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AMP optimistic in suit to invalidate patents on breast cancer genes

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Public release date: 27-Mar-2012 [ | E-mail | Share ]

Contact: Mary Steele Williams mwilliams@amp.org 301-634-7921 Association for Molecular Pathology

Bethesda, MD -- Now that the Supreme Court has remanded Association for Molecular Pathology et al. v. Myriad Genetics, Inc., et al. (AMP v. Myriad) to the Court of Appeals for the Federal Circuit for further consideration, AMP is optimistic that it will ultimately prevail in its lawsuit to invalidate patents on two genes that are known to cause breast cancer.

"Our members have witnessed the adverse effects of gene patents on patient care," stated Iris Schrijver, AMP President. "By awarding monopolies in testing of patented genes, these patents reduce patient access to genetic tests, increase test prices, and stand in the way of innovations in diagnostic methods." Further, Dr. Schrijver added, "Because variation in gene sequences plays an important role in the development and progression of many diseases, through gene patents patent holders can essentially gain ownership of the understanding of some diseases and of certain areas of patient care itself."

Stated Roger D. Klein, MD, JD, Chair of the AMP Professional Relations Committee: "We were extremely encouraged by the Supreme Court's reaffirmation in its Prometheus decision of the longstanding principle that natural phenomena are not patent eligible. In Prometheus, the Supreme Court clearly ruled that the correlation between a biomarker and a clinical phenotype cannot be patented. Similarly, in light of this decision we expect that the Court of Appeals for the Federal Circuit will ultimately find that patents on natural products, in this case BRCA1 and BRCA2, cannot be used to exclude physicians and others from examining their patient's genes for disease-related variants."

In its original decision, the Appeals Court held that human gene sequences are patentable subject matter when separated from their native state within cells. This is really a 'form versus substance' argument, said Mary Williams, AMP Executive Director. "A disease-causing mutation means the same thing for the patient irrespective of whether a gene is examined inside or outside the patient's body."

"AMP is looking forward to the proceedings in the lower court. We are confident that optimal patient care and sound science will ultimately prevail," stated Williams.

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ABOUT AMP:

The Association for Molecular Pathology (AMP) is an international medical professional association dedicated to the advancement, practice, and science of clinical molecular laboratory medicine and translational research based on the applications of molecular biology, genetics, and genomics. For more information, please visit http://www.amp.org.

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AMP optimistic in suit to invalidate patents on breast cancer genes

Nutrition: That's not ice cream… it's 'pink slime'

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Take a cow. Chop it into pieces. Sell the edible bits to supermarkets, ship its hide to a handbag factory, send leftover bones and organs to a rendering plant. Now, what's left? In most of the developed world, the answer is simple: pet food. The sinew, gristle and fat regarded as unfit for human consumption are taken away by Mr Pedigree Chum and turned into something the salmonella-resistant stomach of your average Labrador will find vaguely digestible.

But in America, they do food differently. Here, in the land of GM corn, 26 per cent obesity and a government which classifies pizza as a "vegetable", scientists have discovered a way to turn bacteria-ridden scraps from the abattoir floor into a substance called "pink slime", which is then sold to unwitting consumers of hamburgers, tacos and other beef-based junk products. The process involves sticking bovine off-cuts in a heated centrifuge, so they separate into a mixture of liquid fat and a putty-coloured paste. That substance is then treated with ammonium hydroxide (a chemical used in household cleaners and home-made bombs) to kill off salmonella and e-coli. Then it's mixed with regular beef and hey presto! you have "all natural" mince.

In 2001, it became legal to sell "pink slime" in America. Today, more than half the ground beef sold in America contains the stuff. The US Department of Agriculture (USDA), which supposedly regulates the food industry, does not require it to be mentioned on ingredient lists. Since its provenance is a cow, they insist, you can call it "beef". If you think that's a bit rum, you're not alone. For years, US foodies have earnestly cited "pink slime" as exhibit A in the list of liberties taken by a rapacious food industry.

Not for nothing, they argue, has the stuff been banned in Europe, where mechanically-separated meat from cows and sheep has been prohibited since the era of BSE.

It took an Englishman, however, to turn their complaints into national outrage. A year ago, Jamie Oliver jollified the US version of his Food Revolution TV show by using a cow called Scarlet and a tumble dryer to demonstrate how something he calls "crap" became a staple of the American diet. Video of his stunt was uploaded to YouTube, and shared via social media. Opposition to "pink slime" slowly built.

In January, McDonalds announced the removal of "pink slime" from its burgers. So did Burger King and Taco Bell. This month, as the product became a burgeoning national talking point, several major supermarkets went slime-free. School districts were allowed to start banning it and dozens swiftly did. Yesterday, Beef Products Inc, pink slime's leading manufacturer, shut down three of its four plants, citing swiftly cratering demand. According to the American Meat Institute, 600 jobs could now be lost.

"It's a sad day for the families," claimed a spokesman. Though not, one must presume, for their diets.

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Nutrition: That's not ice cream... it's 'pink slime'

Did Mead Johnson Nutrition Squander Its Latest Sales Increase?

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Margins matter. The more Mead Johnson Nutrition (NYSE: MJN) keeps of each buck it earns in revenue, the more money it has to invest in growth, fund new strategic plans, or (gasp!) distribute to shareholders. Healthy margins often separate pretenders from the best stocks in the market. That's why we check up on margins at least once a quarter in this series. I'm looking for the absolute numbers, so I can compare them to current and potential competitors, and any trend that may tell me how strong Mead Johnson Nutrition's competitive position could be.

