Biology professor gets grant to catalogue Indonesian species

Assistant Biology Professor Eric Smith received a $725,000 grant from the National Science foundation to catalogue new species in Indonesia, according to a press release Thursday..

Smith begins work later this year as the lead investigator with a team of researchers, which will include UTA students. The grant funds the project for three years.

Alumnus Michael Harvey, now a Broward College associate professor, will join Smith as co-principal investigator.

Harvey and Smith traveled to Indonesia in 1996 while attending UTA to study amphibians and reptiles. The two published scientific papers about the new species they discovered.

We calculated we were getting a new species of reptile or amphibian every four hours, Smith said in the release. So thats how much work the area needed. Its a huge place and it will take a long time to explore what is there.

Some of whatever the research team finds in the upcoming trip will come to UTA for further study.

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Biology professor gets grant to catalogue Indonesian species

PerkinElmer's 'Ensemble for Biology' Suite Arises from 2011 Informatics Acquisitions

Knome has added some new faces to its executive team, naming Jay Therrien as senior VP and head of global sales, Charles Abdalian as chief financial officer, and Adam Rosenberg as senior VP and head of corporate development.

Therrien was VP of commercial operations and sequencing at Life Technologies, and also had spent five years in various sales leadership roles at Illumina. Abdalian recently was senior VP and CFO of Molecular Insight Pharmaceuticals, and he was senior VP of finance and CFO at Coley Pharmaceutical. Rosenberg previously was an adviser for emerging life sciences companies, co-founder of Clean Membranes, and CEO of Link Medicine.

The company also has appointed Hugh Reinhoff to serve on its scientific advisory board. Reinhoff is currently a managing director of Life Science Venture Partners, an adjunct scientist at the Children's Hospital Oakland Research Institute, and CEO of FerroKin BioSciences.

Pacific Biosciences said this week that Hugh Martin has resigned from its board of directors for personal reasons, effective immediately. Martin was previously the firm's president and CEO but resigned at the beginning of this year and was replaced by Michael Hunkapiller. He had led the company since 2004 and has been battling multiple myeloma, with which he was diagnosed in 2009.

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PerkinElmer's 'Ensemble for Biology' Suite Arises from 2011 Informatics Acquisitions

Synthetic Genetic Evolution

Scientists show that manmade nucleic acids can replicate and evolve, ushering in a new era in synthetic biology.

Synthetic genetic polymers, broadly referred to as XNAs, can replicate and evolve just like their naturally occurring counterparts, DNA and RNA, according to a new study published today (April 19) in Science. The results of the research have implications not only for the fields of biotechnology and drug design, but also for research into the origins of lifeon this planet and beyond.

Its a breakthrough, said Gerald Joyce of The Scripps Research Institute in La Jolla, California, who was not involved in the studya beautiful paper in the realm of synthetic biology.

It shows that you dont have to stick with the ribose and deoxyribose backbones of RNA and DNA in order to have transmittable, heritable, and evolvable information, added Eric Kool of Stanford University, California, who also did not participate in the research.

Over the years, scientists have created a range of XNAs, in which the ribose or deoxyribose portions of RNA and DNA are replaced with alternative molecules. For example, threose is used to make TNA, and anhydrohexitol is used to make HNA. These polymers, which do not exist naturally, are generally studied with various biotechnological and therapeutic aims in mind. But some researchers, like Philipp Holliger of the MRC Laboratory of Molecular Biology in Cambridge, UK, think XNAs might also provide insights into the origins of life. They might help to answer questions such as, why is life based on DNA and RNA, and, if we ever find life beyond earth, is it likely to be based on the same molecule or could there be other possibilities? Holliger said.

To get at some of these questions, Holliger and his colleagues had to first create enzymes that could replicate XNAs, a necessary first step to evolution. They did this both by randomly mutating and screening existing DNA polymerases for their ability to read XNA, and by an iterative process of selecting polymerase variants with capacities for XNA synthesis. In the end, they had several polymerases that could synthesize six different types of XNA.

To see whether XNAs could evolve, they generated random HNA sequences, then selected for those that could bind to two target molecules. After selection, the HNAs were amplified by the newly designed polymerases and again selected for their ability to bind the targets. Eight rounds of selection later, the HNA sequences were no longer random, as those with a particular target-binding motif became more abundant. Through selection and replication, the HNAs had evolved.

