‘shovel-ready’ infrastructure and construction projects. At agencies such as the NSF and the Department of Energy’s (DoE) office of science, however, much of the money will be spent on grants, and details are emerging this week of how those grants will be awarded.

>>>> Article in Nature

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The February, 2009 issue of the American Association for Cancer Research journal Cancer Epidemiology, Biomarkers & Prevention published the discovery of researchers from the University of California, San Diego, the University of Arizona, and other research centers of a positive effect of high carotenoid intake on recurrence-free survival in breast cancer patients. Carotenoids, such as beta-carotene, occur in most fruits and vegetables. Diets high in these plant foods have been linked with a protective effect against various cancers in a number of studies.

>>>> Article in Life Extension site

Postmenopausal women who take multivitamins appear to have the same risk of most common cancers, cardiovascular disease or dying of any cause as women who do not take multivitamin supplements, according to a report in the February 9 issue of Archives of Internal Medicine, one of the JAMA/Archives journals. Read the rest of this entry »

A simple, chemical materials model may lead to a better understanding of the structure and organization of the cell according to a Penn State researcher.

“Cells are interesting because they show organization even at the level of the cytoplasm, and while it is thought to be important for cell functions, it is not always clear how this organization is achieved,” said Christine Keating, associate professor of chemistry. “We are taking a materials chemistry approach in developing simple experimental models for cytoplasm organization,” she told attendees at the 2009 Annual Meeting of the American Association for the Advancement of Science.

Christine Keating, Penn State

Caption: These are images of primitive artificial cell created with lipid membrane and two large molecules. Top images are when cells form. The bottom images are after fluid is removed via osmotic stress. The left images are by transmitted-light, Differential Interference Contrast microscopy. The images on the right are false colored fluorescent images. The scale bar is 10 micrometers. Credit: Christine Keating, Penn State

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Scientists from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, and the University of California, San Diego have developed a set of molecular tools that provide important insight into the complex genomes of multicellular organisms. The strategy promises to clarify the longstanding mystery of the role played by vast stretches of DNA sequence that do not code for the functional units—genes—that nevertheless may have a powerful regulatory influence. The research is described in the 12 February edition of the journal Nature.

Axel Visel, Lawrence Berkeley National Laboratory

Caption: Activity pattern of one of nearly 5000 potential genetic switches (enhancers) identified by Visel et al. This particular switch is located on human chromosome 5 and turns on genes in developing mammalian limbs, as shown here by reporter gene staining (dark blue) in a transgenic mouse embryo. Credit: Axel Visel, Lawrence Berkeley National Laboratory

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The heart tissue is created by induced pluripotency, which genetically reprograms adult cells into a near-embryonic state, capable of becoming almost any cell type.

Video: University of Wisconsin

Researchers at Canada’s largest children’s rehabilitation hospital have developed a technique that uses infrared light brain imaging to decode preference – with the goal of ultimately opening the world of choice to children who can’t speak or move.

In a study published this month in The Journal of Neural Engineering, Bloorview scientists demonstrate the ability to decode a person’s preference for one of two drinks with 80 per cent accuracy by measuring the intensity of near-infrared light absorbed in brain tissue Read the rest of this entry »

Amanda Kitts lost her left arm in a car accident three years ago, but these days she plays football with her 12-year-old son, and changes diapers and bearhugs children at the three Kiddie Cottage day care centers she owns in Knoxville, Tenn.

Ms. Kitts, 40, does this all with a new kind of artificial arm that moves more easily than other devices and that she can control by using only her thoughts. Her turnaround is the result of a new procedure that is attracting increasing attention because it allows people to move prosthetic arms more automatically than ever before, simply by using rewired nerves and their brains.

>>>> article in New York Times

Atomic-force microscopy could advance osteoarthritis drug development.

Martin Stolz

Molecular checkup: Atomic-force microscopy images show molecular changes in cartilage decades before symptoms show up. In this image of osteoarthritic cartilage, collagen fibers are lined up instead of randomly ordered, as in healthy cartilage. The white arrows point to a gap in the fibers, and the silvery diamond represents the microscopy probe. Credit: Martin Stolz

Osteoarthritis, which affects about 14 million people in the United States alone, occurs when cartilage between joints degrades and disappears, leaving joint bones to grind painfully against each other. Therapies can alleviate some of the pain, and some patients undergo joint replacements, but there is no cure. Now nanotechnologists at the University of Basel, in Switzerland, have demonstrated that the molecular changes characteristic of the disease’s earliest stages can be detected using an atomic-force microscope (AFM). The researchers hope that using the extremely sensitive technique to monitor response to osteoarthritis therapies will speed the development of more-effective drugs for the disease.

