ASU creating new chemistry forensics study

Staff Writer

Augusta State University is creating a new chemistry track for students who want to become behind-the-scenes scientists.

JACKIE RICCIARDI/STAFF

Chemistry professor Stephanie Myers, shown in her office, will be starting a new forensic science program at Augusta State University.

The Department of Chemistry and Physics will debut a forensic science track in fall 2012, which can lead to jobs testing blood stains on clothes from crime scenes or determining types of drugs found in the bloodstream.

We are a very hands-on department, said Stephanie Myers, professor of chemistry and forensic science advisor. Students get lots of real lab experience. Theyre not watching someone else do it.

Students who sign up for the new track will still graduate with a chemistry degree but with a concentration in the forensic field. ASU Vice President for Academic Affairs Carol Rychly said adding this track to the chemistry department compliments the goals of the merger with Georgia Health Sciences University – creating more options for students and producing more qualified graduates.

One of the things that were looking to as we move toward the new (university) is to build up the programs we already have and making them more robust, Rychly said. Its a win-win. Youre meeting the students needs and youre providing the community employable people.

Rychly said she expects other departments to add more tracks or programs within their field in the next few years. The expansion also provides a chance for collaboration between liberal arts and health sciences, like a possible medical humanities course in the works, she said.

Myers said the forensic track was born out of an interest from the students and opportunity after she received a certificate in forensic science from The University of Florida in 2010.

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New Clinical Data Highlighting Foundation Medicine’s Comprehensive Cancer Genomic Profile to be Presented at 2012 ASCO …

CAMBRIDGE, Mass.–(BUSINESS WIRE)–

Foundation Medicine, Inc., a molecular information company that brings comprehensive cancer genomic analysis to routine clinical care, today announced that new clinical data highlighting the companys comprehensive cancer genomic profile and next-generation sequencing approach in clinical oncology will be presented at the 2012 Annual Meeting of the American Society for Clinical Oncology (ASCO) being held June 1-5, 2012 in Chicago.

The data to be presented at ASCO support Foundation Medicines deep sequencing approach to simultaneously detect all classes of genomic alterations across hundreds of genes known to be related to cancer, said Michael J. Pellini, M.D., president and chief executive officer, Foundation Medicine. In our clinical experience abstract, this approach detected actionable alterations those associated with available targeted treatments or ongoing clinical trials for 74% of tumor samples in the study. Foundation Medicines test has also been shown to identify novel genomic alterations in multiple tumor types, including potentially druggable gene fusions. The combined evidence presented in these studies suggests that fully informative genomic profiling can now become a routine component of cancer patient care.

The schedule for Foundation Medicines oral presentation is as follows:

Date & Time:

Session:

Abstract Number:

Title:

Discovery of recurrent KIF5B-RET fusions and other targetable alterations from clinical NSCLC specimens.

Location:

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FDA Approves Generic Clopidogrels As Plavix Loses Patent Protection

For the second time in the past six months, a cardiology mainstay drug has lost patent protection and gone generic. Today the FDA announced that it had approved several generic versions of clopidogrel (Plavix), the antiplatelet drug that for many years was the second best-selling drug in the world. Last November the best-selling drug of all time, Lipitor (atorvastatin), another cardiology …

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Cardiology expands again

Wednesday, May 16, 2012 Edition

Cardiology expands again Following the addition last fall of state-of-the-art echocardiography equipment to diagnose complex heart conditions, Baptist Medical Center Nassau has taken another giant step forward in cardiac care, says Stephen Lee, hospital president.

DEA honors local detective U.S. Attorney Robert O’Neill presided over a federal awards ceremony last month at the Federal Courthouse in Jacksonville and announced that local narcotics investigator Matt Bowen and his DEA Task Force partner Randy Crews of the Baker County Sheriff’s Office have been named the U.S. Attorney’s Outstanding Law Enforcement Officers for 2011.

HOME AND GARDEN BRIEFS Wine festival Amelia Island Wine Festival is pleased to announce that Bridget Keegan of Old Oaks Vineyard will be a vendor at the Amelia Island Wine Festival.

A local perspective The Fernandina Beach Police Department is committed to the goal of reducing illegal narcotics activity in our City and for that reason we participate in the Jacksonville Regional Drug Enforcement Administration Narcotics Task Force.

PET PROJECTS Garage sale On May 19 from 8 a.m. to noon, the Palmetto Walk shopping center will have its second annual garage sale and Nassau Humane Society will receive 10 percent of sales. To reserve space call Sharon at 321-0588.

WEEKLY UPDATE Heart to Heart Baptist Nassau program on the risks of heart disease and the latest techniques for diagnosis and treatment at a free discussion, Wednesday May 23, with Fernandina Beach cardiologist, Dr. George Le-Bert. The free program takes place at The Journey Church on Sadler Road from 11:45 am to 1:30 pm. Lunch will be available. Reservations are required. Call 904-202-CARE (2273).

PEOPLE AND PLACES ~~ SPECIAL EVENTS Bingo anniversary American Legion Post 54 will celebrate its second anniversary of providing bingo to the public each Thursday on May 17 with lots of door prizes and an extra jackpot game.