The finding in itself is not surprising, said Kool. Chemists have been working for 20 years to find new backbones for DNA and the feeling always was that it would be interesting and quite possible that some of them might be replicated one day. It was, nevertheless, impressive, he added. The hard part was finding the enzymes that could do it. So the big leap ahead for this paper was finding those enzymes.

The new polymerases synthesized XNA through rounds of DNA-to-XNA and XNA-to-DNA synthesis. Generating polymerases that can make XNA direct from XNA will be the next step, Holliger said, but it will be a lot harder because both strands would be foreign to the polymerase.

Holliger also explained that there was actually a benefit to having a DNA intermediate. It allowed us to access the whole gamut of technologies that are available for analyzing DNA sequences. Working with XNAs uniquely, he said, is like being thrown back to the way molecular biology was in the early 1970s, in that we have to develop all our tools afresh.

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Synthetic Genetic Evolution

Boundary between electronics and biology is blurring: First proof of ferroelectricity in simplest amino acid

ScienceDaily (Apr. 19, 2012) The boundary between electronics and biology is blurring with the first detection by researchers at Department of Energy's Oak Ridge National Laboratory of ferroelectric properties in an amino acid called glycine.

A multi-institutional research team led by Andrei Kholkin of the University of Aveiro, Portugal, used a combination of experiments and modeling to identify and explain the presence of ferroelectricity, a property where materials switch their polarization when an electric field is applied, in the simplest known amino acid -- glycine.

"The discovery of ferroelectricity opens new pathways to novel classes of bioelectronic logic and memory devices, where polarization switching is used to record and retrieve information in the form of ferroelectric domains," said coauthor and senior scientist at ORNL's Center for Nanophase Materials Sciences (CNMS) Sergei Kalinin.

Although certain biological molecules like glycine are known to be piezoelectric, a phenomenon in which materials respond to pressure by producing electricity, ferroelectricity is relatively rare in the realm of biology. Thus, scientists are still unclear about the potential applications of ferroelectric biomaterials.

"This research helps paves the way toward building memory devices made of molecules that already exist in our bodies," Kholkin said.

For example, making use of the ability to switch polarization through tiny electric fields may help build nanorobots that can swim through human blood. Kalinin cautions that such nanotechnology is still a long way in the future.

"Clearly there is a very long road from studying electromechanical coupling on the molecular level to making a nanomotor that can flow through blood," Kalinin said. "But unless you have a way to make this motor and study it, there will be no second and third steps. Our method can offer an option for quantitative and reproducible study of this electromechanical conversion."

The study, published in Advanced Functional Materials, builds on previous research at ORNL's CNMS, where Kalinin and others are developing new tools such as the piezoresponse force microscopy used in the experimental study of glycine.

"It turns out that piezoresponse force microsopy is perfectly suited to observe the fine details in biological systems at the nanoscale," Kalinin said. "With this type of microscopy, you gain the capability to study electromechanical motion on the level of a single molecule or small number of molecular assemblies. This scale is exactly where interesting things can happen."

Kholkin's lab grew the crystalline samples of glycine that were studied by his team and by the ORNL microscopy group. In addition to the experimental measurements, the team's theorists verified the ferroelectricity with molecular dynamics simulations that explained the mechanisms behind the observed behavior.

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Boundary between electronics and biology is blurring: First proof of ferroelectricity in simplest amino acid

GenScript Rush Gene Synthesis – Driving Molecular Biology Research Faster

PISCATAWAY, N.J., April 19, 2012 /PRNewswire-Asia/ -- GenScript USA Inc., an internationally recognized biology contract research organization (CRO) has recently launched Rush Gene Synthesis service in the global market on Dec. 22, 2011, and has achieved 100% success and on time delivery rates ever since its kick-off.

"Two decades ago, a 2 Kb gene took me nearly two years to obtain the construct using conventional PCR cloning technologies in my PhD research. I did believe this could be changed. Nowadays, GenScript Rush Gene Synthesis service delivers synthetic genes in as little as 5 business days. The proprietary technology and a dedicated Rush Gene service team are the key points to making GenScript Rush Gene Synthesis service a big success," commented Frank Zhang, the CEO and co-founder of GenScript.

"Delivering synthetic genes in as little as 5 days, GenScript Rush Gene Synthesis service is not only fast but is accurate and worry-free to our customers," says Frank, "all our synthesized genes are packed into cloning vectors, picked from single clones and fully sequence-verified before the delivery. Therefore, none of our customers is bothered with picking up the right gene from the tube. With this rush service, we aim to drive molecular biology research faster than ever."

