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Posts Tagged ‘microbiome

Science Policy Around the Web – August 19, 2016

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By: Ian McWilliams, PhD

Photo source: pixabay

Climate Change

Melting ice sheet may expose cold war base, hazardous waste

During the Cold War, the US Army Corps began a top-secret mission to determine the capability of launching nuclear missiles at Russia from a base in Greenland. The military base constructed for this mission, named Camp Century, lies approximately 125 miles inland from the Greenland coast and was later abandoned in 1964 after the Joint Chiefs of Staff rejected the plans to create a nuclear base. When soldiers abandoned the base, it was thought that leftover fuel and waste material would be safely interred, buried under ice for thousands of years.

However, climate change has now threatened those plans. The increased ice melt could reveal the base as early as 2090 and it is estimated that tens of thousands of gallons of diesel fuel, wastewater, sewage, and other chemicals could be exposed. Adding to concerns is the nuclear generator housed in the frozen base. Although the base never became a site for nuclear weapons, the low-level radioactive coolant from the nuclear generator is still stored in the base. If ice melt continues to occur at an accelerated rate, some have expressed concern that these chemicals could be released into the environment by seeping into waterways causing a potential environmental catastrophe. (Stephen Feller, UPI)


Mouse microbe may make scientific studies harder to replicate

Reproducibility is an issue that has been the subject of much debate in the scientific community recently. Now, scientists are concerned that the microbiome may further complicate the issue. The collection of commensal microorganisms that reside on or within the body is referred to as microbiota, and it is now well known to affect the health of the host. Although researchers have taken meticulous steps to ensure that experimental animals are housed in identical conditions, including sterile bedding, strict temperature control, and standard light cycles, determining experimental variability due to differences in their microbiome have remained elusive. As researchers explore the issue further they have found that mice from different vendors have very different compositions of bacteria in their gut that could explain some inconsistencies in researchers’ experiments.

Although it is not mandated, taking steps to control for microbiome may aid in the reproducibility crisis. Segmented filamentous bacteria (SFB) have been identified as a notable concern, and some vendors are providing SFB positive or SFB negative animals separately. Although it is unlikely that SFB is the only culprit for differences in studies, researchers continue to explore new variables in rodent husbandry in an effort to improve reproducibility of scientific results. To add to the dilemma, because the species that constitute the microbiome are constantly changing, it is difficult to characterize, and impossible to standardize. Since mice share their microbes through eating each other’s feces, cage-mates can have similar microbiomes that provide natural microbiota normalization for littermates. (Kelly Servick, Science)

Precision Medicine

Spiking genomic databases with misinformation could protect patient privacy

New initiatives, like the Precision Medicine Initiative (PMI), are helping to cultivate the human genome into usable sets of data for research purposes. This pursuit is founded upon the willingness of participants to allow their genetic information to be pooled for analyses, but many have expressed concerns over the privacy of this genetic information. It has previously been shown that individuals can be identified from their anonymized genomic data and this has prompted researchers to look for additional security measures. Computer scientists Bonnier Berger and Sean Simmons have developed a new tool to help achieve this goal by using an approach called differential privacy. To increase privacy, a small amount of noise, or random variation, is added to the results of a user’s database query. Although the information returned would provide useful results, it would make it more difficult to conclusively connect this data to a patient’s identity. A similar method has been used by the US Census Bureau and the US Department of Labor for many years.

However, some scientists, including Yaniv Erlich, have concerns that adding noise to the dataset will reduce users ability to generate useful results. Erlich stated that “It’s nice on paper. But from a practical perspective I’m not sure that it can be used”. In the search for privacy, free form access to the data is limited. This “privacy budget” limits the number of questions that can be asked and excludes hundreds or thousands of locations in a genome. Additionally, because noise naturally increases error, it weakens the overall conclusion that can be drawn from the query. Simmons expects that answers will be close enough to be useful for a few targeted questions. The tradeoff for increased security is that databases protected this way could be instantly accessible and searchable, which cuts down on getting access to databases such as those managed by the National Institutes of Health. Simmons added that this method is “meant to get access to data sets that you might not have access to otherwise”. The group plans to continue to refine this method to balance the needs of researchers for access to these data sets while maintaining patient privacy. (Anna Nowogrodzki, Nature)

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August 19, 2016 at 11:08 am

The unseen microbes that rule the world

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By: Jessica Hostetler, B.Sc.

