October 19, 2006, 8:59 PM CT

Affymetrix 500K Array And Memory Gene

Affymetrix Inc. announced recently that scientists at the Translational Genomics Research Institute (TGen) in Phoenix, Arizona have used the Affymetrix 500K Array to discover a gene--called Kibra--linked to memory performance in humans. The team's findings may be used to develop new medicines for memory-based diseases such as Alzheimer's and Parkinson's by providing researchers with a better understanding of how memory works at the molecular level.

The study entitled, "Common KIBRA alleles are linked to human memory performance," would be reported in the Oct. 20, 2006 issue of Science. The research team was led by Dietrich Stephan, Ph.D., director of TGen's Neurogenomics Division. It included colleagues at the University of Zurich in Switzerland, Banner Alzheimer's Institute and Mayo Clinic Scottsdale.

"Using the latest Affymetrix 500K Array, we have shed light on the fundamental biological process of human memory performance," said Dr. Stephan. "We can use this new understanding to develop drugs that will improve memory function".

Until now, scientists did not have access to the high-density technology needed to examine the genetic components linked to memory performance. The team at TGen used Affymetrix Human Mapping 500K Arrays to analyze 500,000 DNA markers simultaneously, providing a genetic blueprint for the memory-study participants. The scientists discovered the Kibra gene by comparing the genetic blueprints of people with good memory vs. poor memory and looking for the genetic variations consistently present in one group, but not the other. They then validated their discovery by replicating the Kibra gene finding in two separate and distinct groups of subjects.........

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October 18, 2006, 8:42 PM CT

National Center for X-ray Tomography

The National Center for X-ray Tomography (NCXT) has officially been dedicated at the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab). Located at Berkeley Lab's Advanced Light Source (ALS), this new center features a first-of-its-kind x-ray microscope that will enable scientists to perform "CT scans" on biological cells, just one of many unprecedented capabilities for cell and molecular biology studies.

"X-ray microscopy is an emerging new technology that expands the imaging toolbox for cell and molecular biologists, and we are going to make this technology available to the greater biological community," said cell biologist and microscopy expert Carolyn Larabell, who is the principal investigator for the new center. Larabell, holds a joint appointment with Berkeley Lab's Physical Biosciences Division and the Anatomy Department of UC San Francisco. Her co-principal investigator at the center is.

The NCXT is being funded with grants from the U.S. Department of Energy (DOE) and from the National Institutes of Health (NIH). For construction and five years of operation, the Biological and Environmental Research (BER) program in DOE's Office of Science has provided about $7 million. NIH has provided about $5 million through its National Center for Research Resources program, which establishes "biomedical technology resource centers," such as the NCXT, to provide scientists and clinical researchers with "the environments and tools they need to understand, detect, treat, and prevent a wide range of diseases".........

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October 17, 2006, 9:34 PM CT

DNA computing targets West Nile Virus

Scientists say that they have developed a DNA-based computer that could lead to faster, more accurate tests for diagnosing West Nile Virus and bird flu. Representing the first "medium-scale integrated molecular circuit," it is the most powerful computing device of its type to date, they say.

The new technology could be used in the future, perhaps in 5 to 10 years, to develop instruments that can simultaneously diagnose and treat cancer, diabetes or other diseases, as per a team of researchers at Columbia University Medical Center in New York and the University of New Mexico, Albuquerque. Their study is scheduled to appear in the recent issue of the American Chemical Society's Nano Letters, a monthly peer-evaluated journal.

"This is a big step in DNA computing," says Joanne Macdonald, Ph.D., a virologist at Columbia University's Department of Medicine. Macdonald led the research team that developed MAYA-II (Molecular Array of YES and AND logic gates) ¯ a "computer" whose circuits consist of DNA instead of silicon. She likens the significance of the advance to the development of the earliest silicon chips. "The study shows that large-scale DNA computers are possible".

"These DNA computers won't compete with silicon computing in terms of speed, but their advantage is that they can be used in fluids, such as a sample of blood or in the body, and make decisions at the level of a single cell," says the researcher, whose work is funded by the National Science Foundation. Her main collaborators in this study were Milan Stojanovic, of Columbia University, and Darko Stefanovic, of the University of New Mexico.........

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October 17, 2006, 9:31 PM CT

Bacteria Increase Risk Of Stomach Cancer

The bacteria Helicobacter pylori substantially increase the risk of cancer in the lower stomach, but it may decrease the risk of cancer near the junction between the esophagus and the stomach, as per a research studyin the October 19 Journal of the National Cancer Institute. This finding may help explain the changing rates and distributions of these cancers in Western countries over the past century.

