October 17, 2007, 4:36 AM CT

Force-induced Changes in Biomolecule's Conformation

Researchers studying biological systems at the molecular level now have a new hybrid technique to probe the dynamics of the Holliday junction. The Holliday junction is a four-stranded DNA structure that forms during a process known as homologous recombination, which occurs when damaged DNA is repaired. Understanding how DNA repairs itself is an essential step in ultimately developing therapies for inherited disorders.

The hybrid technique is described by principal investigator Taekjip Ha and colleagues at the University of Illinois in the Oct. 12 issue of Science. The Holliday junction is named after geneticist Robin Holliday, who proposed the model of DNA-strand exchange in 1964. To better understand the mechanisms and functions of proteins that interact with the Holliday junction, the scientists needed a way to study the structural and dynamic properties of the junction itself.

"Based on our prior studies, we knew the Holliday junction fluctuated between two structures, but how it moved from one place to the other and what intermediates were visited along the pathway were unknown," Ha said. With this latest work, the scientists have determined that the intermediate structure is similar to that of a Holliday junction bound to its own processing enzyme.

The hybrid technique combines the exquisite force control of an optical trap and the precise measurement capabilities of single-molecule fluorescence resonance energy transfer. To use the technique, scientists first attach two dye molecules--one green and one red--to the molecule they want to study. Next, they excite the green dye with a laser. Some of the energy moves from the green dye to the red dye, depending upon the distance between them. The changing ratio of the two intensities indicates the relative movement of the two dyes. Therefore, by monitoring the brightness of the two dyes, the scientists can determine the motion of the molecule. With the optical trap, a focused laser beam locks onto a microsphere attached to one end of the molecule to be studied. The optical trap can then pull on the molecule like a pair of tweezers......... Posted by: Ashley      Read more         Source

October 16, 2007, 7:18 PM CT

Getting Light to Bend Backwards

While developing new lenses for next-generation sensors, scientists have crafted a layered material that causes light to refract, or bend, in a manner nature never intended.

Refraction always bends light one way, as one can see in the illusion of a "bent" drinking straw when observed through the side of a glass. A new metamaterial crafted from alternating layers of semiconductors (indium-gallium-arsenic and aluminum-indium-arsenic) acts as a single lens that refracts light in the opposite direction.

Refraction is the reason that lenses have to be curved, a trait that limits image resolution. With the new metamaterial, flat lenses are possible, theoretically allowing microscopes to capture images of objects as small as a strand of DNA. The current metamaterial lens works with infrared light, but the scientists hope the technology will expand to other wavelengths in the future.

Earlier efforts have crafted metamaterials that bend light in a similar way, but this is the first to do so using a 3-dimensional structure and a metamaterial comprised entirely of semiconductors. Those traits will prove critical for incorporating the technology into devices such as chemical threat sensors, communications equipment and medical diagnostics tools......... Posted by: Kevin      Read more         Source

October 11, 2007, 10:44 PM CT

New insights on green algae

Culminating a three-year research project, 115 researchers from around the world report in the Oct. 12 issue of the journal Science a "gold mine" of data on a tiny green alga called Chlamydomonas, with implications for human diseases.

The single-celled Chlamydomonas, a slimy organism that grows in soil and ponds, has approximately 15,000 genes, and researchers now know 95 percent of the sequence of its genome. Several years ago, they knew less than 2 percent.

"It's like having a dictionary of genes," said lead author Sabeeha Merchant, professor of biochemistry and associate director of UCLA's Molecular Biology Institute, who has studied the green alga for 20 years. "We know the words and now we want to learn to talk. Without the dictionary, you would be stuck and couldn't learn how to speak or write. We went from having a 200-word vocabulary to a 14,250-word vocabulary. Each of us is trying to learn how to put the words and sentences together in our own research programs.

"Having the genome sequence available fast-forwards our research by 10 or 20 years and allows us to make progress by leaps and bounds," she said. "The genome sequence opens the door for us to access all the genes and target our research on subsets of genes. What was just a dream 10 years ago, we have now accomplished"......... Posted by: Ashley      Read more         Source

October 11, 2007, 4:09 AM CT

Role Of Climate In Neanderthal Extinction

"Our findings suggest that there was no single climatic event that caused the extinction of the Neanderthals" says palaeoanthro-pologist Katerina Harvati. Only a controversial date for very late Neanderthal survival places their disappearance just before a major environmental shift. "Even in this case" continues Harvati "the role of climate would have been indirect, perhaps promoting competition with other human groups".