Besides the world-leading gene synthesis service, GenScript, as a contract research organization (CRO), also provides comprehensive services for biological research and early-phase drug discovery, such as bio-reagents, assay development & screening, lead optimization, antibody drug development and animal model services. The bio-reagents services include custom gene synthesis and molecular biology, custom protein expression and purification, custom peptide synthesis, antibody production, and custom cell line development. Headquartered in Piscataway, New Jersey, GenScript has three subsidiaries located in France, Japan, and China.

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GenScript Rush Gene Synthesis - Driving Molecular Biology Research Faster

Science, Social Media, #SciComm and Sunny San Diego

Your Hip Hop Maven of Science is bustin a move this weekend and headed to San Diego, California. I received an invite to attend the 2012 Experimental Biology Conference. Experimental Biology is one of the largest life sciences professional conferences 14,000 attendees. Its a convocation of several scientific societies under the Federation of American Societies for Experimental Biology (FASEB). I am honored to be speaking at a Science Communication Symposium sponsored by the American Physiological Society (APS), and sharing the dais with the most amazing superstars in online science outreach, EVAH!

I am beyond excited about this. Plus, it gives me a very new arena to network with others FASEB Biologists. Im a biologist and do experiments, but for whatever reason, my science societies arent members of the Experimental Biology sect. FASEB membership includes science societies that focus on applied biology in the health biomedical related research arenas. All of my science societies are part of the American Institute of Biological Sciences (AIBS) yeah, I know the names certainly dont help clear things up. But AIBS societies are more of the basic biology societies covering alot of the taxonomy, natural history, agriculture, and natural resources fields. I can see how they are different. However, in the last year, Ive become acquainted with FASEB and some of its member organizations. And I have to say this much, FASEB offers an incredible amount of support (financial and otherwise) to students and junior professionals. FASEB has an undeniable committement to diversity and inclusion in STEM and higher education. FASEB sponsors a number of minority access programs such as the Minority Access to Research Careers (MARC) and has a very strong presence at the SACNAS and ABRCMS annual meetings. Thanks to Alberto Roca of Minority Postdoc.org for introducing me to these amazing organizations and facilitating my attendance to each.

In fact, Ill be presenting a version of this talk at APS: Blogging, Tweeting, & Writing: How an Online Presence can Impact Science and Your Career. But since the goal of the panel is provide wisdom to thec rowd, I expect it be very interactive. And I know my co-panelists, itll sure to be as much fun as it is informative. In fact, theyve each made announcements. Jason Goldman Science and Social Media at Experimental Biology in San Diego Dr. Isis Sessions of Interest at#EB2012 PH Lane Packing for #EB2012 (which reminds me to pack some nice clothes for this trip).

Some folks have asked about live streaming. Im not sure about that, but you can follow the hashtag #apsComm and us on twitter @DNLee5, @DrIsis, @PHLane, @JGold85. Were speaking at 3 pm PST.

Some other #SciComm friends will be at #EB2012 the official hashtag of the meeting such as @SciCurious whose an official blogger for the American Society for Pharmacology and Experimental Therapeutics,@hapsci, official meeting blogger for ASBMB, and @Comprendia who is co-hosting an event with ASBMB at the meeting. Cant wait to see all of these great people and many more.

Also check out: Experimental Biology @ExpBio and American Physiology Society Executive Director @ExecDirectorAPS

Although, there wont be many talks or posters in my specific field, I am a science nerd in general. I love learning new things. So I have no doubt Ill be engaged, plus Im a complete nut for Exhibit Hall Swag. However, I am looking forward to any presentations on physiology ad behavior and Ive got my eye out for anyone who does ANY kind of bio-behavior work with rodents. Ive got some experimental design work to do and I think I can get some new insight from researchers who see things a little differently than I do. So all in all, Im looking forward to the entire thing: the presenting, the presentations, the networking, the professional development (and the partying). Ha!

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Science, Social Media, #SciComm and Sunny San Diego

Could a newly discovered viral genome change what we thought we knew about virus evolution?

Public release date: 18-Apr-2012 [ | E-mail | Share ]

Contact: Dr. Hilary Glover hilary.glover@biomedcentral.com 44-203-192-2370 BioMed Central

A study published in BioMed Central's Biology Direct journal reports the existence of a previously undetected group of viruses and, more importantly, a new type of viral genome that could have huge implications for theories of viral emergence and evolution.

