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Science Teaching Goes Viral

 :: Posted by American Biotechnologist on 02-04-2014

An alternative approach to the traditional introductory laboratory course at the undergraduate level significantly increases student retention rates, according to research published in mBio, the online open-access journal of the American Society for Microbiology.

In 2012, the President’s Council of Advisors on Science and Technology reported that there is a need for an additional one million science, technology, engineering and mathematics (STEM) graduates in the United States over the next decade to meet U.S. economic needs. The report noted that even a modest increase in the persistence of STEM students in the first two years of their undergraduate education would alleviate much of this shortfall and recommended replacing conventional introductory laboratory courses with discovery-based research courses.

Launched in 2008 with only 12 schools, the Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) has spread to more than 73 institutions and so far has involved 4,800 students. SEA-PHAGES integrates course-based learning within a framework of scientific activity including real-world research into mycobacteriophage genomics, professional networking, and the opportunity to publish in a scientific journal.

“As direct participants in scientific discovery our goal is to engage, excite, increase confidence and draw students into a cycle of self-motivation,” says Graham F. Hatfull of the University of Pittsburgh, an author on the study who leads the program for HHMI. “Phages are people-friendly viruses and their population size and diversity provide an inexhaustible wealth of biological novelty that imposes no obvious limits on the number of students who can participate in SEA-PHAGES.”

First-year undergraduates and high school students isolate novel mycobacteriophages from local soil samples, sequence their genomes and then annotate, analyze and compare them to those of other phages. Because each isolated phage is new and they can name them, students have a sense of ownership which helps motivate them to explore viral secrets. The more than 600 genomes so far sequenced include phages called Sunflower, Yo Yo, Funbox, Lucky, Che, Roscoe, and Hercules.

To analyze the effect of the SEA-PHAGES course on student persistence, Hatfull and his colleagues compared retention of students enrolled in the course with retention of all students and STEM majors at 20 institutions. They found that SEA-PHAGES students continued on to their second year at significantly higher rates (over 90%) than the other groups (both less than 85%.)

“Our core hypothesis was that participation in phage research would not only elevate student engagement in science, it would also provide invaluable insights into phage diversity and evolution,” Hatfull notes.

“Seven weeks in, and I still have no idea what I’m doing. But there’s a key difference now. Seven weeks ago I was beyond frustrated in my lack of knowledge. Now I have come to realize that this is what science truly is: guess and check, take a leap of faith and hoping you get lucky, making mistakes and learning to correct them,” says student phage hunter Allyson Roberts. “And that has finally inspired me to be intrigued by what I’m doing and what lies ahead of me in this course and in the future that awaits me.”

SEA-PHAGES evolved from the Phage Hunters Integrating Research and Education Program (PHIRE), begun by Hatfull several years ago at the University of Pittsburgh.

Seasoned phage hunter, Forest Rohwer at San Diego University, who was not involved in this study, calls SEA-PHAGES a “great idea,” noting that it has already proved “extremely successful at teaching people about both phages and genomics.”

Thanks to the American Society of Microbiology for this story.

Genomics for Judges

 :: Posted by American Biotechnologist on 01-27-2014

Genomic research will eventually uncover a complete picture of how our genetic information, acting in concert with our experiences, influences our behavior, our risk for disease, and our responsiveness to medical treatments. These are all subjects of great academic and personal interest, but what happens when they are connected to a question of legality? When considering whether an individual’s genetic inheritance can be blamed for criminal behavior, or how information on disease predisposition should be used, who is qualified to testify, and what kinds of knowledge are needed to make sound judicial decisions?

The Supreme Court of Illinois and its Administrative Office of the Illinois Courts, in coordination with members of the Illinois Judicial Conference Committee on Education, appointed by the Supreme Court, are responsible for facilitating educational resources for Illinois judges, including those pertaining to sciences in the law. The Institute for Genomic Biology (IGB) at the University of Illinois had the unique opportunity to work with the AOIC in offering a new seminar, “Genomics for(TM) Judges,” that was designed to prepare judges to grapple with legal questions involving DNA sequencing and analysis, as well as related technologies, in the courts today and in the future.

Read more…

Researchers propose alternative way to allocate science funding

 :: Posted by American Biotechnologist on 01-13-2014

Researchers in the United States have suggested an alternative way to allocate science funding. The method, which is described in EMBO reports, depends on a collective distribution of funding by the scientific community, requires only a fraction of the costs associated with the traditional peer review of grant proposals and, according to the authors, may yield comparable or even better results.

“Peer review of scientific proposals and grants has served science very well for decades. However, there is a strong sense in the scientific community that things could be improved,” said Johan Bollen, professor and lead author of the study from the School of Informatics and Computing at Indiana University. “Our most productive researchers invest an increasing amount of time, energy, and effort into writing and reviewing research proposals, most of which do not get funded. That time could be spent performing the proposed research in the first place.” He added: “Our proposal does not just save time and money but also encourages innovation.”