THIS WEEK Maritime Museum The Maritime Museum of Amelia Island hosts a program on a current topic every Friday at 5 p.m. The programs are jointly sponsored by the museum and Amelia Research and Recovery, LLC, the Amelia-based company that searches for and recovers sunken treasure from Spanish Galleons. The museum is located at 1335 S. Eighth St. No reservations are needed. Call (904) 838-6688 or (904) 838-6619.

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Panel of Top Industry Executives to Discuss Biotech and Big Pharma – What’s Next? – 2012 BIO International Convention …

WASHINGTON–(BUSINESS WIRE)–

The Biotechnology Industry Organization (BIO) announced today that a panel of top industry executives will discuss where biotech will be in the next ten years and how the pharmaceutical industry landscape is changing. With the biotech and pharmaceutical industries facing considerable challenges but also tremendous growth opportunities, attendees can expect to gain valuable insights into the future of biotech and big pharma.

Biotech and Big Pharma Whats Next? panelists include: Moderator: Joshua Boger, PhD, Founder and CEO (Retired), Vertex Pharmaceuticals Incorporated Panelists: Rachel K. King, Chief Executive Officer, GlycoMimetics, Inc; Christopher A. Viehbacher, Chief Executive Officer, Sanofi, Chairman, Genzyme and H. Thomas Watkins, President and Chief Executive Officer, Human Genome Sciences

Wednesdays Keynote session is sponsored by Amgen, a leading human therapeutics company in the biotechnology industry.

Immediately preceding the Keynote panel, Senator John Kerry (D-MA) will address the 2012 BIO International Convention, this years global event for biotechnology, which will take place June 18-21, 2012 at the Boston Convention and Exhibition Center in Boston, MA. Additionally, the Keynote will feature the presentation of awards for the Biotech Humanitarian of the Year and the Governor of the Year.

Senator Kerrys speech will address the major challenges to the life sciences innovation ecosystem. He is scheduled to speak Wednesday, June 20th at 12:00 p.m., during the Keynote luncheon.

Each year, we strive to provide attendees with a Keynote address by an industry thought leader to share their perspective on the state of the industry, said Robbi Lycett, Vice President of Conventions & Conferences at BIO. We anticipate Senator Kerry will continue this tradition and share his insights and vision for the future with our attendees.

John Kerry was elected to the United States Senate in 1984 and he has won reelection four-times since. He is now serving his fifth term. Senator Kerry has fought to protect our natural environment and has proved to be a leader on the global AIDS issue and confronting the climate crisis.

In 2003, Senator Kerry announced that he would be a candidate for President of the United States and he went on to mount a come from behind campaign that won the Democratic nomination and was nearly elected President.

Today, Senator Kerry is the tenth most senior Senator and the second longest serving Senator in his seat. He is chairman of the Foreign Relations Committee as well as holds a senior position on the Finance, Commerce and Small Business Committees.

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DGAP-News: Cytos Biotechnology Ltd Announces Updates to the Board of Directors

NOT FOR RELEASE, PUBLICATION OR DISTRIBUTION IN WHOLE OR IN PART, IN, INTO OR FROM THE UNITED STATES OF AMERICA (THE UNITED STATES OR U.S.), CANADA, JAPAN OR AUSTRALIA OR ANY OTHER JURISDICTION WHERE TO DO SO WOULD CONSTITUTE A VIOLATION OF THE RELEVANT LAWS OF SUCH JURISDICTION.

Cytos Biotechnology Ltd Announces Updates to the Board of Directors

Schlieren (Zurich), Switzerland, May 18, 2012 – Cytos Biotechnology Ltd (Cytos) announced today that its Board of Directors, consisting of Joseph Anderson, John Berriman, Paul Brooke, Thomas Hecht, Arthur Krieg, Jakob Schlapbach and Kurt von Emster constituted itself as follows:

– Thomas Hecht, Executive-Chairman of the Board of Directors

– John Berriman, Vice Chairman of the Board of Directors and Chairman of the Compensation Committee

– Arthur Krieg, Vice Chairman of the Board of Directors and member of the Nomination and Corporate Governance Committee

– Joseph Anderson, member of the Board of Directors and Chairman of the Nomination and Corporate Governance Committee

– Paul Brooke, member of the Board of Directors and Chairman of the Audit Committee and member of the Compensation Committee

– Jakob Schlapbach, member of the Board of Directors and member of the Audit Committee and the Compensation Committee

– Kurt von Emster, member of the Board of Directors and member of the Audit and Nomination and Corporate Governance Committee

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Puma Biotechnology to Present Clinical Data on PB272 at ASCO 2012 Annual Meeting

LOS ANGELES–(BUSINESS WIRE)–

Puma Biotechnology, Inc. (OTCBB: PBYI.OB – News), a development stage biopharmaceutical company, announced that clinical data for its lead drug candidate PB272 (neratinib) in patients with metastatic breast cancer will be presented in the HER2/ER Breast Cancer poster session at the American Society of Clinical Oncology (ASCO) 2012 Annual Meeting. The ASCO Annual Meeting will be held June 1 5, 2012, in Chicago.

