Showing posts with label BY SAI KIRAN REDDY. Show all posts

Flu Jab for Bacteria


Sai kiran (Apr. 7, 2010) — Viruses can wreak havoc on bacteria as well as humans and, just like us, bacteria have their own defence system in place, explains Professor John van der Oost, at the Society for General Microbiology's spring meeting. Uncovering the workings of the bacterial "immune system" could be used to keep industrial microbes at peak performance.

The key experiment shows the successful protection of a phage-sensitive bacterial strain against a virus. Top-right - bacterial lawn growing in absence of virus; Top-left -holes in the lawn (plaques) caused by growth perturbation due to phage; Bottom - when equipped with the right components of the CRISPR/Cas defense system, the bacteria became resistant to virus infection. (Credit: John van der Oost)


Professor van der Oost and his team at Wageningen University in the Netherlands have spent the last three years working out the molecular details of the immune system called CRISPR that is present in bacteria. The recently discovered CRISPR defence system differs from the immune system in higher organisms in that acquired immunity can be passed down future generations. This means bacterial offspring are protected from viral attack even before they are exposed to the invading virus.
Specific bacterial proteins recognise infectious viruses, called bacteriophages, by detecting foreign DNA. These proteins take the viral DNA and insert it into the bacterial genome at very specific locations. "Storing the information in this way gives the bacteria a lasting 'memory' of the harmful virus that subsequently confers immunity- much like our own immune systems," said Professor van der Oost. Upon future attack by the same virus, the DNA sequence of the invader is quickly recognised and destroyed by the bacteria.
Understanding the exact mechanisms of the CRISPR defence system could have big economic rewards for industry. "We can exploit this system and expose bacteria to artificial or modified bacteriophages whose DNA could be stored. This would be exactly like giving them a flu jab and protect them against a real attack in the future. For industrially-important bacteria this could be a great cost-saving method to reduce viral infections that may compromise yields of bacterial products. It's a classic example of vaccinating the workforce to increase its productivity."

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Form or Function? Evolution Takes Different Paths, Genetic Study Shows


Sai kiran (Apr. 7, 2010) — Biologists long have known that both the appearance of organisms and their inner workings are shaped by evolution. But do the same genetic mechanisms underlie changes in form and function? A new study by scientists at the University of Michigan and Taiwan's National Health Research Institutes suggests not.
Do the same genetic mechanisms underlie changes in form and function? Researchers recently turned to a database of knockout mice -- lab mice that have been engineered to lack particular genes -- to answer that question. (Credit: iStockphoto

The research is scheduled for online publication in the Proceedings of the National Academy of Sciences.
In the study, U-M evolutionary biologist Jianzhi "George" Zhang and colleagues Ben-Yang Liao and Meng-Pin Weng set out to systematically test a hypothesis proposed by molecular biologist Sean Carroll in 2005. Carroll posited that changes in morphology (such things as shape, color and structure of external and internal parts) occur through different genetic mechanisms than changes in physiology (inner workings). Carroll backed up his assertion with examples, but the idea, which challenged previous dogma, was controversial, Zhang said.
To test the hypothesis, Zhang's team turned to a database of knockout mice -- lab mice that have been engineered to lack particular genes.
"We found about 5,200 genes that have been knocked out in the mouse and the resulting effects studied," said Zhang, a professor of ecology and evolutionary biology. "From those genes, we looked for genes that, when knocked out, affect only morphological traits, not physiological traits. We got about 900 of those genes, which we call morphogenes."
The researchers also found about 900 "physiogenes" -- genes that affect only physiological traits, not morphology.
"Next, we compared the two groups of genes to see if there are differences in the molecular roles of their products," Zhang said. "We found very large differences." Morphogenes were more likely to carry instructions for transcription -- the step that determines whether a gene should be turned on and how much gene product should be manufactured. Physiogenes were more likely to be blueprints for enzymes, receptors, transporters and ion channels (molecules that control the flow of ions across cell membranes).
The next step was to examine patterns of evolution in the two groups of genes.
In a classic paper published in 1975, evolutionary biologists Mary-Claire King and Allan Wilson argued that evolution of both morphology and "ways of life" (physiology and behavior) occurred through changes in the way genes are turned on and off, rather than through direct changes in gene products themselves. In the parlance of geneticists, these traits were shaped over time through changes in gene expression, not changes in protein sequence. King and Wilson supported their claim with the example of chimpanzees and humans, which are remarkably similar at the protein sequence level, but quite different in appearance and behavior. It was this influential paper that Carroll commemorated 30 years later, but he suggested instead that physiological changes are due to protein sequence changes, while morphological changes result from changes in gene expression.
With their new analysis, Zhang and colleagues found that, at the protein sequence level, physiogenes evolved much faster than morphogenes. "This is consistent with the idea that physiological changes tend to be caused by protein sequence changes," Zhang said.
Next, the researchers examined gene expression data, looking to see how similarly or differently genes are turned on or off in identical tissues from different species, such as the livers of mice and humans. Greater differences indicate more rapid evolutionary change.
"We found more differences in morphogenes than in physiogenes," Zhang said. "In other words, morphogenes evolve faster, with respect to expression patterns, than do physiogenes -- a finding that supports the idea that morphological changes result mainly from gene expression changes."
The finding that morphology and physiology are shaped by different evolutionary genetic processes can not only aid in future evolutionary studies, but can also be helpful in the study of human disease, Zhang said. "Our analysis of the knockout mouse data suggests that morphological defects are more likely due to problems with gene expression. This knowledge could help identify the disease-causing mutations more quickly, because it narrows the set of candidate genes and mutations that one needs to search from."
Zhang's coauthors, Liao and Weng, are at the National Health Research Institutes (NHRI) in Taiwan. Funding was provided by the National Institutes of Health and NHRI.