The new approach is possible due to recent advances in mathematics and computer technologies. The system involves giving all scientists an annual, unconditional fixed amount of funding to conduct their research. All funded scientists are, however, obliged to donate a fixed percentage of all of the funding that they previously received to other researchers. As a result, the funding circulates through the community, converging on researchers that are expected to make the best use of it. “Our alternative funding system is inspired by the mathematical models used to search the internet for relevant information,” said Bollen. “The decentralized funding model uses the wisdom of the entire scientific community to determine a fair distribution of funding.”

The authors believe that this system can lead to sophisticated behavior at a global level. It would certainly liberate researchers from the time-consuming process of submitting and reviewing project proposals, but could also reduce the uncertainty associated with funding cycles, give researchers much greater flexibility, and allow the community to fund risky but high-reward projects that existing funding systems may overlook.

“You could think of it as a Google-inspired crowd-funding system that encourages all researchers to make autonomous, individual funding decisions towards people, not projects or proposals,” said Bollen. “All you need is a centralized web site where researchers could log-in, enter the names of the scientists they chose to donate to, and specify how much they each should receive.”

The authors emphasize that the system would require oversight to prevent misuse, such as conflicts of interests and collusion. Funding agencies may need to confidentially monitor the flow of funding and may even play a role in directing it. For example they can provide incentives to donate to specific large-scale research challenges that are deemed priorities but which the scientific community can overlook.

“The savings of financial and human resources could be used to identify new targets of funding, to support the translation of scientific results into products and jobs, and to help communicate advances in science and technology,” added Bollen. “This funding system may even have the side-effect of changing publication practices for the better: researchers will want to clearly communicate their vision and research goals to as wide an audience as possible.”

Awards from the National Science Foundation, the Andrew W. Mellon Foundation and the National Institutes of Health supported the work.

From funding agencies to scientific agency: Collective allocation of science funding as an alternative to peer review
Johan Bollen, David Crandall, Damion Junk, Ying Ding, and Katy Börner

Read the paper:
doi: 10.1002/embr.201338068

Thank you to EMBO for contributing this story.

Closer to Understanding the ‘Contagion’ Virus

 :: Posted by American Biotechnologist on 12-16-2013

A team of scientists from Washington State University has discovered how one of the planet’s most deadly known viruses employs burglary-ring-like teamwork to infiltrate the human cell.

Nipah virus is so menacing that the nation’s top infectious disease experts served as consultants in the filmmaking of the 2011 medical thriller, “Contagion,” which is based on a global Nipah outbreak.

The WSU researchers, led by virologist Hector Aguilar-Carreno, have found that two proteins on the surface of the virus communicate in a way similar to two skilled burglars – with one casing the human cell while the other waits for a signal to launch the break-in. Their findings were recently published in the medical journal PLOS Pathogens. (Go to PLOS for the full article).

Those include measles, mumps, respiratory syncytial virus in humans and distemper in dogs, he said.

Invasion from inner space

Working with disabled Nipah microbes that can’t cause infection, Aguilar-Carreno and his colleagues determined that two proteins act as forward scouts, with protein G sensing an opportunity to activate the break-and-enter and then signaling the go-ahead to protein F to start the fusion process.

This signal exchange is so efficient that it helps explain how a single, miniscule virus can launch full-blown disease, said Aguilar-Carreno.

“The virus is able to fuse its own membrane with the membrane of a healthy cell and then invade with its RNA. Once inside its cell host, Nipah multiplies by the thousands and the infection process begins,” he said.

Flu-like, but worse

Nipah virus, identified 14 years ago during an epidemic in Malaysia, causes flu-like symptoms and convulsions due to swelling of the brain. Outbreaks of the virus inflict a high mortality rate, usually killing more humans than are spared.

Because the pathogen spreads from certain animals to humans and from person to person, the World Health Organization has identified it as a potential source of a global pandemic.

And it might start with a single cough.

As the movie “Contagion” portrays, the microbe is believed to have spread from the tropical fruit bat to pigs before making a leap to humans.

The disease hasn’t been diagnosed outside remote areas of Southeast Asia. But the concern is that the pathogen could spread to other regions if an infected person travels on a plane or if the fruit bat – with its six-foot wing span – ventures farther in search of food and habitat. The virus doesn’t sicken the bats; instead they are reservoir hosts.

Higher death tolls

“Since Nipah virus was identified, we’ve seen at least one outbreak each year, each resulting in a high percentage of deaths,” said Aguilar-Carreno.