Details of the poster presentation are as follows:

Abstract #611: A phase I dose-escalating study evaluating weekly paclitaxel with neratinib and trastuzumab in women with metastatic HER-2 positive breast cancer, NSABP FB-8. Rachel C. Jankowitz, MD Poster Board #10F, S Hall A2, Saturday, June 2, 8:00 a.m. 12 Noon

About Puma Biotechnology

Puma Biotechnology, Inc. is a development stage biopharmaceutical company that acquires and develops innovative products for the treatment of various forms of cancer. The Company focuses on in-licensing drug candidates that are undergoing or have already completed initial clinical testing for the treatment of cancer and then seeks to further develop those drug candidates for commercial use. The Company is initially focused on the development of PB272 (oral neratinib), a potent irreversible tyrosine kinase inhibitor, for the treatment of patients with HER2 positive metastatic breast cancer.

Further information about Puma Biotechnology can be found at www.pumabiotechnology.com.

Forward-Looking Statements:

This press release contains forward-looking statements that involve risks and uncertainties that could cause the Company’s actual results to differ materially from the anticipated results and expectations expressed in these forward-looking statements. These statements are based on current expectations, forecasts and assumptions, and actual outcomes and results could differ materially from these statements due to a number of factors, which include, but are not limited to, the risk factors disclosed in the periodic reports filed by the Company with the Securities and Exchange Commission from time to time. Readers are cautioned not to place undue reliance on these forward-looking statements, which speak only as of the date hereof. The Company assumes no obligation to update these forward-looking statements, except as required by law.

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Slow-motion film reveals what happens when lizards drop their tails

Timothy Higham is an assistant professor of biology at UC Riverside. He is seen here holding a lizard that has self-amputated its tail. Credit: National Geographic.

Timothy Higham, an assistant professor of biology at the University of California, Riverside, will be featured in the program Animal Superpowers: Extreme Survivors on the National Geographic Wild Channel, 8 p.m., ET and PT, Sunday, June 3.

Broadcast internationally, the series Animal Superpowers is hosted by the actor Sir Patrick Stewart. On the Extreme Survivors episode, Higham will discuss what happens when a lizard drops its tail an escape plan unique in nature that lizards use when they are attacked. Using high-speed cameras, Higham reveals precisely how the tail fools predators, allowing the lizard to escape and survive. The research may, in the future, help humans with spinal cord injuries.

Lizards are incredible in their ability to self-amputate their tail when they encounter a predator, Higham said. The tail, containing a portion of the spinal cord, is voluntarily detached by muscular contractions that break the tail at a weak point within a single vertebra. The tail contains many of these weak points, so the lizard can break off variable amounts of the tail.

Higham explained that the tail, once dropped by the lizard, continues to move around vigorously, doing flips and swinging back and forth. This movement distracts the predator while the lizard is able to run away and avoid being eaten.

Enlarge

Lizards use an escape plan unique in nature when they are attacked. Credit: National Geographic.

Highams lab focuses on biomechanics, functional morphology, and comparative physiology of vertebrate locomotion and feeding. He received his doctoral degree in molecular, cellular and integrative physiology from UC Davis in 2006. Following a postdoctoral appointment at Harvard, he spent three years as an assistant professor of biological sciences at Clemson University. He joined UC Riverside last year.

Viewers are encouraged to check their local listings for Animal Superpowers: Extreme Survivors on the National Geographic Wild Channel.

More information: http://animals.nat hedule/wild/

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Forest diversity from Canada to the sub-tropics influenced by family proximity

ScienceDaily (May 17, 2012) How species diversity is maintained is a fundamental question in biology. In a new study, a team of Indiana University biologists has shown for the first time that diversity is influenced on a spatial scale of unparalleled scope, in part, by how well tree seedlings survive under their own parents.

Data from over 3 million trees in the eastern half of the U.S. were aggregated into two-degree-latitude-by-longitude cells in order to study regional patterns of conspecific negative density dependence, a process where the mortality of a species rises in coincidence with its increasing abundance.

Scientists have long considered conspecific negative density dependence (CNDD), a process where the mortality of a species rises in coincidence with its increasing abundance, to be a key mechanism maintaining diversity at the local scale. In new research to be published May 17 in the journal Science, the IU researchers show that this mechanism is driving diversity from the boreal forests to sub-tropical forests.

The report, “Conspecific negative density dependence and forest diversity,” is authored by Daniel Johnson, a doctoral student in the IU Bloomington College of Arts and Sciences’ Department of Biology. Co-authors are Wesley T. Beaulieu, also a doctoral student in the Department of Biology, and biology professors James D. Bever and Keith Clay, Johnson’s major advisor.

Their work analyzed data on forest composition from over 200,000 plots containing more than 1.3 million trees and from paired plots containing over 1.7 million seedlings of 151 different tree species. The plots were located from the Canadian border south to Florida and from the Atlantic coast to the 100th meridian and covered over 1.5 million square miles. The U.S. Forest Service spends about $62 million each year to gather the publicly available forest inventory data used in the IU study.

