martedì 28 agosto 2007

World's Oldest Bacteria Found Living In Permafrost


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Science Daily — A research team has for the first time ever discovered DNA from living bacteria that are more than half a million years old. Never before has traces of still living organisms that old been found.
The exceptional discovery can lead to a better understanding of the aging of cells and might even cast light on the question of life on Mars. The discovery was made by Professor Eske Willerslev from the University of Copenhagen and his international research team.
All cells decompose with time. But some cells are better than others to postpone the decomposing and thus delay aging and eventually death. And there are even organisms that are capable of regenerate and thereby repair damaged cells. These cells -- their DNA -- are very interesting to the understanding of the process of how cells break down and age.
The research team, which consists of experts in, among other things, DNA traces in sediments and organisms, have found ancient bacteria that still contains active and living DNA. So far, it is the oldest finding of organisms containing active DNA and thus life on this earth. The discovery was made after excavations of layers of permafrost in the north-western Canada, the north-eastern Siberia and Antarctica.
The project is about examining how bacteria can live after having been frozen down for millions of years. Other researchers has tried to uncover the life of the past and the following evolutionary development by focusing on cells that are in a state of dead-like lethargy. "We, on the other hand, have found a method that makes is possible to extract and isolate DNA traces from cells that are still active. It gives a more precise picture of the past life and the evolution towards the present because we are dealing with cells that still have a metabolistic function -- unlike "dead" cells where that function has ceased," says Eske Wilerslev.
After the fieldwork and the isolation of the DNA, the researchers compared the DNA to DNA from a worldwide gene-bank in the US to identify the ancient material. Much in the same way the police compares fingerprints from a crime, the researchers were able to place the DNA more precisely and to place it in a context.
There is a very long way, of course, from our basic research towards understanding why some cells can become that old. But it is interesting in this context to look at how cells break down and are restored and thus are kept over a very long period. The researchers' methods and results can be used to determine if there was ever life on Mars the way we perceive life on earth.
And then there is the grand perspective in relation to Darwin's evolution theory. It predicts that life never returns to the same genetic level. "But our findings allows us to post the question: are we dealing with a circular evolution where development, so to speak, bites its own tail if and when ancient DNA are mixed with new?" says Eske Willerslev.
The discovery is being published in the current issue of PNAS (Proceedings of The National Academy of Sciences).
Note: This story has been adapted from a news release issued by University of Copenhagen.

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Social Habits Of Cells May Hold Key To Fighting Diseases


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Science Daily — Scientists in Manchester are working to change the social habits of living cells -- an innovation that could bring about cleaner and greener fuel and help fight diseases such as cancer and diabetes.
As part of a new £18 million project spanning six countries, The Manchester Centre for Integrative Systems Biology at The University of Manchester will spearhead important new research into an emerging field of science and engineering known as Systems Biology*.
Scientists have recently discovered that networking in living cells may determine whether a cell causes diabetes or cancer or helps to maintain our health.
By adjusting and modifying the way cells network, researchers believe it's possible to adjust the behaviour of living cells and reduce the chances of disease occurring.
Using this approach Manchester researchers working on the Systems Biology of Microorganisms (SysMO) research programme will also drive a project that looks at how the yeast used in the production of beer and bread can be turned into an efficient producer of bioethanol.
Other work to be carried out in Manchester includes the investigation of 'lactobacilli'. Some of these occasionally turn into flesh-eating bacteria or cause human diseases such as strep throat and rashes, whereas others are completely safe and are used in the production of cheeses and yoghurts.
It's hoped the work will lead not only to greater understanding of how 'wrong' networks lead to disease, but also to the production of drugs and other foods more efficiently and safely.
Academics will also look at 'pseudomonads' -- soil bacteria that may make people ill but can also be used to degrade nasty compounds in the environment, or to create compounds now being made by chemical industries.
Researchers will also focus on 'thermophilic' organisms that live naturally in hot springs, and examine how their networks enable them to survive high and varying temperatures. It's hoped that this research will reveal how to make any living organism cope better with extreme conditions. It may also lead to better performance of detergents and cosmetics.
All research will be carried out in the Manchester Interdisciplinary Biocentre (MIB) -- a unique, purpose-built, £38m facility that brings together experts from a wide range of disciplines in order to tackle major challenges in quantitative, interdisciplinary bioscience.
Professor Douglas Kell, Director of the MCISB, said: "Manchester is a leading centre for Systems Biology research and it is very exciting that so many of the SysMO projects have a Manchester component. Our involvement in these projects will allow us to achieve much added value and to develop and show best practice across all of them."
Professor Hans Westerhoff, AstraZeneca Professor of Systems Biology and Director of the Doctoral Training Centre on Systems Biology at The University of Manchester, said: "This is a unique opportunity to begin to understand how networking contributes to the functioning of living cells inside and outside our bodies.
"It enables us to integrate the best groups from six European countries and will address four concrete issues of energy, the disease-benefit balance, white biotechnology and robustness."
Systems Biology combines molecular biology and mathematics, which have traditionally been seen as the equivalents of fire and water. This type of research is still viewed as controversial by some in the scientific community.
But researchers involved in SysMO believe this approach will allow them to obtain a very large set of mathematical equations that describe living cells. This may then allow those cells to be engineered in a number of ways, with numerous benefits in the field of medicine and in the commercial world.
The SysMO scheme is funding a total of 11 programmes that run for three years in the first instance. It is being financed by the UK, Austria, Germany, The Netherlands, Spain and Norway.
The MCISB brings together researchers from across the faculties of Engineering and Physical Sciences and Life Sciences. It is funded by the Biotechnology and Biological Science Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC).
*Systems biology is a new approach to bioscience that combines theory, computer modelling and experiments. It is revolutionising how bioscientists think and work and will make the outputs on their work more useful, and easier to use in industry and policymaking.
Instead of using the traditional biology approach of observation and experiment, systems biology uses computer simulations and modelling to process results, design new, more quantitative experiments and generate predictive solutions.
Note: This story has been adapted from a news release issued by University of Manchester.