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Aging Gene Found to Govern Lifespan, Immunity and Resilience


Sai kiran (Apr. 4 2010) — Scientists funded by the Biotechnology and Biological Sciences Research Council (BBSRC) at the University of Birmingham have discovered that a gene called DAF-16 is strongly involved in determining the rate of ageing and average lifespan of the laboratory wormCaenorhabditis elegans (C. elegans) and its close evolutionary cousins. DAF-16 is found in many other animals, including humans. It is possible that this knowledge could open up new avenues for altering ageing, immunity and resistance to stresses in humans.

A nematode worm that has a bacterial infection (highlighted in green). (Credit: Dr Robin May, University of Birmingham (92KB))

The research is published April 1 inPLoS ONE.
Dr Robin May, who led the research said: "Ageing is a process that all organisms experience, but at very different rates. We know that, even between closely related species, average lifespans can vary enormously.
"We wanted to find out how normal ageing is being governed by genes and what effect these genes have on other traits, such as immunity. To do that, we looked at a gene that we already knew to be involved in the ageing process, called DAF-16, to see how it may determine the different rates of ageing in different species."
Dr May and colleagues compared longevity, stress resistance and immunity in four related species of worm. They also looked for differences in the activity of DAF-16 in each of the four species and found that they were all quite distinct in this respect. And, importantly, the differences in DAF-16 corresponded to differences in longevity, stress resistance and immunity between the four species -- in general higher levels of DAF-16 activity correlated with longer life, increased stress resistance and better immunity against some infections.
Dr May continued: "DAF-16 is part of a group of genes that drive the biological processes involved in ageing, immunity and responses to physical or environmental stresses. The fact that subtle differences in DAF-16 between species seem to have such an impact on ageing and health is very interesting and may explain how differences in lifespan and related traits have arisen during evolution."
The research in Birmingham is now moving on to look at the way in which DAF-16 coordinates a complex network of genes in order to balance the differing needs of an individual's immune system over time.
Professor Douglas Kell said: "Research using model organisms that uncovers the biology underpinning ageing gives us the opportunity to understand some of the mechanisms that determine how humans age in a healthy, or at least normal, way. It is very important to develop a good understanding of healthy ageing if we are to appreciate what happens to an older person's physiology when they become unwell or experience difficulties with everyday tasks such as recalling memories or moving around. Improving the healthspan to mirror increases in the lifespan is an important subject of BBSRC research."

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Jaw Bone Grown from Adult Stem Cells


Sai kiran (apr 2, 2010) — A Columbia scientist has become the first to grow a complex, full-size bone from human adult stem cells.
gordana Vunjak-Novakovic, a professor of biomedical engineering at the Fu Foundation School of Engineering and Applied Science, reports that her team grew a temporomandibular joint (TMJ) from stem cells derived from bone marrow. Her work is reported in the onlineEarly Edition of the journalProceedings of the National Academy of Sciences this month.
Vunjak-Novakovic used CT images (A and B) to build a TMJ-shaped scaffold (C). (Credit: Image courtesy of The Record, Columbia University)

"The TMJ has been widely studied as a tissue-engineering model because it cannot be generated easily, if at all, by current methods," says Vunjak-Novakovic, whose co-authors include Warren L. Grayson, then a post-doctoral student in her lab and now an assistant professor at Johns Hopkins University. Around 25 percent of the population suffers from TMJ disorders -- including those who suffer from cancer, birth defects, trauma and arthritis -- which can cause joint deterioration. Because the TMJ is such a complex structure, it is not easily grafted from other bones in a patient's body. "The availability of personalized bone grafts engineered from the patient's own stem cells would revolutionize the way we currently treat these defects," she says.
Current methods of treating traumatic injury to the jaw include taking a bone from the patient's leg or hip to replace the missing bone. "Wouldn't it be wonderful if we could get the patient's own stem cells and grow a new jaw?" says Dr. June Wu, a craniofacial surgeon at Columbia University Medical Center who advised Vunjak-Novakovic on her research.
Vunjak-Novakovic's technique for turning stem cells into bone was inspired by the body's natural bone-building process. Her team started by analyzing digital images of a patient's jawbone in order to build a scaffold into the precise shape of a TMJ joint. The scaffold itself was made from human bone stripped of living cells. The team then seeded the scaffold with bone marrow stem cells and placed it into a custom-designed bioreactor. The reactor, filled with culture medium, nourished and physically stimulated the cells to form bone. "Bone tissue is metabolically very active," she says. Bone tissue develops best when it is bathed in fluid flowing around it. Vunjak-Novakovic and the team looked into the exact flow rates one needs for optimal effects. After five weeks, they had a four-centimeter-high jawbone that was the precise size and shape of a human TMJ.
The technique can be applied to other bones in the head and neck, including skull bones and cheek bones, which are similarly difficult to reconstruct, but Vunjak-Novakovic started with the TMJ because, "We thought this would be the most rigorous test of our technique," she said. "If you can make this, you can make any shape."
Her team's next step is to develop a way to connect the bone graft to a patient's blood supply to ensure that the graft grows with the person's body. "Our bones change, and these biological grafts would change with us," says Vunjak-Novakovic.

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Genetically Engineered Tobacco Plant


Genetically Engineered Tobacco Plant Cleans Up Environmental Toxin

Sai kiran (Mar. 6, 2010) — Tobacco might become as well known for keeping us healthy as it is for causing illness thanks to researchers from the U.K.