“We are now able to provide robust evidence that CNDD is pervasive in forest communities from boreal to sub-tropical regions and that it can significantly affect the relative abundance and richness of species with and between forests,” Johnson said. “And we now see that the ability to which one tree species can sustain itself in the same area has profound impacts on the diversity of species at a spatial scale that has not been attainable previously. This is the first time it’s been shown to be happening not just at a local spatial scale but over the entire eastern US.”

The concept of CNDD is based on the well-known Janzen-Connell hypothesis, which proposes that the close proximity of adults reduces seedling survival of that species through increased attack by host-specific pests and pathogens.

Studies of CNDD in the past have mostly focused on forest communities at single sites or of a single species, with the most recent work showing that in tree species, composition and abundance can be influenced by CNDD at the scale of individual trees.

“Local interactions have previously been considered to affect species diversity at a local scale, but our findings indicate that local interactions feed back to species richness and abundance over much larger geographical scale, spanning most of eastern North America,” Johnson said.

Evidence that local interactions underlie regional species richness is in contrast to the current understanding that patterns of forest diversity are primarily driven by temperature, precipitation and other physical aspects of the environment. This discovery has implications for how forest modeling is conducted and conservation and management decisions are made.

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Reed College biology professor wins prestigious $986,000 National Science Foundation grant

Schaack received the foundation’s Faculty Early Career Development Program grant. The five-year award is the foundation’s most prestigious for junior faculty. It rewards professors who serve as research mentors and integrate their research into their teaching and their college’s mission.

Schaack’s research focuses on understanding genetic mutation rates, genetic variations and the role of mobile DNA in mutations. She draws on the help of advanced undergraduate and post-doctoral students in her research and uses it to provide students hands-on laboratory exercises.

She also provides public lectures and workshops about genome biology, including Pub Talks in the Portland area in conjunction with the Oregon Museum of Science and Industry. She, for example, spoke at Hotel Oregon in McMinnville about “Promiscuous DNA: The Invasion, Spread and Impact of Mobile Genes.”

The professor earned her bachelor’s in biology from Earlham College in Richmond, Ind., her master’s in zoology from the University of Florida in Gainesville and her doctorate in biology from Indiana University.

— Bill Graves

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Wanna Learn Marine Biology? There's an App for That

Killer photos of orcas, stellar images of Stellar sea lions, and full-color images of gray whales can be seen by even the most landlocked of animal lover by downloading the SeaPhoto app onto their smart phones.

The National Oceanic and Atmospheric Administration’s Monterey Bay National Marine Sanctuary released the app, which features more than 1,300 images of animals that call the sanctuary home. From the abalone jingle (a bivalve, Pododesmus cepio) to yellowtail rock fish (Sebastes flavidus), 550 species populate the app along with an ecological profile of the animal.

For those who haven’t joined the smart phone set, the photos are available here.

The right combination of apps can turn a smart phone into a tool of science by putting biological field stations in the palms of millions of curious students, teachers, researchers and maybe even a few orangutans.

ANALYSIS: Apes Get Apps and iPads

Some apps allow anyone to act as the eyes and ears for biologists and wildlife conservationists. For example, amateur game wardens can use the IveGot1 app to report invasive species in Florida.

COOKBOOK SLIDESHOW: Invasive Species Recipes

Another, Instant Wild uses crowd sourcing to identify animals seen in wildlife camera traps. The app sends the photo to users who then help identify the species and report endangered species. Users can even choose the region they want to monitor so they can watch for favorite species, such as elephants in the Tsavo of Kenya. Having an army of volunteer research assistants to sift through camera trap photos could speed up a task that consumes weeks of a researcher’s time.

Apps also exist that help users identify species. Some function like electronic field guides by providing images to compare to what a user finds in the natural world. Others use visual recognition to determine a species using a photo snapped by the phone. LeafSnap, a free app from Columbia University, will try to identify a tree based on a photo of the leaf by analyzing the shape and margins. It then keeps a record of trees it’s identified.

IMAGE:

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Singularity University launches synthetic biology accelerator

The new program will give three initial companies a leg up in getting their startups off the ground. The accelerator will be modeled on those that traditionally work with tech and biotech startups.

Singularity University announced the SuynBio Startup Launchpad accelerator program today.

Synthetic biology startups have a new friend in Silicon Valley.

Today, Singularity University pulled back the wraps on its new SynBio Startup Launchpad, an accelerator program designed to boost the prospects of entrepreneurs in the blossoming field.

As part of the unveiling of the accelerator program, Singularity University announced the first three companies that are “seeking to apply the rapid-cycle, low-cost approaches employed by tech and biotech startups.”

Those companies are Evolutionary Solutions, which is building a genome synthesis device; Modern Meadow, which is using tissue-engineering techniques to generate large amounts of animal protein for textiles and food; and SoilGene, which is blending bioinformatic and metagenomic strategies to “survey land opportunities for the natural resources and agricultural sectors.”

Following the model set by traditional tech and biotech startups is an approach that makes sense for a new accelerator program that will place its participating companies in Newark, Calif., less than 20 miles from the heart of Silicon Valley, where Singularity University is based.

And while Singularity University has for several years been providing talented graduate-school level and executive students with an intensive introduction into exponentially developing technologies, this is the first time the institution has launched an effort to formally support new startups working in those areas.