Viruses are the most abundant organisms on earth, yet little is known about their evolutionary history since they have exceptionally high rates of genetic mutation which are difficult to track. Viral metagenomics, however, is becoming an increasingly useful tool with which to glimpse virus evolution, as it makes available vast amounts of new sequence data for analysis.

Kenneth M Stedman's team from Portland State University in Oregon, USA, used a metagenomics approach to investigate virus diversity in Boiling Springs Lake in Lassen Volcanic National Park, USA, an acidic, high temperature lake (ranging from 52-95C, with a pH of ~2.5) that sustains a purely microbial ecosystem.

Astonishingly, they found a unique viral genome that has never before been reported - a circular, single-stranded DNA virus encoding a major capsid protein seen previously only in RNA viruses. This unusual genome provides proof that integration of an RNA virus into a DNA virus may have occurred between two unrelated virus groups at some point in evolution - something that has not been observed before. Moreover, this suggests that entirely new virus types may emerge via recombination of functional and structural modules between vastly different viruses, using mechanisms that are as-yet unknown.

The team observed that the Boiling Springs Lake RNA-DNA hybrid virus (BSL RDHV) genome is circular, but its size is roughly double that of typical circoviruses, with the ORFs arranged in an uncommon orientation. They compared the BSL RDHV genome to other metagenomic DNA sequences from the Global Ocean Survey, and found strong evidence to conclude that previously undetected BSL RDHV-like viruses could be widespread in the marine environment and are likely to be found in other environments as well.

No mechanism has been proposed to account for the inferred instances of interviral RNA-DNA recombination, but the team speculate that a DNA circovirus-like progenitor may have acquired a capsid protein gene from a ssRNA virus via reverse transcription and recombination.

Lead author Kenneth M Stedman said, "As more viral metagenomic data are generated and analyzed, additional evidence of recombination between RNA and DNA virus groups will likely be discovered. The discovery that novel virus groups can emerge via recombination between highly disparate virus types will have broad implications for the early evolution of viruses and extends the modular theory of virus evolution to encompass a much broader range of possibilities than previously thought."

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Could a newly discovered viral genome change what we thought we knew about virus evolution?

Experimental Biology 2012: Conference Blogging Basics

Sci is flying out tomorrow to take part in (and blog about) the Experimental Biology meeting in San Diego. I will be blogging on behalf of the American Society for Pharmacology and Experimental Therapeutics, so itll be all things pharmacology from here on out! Make sure to check out the blog and follow along on Twitter! See you in San Diego!

But perhaps I have emailed you, and asked to blog your poster, and perhaps you are considering emailing me about your latest and greatest workand you pause. What IS this conference blogging, exactly? What is it for?

Well, look no further. Because this post (a re-post from my previous blogging of the Society for Neuroscience Meeting) is all about explaining what Im planning for the conference, how Im going to go about it, and what you can look forward to as a scientist when I blog your poster or talk. And because the more you know, the better prepared we will all be!

(source)

I covered much of this information in a guest post over at the Science of Blogging, where I talked about tips for blogging a conference. But that post is from a bloggers point of view, whereas this one will be from the perspective of you, the scientist.

So this is how it goes:

1. Over the next few days, I will either contact you, or you can contact me (scicurious at gmail) with your poster/presentation details. I will set up a time to come by your poster, and possibly also to meet with you for 30 minutes before or after your presentation.

2. If we meet up, I would like to hear from you about your work in detail. I will be reading the abstract that you submitted ahead of time, but If you could bring a copy of your poster or presentation (or send it ahead of time!) that would be wonderful! I will NOT use any of the graphs, tables, or images that you send in any post I may write up. What I will do is use your poster to give my my writing context and help me to remember and understand what weve talked about and the significance of your findings.

2a. If you are a student presenter (or heck, a postdoc!), you may want to bring your advisor along while we talk, if you are worried. Additionally, if your advisor requires credentials, let me know and I will provide them.

3. Once Im done grilling you (gently!) about your work, Ill head back, and start writing! I will try to get the post done before the next day.

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Experimental Biology 2012: Conference Blogging Basics

New discovery may lead to effective prevention and treatment of graft-versus-host dsease

Public release date: 1-Apr-2012 [ | E-mail | Share ]

Contact: Cody Mooneyhan cmooneyhan@faseb.org 301-634-7104 Federation of American Societies for Experimental Biology

Bethesda, MD -- A new discovery in mice may lead to new treatments that could make bone marrow transplants more likely to succeed and to be significantly less dangerous. According to new research findings published in the Journal of Leukocyte Biology (https://www.jleukbio.org) Brazilian scientists may have found a way to prevent the immune system from attacking transplant grafts and damaging the host's own cells after a bone marrow transplant.