Tobacco growing in a field (Credit: Courtesy of USDA-ARS; photo by Alvin Simmons)




In a new research report appearing in the March 2010 print issue of theFASEB Journal, scientists explain how they developed a genetically modified strain of tobacco that helps temper the damaging effects of toxic pond scum, scientifically known as microcystin-LR (MC-LR), which makes water unsafe for drinking, swimming, or fishing. This plant could serve as a major tool for helping keep water sources safe to use, especially in developing nations.
"We hope that our study will ultimately lead to a reduction in the exposure of humans, livestock, and wildlife to environmental pollutants," said Pascal M.W. Drake, Ph.D., co-author of the study, from the Centre for Infection at St. George's University of London.
To develop this type of tobacco, Drake and colleagues genetically altered a tobacco plant to produce an antibody to MC-LR, by inserting genes which code for the production of this antibody. With the genes in place, the new strain of tobacco produced the antibody in its leaves and secreted the antibody from its roots into the surrounding hypotonic growth medium. When the toxin from MC-LR was added to the plant's surrounding hypotonic growth medium, the antibody bound to the toxin, rendering it harmless. This is the first example of a transgenic plant expressing an antibody that remediates an environmental toxin, but according to Drake, more plants like these will be developed in the future to address different environmental problems.
"Tobacco is perhaps one of the most cultivated non-food crop in human history," said Gerald Weissmann, M.D., Editor-in-Chief of the FASEB Journal, "and for centuries it has hurt human health. Now, with smart genetic tweaking, tobacco may prove more valuable in the field than in the pipe."


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Hot Road to New Drugs


Hot Road to New Drugs: Efficient Identification of Drug Candidates

Sai kiran (Mar. 6, 2010) — The search for new therapeutic agents is time-consuming and expensive. Pharmaceutical companies may have to screen thousands of compounds for the ability to bind a target molecule before they hit upon a promising drug candidate. 

A group of Biophysicists at LMU Munich led by Professor Dieter Braun, a member of the Cluster of Excellence "Nanosystems Initiative Munich" (NIM), and a partner in NanoTemper (an LMU spin-off), have now developed a unique technology called "microscale thermophoresis" that allows to measure intereactions under close-to-native conditions, thus improving the decision making process in drug development.
The technique takes advantage of the Soret effect -- the tendency of molecules to drift along temperature gradients, usually from warm to cold. If a compound encounters and binds to another molecule, its thermophoretic parameters change, and its trajectory may even be reversed. This phenomenon can be exploited to determine whether a molecule that is known to play a causative role in a given disease binds to a test substance. In the test, which can be carried out directly on blood samples, the thermodiffusion of a labelled biomolecule of interest is measured in the presence and absence of a candidate binding agent. If the two bind together to form a complex, the resulting change in their thermophoretic behaviour can be detected.A group of Biophysicists at LMU Munich led by Professor Dieter Braun, a member of the Cluster of Excellence "Nanosystems Initiative Munich" (NIM), and a partner in NanoTemper (an LMU spin-off), have now developed a unique technology called "microscale thermophoresis" that allows to measure intereactions under close-to-native conditions, thus improving the decision making process in drug development.
"Detection of binding activity is the first step on the road to a new drug," says Braun. "The new method also has potential applications in medical diagnostics, and in food and environmental monitoring."
The procedures conventionally used to identify candidate drugs are normally carried out in artificial buffer solutions, and the results often have little relationship to a compound's binding affinity for its target in the blood.
The new thermophoretic technique, on the other hand, allows one to perform the binding test directly in a blood sample and therefore gives more reliable results. The substance to be tested is mixed with a blood sample containing a target that is known to be associated with a disease state and has been labelled with a fluorescent tag. A tiny drop of the mixture is taken up into a thin glass capillary tube, and a focused beam of IR-laser light is used to heat a small volume of the solution in the middle of the tube. This gives rise to a temperature gradient that falls off towards the outside. The response of the labelled molecule to the variation in temperature can then be followed using fluorescence methods.
Upon heating of the sample, it immediately becomes apparent whether or not the fluorescent target-molecules in the sample behave differently in the presence of the drug test compound than they do in its absence. Any difference in thermophoresis between the two samples indicates that the test substance binds to the labelled target, and provides the first hint that it may have therapeutic potential.
"Our method will not only be a boon to drug discovery," says Braun. "It can also be used in medical diagnostics, food testing and environmental monitoring. One could, for instance, employ it to diagnose autoimmune diseases and infections, or as the basis for a rapid test for the presence of antibiotics in milk or toxic substances in water."

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Hormone Study


Hormone Study Gives Scientists a Sense of How Animals Bond

Sai kiran (Mar. 6, 2010) — Scientists have pinpointed how a key hormone helps animals to recognise others by their smell.Researchers at the University of Edinburgh have shown that the hormone vasopressin helps the brain differentiate between familiar and new scents.



Scientists have pinpointed how a key hormone helps animals to recognise others by their smell. (Credit: iStockphoto)
the study published in the journalNature, suggests that when the hormone fails to function, animals are unable to recognise other individuals from their scent.Researchers at the University of Edinburgh have shown that the hormone vasopressin helps the brain differentiate between familiar and new scents.
The ability to recognise others by smell is crucial in helping animals to establish strong bonds with other animals.
The research, funded by the Biotechnology and Biological Sciences Research Council (BBSRC), may offer clues about the way people make emotional connections with others through smell and deepen our understanding of the role scent plays in memory.
Many scientists think a failure in this recognition system in humans may prevent them from forming deep emotional bonds with others.
It is thought that it may be at the root of conditions such as some forms of autism and social phobia.
Researchers, including scientists in Germany and Japan, reached their conclusion by studying the way rats familiarise themselves with other rats through smell.
They placed an adult rat in an enclosure with a baby rat and left them to sniff and interact with each other.
After a short separation, they placed the baby back in the adult's enclosure, together with an unknown baby.
Adult rats whose vasopressin had been blocked failed to recognise the baby they had already met.
Professor Mike Ludwig, who led the study at the University of Edinburgh, said: "This study gives us a window into understanding the biological basis of social interactions.
It may be that vasopressin helps to filter sensory information according to its emotional significance."
Professor Janet Allen, BBSRC Director of Research said, "Research that helps us to gain a fundamental understanding of how our brains work is vital if we are to know what is happening when something has gone wrong. The biological basis of psychological responses can often be extremely complicated, so finding this direct relationship between a hormone and a psycho-social phenomenon could open up a whole wealth of knowledge in this area."