As part of their participation in the program, the three companies chosen for the accelerator will be based at Triple Ring Technologies, which was selected because of its lab and engineering facilities, as well as its staff’s substantial expertise in the commercialization and innovation in the life sciences. Each of the three companies will spend four months receiving intense personal mentoring and help with bringing their work to market.

The accelerator was the brainchild of Singularity University biotechnology and bioinformatics track chair Andrew Hessel, and NASA Ames Research Center synthetic biologist John Cumbers.

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Thomasians Dominate National Biology Awards

MANILA, Philippines – Thomasian biologists sweep six out of six awards given by the Biology Teachers Association (BIOTA), Philippines during its 47th Annual National Convention and Scientific Sessions held at the Ateneo de Naga University, Naga City last April 12-14, with the theme “The 21st Century Biology: Pedagogy and Scientific Research”.

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Singularity University Announces Inaugural Synthetic Biology Accelerator Program

MOUNTAIN VIEW, Calif., May 17, 2012 (GLOBE NEWSWIRE) — Singularity University today announced the companies selected to participate in its inaugural synthetic biology accelerator program, SynBio Startup Launchpad. The program will nurture aspiring SynBio entrepreneurs seeking to apply the rapid-cycle, low-cost approaches employed by tech and biotech startups. Synthetic biology is genetic engineering using software-based design tools coupled with low-cost DNA synthesis and assembly.

The SynBio Accerlator Program was conceived by Andrew Hessel, Co-Chair of SU’s Biotechnology and Bioinformatics track, and John Cumbers, Ph.D, a synthetic biologist at NASA Ames Research Center. As Andrew Hessel explains, “advances in technology are allowing scientists to treat DNA, our genetic code, the same way people use code for software programming.”

The SynBio Startup Launchpad is Singularity University’s first formal initiative to support startups developing exponentially growing technologies. “The SynBio program brings together a powerful community seeking to support startups developing products from the emerging field of synthetic biology to address some of the world’s biggest challenges,” said Gabriel Baldinucci, Singularity University’s Vice President of Strategy and New Venture Development.

Three (3) companies have been selected for the SynBio Program: Evolutionary Solutions, Modern Meadow and SoilGene. Evolutionary Solutions (founders Kettner Griswold and Paul Sebexen) is developing a genome synthesis device. Modern Meadow (co-founder Andras Forgacs) applies tissue-engineering techniques to produce high volumes of animal protein for food and textiles. SoilGene (founders Zachary Apte and Robert Lim) combines metagenomic and bioinformatic approaches to survey land opportunities for the natural resources and agriculture sectors.

A unique aspect of the SynBio program is its partnership with Triple Ring Technologies in Newark, California. The three selected companies will be based at Triple Ring to take advantage of its engineering and lab facilities, and their staff’s extensive expertise in life sciences innovation and commercialization. “We are excited to work with the SynBio entrepreneurs taking innovations to market in the emerging synthetic biology space,” said Joseph Heanue, Ph.D., president and CEO of Triple Ring Technologies.

The selected entrepreneurs will go through four months of comprehensive, customized mentoring and education in bringing their ideas to market. The companies receive close mentorship from a network of experienced advisors, weekly speakers on critical venture topics, networking with their peers, and valuable discounted services to launch their companies.

The first program will conclude in late August with the SynBio Companies pitching their ventures to investors and the community at “demo day” events.

Sandra Miller, newly appointed SU Managing Director of New Venture Development, will be responsible for the management of the SynBio Launchpad as well as other new Singularity University ventures, working closely with Gabriel Baldinucci, VP of Strategy and New Venture Development.

“Creating, incubating and financing companies to positively affect the lives of a billion people are central elements of SU’s vision. We call this 10^9+ impact,” said Dr. Peter H. Diamandis, SU Chairman and Co-Founder.

About Singularity University

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Resolving the ortholog conjecture

Public release date: 17-May-2012 [ | E-mail | Share ]

Contact: Christophe Dessimoz dessimoz@ebi.ac.uk 44-122-349-4695 Public Library of Science

Researchers at the SIB Swiss Institute of Bioinformatics and the EMBL-European Bioinformatics Institute have confirmed the long-held conjecture that studying the genes we share with other animals is a viable means of extrapolating information about human biology. The study, published in the open access journal PLoS Computational Biology, shows how bioinformatics makes it possible to test the conjecture.

Scientists have long looked to model species mice, for example to understand human biology. This is at the root of what is called the ‘ortholog conjecture’: the idea that studying genes which are separated by a speciation event, but retain the same evolutionary ancestor, is useful.

In genetics, scientists must address these issues in order to pinpoint the best genes to study. For example, it may be better to compare genes in mice and humans that directly descend from a common ancestor (orthologs), than to compare copies of genes with a different function (paralogs).

Consider hemoglobins, for example, which are protein complexes used to carry oxygen across diverse animals. Normal hemoglobin in humans is made up of two subunits alpha globin and beta globin. These proteins are related to each other by a duplication event that happened long ago in animal evolution. If one were interested in the human beta globin, would the best model be to study beta globin in mouse (this is the ortholog of human beta globin) or would it be to study alpha globin in humans (alpha and beta globins are paralogs)?