"There are three main limitations to understanding the role of climate in the Neanderthal extinction" explains palaeoecologist Chronis Tzedakis: uncertainty over the exact timing of the Neanderthal disappearance; uncertainties in converting radiocarbon dates to actual calendar years; and the chronological imprecision of the ancient climate record. "Our novel method circumvents the last two problems" adds palaeoclimatologist Konrad Hughen. "We were therefore able to provide a much more accurate picture of the climatic background at the time of the Neanderthal disappearance". "More generally," continues Hughen "our approach offers the huge potential to unravel the role of climate in critical events of the recent fossil record as it can be applied to any radiocarbon date from any deposit".

The new method was applied by the scientists to three possible dates for the Neanderthal extinction obtained from Gorham's cave, Gibraltar - a site thought to have been occupied by some of the latest surviving Neanderthals. The first two of these dates (~32 and ~28 thousand radiocarbon years ago) relate to conditions that are not distinct from the general climatic instability of the last glacial period. The much more controversial date of ~24 thousand radiocarbon years ago places the last Neanderthals just before a major environmental shift, with an expansion of ice sheets and onset of cold conditions in northern Europe. Gibraltar's climate, however, remained relatively unaffected "perhaps as a result of warm water from the subtropical Atlantic entering the western Mediterranean" as per palaeoceanographer Isabel Cacho......... Posted by: William      Read more         Source

October 10, 2007, 7:15 PM CT

Physics professor probes superconductivity

When Eric Hudson was introduced to high-temperature superconductivity as a graduate student, it was still, so to speak, a hot topic.

The phenomenon, discovered in the 1980s, reflects the fact that if you develop the right types of compounds, you can create electrical conductors that are completely resistance-free at temperatures well above the threshold for conventional superconductors.

"With conventional systems, you get to about 25 degrees Kelvin [-415? F] and then plateau," says Hudson, now the Class of 1958 Assistant Professor of Physics at MIT. "With high-temperature superconductivity, you were suddenly at 90 degrees Kelvin".

That figure is well above the mark at which nitrogen gas turns liquid. This meant you could create devices like the high-powered electromagnets used in a number of MRI scanners without having to use costly liquid helium to cool the magnets' coils to superconducting temperatures. (Helium, which liquefies at a hyper-frigid 4 degrees above absolute zero, is a must for conventional superconducting devices.).

More exciting yet, the discovery seemed to signal that room-temperature superconductivity was on its way. This triggered claims that problems like electricity line -losses--the often-hefty amount of power lost to resistance in electrical transmission networks--would soon -disappear......... Posted by: Kevin      Read more         Source

October 10, 2007, 7:10 PM CT

Assessing health risks from chemicals

Determining how thousands of chemicals found in the environment may be interacting with the genes in your body to cause disease is becoming easier because of a new field of science called toxicogenomics. A new report issued today by the National Academies of Sciences (NAS) recognizes the importance of toxicogenomics in predicting effects on human health and recommends the integration of toxicogenomics into regulatory decision making. The NAS report was commissioned by the National Institute of Environmental Health Sciences (NIEHS) part of the National Institutes of Health (NIH) and a leader in the development of toxicogenomic technologies.

Toxicogenomic technologies provide tools to better understand the mechanisms through which environmental agents initiate and advance disease processes. They can also provide important information to help identify individuals that are more susceptible to disease risks posed by certain environmental agents than the general population.

Using toxicogenomic technologies will open the door for public health decision makers who need to decide in a timely and accurate manner what chemicals are safe and which ones are not, says Christopher Portier, Ph.D., Associate Director, NIEHS and Director, Office of Risk Assessment Research......... Posted by: Sarah      Read more         Source

October 10, 2007, 7:08 PM CT

Increase in ethanol production from corn

If projected increases in the use of corn for ethanol production occur, the harm to water quality could be considerable, and water supply problems at the regional and local levels could also arise, says a new report from the National Research Council. The committee that wrote the report examined policy options and identified opportunities for new agricultural techniques and technologies to help minimize effects of biofuel production on water resources.