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Offering Hope for Tissue Regeneration


Offering Hope for Tissue Regeneration

Sai kiran (Mar. 5, 2010) — Researchers at Rhode Island Hospital have discovered how cells communicate with each other during times of cellular injury. The findings shed new light on how the body repairs itself when organs become diseased, through small particles known as microvesicles, and offers hope for tissue regeneration. The paper is published in the March 2010 edition of the journalExperimental Hematology and is now available online in advance of publication.

Aliotta is also an assistant professor of medicine at The Warren Alpert Medical School of Brown University and a physician with University Medicine Foundation, Inc. He says, "What we attempted to understand is how cells within the bone marrow are able to repair organs that are unrelated to those bone marrow cells, such as the lung. Our work suggests that when the lung is injured or diseased and cells within the lung are stressed or dying, they shed microvesicles. Those microvesicles are then consumed by cells within the bone marrow, including stem cells, which are present in small numbers within the circulatory system. Those bone marrow cells then turn into lung cells."Lead author Jason Aliotta, MD, a physician researcher in the pulmonary/critical care and hematology/oncology departments at Rhode Island Hospital, and his colleagues focused their work on the microvesicles. These particles are several times smaller than a normal cell and contain genetic information such as messenger ribonucleic acid (RNA), other species of RNA and protein. The paper shows a novel mechanism by which the cells communicate with each other through these microvesicles. During times of cellular injury or stress, or with certain diseases like cancer, infections and cardiovascular disease, these particles are shed and then taken up by other cells in the body. The genetic information and protein in the microvesicles helps to reprogram the accepting cell to behave more like the cell from which the particle was derived.
Other researchers have reported similar findings over the last couple of years, however, microvesicles have been known about for over 40 years and have often been considered irrelevant.
Aliotta adds, "We are now recognizing the relevance of microvesicles: They are important mediators of cell-to-cell communication. What is unique to our research is the finding that microvesicles not only supply information to stem cells with lung injury, but this process also occurs in other organs as well, like the heart, liver and brain."
The researchers report unique findings, noting that the change in those stem cells that have consumed microvesicles made by injured lung cells is very stable -- the change appears to be permanent. Stem cells are reprogrammed due to the transfer of microvesicle-based transcription factors. These factors cause cells to behave atypically. As Aliotta says, "This would be relevant to any type of disease -- if you want to repair damaged tissue, these microvesicles potentially provide a durable fix, and the hope is that it would be fixed forever."
The study is part of ongoing stem cell research at Rhode Island Hospital under the direction of Peter Quesenberry, MD, director of hematology/oncology at Rhode Island Hospital, who is a co-author on the paper. He is the principal investigator for a recent $11 million Center of Biomedical Research Excellence (COBRE) grant to Rhode Island Hospital from the National Center for Research Resources of the National Institutes of Health (NIH).
Quesenberry says, "We believe this research presents a novel finding in the understanding of stem cells and signifies practical implications for the world of medicine. These microvesicles can change the basic nature of adjoining cells, and that presents a world of possibilities in tissue restoration efforts." Quesenberry, who is a physician with University Medicine Foundation, Inc., also holds the Paul Calabresi, MD, professorship in oncology and is director of the division of hematology/oncology at Alpert Medical School.
Among the practical implications from their findings is an understanding of the mechanism of tissue repair and determining whether or not microvesicles can be used in a therapeutic fashion. Aliotta explains, "If you have an injured organ, our hope is that if we were to deliver large numbers of microvesicles to that injured organ, it would help the repair process."
Based on their findings, the researchers also hypothesize that microvesicles could potentially be mediators of cancer metastasis. It is known that in cancer there are higher levels of circulating microvesicles, and these microvesicles may be responsible for transferring the traits of the cancer to other organs. Aliotta notes, "If we can define the microvesicles that are shed from cancer cells, we can identify unique characteristics, which might help us to block their uptake into normal cells. This could, in theory, stop the metastasis of cancer."
Quesenberry concludes, "Our work explained in this paper and the work still to come from our COBRE grant hold great promise in terms of future treatment of tissue repair and cancer."
The study was funded through grants from the National Institutes of Health. Along with Aliotta and Quesenberry, other researchers in the study include Mandy Pereira, Kevin Johnson, Nicole dePaz, Mark Dooner, Napoleon Puente, Carol Ayala, Kate Brilliant, David Lee, Bharat Ramratnam, Paul McMillan and Douglas Hixson, all of Rhode Island Hospital and Alpert Medical School.

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Protein Shown to Be Natural Inhibitor


Protein Shown to Be Natural Inhibitor of Aging in Fruit Fly Model

Sai kiran (Mar. 5, 2010) — Scientists at the University of California, San Diego School of Medicine, have identified a protein called Sestrin that serves as a natural inhibitor of aging and age-related pathologies in fruit flies. They also showed that Sestrin, whose structure and biochemical function are conserved between flies and humans, is needed for regulation of a signaling pathway that is the central controller of aging and metabolism.
Sestrins are highly 