For the past 40 years, scientists have used orthologs by studying genes in model species, and this has provided invaluable insights in all areas of biology. Until now, there hasn’t been enough data to use orthologs with empirical authority. However, with advances in biotechnology producing vast quantities of data, there is finally enough data to settle the debate.

Using advanced computational techniques on data derived from tens of thousands of scientific articles, the researchers analysed 400,000 pairs of genes (orthologs and paralogs) from 13 different species. The team compared the two approaches and observed only a weak decrease in functional similarity between orthologs.

“We have the data to prove that the study of orthologs is indeed useful, but we are only at the beginning,” says Prof. Marc Robinson-Rechavi of SIB and the University of Lausanne. “This is at the heart of all of comparative genomics, in which we try to extrapolate knowledge from a handful of organisms and apply it to all of life.”

“We found that current experimental annotations do support the standard model,” explains Christophe Dessimoz of EMBL-EBI. “Our work corroborates the assumption that studying the genes of other species whether mice, yeast, or even bacteria can elucidate aspects of human biology.”

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A long-held assumption confirmed: We can learn a lot from other species' genes

Researchers at the SIB Swiss Institute of Bioinformatics and the EMBL-European Bioinformatics Institute have confirmed the long-held belief that studying the genes we share with other animals is useful. The study, published today in the open access journal PLoS Computational Biology, shows how bioinformatics makes it possible to test the fundamental principles on which life science is built.

Studying genes helps life science researchers understand how our bodies work and how diseases progress. Scientists have long looked to model species mice, for example to understand human biology. This is at the root of what is called the ‘ortholog conjecture’: the idea that we can take what we learn from a few species and apply it to many.

The ortholog conjecture

To get an idea of what orthologs are about, consider wolf teeth. If we want to know more about our canine teeth, would we learn more by looking at the canines of wolves? Or would it be better to look at our molars? The answer might not be straightforward. In genetics, scientists address a similar question: Is it better to compare genes in mice and humans that directly descend from a common ancestor (these are called ‘orthologs’) or to compare imperfect copies of genes within a human being (the ‘paralogs’)?

Assume nothing

For the past 40 years, scientists have gone with Plan A: the orthologs, and this has worked quite well. Studying genes in model species has provided invaluable insights in all areas of biology. But until now, there hasn’t been enough data to answer this question with authority. With advances in biotechnology producing vast quantities of data every day, there is finally enough to settle the debate.

Using advanced computational techniques on data derived from tens of thousands of scientific articles, the researchers analysed 400 000 pairs of genes (orthologs and paralogs) from 13 different species. The team compared the two approaches and picked a winner.

“We have the data to prove that the study of orthologs is indeed useful, but we are only at the beginning,” says Prof. Marc Robinson-Rechavi of SIB and the University of Lausanne. “This is at the heart of all of comparative genomics, in which we try to extrapolate knowledge from a handful of organisms and apply it to all of life.”

“We found that current experimental annotations do support the standard model,” explains Christophe Dessimoz of EMBL-EBI. “Our work corroborates the assumption that studying the genes of other species whether mice, yeast, or even bacteria can elucidate aspects of human biology.”

The same question has recently been addressed by Matthew Hahn and colleagues (University of Indiana, USA), whose different conclusion sparked some debate. The new research demonstrates that these controversial results were due to overlooked biases in the collective knowledge of gene function. Controlling for these, the new study unequivocally supports the ortholog conjecture and the fact that studying species we are only distantly related to even worms, flies, yeasts or bacteria is relevant and useful.

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We can learn a lot from other species

Public release date: 17-May-2012 [ | E-mail | Share ]

Contact: Irene Perovsek irene.perovsek@isb-sib.ch 41-078-876-1129 Swiss Institute of Bioinformatics

Researchers at the SIB Swiss Institute of Bioinformatics and the EMBL-European Bioinformatics Institute have confirmed the long-held belief that studying the genes we share with other animals is useful. The study, published today in the open access journal PLoS Computational Biology, shows how bioinformatics makes it possible to test the fundamental principles on which life science is built.

Studying genes helps life science researchers understand how our bodies work and how diseases progress. Scientists have long looked to model species mice, for example to understand human biology. This is at the root of what is called the ‘ortholog conjecture’: the idea that we can take what we learn from a few species and apply it to many.

The ortholog conjecture

To get an idea of what orthologs are about, consider wolf teeth. If we want to know more about our canine teeth, would we learn more by looking at the canines of wolves? Or would it be better to look at our molars? The answer might not be straightforward. In genetics, scientists address a similar question: Is it better to compare genes in mice and humans that directly descend from a common ancestor (these are called ‘orthologs’) or to compare imperfect copies of genes within a human being (the ‘paralogs’)?

Assume nothing

For the past 40 years, scientists have gone with Plan A: the orthologs, and this has worked quite well. Studying genes in model species has provided invaluable insights in all areas of biology. But until now, there hasn’t been enough data to answer this question with authority. With advances in biotechnology producing vast quantities of data every day, there is finally enough to settle the debate.