Here's the current margin snapshot for Mead Johnson Nutrition over the trailing 12 months: Gross margin is 63.0%, while operating margin is 23.3% and net margin is 13.8%.

Unfortunately, a look at the most recent numbers doesn't tell us much about where Mead Johnson Nutrition has been, or where it's going. A company with rising gross and operating margins often fuels its growth by increasing demand for its products. If it sells more units while keeping costs in check, its profitability increases. Conversely, a company with gross margins that inch downward over time is often losing out to competition, and possibly engaging in a race to the bottom on prices. If it can't make up for this problem by cutting costs -- and most companies can't -- then both the business and its shares face a decidedly bleak outlook.

Of course, over the short term, the kind of economic shocks we recently experienced can drastically affect a company's profitability. That's why I like to look at five fiscal years' worth of margins, along with the results for the trailing 12 months, the last fiscal year, and last fiscal quarter (LFQ). You can't always reach a hard conclusion about your company's health, but you can better understand what to expect, and what to watch.

Here's the margin picture for Mead Johnson Nutrition over the past few years.

Source: S&P Capital IQ. Dollar amounts in millions. FY = fiscal year. TTM = trailing 12 months.

Because of seasonality in some businesses, the numbers for the last period on the right -- the TTM figures -- aren't always comparable to the FY results preceding them. To compare quarterly margins to their prior-year levels, consult this chart.

Source: S&P Capital IQ. Dollar amounts in millions. FQ = fiscal quarter.

Here's how the stats break down:

With recent TTM operating margins below historical averages, Mead Johnson Nutrition has some work to do.

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Did Mead Johnson Nutrition Squander Its Latest Sales Increase?

Has modern science become dysfunctional?

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Public release date: 27-Mar-2012 [ | E-mail | Share ]

Contact: Jim Sliwa jsliwa@asmusa.org 202-942-9297 American Society for Microbiology

The recent explosion in the number of retractions in scientific journals is just the tip of the iceberg and a symptom of a greater dysfunction that has been evolving the world of biomedical research say the editors-in-chief of two prominent journals in a presentation before a committee of the National Academy of Sciences (NAS) today.

"Incentives have evolved over the decades to encourage some behaviors that are detrimental to good science," says Ferric Fang, editor-in-chief of the journal Infection and Immunity, a publication of the American Society for Microbiology (ASM), who is speaking today at the meeting of the Committee of Science, Technology, and Law of the NAS along with Arturo Casadevall, editor-in -chief of mBio, the ASM's online, open-access journal.

In the past decade the number of retraction notices for scientific journals has increased more than 10-fold while the number of journals articles published has only increased by 44%. While retractions still represent a very small percentage of the total, the increase is still disturbing because it undermines society's confidence in scientific results and on public policy decisions that are based on those results, says Casadevall. Some of the retractions are due to simple error but many are a result of misconduct including falsification of data and plagiarism.

More concerning, say the editors, is that this trend may be a symptom of a growing dysfunction in the biomedical sciences, one that needs to be addressed soon. At the heart of the problem is an economic incentive system fueling a hypercompetitive environment that is fostering poor scientific practices, including frank misconduct.

The root of the problem is a lack of sufficient resources to sustain the current enterprise. Too many researchers are competing for too little funding, creating a survival-of-the-fittest, winner-take-all environment where researchers increasingly feel pressure to publish, especially in high-prestige journals.

"The surest ticket to getting a grant or job is getting published in a high profile journal," says Fang. "This is an unhealthy belief that can lead a scientist to engage in sensationalism and sometimes even dishonest behavior to salvage their career."

Funding is just one aspect of a very complex problem Casadevall and Fang see growing in the biomedical sciences. In a series of editorials in the journal Infection and Immunity they describe their views in detail, arguing that science is not as healthy as it could be or as it needs to be to effectively address the challenges facing humanity in the 21st century.

"Incentives in the current system place scientists under tremendous stress, discourage cooperation, encourage poor scientific practices and deter new talent from entering the field," they write. "It is time for a discussion of how the scientific enterprise can be reformed to become more effective and robust."

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Has modern science become dysfunctional?

S.A. Life column will focus on aging, health

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Long before Steven Austad became a respected scholar in aging research, he wrangled lions, tigers, cougars and the occasional bear and elephant for the Hollywood film industry.

As a professor and interim director of the Barshop Institute for Longevity and Aging Studies at the UT Health Science Center at San Antonio, he also works with animals this time, studying a wide range of species to discover how they age.

Besides the usual lab rats and mice, his research subjects include clams that live up to 500 years.

There are hearts out there that have been beating since before Shakespeare was born, says Austad, 65. We're hoping that by studying some of these animals that have been so successful at resisting aging, we'll figure out ways to help humans stay healthy longer as well.

Austad joins S.A. Life today as a columnist writing about aging. His columns will appear every other Sunday.

Seventy-five percent of how well we age has to do with our lifestyle habits, not our genes, according to Austad.

So you're really in control of your health destiny, he says.

While researchers are close to having effective medications for aging, he says, at this point we can't tell you more than what your mother probably did, Austad says, which is all things in moderation, stay active mentally and physically and avoid bad habits, such as smoking, such as eating too much and drinking too much.

His column will address ways in which people can affect their health destiny, but also will inform his audience about this wonderfully interesting and complex process of aging that not just people but everything undergoes, he says.

Austad earned bachelor's degrees in English literature from UCLA and biology from California State, Northridge. His Ph.D. in biology is from Purdue University.