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lunedì 27 agosto 2007

Feeling Hot, Hot, Hot: New Study Suggests Ways To Control Fever-induced Seizures


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Science Daily — When your body cranks up the heat, it's a sign that something's wrong--and a fever is designed to help fight off the infection. But turning up the temperature can have a down side: in about one in 25 infants or small children, high fever can trigger fever-induced (febrile) seizures. While the seizures themselves are generally harmless, a prolonged fever resulting from infection or heatstroke of over 108 °F (42 °C) can eventually lead to respiratory distress, cognitive dysfunction, brain damage or death.
New research by scientists at the University of Toronto Mississauga and Queen's University has shown that genetic variation in the foraging gene results in different tolerance for heat stress, and demonstrates how the use of specific drugs can replicate this effect in fruit flies and locusts. While the findings are at an early stage, the researchers suggest that since this genetic pathway is found in other organisms, it could lead to ways to rapidly protect the brain from extremely high fevers in mammals, including humans.
"Our research suggests that manipulation of a single gene or genetic pathway will be sufficient to rapidly protect the nervous system from damage due to extreme heat stress," says senior researcher, Professor Marla B. Sokolowski, who holds a Canada Research Chair in Genetics.
In their research, post-doctoral fellow Ken Dawson-Scully and Sokolowski demonstrate that the foraging gene, responsible for a protein called PKG, protects against heat-induced neural failure in fruit flies and locusts. When they increased the temperature by 5°C per minute (starting from 22°C and rising to 42°C), they found that fruit flies with a lower level of PKG experienced neural failure at much higher temperatures than those with higher levels of PKG.
Using drugs that interact with the PKG molecule, the researchers showed it is possible to induce an extremely rapid protection of neural function during heat stress. Queen's biologists Gary Armstrong and Mel Robertson exposed locusts to increasing heat while monitoring the neural circuit that controls breathing. At approximately 30ÚC (about three minutes before expected neural failure), the researchers injected the locusts with a PKG inhibitor. Compared to locusts who received a placebo injection, the treated locusts showed a rapid and significant protection of their neural circuitry.
"During heat trauma to the brain, there exists a window of opportunity between the time of occurrence of neural dysfunction and eventual brain damage or death," says Dawson-Scully. "Manipulation of the PKG pathway during this period should increase an individual's chance of survival."
The research was supported by the Heart and Stroke Foundation of Canada, the Canadian Institutes of Health Research and the Natural Sciences and Engineering Research Council of Canada.
The new study appears in the August 22 issue of the journal PLoS One.
Citation: Dawson-Scully K, Armstrong GAB, Kent C, Robertson RM, Sokolowski MB (2007) Natural Variation in the Thermotolerance of Neural Function and Behavior due to a cGMP-Dependent Protein Kinase. PLoS One 2(8): e773. doi:10.1371/journal.pone.0000773
Note: This story has been adapted from a news release issued by Public Library of Science.

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Folate Mystery Finally Solved


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Science Daily — Some biochemical processes, especially those in bacteria, have been so well studied it's assumed that no discoveries are left to be made. Not so, it turns out, for Johns Hopkins researchers who have stumbled on the identity of an enzyme that had been a mystery for more than 30 years.
"It was really quite a surprise when we realized we had discovered the unknown player in how bacteria make the B vitamin folate, a player that we've known of since 1974," says study author L. Mario Amzel, Ph.D., professor and director of biophysics and biophysical chemistry at Hopkins. "Basic research can be so serendipitous at times."
Amzel and colleague Maurice Bessman and their labs were in the middle of systematically characterizing how members of a family of related enzymes in bacteria can recognize specific molecules. With each family member, they isolated purified enzyme, grew crystals of pure enzyme, and figured out the enzyme's 3-D structure by using techniques that use X-rays.
Armed with the 3-D structure, they then used computer modeling to analyze how the enzyme binds to and acts on another molecule, its substrate.
"We still didn't know that it was anything special until Maurice started searching old publications," says study author Sandra Gabelli, Ph.D. "As it turns out, Suzuki and coworkers in 1974 had published evidence of an enzyme in the bacteria E. coli with similar characteristics to ours that could initiate folate biosynthesis."
"So we had to ask, Can the bacteria make folate if we remove the orf17 gene"" says Amzel. Bessman and colleagues then "knocked-out" the gene and, predictably, the bacteria made 10 times less folate than usual.
"It was such a sweet discovery," says Gabelli. "It's scientific discovery the old-fashioned way, finding something we weren't looking for."
The mechanics behind how bacteria make folate are of particular interest to scientists who want to design more powerful antibacterial drugs. Humans cannot make folate because they do not have any of the same molecular machinery. Therefore, it's possible to design drugs that target the bacterial folate machinery that would not lead to side effects in humans.
Their discovery, says Amzel, identifies yet another potential antibacterial target. "We are not in that business of drug design--we're focused on the basics, figuring out how things work," he says. "We do hope that others can use what we find to make new drugs."
The full report appears in the May 15 issue of Structure.
The research was funded by the National Institutes of Health.
Authors on the paper are Gabelli, Mario Bianchet, WenLian Xu, Christopher Dunn, Zhi-Dian Niu, Amzel and Maurice Bessman, all of Hopkins.
Note: This story has been adapted from a news release issued by Johns Hopkins Medical Institutions.
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martedì 21 agosto 2007