Using advanced computational techniques on data derived from tens of thousands of scientific articles, the researchers analysed 400 000 pairs of genes (orthologs and paralogs) from 13 different species. The team compared the two approaches and picked a winner.

“We have the data to prove that the study of orthologs is indeed useful, but we are only at the beginning,” says Prof. Marc Robinson-Rechavi of SIB and the University of Lausanne. “This is at the heart of all of comparative genomics, in which we try to extrapolate knowledge from a handful of organisms and apply it to all of life.”

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We can learn a lot from other species

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Bioinformatics: We can learn a lot from other species

ScienceDaily (May 17, 2012) Researchers at the SIB Swiss Institute of Bioinformatics and the EMBL-European Bioinformatics Institute have confirmed the long-held belief that studying the genes we share with other animals is useful. The study, published May 17 in the open access journal PLoS Computational Biology, shows how bioinformatics makes it possible to test the fundamental principles on which life science is built.

Studying genes helps life science researchers understand how our bodies work and how diseases progress. Scientists have long looked to model species — mice, for example — to understand human biology. This is at the root of what is called the ‘ortholog conjecture’: the idea that we can take what we learn from a few species and apply it to many.

The ortholog conjecture

To get an idea of what orthologs are about, consider wolf teeth. If we want to know more about our canine teeth, would we learn more by looking at the canines of wolves? Or would it be better to look at our molars? The answer might not be straightforward. In genetics, scientists address a similar question: Is it better to compare genes in mice and humans that directly descend from a common ancestor (these are called ‘orthologs’) — or to compare imperfect copies of genes within a human being (the ‘paralogs’)?

Assume nothing

For the past 40 years, scientists have gone with Plan A: the orthologs, and this has worked quite well. Studying genes in model species has provided invaluable insights in all areas of biology. But until now, there hasn’t been enough data to answer this question with authority. With advances in biotechnology producing vast quantities of data every day, there is finally enough to settle the debate.

Using advanced computational techniques on data derived from tens of thousands of scientific articles, the researchers analysed 400 000 pairs of genes (orthologs and paralogs) from 13 different species. The team compared the two approaches and picked a winner.

“We have the data to prove that the study of orthologs is indeed useful, but we are only at the beginning,” says Prof. Marc Robinson-Rechavi of SIB and the University of Lausanne. “This is at the heart of all of comparative genomics, in which we try to extrapolate knowledge from a handful of organisms and apply it to all of life.”

“We found that current experimental annotations do support the standard model,” explains Christophe Dessimoz of EMBL-EBI. “Our work corroborates the assumption that studying the genes of other species — whether mice, yeast, or even bacteria — can elucidate aspects of human biology.”

The same question has recently been addressed by Matthew Hahn and colleagues (University of Indiana, USA), whose different conclusion sparked some debate. The new research demonstrates that these controversial results were due to overlooked biases in the collective knowledge of gene function. Controlling for these, the new study unequivocally supports the ortholog conjecture and the fact that studying species we are only distantly related to — even worms, flies, yeasts or bacteria — is relevant and useful.

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Bioinformatics: We can learn a lot from other species

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'Grey's Anatomy' Finale: Bloody Season 8 Sneak Peek (VIDEO)

MONDAY, MAY 14: “Bones”

“Bones” (8 p.m. ET on Fox) season finale
Evil tech genius Christopher Pelant (guest star Andrew Leeds), a suspect in a previous case Brennan and Booth handled, is back in court on appeal. Knowing what he is capable of, Brennan and Booth inform the judge that he is a suspect in two murder cases. Then, Brennan and Booth are called to the scene of a new murder. After determining the victim is Brennan’s friend, who also is linked to Pelant, the Jeffersonian team works to prove he is guilty once and for all. But when law enforcement examines the team’s findings, key pieces of evidence are tied to Brennan and suspicion falls on her.

“Gossip Girl” (8 p.m. ET on The CW) season finale
When Gossip Girl goes after Blair as she’s never done before, Serena admits she may have unintentionally played an important role in Blair’s latest nightmare. Meanwhile, Nate invites Lola to move in with him, and Lily must make a big decision about the future of her marriage. Finally, by episode’s end, Blair will make a choice between the two men in her life … will it be Chuck or will it be Dan? Followed by the finale of the also-renewed “Hart of Dixie.”

“How I Met Your Mother” (8 p.m. ET on CBS) one-hour season finale
On Barney’s future wedding day, when his wife is finally revealed, the gang reminisces about the time they encouraged Ted to follow his heart and go after the one that got away. Followed by the season finales of “Two and a Half Men” and “Hawaii Five-0.”

“Make It or Break It” (9 p.m. ET on ABC Family) series finale
Eight weeks at the USA Training Center have led to this moment: who will make it onto the 2012 Olympic Gymnastics team and who will be left behind in the show’s final episode. Payson decides to rework her floor routine at the risk of losing a spot on the team. Kaylie is at a loss when Jordan refuses her help. Still recovering from surgery, Lauren balances her health with her need to make it to the Olympics. Meanwhile, Kaylie is thrown for a loop when she is told that her drug test came back positive for a banned substance.