Specifically, they found that a receptor for a mediator of the inflammatory process, known as platelet activating factor plays a crucial role in the development of graft-versus-host disease. Platelet activating factor receptor appears to contribute to the attraction of immune cells that lead to graft-versus-host disease. When this mechanism was blocked, there was reduced tissue damage and mortality.

"Platelet activating factor receptor antagonists may decrease suffering caused by graft-versus-host disease in patients undergoing bone marrow transplant," said Vanessa Pinho, Ph.D., a researcher involved in the work from the Departamento de Morfologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais in Brazil. "As graft-versus-host disease also may decrease quality of life, patients treated with platelet activating factor receptor antagonists may live longer and with better quality of life."

To make this discovery, scientists induced graft-versus-host disease by transferring cells between mice which were genetically incompatible. In mice subjected to graft-versus-host disease, there was significant injury to target organs, especially the liver and the intestine. In mice that received cells from genetically modified mice bred to not have platelet activating factor receptors, or in mice treated with platelet activating factor receptor antagonist, there was reduced tissue injury and reduced lethality.

"Immune rejection is one of the biggest risks of any transplant procedure, and this study sheds a new light on a receptor and pathway amenable to therapeutic intervention to reduce the serious complication of graft-versus-host disease," said John Wherry, Ph.D., Deputy Editor of the Journal of Leukocyte Biology. "The next step is to take these observations from the lab and see if the potential suggested by studies in mice hold true in humans with disease."

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The Journal of Leukocyte Biology (http://www.jleukbio.org) publishes peer-reviewed manuscripts on original investigations focusing on the cellular and molecular biology of leukocytes and on the origins, the developmental biology, biochemistry and functions of granulocytes, lymphocytes, mononuclear phagocytes and other cells involved in host defense and inflammation. The Journal of Leukocyte Biology is published by the Society for Leukocyte Biology.

Details: Marina G. M. Castor, Brbara M. Rezende, Carolina B. Resende, Priscila T. T. Bernardes, Daniel isalpino, Anglica T. Vieira, Danielle G. Souza, Tarclia A. Silva, Mauro M. Teixeira, and Vanessa Pinho. Platelet-activating factor receptor plays a role in the pathogenesis of graft-versus-host disease by regulating leukocyte recruitment, tissue injury, and lethality. J Leukoc Biol. April 2012 91: 629-639; doi:10.1189/jlb.1111561 ; http://www.jleukbio.org/content/91/4/629.abstract

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New discovery may lead to effective prevention and treatment of graft-versus-host dsease

Foods in the Year 2000

A lot of proposed synthetic biology applications can seem pretty out there, but some are really out there. NASA is currently advertising open postdoctoral positions in synthetic biology, with particular emphasis on food production in space. Engineered organisms have the potential to do lots of things that would be useful for space colonists, from producing food and fuel to treating wastewater. Because organisms replicate themselves, future astronauts would only have to bring some spores and seeds and empty bioreactors, the organisms would do the rest of the work.

Matt Mansell--Synthetic Biology in Space

I am fascinated by these proposals, and other proposals large and small for how biological engineering might someday impact the way that we produce, process, and prepare our food. The way we eat and the way we imagine the food of the future is really complicated, and has a long and interesting history tied not only to our culinary cultures and the science of nutrition, but often to the hot new science and technology of the day.

In the 1890s, that technology was synthetic chemistry, making it possible to generate organic chemicals from inorganic starting materials. New industries were springing up that replaced old agricultural methods with chemical ones, in particular the production of synthetic dyes and flavors. This led some chemists to speculate on how this technology would be used a hundred years in the future, extrapolating the current industrial transformations into nearly every organic arena. This speculative application of synthetic chemistry to food production is detailed in an 1894 article in McClures Magazine by Henry J.W. Dam titled Foods in the Year 2000: Professor Berthelots Theory that Chemistry Will Displace Agriculture. By 2000, Marcellin Berthelot, considered to be one of the greatest chemists of all time, believed that we would no longer have agriculture, that instead:

The epicure of the future is to dine upon artificial meat, artificial flour, and artificial vegetablesWheat fields and corn fields are to disappear from the face of the earth, because flour and meal will no longer be grown, but madeCoal will no longer be dug, except perhaps with the object of transforming it into bread or meat. The engines of the great food factories will be driven, not by artificial combustion, but by the underlying heat of the globe.