Genetic Phonetics Could Be The Trick To Sounding Out DNA's Meaning

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Science Daily — Most modern attempts to decipher how portions of genetic code are translated into physical characteristics are akin to a first-grader trying to sound out a word letter by letter — or, in this case, base pair by base pair.
But University of Florida researchers have developed a computational method that’s more like reading whole words at a time.
In a world where science’s ability to transcribe an organism’s genetic code is growing faster every day, the technique could offer much needed efficiency in translating the seemingly endless string of characters into information that can cure disease or create new crops.
The researchers, from UF’s Institute of Food and Agricultural Sciences and the UF Genetics Institute, published their verification of the method in PLoS One, an online journal produced by the Public Library of Science.
“We worked very hard to find ways to collect genetic information,” said Rongling Wu, the project’s lead researcher and a UF Research Foundation professor. “We now must work hard to find ways to use it.”
In many respects, researchers think of an organism’s genome as ticker-tape listings of four letters — representing four amino acid bases — repeated in varying orders. The goal is to find meaning within the sequences, to figure out how variations in the pattern affect the organism’s physiology.
Humans, for example, have 3 billion letters in our code. Between any two of us, 99.9 percent of those letters are the same. But it’s that last 0.1 percent of difference, peppered throughout our DNA in the form of single-letter changes, that accounts for our unique identities—from eye color to disease susceptibility.
These differences are called single nucleotide polymorphisms, or SNPs (pronounced “snips”).
The simplest way to find out how a SNP affects an organism is to collect a group of organisms that have different variations of that letter in their genetic code.
But physical traits are typically affected by multiple SNPs that interact in sometimes unpredictable ways — much like the way an “e” at the end of a word can change its pronunciation.
Fortunately, the rules of genetics say that SNPs that affect the same trait are generally related to each other in some way, such as being near each other.
Wu’s model uses these rules in conjunction with statistical analysis of real data from genetically mapped organisms. As a result, the model can find whole groups of SNPs associated with a physical trait.
Just as an understanding of general phonetic principles allows a reader to sound out a whole word, this extra knowledge of genetics allows Wu’s model to find whole pictures of genome/physical correlations.
“The real promise of Wu’s work is that it could offer the opportunity for a researcher to not spend a really disheartening amount of time parsing out individual nucleotides, and move more directly to doing the type of genetic work that’s going to have a greater significance,” said Rory Todhunter, a researcher working with canine genetics at Cornell University.
In the paper, the researchers verified their model using genetic and physical information from mice that was first collected from the Washington University lab of James Cheverud in the mid-1990s. They then compared their results with several years’ worth of genetic analysis.
This validation was important, said Wei Hou, the first author of the paper and an assistant professor at UF’s department of epidemiology and health policy research. But the analysis of modern data will be the real key to the technique’s importance. For example, the mouse genetic information used in this paper featured only a few thousand SNPs. The July 29 issue of the journal Nature cited more than 8 million SNPs for the mouse genome.
“This shows how we need to move beyond looking at genomes SNP by SNP,” Cheverud said. “Imagine the work that’s ahead of us if we don’t.”
Note: This story has been adapted from a news release issued by University Of Florida.