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S.A. Life column will focus on aging, health

DNA traces cattle back to a small herd domesticated around 10,500 years ago

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Public release date: 27-Mar-2012 [ | E-mail | Share ]

Contact: Clare Ryan clare.ryan@ucl.ac.uk 44-020-310-83846 University College London

All cattle are descended from as few as 80 animals that were domesticated from wild ox in the Near East some 10,500 years ago, according to a new genetic study.

An international team of scientists from the CNRS and National Museum of Natural History in France, the University of Mainz in Germany, and UCL in the UK were able to conduct the study by first extracting DNA from the bones of domestic cattle excavated in Iranian archaeological sites. These sites date to not long after the invention of farming and are in the region where cattle were first domesticated.

The team examined how small differences in the DNA sequences of those ancient cattle, as well as cattle living today, could have arisen given different population histories. Using computer simulations they found that the DNA differences could only have arisen if a small number of animals, approximately 80, were domesticated from wild ox (aurochs).

The study is published in the current issue of the journal Molecular Biology and Evolution. Dr Ruth Bollongino of CNRS, France, and the University of Mainz, Germany; lead author of the study, said: "Getting reliable DNA sequences from remains found in cold environments is routine.

"That is why mammoths were one of the first extinct species to have their DNA read. But getting reliable DNA from bones found in hot regions is much more difficult because temperature is so critical for DNA survival. This meant we had to be extremely careful that we did not end up reading contaminating DNA sequences from living, or only recently dead cattle."

The number of animals domesticated has important implications for the archaeological study of domestication.

Prof Mark Thomas, geneticist and an author of the study based at the UCL Research Department of Genetics, Evolution and Environment: "This is a surprisingly small number of cattle. We know from archaeological remains that the wild ancestors of modern-day cattle, known as aurochs, were common throughout Asia and Europe, so there would have been plenty of opportunities to capture and domesticate them."

Prof Joachim Burger, an author of the study based at the University of Mainz, Germany, said: "Wild aurochs are very different beasts from modern domestic cattle.

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DNA traces cattle back to a small herd domesticated around 10,500 years ago

Posted in DNA

DNA Sequencing Market Expected to Double to $6.6 Billion by 2016

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FARMINGTON, Conn., March 27, 2012 /PRNewswire-iReach/ -- Global Information Inc. is pleased to announce a new market research report, "DNA Sequencing: Emerging Technologies and Applications" by BCC Research, as well as remaining available registration for the Sample Prep 2012 Conference in San Diego, CA.

(Photo: http://photos.prnewswire.com/prnh/20120327/CG77328)

DNA Sequencing: Emerging Technologies and Applications

The value of the global market for sequencing products and services is forecast to more than double to a value of $6.6 billion by 2016, growing from nearly $3 billion in 2011 at a compound annual growth rate (CAGR) of 17.5% according to BCC Research's new market research report DNA Sequencing: Emerging Technologies and Applications.

The sequencing products market can be broken down into three segments: instruments and consumables, services, and workflow products. Instruments and consumables accounted for nearly $1.6 billion in 2011 will reach $2.2 billion in 2016. Services were valued at $987.6 million in 2011 and are expected to increase at a remarkable CAGR of 29% to reach $3.5 billion in 2016. Workflow products, worth nearly $410 million in 2011, should reach $883.6 million in 2016 at a CAGR of 16.6%.

Life science research tools suppliers will find this report particularly valuable, as will pharmaceutical, diagnostics, nanotechnology, bioinformatics, semiconductor, and biotechnology companies. Also, companies seeking to benefit from genome sequencing projects, microarray companies seeking an entry into the sequencing market, informatics companies who wish to expand their market reach, and in vitro diagnostics companies who want to add sequencing platforms to their portfolios will also find valuable insights in the full report.

An abstract and free sample for this report are available from Global Information, Inc: http://www.giiresearch.com/report/bc233598-dna-sequencing-emerging-technologies-applications.html

5th Annual Sample Prep International Conference 2012

Sample Prep 2012 is the fifth annual event in an internationally recognized series for experts in sample preparation for detection and identification of viruses, toxins and pathogens. This conference will address the major issues and current state-of-the-art in the technologies related to the important phases of real-world sample preparation such as sample collection, lysis, target extraction, and transfer to analytical modules.

New and novel robust sampling and bioforensic techniques will be discussed with in the contexts of to biodefense, field and point-of-care biomedical and clinical applications, food and water testing, and environmental and agricultural sampling. A panel of leading experts from government, academia and industry will also address topical issues and areas of focused technology development and implementation including sample prep with microfluidics; sample prep-on-a-chip; alternative sample prep technologies for viruses; toxins & pathogens; sample prep as separate vs. integrated module approach; nanotechnology challenges for sample preparation; robust sampling methodologies; food, water, air, and environmental sampling; novel methods of extraction from tough (non-filterable) matrices; single use sample concentration modules; advanced lateral flow assays for sample prep; nucleic acid or protein based sample prep for next generation sequencing; and sample prep technologies for detection/diagnostics vs. pharma.

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DNA Sequencing Market Expected to Double to $6.6 Billion by 2016

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Synthetic Biology Survey Requires Industry Response

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The Woodrow Wilson Synthetic Biology Project has released a public survey soliciting opinions on synthetic biology. It is a follow up to a recent paper on synthetic biology released in Nature, and it is filled with biased questions that revive some of the oldest misconceptions about the biotechnology industry. The results of the survey are expected to be released in May 2012.

BIO is encouraging members of the industry to participate in the survey and use the opportunity to address some of the biases and misconceptions.