What would this food synthesized from coal with geothermal power look like? What would it taste like?

We shall give you the same identical food, however, chemically, digestively, and nutritively speaking. Its form will differ, because it will probably be a tablet. But it will be a tablet of any color and shape that is desired, and will, I think, entirely satisfy the epicurean senses of the future.

Food pills are a common theme in science fiction, especially for space travel where astronauts have to travel light, and its interesting to see how that has transformed, with NASA now thinking beyond synthetic chemistry to synthetic biology. But its the scientific language of Professor Berthelot thats particularly interesting to me:

In order to clearly conceive these impending changes, it must be remembered that milk, eggs, flour, meat, and indeed, all edibles, consist almost entirely (the percentage of other elements is very small) of carbon, hydrogen, oxygen, and nitrogenThese four elements, universally existing, are destined to furnish all the food now grown by nature, through the rapid and steady advance of synthetic chemistry.

Synthetic chemistry is the special science which takes the elements of a given compound, and induces them to combine and form that compound. It is the reverse of analytic chemistry, which takes a given compound, and dissociates and isolates its elements. Analytic chemistry would separate water into oxygen and hydrogen, and synthetic chemistry would take oxygen and hydrogen, mix them, put a match to the mixture, and thus form water. For many years past synthetic chemistry has had an eager eye upon food-making.

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Foods in the Year 2000

Biology professor wins national award for contributions to citizen science

MEDIA CONTACT: Hilary Dickinson at dickinsonh@beloit.edu or 608-363-2849

Marion Field Fass named 2012 winner by the National Center for Science and Civic Engagement

Marion Field Fass, biology professor and co-chair of Beloits health and society interdisciplinary program, has won the 2012 William E. Bennett Award for Extraordinary Contributions to Citizen Science. The announcement was made on Wednesday by the Science Education for New Civic Engagements and Responsibilities.

Dr. Fass has been a distinguished, long-time, unflagging, unfailing, and imaginative contributor to the precursor health and higher education and HIV/AIDS education work that led to the creation of Science Education for New Civic Engagements and Responsibilities (SENCER), wrote David Burns, the executive director of the National Center for Science and Civic Engagement, in a letter to Beloit College President Scott Bierman.

First presented in 2009, the William E. Bennett Award for Extraordinary Contributions to Citizen Science was established by NCSCE and named in honor of its first recipient for his lifetime contributions to citizen science. The award is given annually to an individual and/or a team whose SENCER and other related activities have made exemplary and extraordinary contributions to citizen science.

I'm really honored to be receiving the Bennett Award for Contributions to Citizen Science, Fass said. It is really an honor for the institution that has nurtured and supported SENCER approaches across the curriculum. Science at Beloit College is exceptional in that we encourage students to focus on real world problems as they learn the basic concepts and methods of these disciplines. The SENCER approach complements the work of the BioQUEST Curriculum Consortium and the CHEMLinks project, which both originated at Beloit College, that have really pushed the boundaries of science pedagogy.

Fass will be honored at the annual SENCER Summer Institute in San Jose, Calif., in August when she will share her thoughts on her work and this award. She was nominated for the award by her colleagues in the department of biology and the health and society program.

Marion has demonstrated unwavering dedication to the creation and communication of interdisciplinary opportunities that guide students and faculty to a better understanding of the intersection and overlap between science and civic issues, wrote Fasss colleagues in their nomination letter.

Fass has taught biology at Beloit College since 1991 and served as chair of the department from 2009-2011. Among her many affiliations, she is currently a faculty member at the SENCER Summer Institute, a SENCER leadership fellow, a member of the American Public Health Association, and an executive board member of the Wisconsin Health Education Network. Fass earned a B.A. from the University of Pennsylvania and a doctorate from Johns Hopkins University. For more information on Fass, see her biography here.

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Biology professor wins national award for contributions to citizen science

Pine Manor College Awarded $600,000 National Science Foundation Grant to Support Women Studying Biology

BOSTON, MA--(Marketwire -03/29/12)- Pine Manor College announced today it is the recipient of a $600,000 grant from the National Science Foundation. The grant will provide 20 Pine Manor biology students with targeted educational support, research opportunities and financial aid, enabling them to continue their studies and enter the workforce or pursue graduate degrees.