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lunedì 20 agosto 2007

Features Of Replication Suggest Viruses Have Common Themes, Vulnerabilities

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Science Daily — A study of the reproductive apparatus of a model virus is bolstering the idea that broad classes of viruses - including those that cause important human diseases such as AIDS, SARS and hepatitis C - have features in common that could eventually make them vulnerable to broad-spectrum antiviral agents.
In a study published August 14 in Public Library of Science Biology, a team of researchers from the Howard Hughes Medical Institute (HHMI) at the University of Wisconsin-Madison describes in fine detail how an RNA virus known as flock house virus co-opts a cell's membranes to create an intracellular lair where it can safely replicate its genes.
The results provide strong evidence that at least some of the machinery four of the seven distinct classes of known viruses use to reproduce have common attributes. Such a discovery is important because it reveals a common viral theme that may be vulnerable to disruption and could lead to the development of drugs to treat many different kinds of viral infections, much like antibiotics are used to attack different kinds of bacterial pathogens.
"It turns out that viruses previously thought of as distinct share common features," says Paul Ahlquist, an HHMI investigator and virologist at UW-Madison. "We've found some features of replication that appear to cross over among many viruses."
Using powerful electron microscopy techniques, Ahlquist's group and their collaborators made the first three-dimensional maps of a viral replication complex using flock house virus, which, like all viruses, requires a host cell to make new genetic material and maintain the chain of infection.
In the case of flock house virus, the Wisconsin group found, the virus co-opts intracellular membranes of mitochondria, critical energy-regulating structures found in most eukaryotic cells.
Squeezing into the space between the inner and outer membrane of the double-lined mitochondria, the virus creates tens of thousands of protein-lined, balloon-like pockets where it can make new copies of the viral genome while safe from surveillance and defense mechanisms of the host.
" The virus has developed a very elegant strategy," says Ahlquist. "It creates for itself a new compartment for RNA synthesis, where it can collect its (constituent) components, organize successive steps of replication, and sequester these steps from other processes in the cell, most importantly, host defense responses."
In essence, the virus is reorganizing the cell to make a new intracellular architecture for its own purposes, according to Ahlquist. "The virus is reorganizing the cell to make a new organelle. It is a way to keep out competing processes and alarm-ringers and have a place where it can carry out its processes efficiently and for long periods of time."
The balloon-like sacs or spherules observed by Ahlquist and his colleagues all had narrow necks that transcended the membrane of the organelle to the cytoplasm, the medium inside the cell and in which the organelle is suspended. The neck is a gateway that appears to permit substrates needed for replication to enter and newly made viral genomes to exit.
The virus begins to co-opt the cell as a critical viral protein and viral RNA localize to the budding organelles, Ahlquist explains. "The virus takes over most of the available membrane. The protein creates a shell inside the spherule" to provide stability, and it is this use of a protein shell in replicating viral genes, the Wisconsin virologist suggests, that could be one of several common themes among different groups of viruses.
"Multiple features in the structure and function of these replication compartments appear similar across several virus classes," says Ahlquist. "This includes ways in which cell membranes are used to organize virus replication."
The shared features extend to most RNA viruses and a group known as reverse transcribing viruses, which include retroviruses such as HIV, suggesting a possible evolutionary link from a common ancestor.
The new work was made possible by the use of electron microscope tomography, a technique that can provide detailed cross sections and composite three-dimensional images of structures within the cell. The imaging was conducted at the National Center for Microscopy and Imaging Research at the University of California San Diego by UW-Madison graduate student Benjamin G. Kopek, in collaboration with Guy Perkins and Mark H. Ellisman of UC-San Diego. David J. Miller of the University of Michigan is also a co-author of the paper.
Note: This story has been adapted from a news release issued by University of Wisconsin-Madison.
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Creating Males With Female Sex Chromosomes: Brain Gene Flicks The Switch On Gender


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Science Daily — University of Adelaide researchers have discovered a way of creating a male mouse without a Y chromosome by manipulating a single gene in the developing foetus.
Normally males have one X and one Y chromosome and females have two X chromosomes. But Postdoctoral Research Officer Dr Edwina Sutton has produced male mice with two X chromosomes by artificially activating a gene in the developing gonads.
"The gene - Sox3 on the X chromosome - is well known for its impact on brain development, but this is the first time it's ever been shown to change sexual development. By making this brain gene active in the developing gonads of mice with two X chromosomes during the critical stage of development, we switched off female development and switched on 'maleness'," said Dr Sutton.
"This is not only important for our knowledge of evolution of the sex chromosomes, but it also has potentially significant implications for people with disorders of sexual development, the causes of which we know very little about. We can use these mice to increase our understanding of these disorders which occur with a high frequency in our community and, ultimately, develop therapies or technologies to improve clinical outcomes."
This discovery came about by chance. Dr Sutton and her supervisor Research Fellow Dr Paul Thomas, both in the University's School of Molecular and Biomedical Science, were investigating the role of Sox3 in brain development and discovered they had produced 80% XX male offspring. Although completely male in appearance, reproductive structures and behaviour, the XX males are all sterile.
Dr Sutton's findings were recently presented at the First Pan American Congress in Developmental Biology in Cancun, Mexico.
Note: This story has been adapted from a news release issued by University of Adelaide.