>>>> Article in MIT Tech Review

The shapes of some of the tiniest cellular structures are coming into sharper focus at the Howard Hughes Medical Institute’s Janelia Farm Research Campus, where scientists have developed a new imaging technology that produces the best three-dimensional resolution ever seen with an optical microscope.

With this new tool, scientists can pinpoint fluorescent labels in their images to within 10-20 nanometers – about ten times the size of an average protein – in all three dimensions. The researchers say they now have an extremely powerful technology that will help reveal how biomolecules organize themselves into the structures and signaling complexes that drive cellular functions.

The three-dimensional distribution of membrane proteins within a cell revealed through iPALM imaging. The vertical position of fluorescently labeled farnesyl proteins has been color coded, with red molecules being the deepest and purple the highest.

The three-dimensional distribution of membrane proteins within a cell revealed through iPALM imaging. The vertical position of fluorescently labeled farnesyl proteins has been color coded, with red molecules being the deepest and purple the highest.

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Scientists from the California Institute of Technology (Caltech) have uncovered the Transformer like properties of molecules responsible for carrying and depositing proteins to their correct locations within cells. The research could eventually lead to novel treatments for diseases that result from flaws in protein delivery as well as the development of new types of antibiotics. Read the rest of this entry »

A team of researchers led by Rutgers’ Samuel Gunderson has developed a novel gene silencing platform with very significant improvements over existing RNAi approaches. This may enable the development and discovery of a new class of drugs to treat a wide array of diseases. Critical to the technology is the approach this team took to specifically target RNA biosynthesis. Read the rest of this entry »

A net with large holes won’t catch small fish. Likewise, the microscopic fibers in the protective mucus coatings of the eyes, lungs, stomach or reproductive system naturally bundle together and allow the tiniest disease-causing bugs, allergens or pollutants to slip by. But Johns Hopkins researchers have discovered a way to chemically shrink the holes in the mucus layer’s netting so that it will keep out more of the unwanted particles.
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In research scheduled for presentation at the 11th International Symposium on Amino Acids, to be held in August, 2009 in Vienna, Austria, scientists at Texas A & M University have shown that the amino acid arginine helps reduce fat gain in obese rats, a finding that may prove to be useful against human obesity. Read the rest of this entry »

It’s a commonly held belief that information from the outside world impinges upon our brains through our senses to cause perception, then action. But this reasonable assumption now appears to be false.

>>>>> Article in SEED magazine

New imaging probes show whether cancer drugs will work.

Radiology

Devising the right chemotherapy regimen as soon as possible can spare cancer patients from painful side effects and increase their chances of survival. Two new imaging contrast agents could help by showing doctors whether a drug will reach the target tumor before it is administered.

>>> Article in MIT Tech Review

Go for the jugular: A new imaging probe accumulates in leaky tumor blood vessels, just like the drug doxil, and helps researchers predict whether the drug will work. This fluorescence-microscopy image shows a tumor removed from a mouse that was treated with the imaging agent, which is labeled red. Credit: Radiology

A team of researchers are reporting the ongoing emergence of a new species of fruit fly–and the sequential development of a new species of wasp–in the February 6 issue of the journal Science.

Jeff Feder, a University of Notre Dame biologist, and his colleagues say the introduction of apples to America almost 400 years ago ultimately may have changed the behavior of a fruit fly, leading to its modification and the subsequent modification of a parasitic wasp that feeds on it.

The result is a chain reaction of biodiversity where the modification of one species triggers the sequential modification of a second, dependent species. The National Science Foundation supports the research. Read the rest of this entry »

A University of Iowa study is apparently the first to make a connection between a rare, hereditary premature aging disease and cell damage that comes from smoking. The study results point to possible therapeutic targets for smoking-related diseases.

The investigation found that a key protein that is lost in Werner’s syndrome is decreased in smokers with emphysema, and this decrease harms lung cells that normally heal wounds. The findings appear in the Feb. 6 issue of the American Journal of Respiratory and Critical Care Medicine.

University of Iowa/Nyunoya

Caption: Normal human lung fibroblasts (shown on left) divide and maintain structural integrity. In contrast, lung fibroblasts exposed to cigarette smoke (shown on right) stop dividing and accumulate beta galactosidase (appears in blue), an enzyme that is a marker of an aging cell. Credit: University of Iowa/Nyunoya

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The bacterium behind one of mankind’s deadliest scourges, tuberculosis, is helping researchers at the Commerce Department’s National Institute of Standards and Technology (NIST) and the Department of Energy’s Brookhaven National Laboratory (BNL) move closer to answering the decades-old question of what controls the switching on and off of genes that carry out all of life’s functions.