"We're proud of this partnership with the National Science Foundation and its decision to invest in Pine Manor's students," said Dr. Alane Shanks, president of Pine Manor College. "This grant is really a tribute to the outstanding work of our students and faculty."

In 2008, the National Science Foundation awarded Pine Manor a grant of more than $570,000 to help educate the first 20 BioScholars. Building on this success, with the 2012 grant, Pine Manor will select 20 new students during the next two years.

"We believe this program makes a real difference in the lives of these students and allows women to pursue careers in science after receiving the excellent education Pine Manor offers," President Shanks said. "Each year, a number of promising biology students lack the resources to stay in school and graduate. Our experience with this program has taught us that access plays a crucial role in helping students continue to graduation and beyond."

Each participant will receive a scholarship up to a maximum of $10,000 annually. This scholarship support will continue for the BioScholars through to graduation.

The students will also be enrolled in an Honors Colloquium in Biology, a senior research internship, and workshops to help them obtain graduate school admission and/or life sciences employment. Biology and math tutors will also work with the BioScholars.

Pine Manor College, one of the most diverse liberal arts colleges in the nation, is celebrating its centennial this year.

About Pine Manor CollegePine Manor College is a private, affordable four-year liberal arts college dedicated to preparing women for roles of inclusive leadership and social responsibility in their workplaces, families and communities. The College consistently ranks among the most diverse B.A. liberal arts colleges in the nation, according to US News & World Report's America's Best Colleges. Pine Manor College is located in Chestnut Hill, Mass., five miles from Boston. http://www.pmc.edu.

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Pine Manor College Awarded $600,000 National Science Foundation Grant to Support Women Studying Biology

Critics raise safety concerns with biotech labs at Berkeley forum

No one disputes that the Lawrence Berkeley National Laboratory campus that's coming to Richmond will generate jobs and tax revenues.

But concerns persist about the work that will be done there, especially in synthetic biology, and the risks posed to the surrounding community.

That was among the topics at a news conference and public forum in Berkeley on Wednesday, touted as the first gathering in the area of local, national and international speakers to address concerns about synthetic biology, an emerging science that implants genetic material into cells to produce fuels and other industrial products.

Titled "Bay Area Biotech Labs Bring Unforeseen Risks," the panel presentation at the Center for Genetics and Society featured five prominent critics of synthetic biology.

The national lab, which selected Richmond for its next site thanks in part to broad support among Richmond city leaders, is not all that it appears, said panelist Gopal Dayaneni, co-director of the Movement Generation Justice and Ecology Project.

"What we're experiencing (with LBNL) is a wolf in sheep's clothing," Dayaneni said. "Actually, a wolf genetically engineered to look like a sheep."

Dayaneni, like the other panelists, said the lab enjoys the "shiny veneer" of legitimacy lent by UC Berkeley but is actually a secretive, poorly regulated merger of public and private interests that will be operating on the scientific fringes with potentially

"(Synthetic biology) is genetic engineering on steroids," said Jim Thomas of the ETC Group, a watchdog organization that monitors emerging technologies. "It's a $1.6 billion industry, and the Bay Area is absolutely the heart of that. ... A key institution is the new Richmond lab."

Panelists called for safeguards to bar "human applications" of synthetic biology, a more robust regulatory structure and better protections for workers.

Becky McLain, a molecular biologist who won a 2010 lawsuit against her former employer, pharmaceutical giant Pfizer, said the safety risks that may face workers in Richmond will be even more volatile than those she encountered in an embryonic stem cell lab. A federal jury awarded McLain $1.37 million in damages after she was exposed to a genetically engineered virus that caused her recurring paralysis and other illnesses.

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Critics raise safety concerns with biotech labs at Berkeley forum

Biology students contribute to science community, preterm birth research

Three biology students held a symposium to present their research on causes of preterm birth, the mechanism itself and treatment options earlier this month.

Bao-Tran Nguyen, John Schwabe and Siobhan Donnelly presented their theses and will graduate and pass on their part of the research this May.

"We're going to have students working on this for years," Schwabe said. "It's great to be a part of research with this magnitude and breadth, especially as an undergraduate."

A total of ten students are currently working on the project with Chishimba Mowa, an associate professor in the department of biology.

Nguyen said Mowa's lab is one of the few looking specifically at cervical remodeling to understand why preterm births occur.