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domenica 19 agosto 2007

Interaction Of Just Two Genes Governs Coloration Patterns In Mice


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Science Daily — Biologists at Harvard University and the University of California, San Diego, have found that a simple interaction between just two genes determines the patterns of fur coloration that camouflage mice against their background, protecting them from many predators.
The work, published recently in the journal PLoS Biology, marks one of the few instances in which specific genetic changes have been linked to an organism's ability to survive in the wild."Our work shows how changes in just a few genes can greatly alter an organism's appearance," says Hopi E. Hoekstra, John L. Loeb Associate Professor of the Natural Sciences in Harvard's Faculty of Arts and Sciences. "It also illuminates the pathway by which these two genes interact to produce distinctive coloration. There's reason to believe this simple pathway may be evolutionarily conserved across mammals that display lighter bellies and darker backs, from mice to tuxedo cats to German Shepherds."Hoekstra and co-authors Cynthia C. Steiner at UCSD and Jesse Weber at Harvard studied Peromyscus, a mouse that is the most widespread mammal in North America. Within the last several thousand years, these mice have migrated from mainland Florida to barrier islands and dunes along the Atlantic and Gulf coasts, where they now live on white sand beaches. In the process, the beach mice's coats have become markedly lighter than that of their mainland brethren."In nature there is a tremendous amount of variation in color patterns among organisms, ranging from leopard spots to zebra stripes, that help individuals survive," says Steiner, a postdoctoral researcher in UCSD's Division of Biological Sciences. "However, we know surprisingly little about how these adaptive color patterns are generated. In this paper, we identify the genetic changes producing a simple color pattern that helps camouflage mice inhabiting the sandy dunes of Florida's Gulf and Atlantic coasts. These 'beach mice' have evolved a lighter pigmentation than their mainland relatives, a coloration that helps camouflage them from predators that include owls, herons, and hawks."Previous research has shown that such predators, all of which hunt by sight, will preferentially catch darker mice on the white sand beaches, providing a powerful opportunity for natural selection to evolve increased camouflage.Through a detailed genomic analysis, Hoekstra, Steiner, and Weber identified two pigmentation genes, for the melanocortin-1 receptor (Mc1r) and an agouti signaling protein (Agouti) that binds to this receptor and turns it off. A single amino-acid mutation in Mc1r gene can weaken the receptor's activity, or a mutation in the Agouti gene can increase the amount of protein present without changing the protein's sequence, also reducing Mc1r activity and yielding lighter pigmentation.Both genes affect the type and amount of melanin in individual hairs. When both genes are turned on, the mouse is dark in color. A mutation that changes either gene leads to a somewhat blonder mouse, but it is the combination of mutations in both genes that produces a mouse very light in color."Thus, two different types of mutations in two different genes each contribute to the light coloration of beach mice," Hoekstra says. "This work represents a first step into understanding how unique patterns of fur color are produced via a simple interaction between genes."Hoekstra, Steiner, and Weber's work was funded by the National Science Foundation and the National Institutes of Health.
Note: This story has been adapted from a news release issued by Harvard University.

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giovedì 16 agosto 2007

Gene Mutation Turned West Nile Virus Into Killer Disease Among Crows


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Science Daily — A gene mutation that appears to be responsible for changing relatively mild forms of the West Nile virus into a highly virulent and deadly disease in American crows has been identified by a team of scientists led by a researcher at the University of California, Davis.Because it is highly susceptible to West Nile virus, the American crow has served as the major sentinel species, playing an important role in alerting scientists and health professionals to the movement of the disease across North America.