Some of the loaded questions survey takers are asked to rate the relative importance of include:

Among these questions, ironically, is an admission that there currently is no widely agreed upon definition of synthetic biotechnology:

As members of the biotechnology industry, this survey presents an opportunity to get engaged and help fight misconceptions that have existed since the start of the biotech industry. Broad industry participation in filling out this survey and encouraging others to do so can help ensure the results, which will be released in May, will present a balanced view of synthetic biology and the biotechnology industry. We would hope the results rank developing a clear definition of synthetic biology as a higher priority than banning or labeling it.

You can also vote against a moratorium on synthetic biology in this poll in a Genetic Engineering & Biotechnology News article that looks at how fear has influenced public perception of most novel scientific endeavors like synthetic biology.

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Synthetic Biology Survey Requires Industry Response

Powerful systems biology

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The methods of modern biology have made such leaps in recent years that it is easy to amass vast quantities of measurement data nowadays. Not only have we long been able to decode the genetic material of a living organism; at the same time, we can also determine which genes are activated how strongly in which cells, which cellular regulating molecules are present, which proteins are produced and which metabolic products are present in which concentrations. Far more difficult than collecting the data, however, is analysing it, generating new knowledge from it or proposing new scientific hypotheses. On the one hand, we are practically drowning in the flood of data in biologynowadays; on the other hand, we often lack key data, says Uwe Sauer, a professor at the Institute of Molecular Systems Biology.

According to Sauer, new computer methods can help analyse huge amounts of data. Together with Jrg Stelling, a professor at the Department of Biosystems, and an international team of researchers, he has now demonstrated the possibilities computer-aided biology can offer on the bacterium Bacillus subtilis.

Largest dataset

The researchers began by compiling an extensive collection of hundreds of thousands of specific biological values for the bacterium. What is exceptional about this data pool is that it does not reflect the state of the bacteria at a particular time, but rather a measuring sequence of anadaptation of the micro-organisms to environmental changes over several hours.

The scientists allowed the bacteria to grow on glucose in the lab first before supplementing it with malic acid, which the micro-organisms can use as an alternative nutrient. They then repeated the experiment the other way round. They took all the measurements of the biological parameters available to them at short time intervals, thus generating the largest dataset there currently is for such transitions.

More complex than thought

With the aid of newly developed and existing computer analysis methods, in this dataset the scientists were able to showthat the bacteria alter their metabolism and the basic control mechanisms inside the cell greatly for the comparatively simple adaptation to a new food source,for instance. The metabolic processes in the bacterium are very strongly linked and nature uses a far more complex control mechanism here than the simplest one possible that is theoretically imaginable, says Stelling. Instead of the expected changes of two handfuls of genes, almost half of the bacteriums 4,000 genes altered their activity.

The researchers were also able to ascertain why Bacillus subtilis can adapt much more quickly to malic acid than glucose. Using the computer methods, they were able to recognise genes that effectively act as a brake in the adaptation to glucose because they only adapt their activity slowly to the changed conditions.

Extensive possibilities of systems biology

Thanks to the analysis, the scientists ultimately found a hundred previously unknown regions in the bacteriums genetic material that perform a control function in the organism. And in a series of genes that had not yet been described more precisely until now, they were able to predict a function.

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Powerful systems biology

TRADE NEWS: Agilent Technologies Adds New Integrated Biology Capabilities to Bioinformatics Suite

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Agilent Technologies Inc. (NYSE:A) today released GeneSpring 12.0, a major expansion of its popular bioinformatics software designed to enable a new level of medical science breakthroughs. With the new release, GeneSpring users can now analyze next-generation sequencing data and conduct joint analysis at the pathway level across multiple omics platforms in a familiar software environment.

These new capabilities expand on existing GeneSpring modules for transcriptomic, genetic, metabolomic and proteomic data analysis.

With the release of GeneSpring 12.0, Agilent is continuing to deliver on its strong commitment to help researchers realize the promise of systems biology by providing advanced instrumentation and powerful software tools, said Gustavo Salem, Agilent vice president and general manager, Biological Systems Division. The GeneSpring bioinformatics software suite enables a new breed of integrated biology research with sophisticated analytical, visualization and data-management software.

GeneSpring 12.0 with the new integrated Pathway Architect module is available to all customers for a free evaluation period, now through Aug. 17.

The new release includes an NGS module for next-generation sequencing. The NGS module was designed and tested for use with Agilents SureSelect target-enrichment platform as well as un-targeted next-gen sequencing experiments. An integral part of the NGS module is the QC manager, which provides tools for graphical target enrichment, base quality, mapping and alignment QC. DNA-SEQ workflows in the GeneSpring NGS module include tools for identifying and profiling known and novel variants, annotating SNPs, predicting SNP effects, and detecting structural variants. RNA-SEQ workflows support mRNA profiling in absolute and relative space, including detection and differential expression analysis of genes and splice variants. This includes novel gene and exon detection, gene fusion analysis, and sophisticated statistical and pathway analysis tools.

Agilents new bioinformatics software makes it easy for biologists with little experience in next-generation sequencing bioinformatics to manage and analyze their data by guiding them through wizard-driven workflows. It provides a convenient way to group, classify and explore data processed by a bioinformatics facility. GeneSpring 12.0 is also integrated with Agilents free eArray portal, enabling users to custom-design experiments through an easy-to-use interface.

Integrating data from heterogeneous omics technologies is a key component of systems biology research, which involves measuring the abundance of various biological entities in the same or closely related biological samples. The GeneSpring Pathway Architect module is designed to enable researchers to conduct joint pathway-level analysis of virtually any biological entity. This includes transcripts and splice variants, affected gene panels from variant analysis, metabolites and proteins.