     
conserved small proteins that are produced in high amounts when cells experience stress. Sestrin function, however, remained puzzling until the Karin group found that these proteins function as activators of AMP-dependent protein kinase (AMPK), and inhibitors of the Target of Rapamycin (TOR). AMPK and TOR are two protein kinases that serve as key components of a signaling pathway shown to be the central regulator of aging and metabolism in a variety of model organisms, including the wormCaenorhabditis elegans, the fruit fly Drosophila melanogasterand mammals.The work, led by Michael Karin, PhD, Distinguished Professor of Pharmacology in UCSD's Laboratory of Gene Regulation and Signal Transduction, is the cover story of the March 5 issue of the journalScience.
AMPK is activated in response to caloric restriction, a condition that slows down aging, whereas TOR is activated in response to over-nutrition, a condition that accelerates aging. Activation of AMPK inhibits TOR, and drugs that activate AMPK or inhibit TOR can delay aging in several different model organisms including mammals. But how the body keeps the activity of these two protein kinases in balance to prevent premature aging was unknown. Additionally, the presence of three different genes encoding Sestrins in mammals made it difficult to identify their exact physiological function in live animals.
The new study took advantage of the finding that the fruit flyDrosophila, whose AMPK-TOR signaling pathway functions in the same manner as its mammalian equivalent, contains a single Sestrin gene. Using a variety of genetic techniques, first author Jun Hee Lee inactivated the Sestrin gene of Drosophilaand found that although Sestrin-deficient flies do not exhibit any developmental abnormalities, they suffer from under-activation of AMPK and over-activation of TOR -- confirming that Sestrin is needed for keeping this pathway in check. Most importantly, the biochemical imbalance incurred by loss of Sestrin expression resulted in several age-related pathologies.
"Strikingly, the pathologies caused by the Sestrin deficiency included accumulation of triglycerides, cardiac arrhythmia and muscle degeneration that occurred in rather young flies," said Karin. "These pathologies are amazingly similar to the major disorders of overweight, heart failure and muscle loss that accompany aging in humans."
Lee and colleagues at UC San Diego and the Sanford-Burnham Institute in La Jolla, California, went on to demonstrate that feeding flies with drugs that either activate AMPK or inhibit TOR conferred protection against most of these early aging, degenerative symptoms. The researchers also found that over-activation of TOR is likely to accelerate aging of heart and skeletal muscles by disrupting an important "quality control" process called autophagy. Autophagy allows cells to rid themselves of and replace damaged mitochondria, the little power plants that provide all cells, especially muscles, with energy. However, when mitochondria get old, they produce high concentrations of reactive oxygen species (ROS), or free radicals, that can lead to tissue damage.
Karin explained that the process of autophagy -- which counteracts aging -- allows the replacement of "old" and defective mitochondria with "brand new" mitochondria. Sestrin-deficient flies, however, were found to exhibit accumulation of damaged mitochondria and ROS several days prior to the detection of muscle degeneration. Feeding these flies vitamin E, an antioxidant which neutralizes free radicals, prevented premature muscle degeneration and heart failure.
In future work, the Karin group plans to examine whether the mammalian Sestrins also control aging and metabolism, and whether defects in proper Sestrin expression will provide the explanation to some of the currently unexplainable degenerative diseases associated with old age.
"Maybe one day we will be able to use Sestrin analogs to prevent much of the tissue failure associated with aging, as well as treat a number of degenerative diseases, whose incidence goes up with old age, including sarcopenia and Alzheimer's disease," said Karin.
Additional contributors to the study -- a collaboration between three laboratories at UC San Diego School of Medicine, UCSD Division of Biology and the Sanford-Burnham Institute -- are Andrei V. Budanov, Eek Joong Park, Ryan Birse, Teddy E. Kim, Guy A. Perkins, Karen Ocorr, Mark H. Ellisman, Rolf Bodmer and Ethan Bier.
The research was funded by the National Institutes of Health, the Superfund Basic Research Program and American Cancer Society.

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Sorting Device for Analyzing Biological Reactions Puts the Power of a Lab in a Researcher’s Pocket


Sorting Device for Analyzing Biological Reactions Puts the Power of a Lab in a Researcher’s Pocket

biotech,sai kiran (Mar. 4, 2010) — Fictional candy maker Willy Wonka called his whimsical device to sort good chocolate eggs from bad, an eggucator. Likewise, by determining what enzymes and compounds to keep and which to discard, scientists are aiming to find their own golden eggs: more potent drugs and cleaner sources of energy.