In a Journal of Biological Chemistry paper* posted online this week, the NIST/BNL team reports that it has defined—for the first time—the structure of a “metabolic switch” found inside most types of bacteria—the cyclic AMP (cAMP) receptor protein, or CRP—in its “off” state. CRP is the “binding site” (attachment point) for cAMP, a small molecule that, once attached, serves as the signal to throw the switch. This “on” state of CRP then turns on the genes that help a microbe survive in a human host.

Travis Gallagher, NIST

Caption: This is a computer model of the defined structure for the cyclic AMP receptor protein (CRP) found in Mycobacterium tuberculosis. The two subunits of the protein (colored purple on the left and green on the right) are genetically identical but, surprisingly were found to be asymmetric (different in shape) for the areas shown in white (top). This is the "off" state of the CRP that is unable to activate genes necessary for the microbe's survival. Credit: Travis Gallagher, NIST

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Fascinating documentary about a toddler born with eight limbs and believed by some to be the reincarnation of the multi-limbed Hindu goddess Lakshmi(correction.) She is set to undergo a 40-hour operation to remove half of her limbs.

Lakshmi Tatma was born joined to a ‘parasitic twin’ and will go under the knife at the hands of 30 surgeons to remove two of her useless arms and legs. The headless ‘twin’ is joined to Lakshmi at the pelvis and has its own spinal column and kidney.

Women who carry mutations in the BRCA1 and BRCA2 genes have a dramatically increased risk of developing breast cancer: a 36 to 85 percent chance of developing the disease during their lifetime, which is three to five times greater than the average risk rate. Ken Offit, chief of the clinical genetics service at Memorial Sloan-Kettering Cancer Center, in New York, wants to know how the other 15 to 64 percent escape unscathed.

>>>>> Article in MIT Technology Review

Scientists have discovered a gene that when mutated causes obesity by dampening the body’s ability to burn energy while leaving appetite unaffected.

The new research could potentially lead to new pharmacologic approaches to treating obesity in humans that do not target the brain, according to study senior author Yi Zhang, Ph.D., professor of biochemistry and biophysics in the University of North Carolina School of Medicine.

The findings also add new knowledge to the burgeoning field of epigenetics, in which heritable changes in gene expression or physical appearance are caused by mechanisms besides changes in the underlying DNA. Read the rest of this entry »

In the February, 2009 issue of Mayo Clinic Proceedings,  a study found that men between the ages of 40 and 49 who experience erectile dysfunction (ED) have a significantly higher risk of developing heart disease compared to those not affected by the condition.

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With the support of NASA, Google and a broad range of technology thought leaders and entrepreneurs, a new university will launch in Silicon Valley this summer with the goal of preparing the next generation of leaders to address “humanity’s grand challenges.” Singularity University (SU) (www.singularityu.org) will open its doors in June 2009 on the NASA Research Park campus with a nine-week graduate-level interdisciplinary curriculum designed to facilitate understanding, collaboration, and innovation across a broad range of carefully chosen scientific and technological disciplines whose developments are exponentially accelerating.

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A variation in the gene FOXO3A has a positive effect on the life expectancy of humans, and is found much more often in people living to 100 and beyond – moreover, this appears to be true worldwide. A research group in the Faculty of Medicine at the Christian-Albrechts-University in Kiel (CAU) has now confirmed this assumption by comparing DNA samples taken from 388 German centenarians with those from 731 younger people. Read the rest of this entry »

Amanda Clark

Fertile ground: Researchers at UCLA prodded iPS cells to develop into egg- and sperm-cell precursors. But before they could do so, the researchers had to find a way to identify and isolate them from surrounding cells. Cell-surface markers (shown here in green) allowed them to do just that. Credit: Amanda Clark

For couples who can’t seem to get pregnant, one of the more common causes is egg or sperm quality: sperm that never make it to the egg or that can’t fertilize it once they’re there, and eggs that resist fertilization or implantation in the uterine wall. Now, for the first time, scientists have turned adult cells into egg- and sperm-cell precursors, an achievement that could one day help infertile couples conceive a child that shares their DNA.

Amanda Clark, a developmental biologist at the University of California, Los Angeles, created the egg and sperm precursors using an existing line of induced pluripotent stem (iPS) cells, so named for their ability to turn into just about any tissue type and lauded for their potential in regenerative medicine.