The White House Office of Science and Technology Policy (OSTP) announced on May 13th, 2016, the formation of a National Microbiome Initiative (NMI). It is the latest in a series of scientific initiatives aimed at solidifying the legacy of the Obama administration, joining efforts aimed at curing cancer, delivering on the promise of personalized medicine, mapping the human brain, and developing new antibiotics. Why might this latest effort matter? The NMI has the potential to have a huge positive impact for human health and society, and it may prove to be one of the most productive of the programs initiated by the Obama administration.

Why microbes matter: a brief history of microbiome research

Microbiome research grew quickly on the heels of revolutionary advances in DNA sequencing technologies in the early 2000’s. These changes made sequencing DNA exponentially cheaper and faster than earlier technologies. Early work in the field of “metagenomics” aimed to understand the microbes present in a variety of ecosystems, starting with microorganisms in acid mines, wastewater, the human gut and the world’s oceans. Many species of bacteria will not grow in a laboratory setting or petri dish (in vitro), leaving researchers to try sequencing all the DNA from a mixture of organisms in these ecosystems. After the jumble of sequences were generated, scientists developed software to categorize DNA sequences and try to determine what kinds of microbes were present in the samples. The Global Ocean Sampling (GOS) project from the J. Craig Venter Institute in 2007 nearly doubled the number of known protein sequences at that time, pointing to potentially thousands of new biochemical pathways.

Scientists quickly expanded on this early work by integrating the knowledge gained from the study of microbes and applying it to human beings to understand the microbiome’s impact on human health. Initiatives such as the National Institutes of Health’s Human Microbiome Project (HMP), launched in 2007, aimed to push the field significantly forward by investing $215 million in research projects from 2007-2014. The program generated nearly 50,000 files of publicly available sequencing data which have been accessed by 75,000 users from 178 countries. Human microbiome research is already yielding health benefits, such as the use of fecal microbiome transplantation for curing Clostridium difficile infections in up to 90% of cases. Microbiome diagnostic tests for predicting which pregnant women are at risk for preterm labor (a leading cause of infant death) are under active development by The Mayo Clinic’s Center for Individualized Medicine and Whole Biome.

Why do we need a national microbiome initiative?

Microbiome research is a vastly expanding and productive field, but the pace of growth leaves huge potential for wasted resources through redundant research initiatives. A dozen federal agencies invested $922 million into microbiome research from 2012-2014 alone, with numerous individual initiatives at universities and private companies.

In October of 2015, a commentary in the prominent scientific journal, Science, put out a call for creating a coordinated, microbiome research effort to push the field forward. A high profile group of microbiome researchers and the newly formed Unified Microbiome Initiative Consortium argued that a greater understanding of “microbial functions or community dynamics” has the potential to “transform our understanding of the world and launch innovations in agriculture, energy, health, the environment, and more.” The commentary highlighted key research areas that can be effectively tackled with a united effort, including the following:

  • Better technology: Research must improve tools for predicting the function of the many uncharacterized genes uncovered, and a vast improvement must be made in understanding all of the chemical compounds produced in the biochemical pathways of microbes. One recent report found that only 2% of the data could be matched to known chemical compounds.
  • Jumping from gene to genome: Much of the current microbiome research focuses largely on the gene content of a given microbiome, but teasing out what genes are part of what organism will be essential to fully understand the whole “community function and dynamics.” This will require significant improvements in DNA sequencing and assembling technologies.
  • Integrating all the data: Studies often focus on different aspects of microbial communities, such as genes, expression of genes, proteins made, and chemicals produced. All of this data needs to be integrated along with potentially new high resolution imaging data to get a big picture view of the function of microbes in an ecosystem.
  • Translating observational research into action: Most research currently involves describing what microbes are present, i.e. in a healthy gut versus the gut of a person suffering from a disease. New methods are needed to move research in the direction of making changes in microbial communities to potentially generate disease treatments and environmental improvements. DNA editing technologies like CRISPR/Cas9 may play a role on this front.

What will NMI do?