Toward that end, Harvard researchers and a team of international collaborators demonstrated a new microfluidic sorting device that rapidly analyzes millions of biological reactions. Smaller than an iPod Nano, the device analyzes reactions a 1,000-times faster and uses 10 million-fold less volumes of reagent than conventional state-of-the-art robotic methods.
The scientists anticipate that the invention could reduce screening costs by 1 million-fold and make directed evolution, a means of engineering tailored biological compounds, more commonplace in the lab.
"Our finding is not so much a scientific discovery, but the first demonstration of a new technology," says project leader Jeremy Agresti, a former research associate in the lab of co-author David Weitz, Mallinckrodt Professor of Physics and of Applied Physics in the Harvard School of Engineering and Applied Sciences (SEAS) and Department of Physics. "What limits new areas of research in biology and biotechnology is the ability to assay or to do experiments on many different variables in parallel at once."
The team's technology, first reported in the February 8th online Early Edition of the Proceedings of the National Academy of Sciences, bypasses conventional limitations through the use of drop-based microfluidics, squeezing tiny capsules of liquid through a series of intricate tubes, each narrower than a single human hair.
"Each microscopic drop can trap an individual cell and thus it becomes like a miniature test tube," explains Amy Rowat, a postdoctoral fellow at SEAS. "The drops are coated with a surfactant, or stabilization molecule, that prevents the drops from coalescing with each other and also prevents the contents from sticking to the wall of the drops."
To sort, the system removes inactive and unwanted compounds, dumping the drops into a "bad egg" bin, and guides the others into a "keep" container. Specifically, as the drops flow through the channels they eventually encounter a junction (a two-channel fork). Left alone, the drops will naturally flow towards the path of least fluidic resistance, or the waste channel.
The device identifies the desired drops by using a laser focused on the channel before the fork to read a drop's fluorescence level. The drops with greater intensity of fluorescence (those exhibiting the highest levels of activity) are pulled towards the keep channel by the application of an electrical force, a process known as dielectrophoresis.
"Our concept was to build a miniature laboratory for performing biological experiments quickly and efficiently," explains collaborator Adam Abate, a postdoctoral fellow in applied physics at SEAS. "To do this we needed to construct microfluidic versions of common bench-top tasks, such as isolating cells in a compartment, adding reagents, and sorting the good from the bad. The challenge was to do this with microscopic drops flowing past at thousands per second."
"The sorting process is remarkably efficient and fast. By shrinking down the reaction size to 10 picoliters of volumes, we increased the sorting speed by the same amount," adds Agresti. "In our demonstration with horseradish peroxidase, we evolved and improved an already efficient enzyme by sorting through 100 million variants and choosing the best among them."
In particular, the researchers were struck by the ability to increase the efficiency of an already efficient enzyme to near its theoretical maximum, the diffusion limit, where the enzyme can produce products as quickly as a new substrate can bump into it.
Using conventional means, the sorting process would have taken several years. Such a dramatic reduction of time could be a boon for the burgeoning field of synthetic biology. For example, a biofuels developer could use the device to screen populations of millions of organisms or metabolic pathways to find the most efficient producer of a chemical or fuel. Likewise, scientists could speed up the pace of drug development, determining the best chemical candidate compounds and then evolving them based upon desired properties.
"The high speed of our technique allows us to go through multiple cycles of mutation and screening in a very short time," says Agresti. "This is the way evolution works best. The more generations you can get through, the faster you can make progress."
Agresti, Rowat, and Abate's co-authors included Keunho Ahn from SEAS; Eugene Antipov and Alexander M. Klibanov, both from MIT; Jean-Christophe Baret and Andrew D. Griffiths, both from the Université de Strasbourg; and Manuel Marquez from YNano LLC.
The authors acknowledge the support by the Human Frontier Science Program; the National Science Foundation through the Harvard Materials Research Science and Engineering Center; the Centre National de la Recherche Scientifique; the Massachusetts Life Sciences Center; and the Agence National de la Recherche.

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With Just One Enzyme Missing, Mice Show 'Global' Metabolic Improvements


With Just One Enzyme Missing, Mice Show 'Global' Metabolic Improvements

biotechnology,sai kiran (Mar. 4, 2010) — When researchers created mice lacking an enzyme that breaks down and releases stored triglycerides (more properly known as triacylglycerols or TGs), they expected to see animals with better lipid profiles. But according to a report in the March Cell Metabolism, a Cell Press publication, they got more than they bargained for. The triacylglycerol hydrolase (TGH)-deficient mice showed global metabolic benefits, with essentially no downside.
Very low-density lipoproteins (VLDLs) are a form of "bad" cholesterol, Lehner explained. TGH normally frees up triglycerides from their storage place in the liver, releasing them for assembly into VLDLs. Therefore, one might expect that loss of TGH would have ill effects on the liver, as triglycerides would build up there. Indeed, he says, similar experiments with other enzymes have shown such an effect."It was a surprising and unexpected finding," said Richard Lehner of the University of Alberta. "With this gene deleted, not only was there a decline in very low-density lipoproteins in the whole mouse, it also affected metabolism in fat tissue. The insulin-secreting cells became smaller, suggesting that they didn't have to work as hard to secrete insulin, and the mice became more insulin sensitive." The animals ate more, but they also expended more energy and showed no change in body weight.
"We didn't observe that here," Lehner said. "Instead of being stored in liver, triglycerides were directed for oxidation." In other words, they were burned. The liver also compensated by synthesizing less fat.
The studies demonstrate the potential of TGH as a therapeutic target for lowering blood lipid levels, with possible far-reaching beneficial side effects throughout the body. That may be especially worthy of note, given that drug companies already have a TGH blocker. In fact, Lehner's team earlier showed that the TGH-inhibiting drug can lower the secretion of VLDLs from liver cells. But it wasn't clear whether the drug was really acting only on TGH. The new findings add support to the notion that loss of TGH activity alone can have very significant and positive effects.
"But there is a still a lot more work to do," Lehner says. They plan to see what happens when mice on a high-fat diet lose the enzyme, noting that the mice in the current study were eating regular chow. They also want to find out what happens when the enzyme is lost only in specific tissues -- fat tissue, for example -- instead of throughout the body.
One would also want to be careful that the chemical inhibitor targets TGH and not other enzymes in the same family. For the most part, scientists don't know what those other enzymes are doing, he says, and -- at least until they do -- specificity will be key.
"We've answered a small piece of the puzzle, and this is or could be a good target," Lehner says, although he emphasizes caution. "Would it be a magic bullet? Now, that's something else that has yet to be seen."
The researchers include Enhui Wei, University of Alberta, Edmonton, Canada; Yassine Ben Ali, University of Alberta, Edmonton, Canada; James Lyon, University of Alberta, Edmonton, Canada; Huajin Wang, University of Alberta, Edmonton, Canada; Randy Nelson, University of Alberta, Edmonton, Canada; Vernon W. Dolinsky, University of Alberta, Edmonton, Canada; Jason R.B. Dyck, University of Alberta, Edmonton, Canada; Grant Mitchell, CHU Sainte-Justine, Universite´ de Montreal, Montreal, Canada; Gregory S. Korbutt, University of Alberta, Edmonton, Canada; and Richard Lehner, University of Alberta, Edmonton, Canada.