“The Bachelorette” (9.30 p.m. ET on ABC) season premiere
Fan-favorite Emily Maynard — the first single mother in “Bachelorette” history — begins her own search for love in Charlotte, NC in the eighth edition of the romance reality series. Season highlights include trips to Bermuda, London, Dubrovnik and Prague, and appearances from Dolly Parton, Gloriana, Luke Bryant and The Muppets.

“Kurt Sutter’s Outlaw Empires” (10 p.m. ET on Discovery) series premiere
“Sons of Anarchy” creator Kurt Sutter enters the realm of the gangs and families who have dominated our streets and helped shape our nation’s history. Steered by Sutter’s compelling insight, each episode tells the complete story of an iconic American outlaw dynasty — directly from the mouths of people from the inside. Through their no-holds-barred accounts, the series takes an unvarnished look at moment-by-moment experiences that were not only pivotal for the organizations themselves, but life-changing for the individuals telling the stories.

“Smash” (10 p.m. ET on NBC) season finale
The big night is finally here. Tom and Julia race against time to save the show, while Derek makes a decision that will change the lives of Karen and Ivy forever. Ellis reveals his true colors (hmm) — but when he finally makes his move to save “Bombshell,” will it be for or against Eileen? In the midst of it all, another bombshell goes off — this time in Karen and Dev’s relationship.

“Glee” (8 p.m. ET on Fox) double-bill
As the countdown to graduation continues, the kids of New Directions prepare a high-concept routine for Nationals. When Tina bumps her head, the world of New Directions is turned upside down in her eyes. Then, the New Directions perform at Nationals for celebrity judge Lindsay Lohan (guest-starring as herself). Worth watching for the Lohan trainwreck factor alone, no?

“Cougar Town” (8 p.m. ET on ABC) double-bill
Now that the underappreciated (and still genius) comedy has officially made the move to TBS, ABC seems to be in burn-off mode with two weeks of hour-long blocks — but we’re just happy that it’ll be around for another year. In the first episode, Grayson moves in with Jules after the hurricane damages his house, but the sudden togetherness makes them wonder if they’re going to make the same mistakes in their upcoming marriage that they made in their past relationships. In the second, when Jules realizes that the cul-de-sac crew didn’t celebrate Thanksgiving together, she decides to celebrate the holiday, even though it’s spring. The “Private Practice” season finale airs at 10 p.m. ET.

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'Grey's Anatomy' Finale: Bloody Season 8 Sneak Peek (VIDEO)

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'Grey's Anatomy' Recap: Who Met Their Maker in the Deadly Season Finale?

ABC/BOB D’AMICO

“Grey’s Anatomy”

[WARNING: This post contains massive spoilers from Thursday's Season 8 finale of Grey's Anatomy.]

One of Seattle Grace’s best and brightest succumbed to injuries sustained in last week’s shocking plane crash during Thursday’s emotional Season 8 finale of Grey’s Anatomy.

After departing the hospital for Boise to help with complicated surgery involving conjoined twins, Meredith, Derek, Cristina, Arizona, Mark and Lexie each sustained injuries and were in various stages of distress.

STORY: ‘Grey’s Anatomy’ Recap: Whose Lives are Hanging in the Balance?

LEXIE Left pinned down under part of the plane with her legs and pelvis crushed, ultimately it was Little Grey, Lexie (Chyler Leigh), whose injuries were the most severe. Despite Mark (Eric Dane) and Cristina’s (Sandra Oh) best attempts, Lexie ultimately couldn’t be saved. In one of the ABC medical drama’s most emotional scenes in its eight seasons, Lexie tells Mark to relay a message to Meredith: She was a good sister and loved. With Cristina frantically looking for Meredith — who is busy searching for Derek after he was sucked out of the plane — Mark realizes that there’s nothing he can do for Lexie and, in a bittersweet scene as she slips away, he sends her off by telling her that they’ll get married and she’ll have a bright future as a surgeon.

Meredith, meanwhile, is too late to say goodbye and arrives just after Lexie passes away. As the trio start to search for Derek again, Meredith (Ellen Pompeo) she continues to battle her emotions at the thought that she could lose both her sister and husband as Cristina reveals that she’s leaving Seattle if she survives the harrowing ordeal.

STORY: ‘Grey’s Anatomy’s’ Shonda Rhimes on the Deadline Finale: ‘We’re Literally Saying Goodbye to People’

MARK & ARIZONA In shock after Lexie’s death, Mark — who has a huge gash on his chest — passes out and needs heart surgery as Meredith and Cristina saves his live by draining the blood pooling in his heart. With bone exposed in her leg, Arizona is left in shock from the crash and despite her massive injuries, does her best to help keep Mark alive despite coughing up blood. Realizing that he’s slipping away, Mark tells Arizona to take care of “our girl” and realizes that Lexie is waiting for him, as he knows that he’ll be OK. Unwilling to accept it, Arizona tells Mark that Callie and Sophia are waiting for him, too, and she needs him to hold on so they can go home — together. As Mark continues to cling for life, he notes that he should have professed his love for Lexie well before the crash.

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'Grey's Anatomy' Recap: Who Met Their Maker in the Deadly Season Finale?

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