Most alarming is this year’s outbreak in Bangladesh where the virus killed 21 of the 24 people diagnosed, according to that country’s Institute of Epidemiology, Disease Control and Research. Victims’ ages were 8 months to 60 years.

Whether the virus is becoming more deadly or improved surveillance is finding more cases, “it’s too soon to know,” said virologist Paul Rota of the U.S. Centers for Disease Control in Atlanta, which classifies the pathogen in the same hot-agent category as Ebola and smallpox.

Not only does the virus spread among different species, but there is no vaccine or treatment. And that’s where Aguilar-Carreno’s work comes in.

“Our study reveals the intricate steps that one Nipah virus undertakes in order to enter a 10,000-times-larger healthy cell,” he said. “The more we understand about Nipah’s molecular mechanics, the more likely scientists can develop a drug to block it from infecting.”

Majority of Americans believe another government shutdown likely in coming months

 :: Posted by American Biotechnologist on 12-03-2013

Nearly two-thirds (65%) of Americans say it’s likely there will be another government shutdown in the months ahead as Congress continues to debate deficit and budget issues, according to a new national public opinion poll commissioned by Research!America and the American Society of Hematology. This sentiment is shared across party affiliations: Democrats (66%), Republicans (65%) and Independents (65%). There is also consensus across party lines that government dysfunction has consequences. A majority of Americans (57%) say the shutdown in October caused significant harm to many government-funded programs including medical research, defense and education. Democrats (68%) and about half of Republicans (49%) and Independents (51%) agree.

On the topic of sequestration, a plurality (44%) says Congress must tackle tax and entitlement reform to reduce the deficit instead of continuing the 10 years of across-the-board cuts; another 16% say sequestration is not the right way to reduce the deficit. Less than a quarter (23%) believe the across-the-board cuts are a way of ensuring that many government programs share the pain, and 17% say they’re not sure. In general, 62% of Americans say they’re concerned about the long-term effects of sequestration on advances in health care such as the development of new drugs and other treatments.

“Our poll demonstrates uneasiness among many Americans about the ramifications of deep spending cuts to programs that are critical to our health and well-being,” said Mary Woolley, president and CEO of Research!America. “Americans want Congress to reach a budget deal that protects medical and health research, at least in part because of concern that our nation is at risk of losing our global leadership position in science and innovation.”

The poll shows nearly three-quarters (73%) of Americans doubt the U.S. will be the number one world leader in science and technology in 2020, a significant increase from the percentage that doubted U.S. leadership last year (59%). In addition, one-third of respondents believe China will surpass the U.S. in six years. Another 30% are not sure which country will lead in science in 2020. Many believe the federal government must increase investments in medical and health research now to ensure that the U.S. can compete globally (61%), and a vast majority (84%) think it’s important for the U.S. to lead in medical, health and scientific research.

The current level of federal spending for research to combat disease leaves many Americans on edge. Upon hearing the U.S. spends about 5 cents of each health dollar on research and development to prevent, cure and treat disease and disability, nearly half (49%) say it’s not enough. Where the additional funds would come from is another question. A plurality (43%) of Americans states its willingness to pay $1 per week more in taxes if the respondents were certain that all of the money would be spent on additional medical research, with 34% not willing and another 23% uncertain about additional taxes for research.

“By cutting federal funding for research supported by the National Institutes of Health and other agencies, we are literally putting lifesaving research on hold,” said Janis Abkowitz, MD, president of the American Society of Hematology, the world’s largest association of blood specialists. “As someone who has seen firsthand how scientific breakthroughs have led to better treatments for patients with blood diseases, it is encouraging to see that voters view medical research funding as a key issue when deciding who will get their vote.”

Looking ahead to the midterm elections, about two-thirds of respondents (66%) say it’s important for candidates running for office to assign a high priority to funding medical research. More than half (53%) do not believe elected officials in Washington are paying enough attention to combating the many deadly diseases that afflict Americans.

Among other findings:

  • 70% say basic scientific research that advances the frontiers of knowledge is necessary and should be supported by the federal government, even if it brings no immediate benefits.
  • Upon hearing the federal government spends approximately $100 per American per year on medical research on all diseases and disabilities, about half (46%) say that’s not enough.
  • 79% say it’s important that our nation supports research that focuses on improving how our health care system is functioning.
  • 75% of Americans say it’s important to invest in research for job creation and economic recovery.
  • 54% say the cost of health care is the single most important health issue facing the nation.
  • 51% say research to improve health is part of the solution to rising health care costs.
  • 75% say it’s important to conduct medical or health research to understand and eliminate health disparities.

The nationwide survey was conducted by Zogby Analytics for Research!America and the American Society of Hematology. The margin of error is +/-3.2 percentage points. To view the poll, visit: http://www.researchamerica.org/uploads/Nov13nationalpollwithASH.pdf

Thank you to Research!America for this story.