Recent increases in oil prices in conjunction with subsidy policies have led to a dramatic expansion in corn ethanol production and high interest in further expansion over the next decade, says the report. Indeed, because of strong national interest in greater energy independence, in this year's State of the Union address, President Bush called for the production of 35 billion gallons of ethanol by 2017, which would equal about 15 percent of the U.S. liquid transportation fuels.

A National Research Council committee was convened to look at how shifts in the nation's agriculture to include more energy crops, and potentially more crops overall, could affect water management and long-term sustainability of biofuel production. Based on findings presented at a July colloquium, the committee came to several conclusions about biofuel production and identified options for addressing them......... Posted by: Kevin      Read more         Source

October 10, 2007, 5:54 PM CT

Simultaneous Study of Multiple Variables

Researchers at the U.S. Department of Energy's Brookhaven National Laboratory have developed a method for correlating the results of microscopic imaging techniques in a way that could lead to improved understanding, diagnosis, and possibly therapy of a variety of disease conditions, including Alzheimer's disease. The Laboratory has filed a U.S. provisional patent application for the invention.

The invention is essentially a micron-scale metallic marking grid upon which researchers place their samples - biological tissues or inorganic samples such as minerals - previous to imaging with different methods. "When the findings are analyzed, the grid can be used to 'map,' or orient, the images to one another, allowing us to study multiple variables in a single sample and better understand how they relate to one another," said biophysicist Lisa Miller, leader of the team that developed the new method.

Typically for example, a number of diseases such as alzheimer's are characterized by changes in both organic materials, such as proteins, as well as changes in the composition or concentration of inorganic trace metals (e.g., iron, copper, and zinc). Researchers have techniques - infrared spectroscopy and x-ray fluorescence - for studying each of these independently. But without a way to correlate the findings from the two methods, important information about the relationship between the organic and inorganic components can be missed......... Posted by: Kevin      Read more         Source

October 10, 2007, 5:17 PM CT

Biometric sensors no dirtier than doorknobs

While biometric equipment is gaining popularity in a variety of applications, such as ensuring secure access to buildings, industries are finding that a number of users believe the devices are unsanitary and a potential source of germs that could cause illness.

But a Purdue University study has observed that while the platen glass surfaces of devices that scan fingerprints or hand geometry may look more unsanitary due to visible dirt and prints, they in fact harbor about the same amount of bacteria as a typical doorknob.

Christine R. Blomeke, a researcher and doctoral student in Purdue's Biometric Standards, Performance and Assurance Laboratory, performed the study along with lab director Stephen J. Elliott, an associate professor of industrial technology, and Thomas M. Walter, a continuing lecturer in the Department of Biological Sciences.

Blomeke said the study was conducted because of participant comments made during fingerprint and hand-geometry studies at the lab. She said the subjects, who were mandatory to touch their hands or fingers to the sensors, questioned the cleanliness of the surfaces.

"When you look at these devices, finger moisture, dirt and oils cause the surface to appear to be dirty," Blomeke said. "In a study we did on this last year, more than a quarter of the participants indicated that they thought the devices were somewhat unsanitary......... Posted by: Kevin      Read more         Source

October 8, 2007, 9:28 AM CT

Satellite methods for monitoring volcanic activity

The central part of the Andes situated between southern Peru and Chile bears 50 active or potentially volcanoes, spread along a 1500 km-long arc. These volcanic structures mostly rise to between 4000 and 7000 m, are very remote with abrupt slopes and are often cloaked in snow. Few studies have been made on them as such conditions make field surveying extremely difficult. A team of IRD scientists working in partnership with the University of Chile (Santiago) and the Observatoire de Physique du Globe of Clermont-Ferrand (1) focused special attention on the Lastarria-Cordon del Azufre volcanic complex. With a surface area of 1600 km, it is situated in the central Andes Cordillera at the border between Argentina and Chile near Antofagasta.

Research projects on deformations of the earth crust, conducted in this region between 1992 and 2000 by a North American team, had led to the detection of a long wavelength signal over the areas topography, extracted from analysis of data collected by the European Space Agency (ESA) satellite ERS-1. This deformation would correspond to crustal inflation affecting the whole Lastarria-Cordon del Azufre complex. Eventhough this volcano is not considered as active, as the last eruption dates back 9000 years, such inflation could express an underlying activity correlation to the dynamics of a functioning magma chamber......... Posted by: Tyler      Read more         Source