"The findings from this study highlight the potential for viruses like West Nile to rapidly adapt to changing environments when introduced to new geographic regions," said Aaron C. Brault, a virologist at the Center for Vectorborne Diseases in the Department of Pathology, Microbiology and Immunology of the UC Davis School of Veterinary Medicine."The study also suggests that the genetic mutations that create such adaptive changes may result in viral strains that have unexpected symptoms and patterns of transmission," Brault said.About West Nile virusWest Nile virus, which is passed back and forth between birds and mosquitoes and transmitted to humans via mosquito bites, was first identified in 1937 in Uganda. Although it was recognized as a cause of severe encephalitis and meningitis (inflammation of the brain and spinal cord, respectively) during a 1957 outbreak in Israel, it has been primarily associated with mild infections accompanied by fevers in humans in Africa and the Middle East.In 1996, West Nile virus caused an outbreak of encephalitis in Romania, moving on to cause similar outbreaks throughout the next several years in Israel, Tunisia and Russia.In 1999, the virus was first recognized in North America and has since been reported in humans, birds, horses and mosquitoes in Canada and in all of the contiguous U.S. states. It has become the leading cause of encephalitis from a virus transmitted by arthropods, a group of invertebrates that includes insects, spiders and ticks.West Nile in birdsA variety of North American bird species, including ring-billed gulls, house finches, crows and black-billed magpies, are extremely susceptible to West Nile virus. In fact, a hallmark of the West Nile virus in North America has been how deadly the virus has been among wild and captive birds. Particularly vulnerable to West Nile virus is the American crow, which is common in urban and suburban areas as well as in all natural habitats except the Southwestern deserts.Because the American crow is so common and so highly susceptible to West Nile virus, it has served as the sentinel species in North America. Epidemiological studies have found that deaths of American crows due to West Nile virus are associated with higher rates of infection among mosquito populations and clusters of the disease in humans.Although scientists and health professionals have thoroughly described how West Nile virus spreads through both human and animal populations in North America, it has been unclear just how the virus emerged to cause such serious disease in birds, particularly the American crow.Pinpointing the gene mutation siteTo identify how West Nile virus developed into such a deadly disease for birds, the research team looked to the genetic makeup of the virus. West Nile virus is an RNA virus -- its genetic material being composed of RNA, rather than DNA. Although RNA and DNA molecules differ somewhat in structure and function, both play key roles in enabling cells to build the proteins necessary for reproducing and carry out the cells' functions.The researchers analyzed the evolutionary relationships of the West Nile virus genomes, or entire collections of genes, for 21 different strains of West Nile viruses that had been sampled globally in recent years, including strains from North America. Analysis of genetic patterns indicated a disproportionate rate of change at a particular amino acid within one of the viral genes.Onto this genome "tree" for the various strains of West Nile virus, they mapped the mutational changes in the same gene region mentioned above. They found that the same amino acid change had occurred three different times and that the resulting virus had been associated with human disease outbreaks.In order to determine if this mutation was associated with the increased virulence of the West Nile virus in birds and its subsequent ability to spread to humans, the researchers introduced the mutation independently into the low-virulence virus. They also removed that mutation from the highly virulent North American strain.At that location, the researchers made changes in the amino acids, which they suspected might change a relatively mild West Nile virus strain from Kenya into a much more virulent strain and, conversely, could weaken the more potent New York strain.Then they inoculated American crows with either a parent virus or one of the newly created recombinant viruses in order to observe the viruses' activity.As expected, they found that the parent virus from the relatively mild Kenya strain did not become detectable in the crows' bloodstream until two to three days after the birds were infected. However, the new recombinant form of that viral strain quickly became detectable in the crows' bloodstream, and by the third day was present at 10,000 times the concentration of the parent virus from which it was developed, killing nearly all. The researchers then made the reciprocal amino acid change in the parent virus of the virulent New York strain of West Nile virus, drastically reducing its deadliness in crows. This weakened New York strain was comparable to the relatively mild parent virus from Kenya in terms of detectable levels in the bloodstream and its deadliness among the inoculated crows."It appears that the naturally occurring changes in the amino acids at this particular gene site have played an important role in increasing the virulence of West Nile virus in birds before it appeared in North America," Brault said. "Furthermore, these data indicate how much West Nile virus relies on replicating to high levels in birds for efficient transmission of the virus, potentially leading to human disease outbreaks."The results of the study were reported in the August 12 online issue of the journal Nature Genetics.Funding for the study was provided by the Centers for Disease Control and Prevention, the National Institutes of Health and the Pacific Southwest Regional Center for Excellence.
Note: This story has been adapted from a news release issued by Univesity of California, Davis.