Infection with H. pylori, which is known to cause ulcers, has also been linked to certain types of gastric cancer, but the strength of association varies with where the cancer is located in the stomach. Two types of gastric cancer usually exist -- cardia, or cancer of the upper stomach joining the esophagus; and noncardia, or cancer of the lower stomach.

A group of scientists led by Farin Kamangar, M.D., Ph.D., of the National Cancer Institute in Bethesda, Md., selected 234 cardia and noncardia gastric cancer patients in the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study and matched them to controls. They assessed all of the subjects for H. pylori infection by testing their blood for antibodies that indicate previous infection.

The authors observed that the subjects infected with H. pylori had a higher risk of developing noncardia gastric cancer and a lower risk of developing cardia gastric cancer. They suggest that a decrease in H. pylori infections during the past century may be one reason that researchers have observed increasing rates of cardia and decreasing rates of noncardia gastric cancers in Western countries.........

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October 16, 2006, 10:22 PM CT

Chemistry To Predict The Dynamics Of Clotting

University of Chicago chemists have shown for the first time how to use a simple laboratory model consisting of only a few chemical reactions to predict when and where blood clotting will occur. The researchers used microfluidics, a technique that allowed them to probe blood clotting on surfaces that mimic vascular damage on the micron scale, a unit of measurement much narrower than the diameter of a human hair.

Eventhough researchers understand what occurs during a number of of the 80 individual chemical reactions involved in blood clotting, a number of questions about the dynamics of the entire reaction network remain. Rustem Ismagilov, Associate Professor in Chemistry at the University of Chicago, and graduate students Christian Kastrup, Matthew Runyon and Feng Shen have now developed a technique that will enable researchers to understand the rules governing complex biological reaction networks. They will detail their technique in the online early edition of the Oct. 16-20 issue of the Proceedings of the National Academy of Sciences.

Life and death literally depend on a finely tuned blood-clotting system. "Clotting has to occur at the right place at the right time," Ismagilov said. "A strong, rapid clotting response is essential to stop bleeding at a wound, but such a clotting response at the wrong spot can block blood vessels and can be life-threatening".........

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October 16, 2006, 10:15 PM CT

Harmful Algal Bloom Models

A new observation and modeling program focused on the southern Gulf of Maine and adjacent New England shelf waters could aid policymakers in deciding whether or not to re-open, develop, and manage offshore shellfish beds with potential sustained harvesting value of more than $50 million per year. These areas are presently closed to the harvest of certain species of shellfish due to the presence of red tide toxins.

Scientists at the Woods Hole Oceanographic Institution (WHOI) and his colleagues from seven other universities or agencies began the five-year Gulf of Maine Toxicity program, or GOMTOX, on September 1. The $7.5 million dollar program is funded by a grant from the National Oceanic and Atmospheric Administration's (NOAA) National Ocean Service, Center for Sponsored Coastal Ocean Research (NOS/CSCOR) through the ECOHAB program.

The new research effort expands past studies in the Gulf of Maine and builds on data collected during the historic 2005 red tide, which led to closure of both nearshore shellfish beds and offshore beds in federal waters out to Georges Bank. The toxicity also extended for the first time to the islands of Martha's Vineyard and Nantucket.

The Gulf of Maine (GoM) and its adjacent southern New England shelf is a vast region with extensive shellfish resources, large portions of which are frequently contaminated with paralytic shellfish poisoning (PSP) toxins produced by the dinoflagellate Alexandrium fundyense. The 2005 outbreak caused millions of dollars in economic damage, but monitoring programs and cooperation among federal, state and local officials, scientists, and shellfishermen prevented any reported cases of illness from people eating contaminated shellfish.........

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October 16, 2006, 9:31 PM CT

New Details of Mars, Young and Old

During its first week of observations from low orbit, NASA's newest Mars spacecraft is already revealing new clues about both recent and ancient environments on the red planet.

Researchers hope the Mars Reconnaissance Orbiter will answer questions about the history and distribution of Mars' water by combining data from the orbiter's high-resolution camera, imaging spectrometer, context camera, ground-penetrating radar, atmospheric sounder, global color camera, radio and accelerometers.

Between Sept. 29 and Oct. 6, science instruments on the spacecraft viewed dozens of sites that reflect different episodes in Mars' history. The diverse sites provide a good test for the capabilities of the spacecraft instruments. The orbiter will begin its primary science mission phase in early November when Mars re-emerges from passing nearly behind the sun.