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latest news[bio-tech researchs]-2


Sea Squirt Offers Hope for Alzheimer's Sufferers

biotecsynthesis ,sai kiran reddy(Mar. 3, 2010) — Alzheimer's disease affects an estimated 27 million people worldwide. It is the most common form of age-related dementia, possibly the most feared disease of old age. There is no cure, and the available drugs only help to relieve symptoms without slowing progression of the disease. One of the characteristic changes in the brains of Alzheimer's patients is the accumulation of plaques and tangles; currently, the best hope for curing or at least slowing the disease lies in developing drugs that target this buildup. Some drugs are already in clinical trials, but there is still a pressing need for more research, and for more and better drugs directed against both known and novel targets.


Sea squirts are tunicates, marine organisms protected by an outer hard tunic with a soft body inside. Adults spend their lives attached to one spot on underwater structures like the pilings of piers, sucking in water through one siphon, filtering out small plants to eat, and squirting the water back out through another siphon. However, as long ago as Darwin, it has been recognized that sea squirts may be our closest invertebrate relatives; in their immature, tadpole form, they resemble proper vertebrates, and they share about 80% of their genes with us.One of the big problems in rapidly screening potentially useful drugs has been the lack of a good model system in which Alzheimer's plaques and tangles appear quickly. However, Mike Virata and Bob Zeller, scientists working at San Diego State University, California, have come up with a new, and perhaps unlikely candidate; the humble sea squirt, Ciona intestinalis.
Bob Zeller has been a fan of sea squirt tadpoles since starting work with them in the 1990s, when he helped develop a way of introducing foreign DNA into fertilized sea squirt eggs with almost 100% efficiency, opening the way for their use as model organisms. He and his colleague Mike Virata decided to see whether it would be possible to model Alzheimer's disease in the tiny animals, which share all the genes needed for the development of Alzheimer's plaques in humans.
Incredibly, dosing the sea squirt tadpoles with a mutant protein found in human families with hereditary Alzheimer's resulted in aggressive development of plaques in the tadpoles' brains in only a day, and these, along with the accompanying behavioral defects seen in the tadpoles, could be reversed by treating with an experimental anti-plaque forming drug. This is an important breakthrough, as all other invertebrates tested have been unable to process the plaque-forming protein, and vertebrates take months or years to make plaques. These exciting results make it a real possibility that sea squirts are an excellent model for testing new drugs in the fight against Alzheimer's disease.

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latest news[bio-tech researchs]


How Trauma Leads to Inflammatory Response: Mitochondria May Be at Root of Dangerous Complications from Injury

biotecsynthesis (Mar. 3, 2010) — Inflammation is at the root of most serious complications occurring after both infection and injury. But while the molecular course of events that leads from microbial infections to the inflammatory condition called sepsis is fairly well understood, it is far less clear how and why physical injury can result in a similarly dangerous inflammatory response.
Electron micrograph of a mitochondrion from mammalian lung tissue showing its matrix and membranes. (Credit: Courtesy of Wikimedia Commons)


Appearing in the journal Nature, the findings could eventually lead to new strategies in the management of trauma as well as to the development of new tests to help clinicians discriminate between infective and non-infective inflammation.Now a study led by investigators at Beth Israel Deaconess Medical Center (BIDMC) suggests that mitochondria -- the body's cellular "power plants" -- are released into the bloodstream following physical injury. And because mitochondria closely resemble the bacteria from which they originated, they appear to elicit a sepsis-like immune response, changing from a vital source of cellular injury to a dangerous "enemy within."
"The body's vital organs can become dysfunctional when traumatic injury triggers the Systemic Inflammatory Response Syndrome, or SIRS," explains senior author Carl J. Hauser, MD, a trauma and critical care surgery specialist at BIDMC and Visiting Professor of Surgery at Harvard Medical School. "Trauma kills 5 to 10 million people worldwide per year and among U.S. individuals under age 35, trauma accounts for more deaths than all other illnesses combined. Inflammatory complications are directly responsible for about one-third of those deaths."
Hauser, whose laboratory studies focus on neutrophils, circulating white blood cells that can attack the body's organs, wanted to find out how neutrophils might be participating in this dangerous inflammatory cascade.
The mechanisms that underlie both SIRS and sepsis are rooted in the body's "innate immune" response. Unlike "acquired immunity," which develops over time, innate immunity is present from birth, ready to immediately respond whenever immune cells encounter molecular patterns typical of external pathogens such as bacteria or viruses. These "pathogen-associated molecular patterns," or PAMPS, are in turn, detected by pattern recognition receptor molecules (PRR).
"When an infection strikes, PAMPs activate PRR very rapidly, initiating a group of cellular responses collectively described as the 'Danger Response,'" explains Hauser. This response underlies both SIRS and sepsis, and can ignite early reactions to cell threats as well as act as an adjuvant for later acquired immune responses. However, as Hauser notes, infectious pathogens and PAMPs aren't the only cause of the Danger Response.
"Injured or necrotic tissues can activate very similar immune responses," he explains. "Blunt-force trauma can result in the death of significant amounts of tissue, as can burns, cancer chemotherapy, major surgeries and many other diseases. We wondered if tissues that die by such pathologic means, rather than via programmed cell death or apoptosis, were releasing into the body molecular debris not normally encountered by the immune system."
Some normally intra-cellular molecules can activate PRR, and when they do they are called Damage-Associated Molecular Patterns, or DAMPS. Hauser hypothesized that DAMPs might be triggering inflammatory responses after trauma in the same way that PAMPs triggered inflammation in the face of infection -- and that mitochondria might be ultimately responsible.
Mitochondria are structures within cells that burn nutritional energy sources using oxygen and convert it into the ATP that powers the cells. They function autonomously, having their own DNA which is separate and very different from the genetic material contained within the cell's nucleus, and their own machinery for protein synthesis. Because mitochondria share so many similarities with bacteria -- including their method of reproduction, the molecular nature of their DNA and their synthesis of n-formylated proteins -- it is believed that they were once free living bacterial saprophytes that survived by scavenging the waste products of eukaryotic cells. Over time mitochondria took up residence in the cell and became true symbionts, but many of their molecular signatures remained those of bacteria.
"Mechanical trauma disrupts cells, so we hypothesized that injury might be releasing mitochondria and their DAMPs into the circulatory system, activating immunity in the same way that infections do when they release PAMPS," explains Hauser.
To test this hypothesis, the investigators first assayed mitochondrial DNA (mtDNA) from blood samples obtained from a large group of patients who had suffered multiple trauma. As predicted, they found that mtDNA levels were increased but surprisingly, they found that levels were often thousands-of-fold above normal levels.
Through a series of subsequent experiments, the researchers showed that mitochondrial peptides acted as classical G-protein coupled chemoattractants, activating white blood cells through the FPR1 receptor (a receptor that normally senses bacterial proteins) and associated downstream kinases. They similarly showed that mtDNA activates white blood cells through the PRR known as toll-like receptor 9 (TLR9 normally senses bacterial DNA) and its downstream kinases. Interaction of these two DAMPs and their PRRs work synergistically to activate neutrophils. The investigators also found that injection of mitochondria into rats caused peritonitis and reproduced the pulmonary and hepatic inflammation typical of traumatic SIRS.
"This study suggests that mitochondria -- which can spill into the bloodstream following a physical injury -- look enough like the bacteria they originated from to elicit an immune response," notes Scott Somers, PhD, program director at the National Institute of General Medical Sciences. "This work offers important insight into why the body's response to physical trauma mirrors that of bacterial sepsis, and may lead to new strategies for treating severely injured patients."
Adds Hauser, "Since external injuries and events causing sterile tissue death seem to have just as much potential for causing SIRS as does infection, many of the conditions that we've traditionally treated with antibiotics may turn out to not be infections and may, in fact, require very different types of treatment. Going forward, we hope to collaborate with researchers who are working to identify the origins of inflammation in other clinical conditions."
In addition to Hauser, coauthors include BIDMC investigators Qin Zhang, Mustafa Raoof, Yu Chen, Yuka Sumi, Tolga Sursal, Wolfgang Junger, and Kiyoshi Itagaki; and Karim Brohi of Queen Mary University of London.
This study was supported by a grant from the National Institute of General Medical Sciences.