The GeneSpring Pathway Architect module enables scientists to view and analyze curated pathway content. This is accomplished by leveraging WikiPathways, a publicly available resource for building, annotating and querying biological pathways. Mapping of biological identifiers across multiple public and proprietary annotation databases is also supported through integration with BridgeDB, another publicly available resource. Primary data from any of the single-omic experiments can be merged into a multi-omic experiment and used jointly to identify statistically significant pathways involved in many biological processes, such as signaling events, disease progression or toxicity.

GeneSpring 12.0 customization capabilities now include enhanced integration of the Jython and R programming languages. Using the embedded scripting editor, bioinformatics scientists can write, execute, and save their own algorithms and workflows in the GeneSpring 12.0 programming framework.

Agilent GeneSpring 12.0 was developed in partnership with Strand Scientific Intelligence, Inc. It is powered by Strands Avadis platform, which is designed to enable scientists to simplify and solve complex life science challenges.

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TRADE NEWS: Agilent Technologies Adds New Integrated Biology Capabilities to Bioinformatics Suite

Research and Markets: Handbook of Statistical Systems Biology

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Research and Markets (http://www.researchandmarkets.com/research/e3d2e201/handbook_of_statis) has announced the addition of John Wiley and Sons Ltd's new book "Handbook of Statistical Systems Biology" to their offering.

Systems Biology is now entering a mature phase in which the key issues are characterising uncertainty and stochastic effects in mathematical models of biological systems. The area is moving towards a full statistical analysis and probabilistic reasoning over the inferences that can be made from mathematical models. This handbook presents a comprehensive guide to the discipline for practitioners and educators, in providing a full and detailed treatment of these important and emerging subjects. Leading experts in systems biology and statistics have come together to provide insight in to the major ideas in the field, and in particular methods of specifying and fitting models, and estimating the unknown parameters.

Key Features:

- Provides a comprehensive account of inference techniques in systems biology.

- Introduces classical and Bayesian statistical methods for complex systems.

- Explores networks and graphical modeling as well as a wide range of statistical models for dynamical systems.

- Discusses various applications for statistical systems biology, such as gene regulation and signal transduction.

- Features statistical data analysis on numerous technologies, including metabolic and transcriptomic technologies.

- Presents an in-depth presentation of reverse engineering approaches.

- Provides colour illustrations to explain key concepts.

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Research and Markets: Handbook of Statistical Systems Biology

SDSC graduate student awarded NVIDIA Graduate Fellowship

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Public release date: 27-Mar-2012 [ | E-mail | Share ]

Contact: Jan Zverina jzverina@sdsc.edu 858-534-5111 University of California - San Diego

A graduate student working in the Walker Molecular Dynamics laboratory at the San Diego Supercomputer Center (SDSC) at the University of California, San Diego is a recipient of the 2012-2013 NVIDIA Graduate Fellowship Program award for his innovative molecular dynamics research using GPU (graphics processing unit) computing.

Benjamin Madej, a chemistry and biochemistry Ph.D. student at UC San Diego, will receive a $25,000 scholarship to further his research. Madej received his Bachelor of Science in biomedical engineering from Washington University in St. Louis, Missouri, and is currently working on new methods for developing force fields used in molecular dynamics software, specifically the AMBER MD package.

Madej's research proposal focused on not only improving the AMBER Molecular Dynamics GPU engine, but extending the use of GPUs to multiple facets of molecular dynamics development and workflow for new drug discovery.

"We are proud of Ben's achievement in being awarded this prestigious scholarship and recognition," said SDSC Director Michael Norman. "It is very gratifying to see such a high level of accomplishment in computational science as Ben pursues his doctorate here at UC San Diego."

"This fellowship is a testimony to Ben's past work, the importance of GPUs at the frontiers of molecular dynamics and drug discovery, and recognition of the future potential of his contributions to science. The GPU revolution is transforming the field and this fellowship provides vital support for us to continue this cutting-edge research," said Ross C. Walker, an assistant research professor with SDSC and head of the Walker Molecular Dynamics laboratory. Walker also is an adjunct assistant professor in UC San Diego's Department of Chemistry and Biochemistry, as well as an NVIDIA CUDA Fellow.

The NVIDIA Graduate Fellowship Program provides funding to Ph.D. students who are researching topics that will lead to major advances in the graphics and high-performance computing industries, and are investigating innovative ways of leveraging the power of GPUs. Recipients not only receive crucial funding for their research, but are provided access to NVIDIA products, technology, and expertise.

"This year the NVIDIA Foundation joined in our search for top Ph.D. students who are investigating innovative ways to leverage the power of the GPU, especially those that will ultimately benefit humanity," said Chandra Cheij, NVIDIA's research program manager. "Congratulations to Ben and SDSC for this significant achievement."

SDSC's Walker Molecular Dynamics lab is focused on computational chemistry, molecular biology, and high-performance computing. The lab is particularly interested in the development of efficient algorithms for parallel computation of Quantum Mechanical and hybrid Quantum/Molecular Mechanical (QM/MM) techniques, as well as improvements in the computational efficiency and accuracy of classical MM dynamics simulations.

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SDSC graduate student awarded NVIDIA Graduate Fellowship

Continued Smoking Can Spread Cancer

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Newswise Cigarette smoke cannot only cause cancer, but it's also responsible for the spread of it, according to research by UC Merced biochemistry Professor Henry Jay Forman.