>>>> Article in MIT Technology Review

A tiny molecule found in most plant-based foods douses the flames before damaging lesions can form in the colon, according to a study by Texas AgriLife Research scientist Dr. Nancy Turner.

Even better, the compound can be obtained easily by eating vegetables and fruit rather than by taking expensive prescriptions or supplements, Turner said.

The molecule is quercetin. Tiny but potent, quercetin gets into the body through onions, peppers, tomatoes and most other common produce but also in “fun things like wine,” she said. “Just about any plant-based food in the human diet has some level of quercetin.” Read the rest of this entry »

Brown University biomedical engineers can now grow and assemble living microtissues into complex three-dimensional structures in a way that will advance the field of tissue engineering and may eventually reduce the need for certain kinds of animal research.

The team, led by Brown professor Jeffrey Morgan, successfully used clusters of cells grown in a 3-D Petri dish also invented by the group, in order to build microtissues of more complex shapes.

Morgan Lab/Brown University

Researchers are now able to develop complex microtissues (B,D) that take on the shape of molds they have designed into a 3-D Petri dish (A,C). That technique could reduce the need for certain kinds of animal-based research. Credit: Credit: Morgan Lab/Brown University

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Whether condoms or abstinence, most efforts to prevent sexually transmitted diseases have a common logic: keep the pathogen out of your body altogether. While this approach is certainly reasonable enough, it doesn’t help the countless people worldwide who, for a number of reasons, are not in a position to control their sexual circumstances.

Now, Harvard Medical School professor of pediatrics Judy Lieberman, who is also a senior investigator at the Immune Disease Institute, has overseen the development of a topical treatment that, in mice, disables key genes necessary for herpesvirus transmission. Using a laboratory method called RNA interference, or RNAi, the treatment cripples the virus in a molecular two-punch knockout, simultaneously disabling its ability to replicate, as well as the host cell’s ability to take up the virus. Read the rest of this entry »

A transcription factor known to drive the formation of fibroblasts during development also promotes their ability to invade and remodel surrounding tissues, report Rowe et al. in the February 9, 2009 issue of the Journal of Cell Biology.

10.1083/jcb.200810113.

Wild-type fibroblasts (top panel, green) can invade the extracellular matrix (red), whereas fibroblasts lacking Snail1 cannot (bottom panel). Credit: Rowe, R.G., et al. 2009. J. Cell Biol. doi:10.1083/jcb.200810113.

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More than a century after Ivan Pavlov’s dog was conditioned to salivate when it heard the sound of a tone prior to receiving food, scientists have found neurons that are critical to how people and animals learn from experience.

Using a new imaging technique called Arc catFISH, researchers from the University of Washington have visualized individual neurons in the amygdalas of rat brains that are activated when the animals are given an associative learning task.

http://www.sciencedaily.com/images/2008/12/081208180228-large.jpg Read the rest of this entry »

Getty Images

Getty Images

Ed Vul is a graduate student in the Department of Brain and Cognitive Sciences at the Massachusetts Intitute of Technology. He’s also the lead author of a recent paper, “Voodoo Correlations in Social Neuroscience,” which explored the high correlations between measures of personality or emotionality in the individual—such as the experience of fear, or the willingness to trust another person—with the activity of certain brain areas as observed in an fMRI machine. The paper has provoked a flurry of commentary. Mind Matters editor Jonah Lehrer chats with Vul about what this study means for the future of social neuroscience, whether the press is to blame and why we should always make multiple guesses.

>>>>> Article in Scientific American

Abnormal heart rhythms – arrhythmias – are killers. They strike without warning, causing sudden cardiac death, which accounts for about 10 percent of all deaths in the United States.

Vanderbilt investigators have discovered a new molecular mechanism associated with arrhythmias. Their findings, reported in The Journal of Clinical Investigation, could lead to novel arrhythmia treatments. Read the rest of this entry »

A new brain imaging study illustrates what happens to memories as time goes by. The study, in the January 28 issue of The Journal of Neuroscience, shows that distinct brain structures are involved in recalling recent and older events.

The findings support earlier studies of memory-impaired patients with damage limited to the hippocampus. These patients show deficits in learning new information and in recalling events that occurred just prior to their injuries. However, they are able to recall older events, which are thought to involve other regions of the brain, particularly the cortex. Read the rest of this entry »

Researchers have created a precise biosensor for detecting blood glucose and potentially many other biological molecules by using hollow structures called single-wall carbon nanotubes anchored to gold-coated “nanocubes.”