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human genome project information


Medicine and the New Genetics
The Human Genome Project (HGP), sponsored in the United States by the Department of Energy and the National Institutes of Health has created the field of genomics --understanding genetic material on a large scale. The medical industry is building upon the knowledge, resources, and technologies emanating from the HGP to further understanding of genetic contributions to human health. As a result of this expansion of genomics into human health applications, the field of genomic medicine was born. Genetics is playing an increasingly important role in the diagnosis, monitoring, and treatment of diseases.
Diagnosing and Predicting Disease and Disease Susceptibility
All diseases have a genetic component, whether inherited or resulting from the body's response to environmental stresses like viruses or toxins. The successes of the HGP have even enabled researchers to pinpoint errors in genes--the smallest units of heredity--that cause or contribute to disease.
The ultimate goal is to use this information to develop new ways to treat, cure, or even prevent the thousands of diseases that afflict humankind. But the road from gene identification to effective treatments is long and fraught with challenges. In the meantime, biotechnology companies are racing ahead with commercialization by designing diagnostic tests to detect errant genes in people suspected of having particular diseases or of being at risk for developing them.
An increasing number of gene tests are becoming available commercially, although the scientific community continues to debate the best way to deliver them to the public and medical communities that are often unaware of their scientific and social implications. While some of these tests have greatly improved and even saved lives, scientists remain unsure of how to interpret many of them. Also, patients taking the tests face significant risks of jeopardizing their employment or insurance status*. And because genetic information is shared, these risks can extend beyond them to their family members as well.
*Passing of the 2008 Genetic Information Nondescrimination Act should protect against such discrimination. May 2008.
Disease Intervention
Explorations into the function of each human gene--a major challenge extending far into the 21st century --will shed light on how faulty genes play a role in disease causation. With this knowledge, commercial efforts are shifting away from diagnostics and toward developing a new generation of therapeutics based on genes. Drug design is being revolutionized as researchers create new classes of medicines based on a reasoned approach to the use of information on gene sequence and protein structure function rather than the traditional trial-and-error method. Drugs targeted to specific sites in the body promise to have fewer side effects than many of today's medicines.
The potential for using genes themselves to treat disease--gene therapy--is the most exciting application of DNA science. It has captured the imaginations of the public and the biomedical community for good reason. This rapidly developing field holds great potential for treating or even curing genetic and acquired diseases, using normal genes to replace or supplement a defective gene or to bolster immunity to disease (e.g., by adding a gene that suppresses tumor growth).
See an  that speculates about how genetic advances sparked by the Human Genome Project may affect the practice of medicine in the next 20 years.

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array [MAS technology] synthesis


Array Synthesis
Roche NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. Roche NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system.
At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP employing a solid-state array of miniature aluminum mirrors to pattern 786,000 to 4.2 million individual pixels of light. The DMD creates "virtual masks" that replace the physical chromium masks used in traditional arrays.
These "virtual masks" reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that 385,000 to 2.1 million unique probe features are synthesized in a single array.
Array Synthesis
The synthesis of microarrays using NimbleGen MAS technology is very similar to traditional oligonucleotide synthesis with some important exceptions. Unlike conventional oligo synthesis, arrays are synthesized on glass slides rather than controlled pore glass supports. Another key difference is that the deprotection steps are performed by photodeprotection rather than by acid deprotection. The illustration here depicts digital micromirrors reflecting a pattern of UV light, which deprotects the nascent oligonucleotide and allows addition of the next base.
The Digital Micromirror Device's (DMD) micromirrors are displayed in comparison to the tip of a pin. Each of the 786,000 micromirrors is individually addressable, giving unparalleled precision and control over DNA array fabrication chemistry and structure.

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