Forman discovered tobacco smoke activates an enzyme called Src that causes cancer cells to spread to other parts of the body. The study will appear in the April 15 edition of Free Radical Biology and Medicine.

Cigarette smoke is the major cause of lung cancer, Forman said, but nearly half of lung cancer patients remain active smokers. Nonetheless, researchers haven't understood how cigarette smoke causes cancer to metastasize.

The lab was also able to prevent cigarette smoke from activating the enzyme by introducing an antioxidant. Forman's discovery could prove useful in the fight against cancer, as it creates more understanding on how it spreads and how antioxidants can help combat this.

Forman will present his findings on April 21 at the Experimental Biology 2012 conference in San Diego.

Forman coauthored the paper with a professor from the University of Padova in Italy. Forman served as a visiting professor during the summer while also conducting research.

In another paper, recently published in the Journal of Biological Chemistry, Forman collaborated with investigators at USC who are experts in looking at how cells maintain themselves using proteasome, which degrades old and damaged proteins. When cells are under oxidative stress, the proteasomes work faster to remove damaged proteins.

However, the lab discovered the signal used to increase a cell's defenses doesn't happen in old age, causing cells to die and turn malignant. The findings offer more insight into age-related problems, such as Alzheimer's disease. Both studies were supported by the National Institutes of Health.

Forman will continue his research this summer, focusing on three projects: understanding how differences in the expression of a particular enzyme increases human susceptibility to air pollution; studying how people with sickle cell trait may have a sickle cell crisis when doing severe exercise; and studying how cigarette smoke activates an enzyme that regulates changes in lung cancer cells that promote metastasis. The three projects are also funded by the National Institutes of Health.

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Continued Smoking Can Spread Cancer

Midlands Vet Uses Stem Cell Therapy for Pets in Pain

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Columbia, SC (WLTX) --What if your pet couldn't walk anymore? One Midlands vet is using stem cell therapy to help.

For Beth Phibbs it's almost like a turning back of the hands of time.

"I call her my little miracle dog, because she's doing things she used to do," said Phibbs. "Now she's not on any medication, and she can go up and down the steps and she runs and jumps and things that she used to do when she was five."

Phibbs has spent the last 13 years loving and looking after her pet dog Maggie, and when she pet began to develop arthritis and a limp she had to take action. But when the first treatments stopped working, Phibbs and Maggie had to look to another options, dog stem cell therapy.

"I had no idea that animals were able to have they type of procedures," she said.

Dr. Kenneth Banks a veterinarian with the Bank Animal Hospital, performed the surgery for Maggie using her own stem cells in the one day procedure.

Banks said the stem cell therapy not only cost less than some other options, but was less invasive and had a quicker recovery time as well.

Still with about three similar procedures under his belt, even he didn't expect to see a such change in maggie just 40 days after the surgery.

"I wasn't sure we were gonna get the results this fast, we were expecting results, maybe not a good as she's done. We're real happy with her results," said Banks.

Now, after three years on medication and walking with a limp, Maggie's getting used to a new way of life -- one with out pain in her golden years.

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Midlands Vet Uses Stem Cell Therapy for Pets in Pain

Children four and under should move more, sit less and avoid screens

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Canada's first-ever physical activity and sedentary behaviour guidelines for the early years released

TORONTO, March 27, 2012 /PRNewswire/ - Children aged four and under should move more and sit less every day as recommended by the first-ever Canadian Physical Activity and Sedentary Behaviour Guidelines for the Early Years. All children aged one to four should accumulate at least 180 minutes of physical activity throughout the day, and children under the age of one should be physically active several times daily. Parents and caregivers should also limit prolonged sitting for more than one hour at a time and excessive screen time.

The Physical Activity and Sedentary Behaviour Guidelines for the Early Years (ages 0-4 years) are Canada's first systematic evidence-based physical activity guidelines and the world's first standalone sedentary behaviour guidelines for this age group, which puts Canada at the forefront of the emerging body of sedentary research. They are presented by the Canadian Society for Exercise Physiology (CSEP) and ParticipACTION, with support from the Children's Hospital of Eastern Ontario Research Institute, Healthy Active Living and Obesity Research Group (CHEO-HALO).

Although children in the early years are assumed to be naturally busy and active, they spend 73 to 84 per cent of their waking hours being sedentary. In addition, despite the detrimental effects on physical and social development, most young children are exposed to screen time too early in life and for too long.

"Regular physical activity is essential at a young age as it contributes to bone and skeletal health, motor skill development, psychosocial health, cognitive development and healthy body weights," says Dr. Mark Tremblay, Director, CHEO-HALO. "It is also key to avoid the harms associated with excessive sedentary behaviour, in particular the negative effects of screen time exposure, in the earliest years of development. Lifestyle patterns set in the early years predict health outcomes later in life."

For healthy growth and development, the Canadian Physical Activity Guidelines for the Early Years recommend:

Minimizing sedentary behaviour, including screen time, during waking hours is just as important as being physically active. Sedentary behaviours are characterized by little physical movement and low energy expenditure and include sitting or reclining for long periods of time. For healthy growth and development, the Canadian Sedentary Behaviour Guidelines for the Early Years recommend:

"These guidelines place a high value on the benefits of physical activity that begin in a child's early years and accumulate throughout life," says Kelly Murumets, President and CEO of ParticipACTION, the national voice of physical activity and sport participation. "It is crucial for parents and caregivers to give young children regular opportunities to move more, and it can be as simple as getting outdoors to explore the neighbourhood rather than sitting in front of the TV, or by playing on a mat reaching, pushing or crawling rather than keeping children idle in a high chair."