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Where Broken DNA Is Repaired


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Science Daily — Ionizing radiation, toxic chemicals, and other agents continually damage the body's DNA, threatening life and health: unrepaired DNA can lead to mutations, which in turn can lead to diseases like cancer. Intricate DNA repair mechanisms in the cells' nuclei are constantly working to fix what's broken, but whether the repair work happens "on the road" — right where the damage occurs — or "in the shop" — at specific regions of the nucleus — is an unanswered question.That question may now be closer to an answer.
By comparing computer models of damaged human DNA with microscopic images of human cells that reveal focal sites of radiation-induced damage, researchers in the Life Sciences Division (LSD) of the Department of Energy's Lawrence Berkeley National Laboratory, with colleagues at NASA and the Universities Space Research Association, have found evidence that indeed there are specific regions where broken DNA is concentrated for repair. "NASA has long been interested in the radiation hazards in space," says LSD's Sylvain Costes, who led the study. "On a trip to Mars, astronauts will be exposed to cosmic rays for as long as three years, so NASA has been trying to come up with a mechanistic model of DNA repair to estimate the increased risk of cancer. We are helping to develop such a model." Double-strand breaks and radiation-induced fociIn many NASA studies cells have been exposed to particles like those found in cosmic rays, such as energetic iron nuclei produced in accelerators at Brookhaven National Laboratory. The goal is to determine how many double-strand breaks (DSBs) — in which both strands of the DNA double helix are severed — occur per gray of radiation. (One gray is equivalent to 100 rads, an older unit signifying "radiation absorbed dose"; a gray equals one joule of energy absorbed per kilogram of matter.) DSB yield can be measured by pulling apart a cell's radiation-severed DNA using gel electrophoresis: the shorter the fragments in the gel bands, the more frequent the breaks. Interpreting the band patterns thus leads to an estimate of the average number of breaks per cell for a given dose and time following exposure. NASA has developed a computer model based on these measured DSB yields to predict DSB formation in hypothetical human cell nuclei.On the other hand, gel electrophoresis fails to indicate the severity of the damage, or where in the nucleus the double-strand breaks occur. The default assumption has been that DSBs occur randomly in a homogenous distribution of DNA in the nucleus. Most gel electrophoresis studies indicate about 25 to 30 DSBs per gray of gamma rays. In microscopic images of real cells, however, the visible sites that might be assumed to correspond to double-strand breaks — sites called "radiation induced foci," or RIF — occur at a lower rate, only about 15 per gray, depending on the cell type. "What we see through the microscope is not the broken DNA itself but a collection of proteins associated with breaks, which we have labeled with fluorescent stains. These include modified histones, which are part of the chromosomal material, and other proteins that seek out DNA breaks and recruit repair machinery to fix them," says Costes. "The first question we had to answer was how closely RIF are associated with DSBs." Costes recognized that one way to test the association was to calculate how energy was deposited by different kinds of radiation. A high-energy particle, for example, moves through the nucleus in a straight line and may strike DNA at any point along the way; the pattern of hits along the track should be essentially random. "Physicists understand very well how energy is deposited in the cell's DNA," says Costes, "but the challenge was to make a predictive model that was consistent with what a biologist sees through the microscope. To test what should be seen, given a specific radiation dose, I set out to turn NASA's high-resolution DNA damage simulator" — a model based on data from gel electrophoresis — "into artificial microscope images of a nucleus damaged by radiation." To do this, says Costes, "I simulated the optical transformation when imaging events at the nanoscale are viewed with a fluorescent microscope." One optical transformation is blurring, with the result that, in a real microscope, two nearby radiation-induced foci may blend together and look like one. When such factors were taken into account, Costes's initial model, following the NASA model, confirmed random distribution of double-strand breaks at the micron scale. The frequency of DSBs was radiation dependent, however: in the case of cosmic rays (NASA's main concern), which lead to complex double-strand breaks, there was good agreement with the RIF frequencies seen in the microscope. But in the case of gamma rays, which lead primarily to sparse and noncomplex DSBs, measured frequencies in real microscope images were lower. This suggests that RIF correspond to sites of complex double-strand breaks in DNA. Moreover — focusing on cosmic rays for the NASA project — although the DSB frequency was the same as predicted by the models, the RIF in real microscope images were distributed very differently. Model physics, real biology"For one thing, there is a time effect," says Costes. "Just five minutes after cells are exposed to high-energy particles, microscope images already show a nonrandom distribution of RIF." The RIF occur along straight lines, as expected for a particle track, but are not randomly distributed along the lines. "Even though we have the right foci frequency along a track, many foci appear to repulse each other within the first 30 minutes after irradiation" — a suggestion that they might be moving to specific regions of the nucleus. Costes and his colleagues applied the same kinds of models and measurements to gamma rays and found that whereas the model predicted that these breaks would occur in a random pattern in three dimensions throughout the nucleus (not along lines), in fact, under the microscope, radiation-induced foci caused by gamma rays were also distributed nonrandomly. There were fewer RIF due to gamma rays than the model predicted, and they appeared more gradually. The researchers now used a novel technique, "relative DNA image measurements," and analyzed the images to show where the DNA was dense, where it was less dense, and where the two densities met. They wanted to see whether, where RIF occurred, there was an underlying difference in the nature of the DNA. Indeed there was. By comparison to the random distribution that might have been expected, RIF were more frequent in the low-density regions. And a preponderance of RIF coincided with the interfaces between the two kinds of DNA. "In terms of physics, there's no obvious explanation for this observation," says Costes. "In terms of biology, we have some pretty good guesses." What's evident is that the organization of the cell nucleus plays an important role in response to DNA damage. The high-density regions likely are heterochromatin, the parts of the chromosomes where genes are (for the most part) silenced. The low-density regions likely correspond to euchromatin, the parts of the chromosomes where most genes are actively transcribed. While it's possible that damage in condensed regions causes the condensed chromatin to open up and appear less dense, it is more likely, Costes believes, that the damaged sections actually migrate toward the less-dense chromatin and concentrate at the high-density/low-density interface. Researchers have previously proposed the existence of "repairosomes" in mammalian cells, similar to specific regions where DNA is repaired in yeast, although these have never been observed in mammals. The fact that RIF concentrate in specific regions of the human cell nucleus — and apparently tend to move toward shared sites — is highly suggestive of such repair centers, where activities like the necessary clamping and orientation of the broken strands take place. "Our results raise a number of interesting possibilities," says Costes. "If less-dense regions of the nucleus are more susceptible to radiation damage, we may be able to use this knowledge to make tumor cells easier to kill. Repair centers in mammalian cells are probably an efficient way to repair the typically sparse and noncomplex DNA damages of daily cellular life." But there's a downside, Costes says. "Humans didn't evolve with cosmic rays, and the existence of repair centers may not be good news for astronauts — cosmic rays primarily generate spatial clusters of complex DNA breaks. If these breaks are gathered in common locations in the nucleus, they will most likely lead to chromosomal translocation, a process thought to play an initiative role in cancer." Thus the data obtained by Costes and his colleagues through image-based modeling suggests a wealth of new opportunities for research. "Image-based modeling reveals dynamic redistribution of DNA damage into nuclear sub-domains," by Sylvain V. Costes, Artem Ponomarev, James L. Chen, David Nguyen, Francis A. Cucinotta, and Mary-Helen Barcellos-Hoff, appears online in the August 2007 PLoS Computational Biology, (volume 3, issue 8 ).
Note: This story has been adapted from a news release issued by DOE/Lawrence Berkeley National Laboratory.