The device resembles a tiny cube-shaped tetherball. Each tetherball is a sensor and is anchored to electronic circuitry by a nanotube, which acts as both a tether and ultrathin wire to conduct electrical signals, said Timothy Fisher, a Purdue University professor of mechanical engineering.

Jeff Goecker, Discovery Park, Purdue University

This image, taken with a scanning electron microscope and digitally colorized and enhanced, shows a new precise biosensor for detecting blood glucose and other biological molecules using hollow structures called single-wall carbon nanotubes anchored to gold-coated "nanocubes." The device resembles a tiny cube-shaped tetherball anchored to electronic circuitry by a nanotube about 25,000 times thinner than a human hair. Credit: Jeff Goecker, Discovery Park, Purdue University

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Like guards controlling access to a gated community, nuclear pore complexes are communication channels that regulate the passage of proteins and RNA to and from a cell’s nucleus. Recent studies by researchers at the Salk Institute for Biological Studies offer new insights about the pores’ lifespan and how their longevity affects their function.

Their findings, reported in the Jan. 23 issue of Cell, may provide clues to one of the most enduring questions of biology: how and why cells age. They also offer a new, promising avenue of investigation for scientists pursuing intervention strategies for neurodegenerative diseases.

Courtesy of Dr. Maximiliano DAngelo, Salk Institute for Biological Studies.

In aging cells one of the proteins composing nuclear pores becomes damaged and molecules that should be restricted to the cytoplasm invade the nucleus (outline shown in red). In particular, a protein called tubulin (shown in green), which is strictly a cytoplasmic protein, shows up as long filaments that co-opt a large part of the nucleus. Credit: Courtesy of Dr. Maximiliano D'Angelo, Salk Institute for Biological Studies.

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Three billion years ago, a “new” amino acid was added to the alphabet of 20 that commonly make up proteins in organisms today. Now researchers at Yale and the University of Tokyo have demonstrated how this rare amino acid — and, by example, other amino acids — made its way into the menu for protein synthesis. The study appeared in the December 31 advance online publication of the journal Nature.

Marsland/Yale

This is a model of Pyl tRNA and tRNA synthetase interaction. Credit: Marsland/Yale

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A research team including Serge Rivest of University Laval’s Faculty of Medicine has demonstrated the existence of a type of cells that limits brain damage after a stroke. The study was recently published in the online version of Nature Medicine.

Laboratory experiments showed that three days after a stroke, the affected area of the brain is 20% larger in mice without regulatory T (Treg) cells than in normal mice. Effects on locomotor control are also more severe in mice lacking this type of cells. Read the rest of this entry »

Is it possible to share a pain that you observe in another but have never actually experienced yourself? A new study uses a sophisticated brain-imaging technique to try and answer this question. The research, published by Cell Press in the January 29th issue of the journal Neuron, provides insight into brain mechanisms involved in empathy. Read the rest of this entry »

New kinds of bioelectrodes will help researchers study beating hearts and brain trauma.

Babak Ziaie

Cell stretcher: This system, made of a stretchy polymer embedded with four microelectrodes, can be stretched by a micromanipulator (the black clamp) to mimic the electrical and mechanical activity of the heart. Credit: Babak Ziaie

The cells of the heart can be stretched by as much as 100 percent with every beat. But traditional platforms for studying cells are static, limiting researchers’ ability to study these cells in a realistic way in the lab. Now researchers at Purdue University and Stanford University have developed stretchable electrode arrays for studying these cells. These arrays should help develop tissue-engineered grafts to repair the damage caused by heart attacks, and could serve as bio-friendly electrical interfaces in implantable devices. They’re also being used to study how the mechanical stress inflicted during traumatic brain injury changes neurons’ electrical activity over the long term.

>>>>> Article in MIT Technology Review

In a study published by Nature Biotechnology online on February 1, 2009, Mount Sinai Hospital researchers have unveiled a new technology tool that analyzes breast cancer tumours to determine a patient’s best treatment options. The tool can predict with more than 80 per cent accuracy a patient’s chance of recovering from breast cancer. Read the rest of this entry »

A research team at the Broad Institute of Harvard and MIT and Beth Israel Deaconess Medical Center has uncovered a vast new class of previously unrecognized mammalian genes that do not encode proteins, but instead function as long RNA molecules. Their findings, presented in the February 1st advance online issue of the journal Nature, demonstrate that this novel class of “large intervening non-coding RNAs” or “lincRNAs” plays critical roles in both health and disease, including cancer, immune signaling and stem cell biology. Read the rest of this entry »


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