To download a copy of the new Canadian Physical Activity Guidelines and Sedentary Behaviour Guidelines for the Early Years please visit http://www.csep.ca/guidelines and participACTION.com.

About the Canadian Society for Exercise Physiology The Canadian Society for Exercise Physiology (CSEP) is the principal body for physical activity, health and fitness research and personal training in Canada.CSEP fosters the generation, growth, synthesis, transfer and application of thehighest quality research, education and training related to exercise physiology and science. CSEP is the GOLD STANDARD of health and fitness professionals dedicated to getting Canadians active safely by providing the highest quality customized and specialized physical activity and fitness programs, guidance and advice based on extensive training and evidence-based research. For more information, visit http://www.csep.ca.

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Children four and under should move more, sit less and avoid screens

Destruction Anniversary Tour Features Warbringer, Vital Remains, and Pathology

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03/27/2012 . Warbringer will return to the road in May for a North American tour with Destruction for their 30th anniversary tour which will also feature Vital Remains, and Pathology.

The trek will run from May 8th to June 3rd, and after that, Warbringer will appear at various high-profile Summer festival appearances in Europe.

Vocalist John Kevill checked in to comment about these upcoming shows: "Hey all! Checking in at the end of the Iced Earth and Symphony X tour. We had a great time with those guys, there was a slew of incredible shows with awesome heavy metal fans in abundance, and a bunch of good times with both of those fine bands! Shame to say goodbye to them, but we're on our way home now to recuperate Before beginning out next tour with German thrash metal legends Destruction, on their 30th anniversary tour! We never rest long, the war rages on! We'll see you guys out on the road again in May, prepare to be annihilated!

We're also very excited about the way our summer is shaping up. We have about a dozen European festivals confirmed and we look forward to sharing some amazing experiences ravaging the large crowds, big stages and all the fun times to be had with all the other great bands also performing."

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How colds cause coughs and wheezes

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Public release date: 26-Mar-2012 [ | E-mail | Share ]

Contact: Laura Udakis l.udakis@sgm.ac.uk 44-079-908-26696 Society for General Microbiology

Cold-like infections make 'cough receptors' in the airways more sensitive, making asthmatics more prone to bouts of coughing and wheezing, reveal scientists presenting their findings at the Society for General Microbiology's Spring Conference in Dublin. The work could lead to drugs that reduce virus-induced coughing in those suffering chronic lung diseases.

Asthmatics often report bouts of coughing, wheezing and breathlessness when they have a cold and there is no current medicine that sufficiently treats this problem. Researchers at Queen's University Belfast are investigating 'cough receptors' that line the cells of the airway and how these are affected by rhinovirus a virus frequently responsible for the common cold. The team showed that rhinovirus infection caused an increase in the number of these cough receptors making the airways more sensitive.

Dr Hani'ah Abdullah, who is working on the project, explained how these receptors, called transient receptor potential (TRP) receptors, work. "TRP receptors respond to chemical and physical stimuli in the environment such as pollutants in the air, a change in air temperature and some of the toxic chemicals found in cigarette smoke. Once activated, these receptors cause the individual to cough and wheeze." she said.

Professor Louise Cosby and Dr Lorcan McGarvey from the Centre for Infection and Immunity, Queen's University Belfast, are jointly leading the research team of scientists and clinicians. Their group took airway cells from mild asthmatics and healthy individuals and infected them in the laboratory with rhinovirus, which is the most common virus to exacerbate symptoms of asthma. The results showed that rhinovirus infection caused an increase in the number of TRP receptors in the airway cells and that this effect was most pronounced in the mild asthmatics. "The increase in receptor numbers makes individuals more sensitive to environmental stimuli, making them more likely to suffer from prolonged bouts of coughing," explained Dr Abdullah.

The findings of this study may lead to new drugs that reduce virus-induced cough and wheeze in asthmatics and those with other chronic lung diseases. "It's feasible that therapies could be developed that block either the sensitivity of cough receptors or their increase in number. This would keep symptoms under control and ultimately improve the lives of asthmatics," said Dr Abdullah.

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‘Bacterial shock’ to recapture essential phosphate

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Phosphorus in the form of phosphate - is essential for all living things as a component of DNA and RNA and its role in cellular metabolism. Around 38 million tonnes of phosphorus are extracted each year from rock. Most of this extracted phosphorus goes into the production of fertilizers to replace the phosphates that plants remove from the soil. However, it is a scare natural resource and current estimates suggest that reserves of phosphate rock may only last for the next 45-100 years.

Researchers at Queen's University Belfast (QUB) are developing a novel biological process to remove extracted phosphate from wastewater where it ultimately ends up after manufacturing. Dr John McGrath who is leading the project explained, "Phosphate in wastewater is a pollutant that causes increased growth of algae and plants, reducing the oxygen available for aquatic organisms. This is known as eutrophication and poses the single biggest threat to water quality in Northern Ireland and indeed globally."

The work at QUB has focused on microorganisms that capture and store phosphate from wastewater, and how this process varies under different nutritional and environmental conditions. "A variety of microbes in wastewater accumulate phosphorus inside their cells and store it as a biopolymer known as polyphosphate. In some cases, this can represent up to 20% of the dry weight of the microorganism!" explained Dr McGrath. "If we can harness this process we have a feasible biotechnological route to remove and recycle phosphate from wastewater."