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MIT Creates 3-D Images Of Living Cell


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Science Daily — A new imaging technique developed at MIT has allowed scientists to create the first 3D images of a living cell, using a method similar to the X-ray CT scans doctors use to see inside the body.
The technique, described in a paper published in the Aug. 12 online edition of Nature Methods, could be used to produce the most detailed images yet of what goes on inside a living cell without the help of fluorescent markers or other externally added contrast agents, said Michael Feld, director of MIT's George R. Harrison Spectroscopy Laboratory and a professor of physics."Accomplishing this has been my dream, and a goal of our laboratory, for several years," said Feld, senior author of the paper. "For the first time the functional activities of living cells can be studied in their native state."Using the new technique, his team has created three-dimensional images of cervical cancer cells, showing internal cell structures. They've also imaged C. elegans, a small worm, as well as several other cell types. The researchers based their technique on the same concept used to create three-dimensional CT (computed tomography) images of the human body, which allow doctors to diagnose and treat medical conditions. CT images are generated by combining a series of two-dimensional X-ray images taken as the X-ray source rotates around the object."You can reconstruct a 3D representation of an object from multiple images taken from multiple directions," said Wonshik Choi, lead author of the paper and a Spectroscopy Laboratory postdoctoral associate.Cells don't absorb much visible light, so the researchers instead created their images by taking advantage of a property known as refractive index. Every material has a well-defined refractive index, which is a measure of how much the speed of light is reduced as it passes through the material. The higher the index, the slower the light travels. The researchers made their measurements using a technique known as interferometry, in which a light wave passing through a cell is compared with a reference wave that doesn't pass through it. A 2D image containing information about refractive index is thus obtained.To create a 3D image, the researchers combined 100 two-dimensional images taken from different angles. The resulting images are essentially 3D maps of the refractive index of the cell's organelles. The entire process took about 10 seconds, but the researchers recently reduced this time to 0.1 seconds.The team's image of a cervical cancer cell reveals the cell nucleus, the nucleolus and a number of smaller organelles in the cytoplasm. The researchers are currently in the process of better characterizing these organelles by combining the technique with fluorescence microscopy and other techniques."One key advantage of the new technique is that it can be used to study live cells without any preparation," said Kamran Badizadegan, principal research scientist in the Spectroscopy Laboratory and assistant professor of pathology at Harvard Medical School, and one of the authors of the paper. With essentially all other 3D imaging techniques, the samples must be fixed with chemicals, frozen, stained with dyes, metallized or otherwise processed to provide detailed structural information. "When you fix the cells, you can't look at their movements, and when you add external contrast agents you can never be sure that you haven't somehow interfered with normal cellular function," said Badizadegan.The current resolution of the new technique is about 500 nanometers, or billionths of a meter, but the team is working on improving the resolution. "We are confident that we can attain 150 nanometers, and perhaps higher resolution is possible," Feld said. "We expect this new technique to serve as a complement to electron microscopy, which has a resolution of approximately 10 nanometers." Other authors on the paper are Christopher Fang-Yen, a former postdoctoral associate; graduate students Seungeun Oh and Niyom Lue; and Ramachandra Dasari, principal research scientist at the Spectroscopy Laboratory.The research was conducted at MIT's Laser Biomedical Research Center and funded by the National Institutes of Health and Hamamatsu Corporation.
Note: This story has been adapted from a news release issued by Massachusetts Institute of Technology.

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Locked In Glaciers, Ancient Ice May Return To Life As Glaciers Melt


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Science Daily — The DNA of ancient microorganisms, long frozen in glaciers, may return to life as the glaciers melt, according to a paper published recently online in the Proceedings of the National Academy of Sciences by scientists at Rutgers, The State University of New Jersey, and Boston University. The article is scheduled to appear in the print edition on Tuesday, Aug. 14.
The finding is significant, said Kay Bidle, assistant professor of marine and coastal sciences at Rutgers, because scientists didn't know until now whether such ancient, frozen organisms and their DNA could be revived at all or for how long cells are viable after they've been frozen. Bidle is lead author of the article, "Fossil Genes and Microbes in the Oldest Ice on Earth."Bidle and his co-authors, Rutgers colleague Paul Falkowski, SangHoon Lee of Korea's Polar Research Institute and David Marchant of Boston University -- melted five samples of ice ranging in age from 100,000 to 8 million years old to find the microorganisms trapped inside.The researchers wanted to find out how long cells could remain viable and how intact their DNA was in the youngest and oldest ice. "First, we asked, do we detect microorganisms at all"" Bidle said. "And we did -- more in the young ice than in the old. We tried to grow them in media, and the young stuff grew really fast. We recovered them [the microorganisms] easily; we could plate them and isolate colonies. They doubled every couple of days." By contrast, Bidle said, the microorganisms from the oldest ice samples grew very slowly, doubling only every 70 days.Not only were the microorganisms in oldest ice slow to grow, the researchers were unable to identify them as they grew, because their DNA had deteriorated. In fact, the DNA in the five samples examined showed an "exponential decline" after 1.1 million years, "thereby constraining the geological preservation of microbes in icy environments and the possible exchange of genetic material to the oceans." "There is still DNA left after 1.1 million years," Bidle said. "But 1.1 million years is the 'half-life' -- that is, every 1.1 million years, the DNA gets chopped in half." Bidle said the average size of DNA in the old ice was 210 base pairs -- that is, 210 units strung together. The average genome size of a bacterium, by comparison, is 3 million base pairs.The researchers chose Antarctic glaciers for their research because the polar regions are subject to more cosmic radiation than the rest of the planet and contain the oldest ice on the planet. "It's the cosmic radiation that's blasting the DNA into pieces over geologic time, and most of the organisms can't repair that damage." Because the DNA had deteriorated so much in the old ice, the researchers also concluded that life on Earth, however it arose, did not ride in on a comet or other debris from outside the solar system. "...The preservation of microbes and their genes in icy comets may have allowed transfer of genetic material among planets," they wrote. "However, given the extremely high cosmic radiation flux in space, our results suggest it is highly unlikely that life on Earth could have been seeded by genetic material external to this solar system."The five ice samples used in the experiment were taken from two valleys in the Transantarctic Mountains by Marchant, the Boston University glaciologist. "He sent us blocks of ice," said Bidle of Marchant. "Without them, we couldn't have done the work. Dave is also one of the few researchers who is knowledgeable about the age of the ice, and also important information about the formation and geology of the ice."The actual melting of the ice, growing of microorganisms and examination of DNA was carried out by Bidle and Lee, who was a visiting researcher at Rutgers at the time. Falkowski co-directed the research and helped to write the paper.The work was funded by a grant to Falkowski and Bidle from the Gordon and Betty Moore Foundation.
Note: This story has been adapted from a news release issued by Rutgers, the State University of New Jersey.

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