The instruments are seeing details in the shapes and icy composition of geologically young layering near the Martian north pole. Other views offer details of a mid-latitude valley whose upper layers have been eroded away, revealing an underlying clay layer that formed a few billion years ago, when wet conditions produced the clay. Observations of a southern-hemisphere crater show fine-scale details of more recent gullies, adding evidence that they were carved by flowing water.........

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October 16, 2006, 8:56 PM CT

Could Dreams Be A Mechanism To Help Us Prepare For Danger?

Dreams have been interpreted in many different ways through the ages: as messages from the gods, repressed sexual fantasies. or, based on an evolutionist approach that emerged around the turn of the millennium, as a mechanism that helps us to prepare survival strategies in the face of danger.

Antonio Zadra, a professor in the Department of Psychology, likes that last theory. "Among its merits is that it lets us formulate hypotheses that can be tested quite easily," says Zadra, whose initial study tested no fewer than eight hypotheses derived from the new approach.

The theory was developed by Antti Revonsuo, Director of the Consciousness Research Group at the Centre for Cognitive Neuroscience at the University of Turku in Finland. He postulates that dreams developed in our long-ago ancestors to simulate outside threats, enabling the dreamer to put into practice or rehearse avoidance behaviours.

Pleistocene man faced constant threats from predators, rival tribes, and forces of nature. Seeking ways to avoid danger, our ancestors lived in a perpetual state of alert, and so the dream function assumed the form we see today. The theory is also based on the fact that rehearsing an action in your mind can improve the motor skills needed.

Research on dreams lends some credence to the theory. Research in the 1960s showed that 80% of dreams are negative in content, and misfortune occurs seven times more often than good fortune in dreams. In 96% of cases where there is some interaction with an animal, there is aggression. For both men and women, enemies are nearly always strangers - male strangers.........

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October 15, 2006, 8:52 PM CT

Mimicing Lotus Leaves For Self-cleaning PV Arrays

Researchers at the Georgia Institute of Technology are mimicking one of Nature's best non-stick surfaces to help create more reliable electric transmission systems, photovoltaic arrays that retain their efficiency, MEMS structures unaffected by water and improved biocompatible surfaces able to prevent cells from adhering to implanted medical devices.

Based on a collaboration of materials scientists and chemical engineers, the research aims to duplicate the self-cleaning surfaces of the lotus plant, which grows in waterways of Asia. Despite growing in muddy conditions, the leaves and flowers remain clean because their surfaces are composed of micron- and nano-scale structures that - along with a waxy coating - prevent dirt and water from adhering. Despite their unusual surface properties, the rough surfaces allow photosynthesis to continue in the leaves.

"When rain hits the leaves of the lotus plant, it simply beads up," noted C.P. Wong, a Regents Professor in Georgia Tech's School of Materials Science and Engineering. "When the leaves are also tilted at a small angle, the beads of water run off instantaneously. While the water is rolling off, it carries away any dirt on the surface".

The self-cleaning action of the lotus plant has intrigued researchers for decades, and recent studies done by researchers in several different groups have demonstrated the reasons behind the plant's unique abilities.........

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October 15, 2006, 8:42 PM CT

Complex Meteorology At Venus

In its relentless probing of Venus's atmosphere, ESA's Venus Express keeps revealing new details of the Venusian cloud system. Meteorology at Venus is a complex matter, researchers say.

New night-side infrared images gathered by the Ultraviolet, Visible and Near-Infrared Mapping Spectrometer (VIRTIS) in July 2006, clearly show new details of a complex cloud system.

The first (false colour) view - the composite of three infrared images acquired by VIRTIS, was taken on 22 July when the spacecraft was flying around the apocentre of its orbit (point of maximum distance from the planet surface) at about 65 000 kilometres altitude. Venus was in the night side.

Using its capability to observe at 1.7-micrometre wavelenght, VIRTIS could probe at about 15-20 kilometres altitude, below the thick cloud deck situated at about 60 kilometres from the surface. The thermal radiation coming from the oven-hot surface of Venus is represented by the intensity of the colours: the brighter the colour (towards white), the more radiation comes from the surface, so the less cloudy the region in the line of sight between the view and the spacecraft is.

The edge of the images, taken at a time interval of about 30 minutes from each other, do not precisely match. This is due to the fact that clouds on Venus move very rapidly and constantly vary their shape. Venus's atmosphere is certainly the most dynamic among the terrestrial planets that have one, taking only four days to completely rotate around the planet.........

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