The team have recently discovered a physiological 'shock' treatment which significantly increases microbial uptake of phosphorus and its accumulation inside cells. "It's similar to jumping into the sea on a winter's day the first thing you do is take a sharp intake of breath. When we shock the microorganisms, their response is to take in phosphorus," explained Dr McGrath. "We've demonstrated this using activated sludge, containing a variety of microbes, from wastewater treatment works and shown this shock treatment is effective at producing a phosphorus-rich biomass suitable for phosphorus recycling."

Dr McGrath believes that developing such biotechnological processes is essential for regenerating valuable mineral resources. "No alternative to phosphorus exists we urgently need to find ways of recovering and recycling phosphates. It's a pollutant we can't live without." he said. "Phosphates are currently removed from wastewater by chemical methods, however this is expensive and results in the production of large volumes of sludge. In contrast, the process we are developing is sustainable and efficient."

Provided by Society for General Microbiology

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AU senior awarded Fulbright Program scholarship

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An Auburn University senior has been awarded a scholarship from the Fulbright Program to continue studying microbiology in Germany.

Paul Bergen, a microbiology and German double major, will continue his studies at the Technical University of Munich during the 2012-13 academic year.

The receipt of a Fulbright Scholarship to conduct research in Germany is a great honor, Bergen said in an email to the Opelika-Auburn News on Monday. I am excited to be able to continue conducting research in the field of microbiology in the country my ancestors called home. My grandparents emigrated from Germany in the 1950s and my grandmother always told me stories about life there.

After spending eight days in the summer of 2010 in Germany, I knew I wanted to go back. The Fulbright grants me that opportunity, along with the recognition of the excellence of my studies at Auburn University.

Bergen, 21, of Cooper City, Fla., has studied in Auburns Honors College for four years, accumulating a 3.97 overall GPA. In addition to receiving Auburns Presidential Scholarship, he has been selected for two fellowships and was named the College of Sciences and Mathematics top junior during the 2010-11 school year.

Bergen is Auburns fourth student to receive a scholarship from the Fulbright Program in as many years. After his 10-month stint in Germany, Bergen said he plans to pursue a doctorate in microbiology at the University of Missouri and then work on treatments for bacterial and viral diseases either in the private sector or in academia.

"Paul is an inquisitive and engaging young man with a range of interests and activities that go well beyond the lab and range from the study of German politics, culture and language to being an active member of Auburn's nationally recognized mock trial team," Paul Harris, associate director of the Auburn Honors College, said in a university news release. "He will gain so much from his classes and interactions with German students and faculty, and he will represent himself, Auburn University and the United States with distinction."

Sponsored by the U.S. Department of State, the Fulbright Program was founded in 1946. It allows students, scholars and professionals the opportunity to study in more than 155 countries throughout the world.

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The Black Queen Hypothesis: A new evolutionary theory

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Public release date: 27-Mar-2012 [ | E-mail | Share ]

Contact: Jim Sliwa jsliwa@asmusa.org 202-942-9297 American Society for Microbiology

Microorganisms can sometimes lose the ability to perform a function that appears to be necessary for their survival, and yet they still somehow manage to endure and multiply. How can this be? The authors of an opinion piece appearing in mBio, the online open-access journal of the American Society for Microbiology, on March 27 explain their ideas about the matter. They say microbes that shed necessary functions are getting others to do the hard work for them, an adaptation that can encourage microorganisms to live in cooperative communities.

The Black Queen Hypothesis, as they call it, puts forth the idea that some of the needs of microorganisms can be met by other organisms, enabling microbes that rely on one another to live more efficiently by paring down the genes they have to carry around. In these cases, it would make evolutionary sense for a microbe to lose a burdensome gene for a function it doesn't have to perform for itself. The authors, Richard Lenski and J. Jeffrey Morris of Michigan State University, and Erik Zinser of the University of Tennessee, named the hypothesis for the queen of spades in the game Hearts, in which the usual strategy is to avoid taking this card.

"It's a sweeping hypothesis for how free-living microorganisms evolve to become dependent on each other," says Richard Losick of Harvard University, who edited the paper. "The heart of the hypothesis is that many genetic functions provide products that leak in and out of cells and hence become public goods," he says.

As an illustration of the hypothesis, the authors apply it to one particular microbial system that has been a source of some confusion: one of the most common plankton species in the open ocean, Prochlorococcus, which has a much smaller genome than you might expect. Scientists have wondered how Prochlorococcus has managed to be extremely successful while shedding important genes, including the gene for catalase-peroxidase, which allows it to neutralize hydrogen peroxide, a compound that can damage or even kill cells. Prochlorococcus relies on the other microorganisms around it to remove hydrogen peroxide from the environment, say the authors, allowing it to fob off its responsibilities on the unlucky card holders around it. This is an instance of how one species can profit from paring down while relying on other members of the community to help out.

Losick says the Black Queen Hypothesis offers a new way of looking at complicated, inter-dependent communities of microorganisms. "I have a special interest in how bacteria form biofilms, complex natural communities that often consist of many different kinds of bacteria. The Black Queen Hypothesis provides a valuable new way to think about how the members of these biofilm communities coevolved."

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mBio is an open access online journal published by the American Society for Microbiology to make microbiology research broadly accessible. The focus of the journal is on rapid publication of cutting-edge research spanning the entire spectrum of microbiology and related fields. It can be found online at http://mBio.asm.org.

The American Society for Microbiology is the largest single life science society, composed of over 39,000 scientists and health professionals. ASM's mission is to advance the microbiological sciences as a vehicle for understanding life processes and to apply and communicate this knowledge for the improvement of health and environmental and economic well-being worldwide.

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The Black Queen Hypothesis: A new evolutionary theory