"Sometimes it's frustrating because there's not a lot of previous studies, so we have to forage our own way and invent the wheel," Nguyen said.

This type of research is important because preterm birth is the leading cause of newborn death, Nguyen said.

Nguyen, Schwabe and Donnelly plan to publish their findings, Schwabe said.

"We're going to be the first people to publish this kind of study on this tissue," Schwabe said. "We've identified proteins previously unstudied in the cervix that may play a pivotal role in controlling natural birth."

Other students working on this research project are looking into herbs like Echinacea as a treatment option for preterm birth, Donnelly said.

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Biology students contribute to science community, preterm birth research

Synthetic Biology Survey Requires Industry Response

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

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

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

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

Professor, Student Grow as Biomedical Researchers

Dr. Kristy McClellan, Caitlin Hof and the University of Iowa's Dr. Pamela Geyer.

Dr. Kristy McClellan, assistant professor of biology, and Caitlin Hof, a freshman biochemistry, biology and chemistry triple major from Yankton, S.D., were selected to participate in the University of Iowa's Carver College of Medicine FUTURE (Fostering Undergraduate Talent-Uniting Research and Education) in Biomedicine program.

"One of the best aspects of this program was the opportunity to bring a student. It was a great experience to work side-by-side with Caitlin and to see her grow as a scientist," says McClellan.

Over eight weeks, McClellan and Caitlin worked on a collaborative research project in the laboratory of Dr. Pamela Geyer in the Department of Biochemistry. They investigated the role of a Drosophila zinc finger transcription factor in germline and neuronal development. The Drosophila, a fruit fly, is a model for studying how human genes are regulated, says McClellan.

"Caitlin has been working on adapting what we learned in the FUTURE research into a behavioral lab for our neuroscience course which is taught in the fall semester," says McClellan. "This would be an educational lab experience for students utilizing techniques that are being done in research today."

"Before having this experience, I was sold on practicing medicine," says Caitlin. "I thought that was the only way to make a difference or help in people's lives. Now I have learned how research is a huge part of medicine and improving the quality of life for others. I now am looking at MD/ PhD programs to have a research component to my future practice."

McClellan, who started teaching at BVU in 2009, has also had other faculty development opportunities, including a presentation in 2010 at the Society of Neuroscience in San Diego, Calif. Last October, she and a group of students attended the Nobel Conference at Gustavus Adolphus College. This year, she and Caitlin plan to present their FUTURE research at the Iowa Academy of Science.

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Professor, Student Grow as Biomedical Researchers

How Do Cats Survive Massive Falls? [Biology]

Everyone knows that cats can somehow survive falling out of a tree, but last week a cat survived a 19-story fall in Boston. So just how the hell did it manage it?

Science, as usual, can help explain: it's mostly anatomy. But sadly, there is a lack of empirical evidencescientists seem reluctant to throw cats out of windows in pursuit of their studiesbut there has been plenty of research into way they fall.

In comparison to most mammals, they have a large surface area for their weight, which means their terminal velocity is low. In fact, according to a 1987 study by veterinarians Wayne Whitney and Cheryl Mehlhaff, an average-sized cat with its limbs extended achieves a terminal velocity of about 60mph, while an average-sized man reaches a terminal velocity of about 120mph. The result? When a cat hits the ground, it's subjected to smaller forces and suffers fewer injuries.

But there's more. Cats have also evolved a keen sense for knowing which way is up. Weirdly, given a big enough fall, that means that they're capable of righting themselves in mid-air by spinning their tails, to ensure they land feet-first. "Everything that lives in trees has what we call an aerial righting reflex," explains Robert Dudley, a biologist at the animal flight laboratory at the University of California, Berkeley, to the BBC.

Finally, when they do hit the ground, they have legs designed to soak up the impact. "Cats have long, compliant legs," explains Jim Usherwood of the structure and motion lab at the Royal Veterinary College, again to the BBC. "They've got decent muscles. In that they're able to jump quite well, the same muscles divert energy into decelerating rather than breaking bones." And by stretching out the duration of the impact, the forces transmitted through their bodies are once again greatly reduced.

Sadly, not all domestic cats can survive a massive fall, and that's for one reason: they're often overweight because they get fed treats and snacks all day long. But if your cat is lean and agile, it should happily survive a modest drop. Just please don't treat that as an experimental challenge, though. [BBC]

Image by djgis/Shutterstock

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How Do Cats Survive Massive Falls? [Biology]