NMI aims to pull together a number of federal agencies and stakeholders in order to coordinate research and set common goals. The project consists of three broad goals reported in the OSTP announcement:

  1. Supporting interdisciplinary research to answer fundamental questions about microbiomes in diverse ecosystems.
  2. Developing platform technologies that will generate insights and help share knowledge of microbiomes in diverse ecosystems and enhance access to microbiome data.
  3. Expanding the microbiome workforce through citizen science and educational opportunities.

NMI will commit $121 million from the 2016 and proposed 2017 Federal budgets into “interdisciplinary, multi-ecosystem research and tools development.” In a call to action from OSTP, numerous universities and private sector stakeholders committed over $400 million for additional microbiome research and development including projects aimed at the following:

  • Human and agricultural microbiomes (Bill and Melinda Gates Foundation, $100 million)
  • Microbiomes related to type 1 diabetes (JDRF, $10 million)
  • Technology development (Center for Microbiome Innovation, The University of California, San Diego, $12 million)
  • Microbiome data access for researchers, clinicians, and other public health professionals (One Codex)
  • Microbiome data and sample banks including underrepresented groups (The BioCollective, LLC, Health Ministries Network, $250,000)
  • Microbiome research and training programs under the Michigan Microbiome Project (The University of Michigan, Howard Hughes Medical Institute, Procter and Gamble, $3.5 million)
  • Microbiomes of health and disease, developing new therapies via the Center for Medicine and the Microbiome (University of Pittsburgh Schools of the Health Sciences, University of Pittsburgh Medical Center)

A complete list can be found in the OSTP announcement.

In order to be truly effective, however, the efforts to coordinate microbiome research will have to include the global scientific community. A commentary by several international microbiome researchers released in Nature in the fall of 2015 supports the efforts to unify the microbiome research community but goes on to argue that the microbiome research effort must be global in scope. It points out that at least eight separate human microbiome programs from various countries – including the US, Canada, the European Union, China and Japan – have generated huge amounts of data that are not easy to compare. International study standards, forums, and common tools would go a long way in ensuring that the public gets the most return on investment from every research dollar spent.

If NMI can lead the charge in setting the global microbiome research agenda, the world may benefit in a number of ways. The Science commentary notes that microbes have the potential to produce a nearly unlimited number of beneficial compounds, including biofuels and next-generation antibiotics. The study of ocean and soil microbes may paint a clearer picture of climate change. Agriculture may see improvements such as reducing the need for pesticides or rehabilitating soil depleted of nutrients. Human health may see potential interventions for conditions such as “asthma, diabetes, obesity, infectious diseases, psychiatric illnesses, and other afflictions.” Communication driven by NMI among key stakeholders, federal agencies, and the global community will be essential to delivering solutions for all of these areas in the next decade of microbiome research.

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June 1, 2016 at 9:00 am

Science Policy Around the Web – May 17, 2016

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By: Melissa Pegues, Ph.D.

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Zika Virus

WHO’s Zika guidelines don’t include delaying Olympics

With the summer Olympic games slated to begin in Brazil in August, many have expressed concerns about the health risks posed by the recent outbreak of Zika virus in Central and South America. Despite these concerns, the World Health Organization (WHO) released a statement on Thursday making it clear that they are not calling for a cancellation of the Olympic games this summer.

The Zika virus, which is transmitted by mosquitoes, has garnered much attention recently after infection with the virus during pregnancy has been found to cause microcephaly in infants. Microcephaly is a birth defect in which the brain does not develop properly resulting in a smaller than normal head. The virus has also been associated with the development of Guillian-Barre syndrome, a rare form of paralysis.

Although many prominent medical ethicists have publicly called for the postponement or relocation of the games, few athletes have expressed concern over the risks posed by Zika. However, Marcos Espinal, the director of the Zika response of the Pan American Health Organization, has strongly rejected the idea of postponing the games. He cited trends seen from dengue and chikungunya, similar viruses that are also carried by the same Aedes aegypti mosquito, in that infections peak during the summer months and subsequently drop off after the season changes. Furthermore, he noted that the games are occurring in the winter months of August and September when mosquitoes are not so abundant. International Olympic Committee (IOC) director, Richard Budgett, reaffirmed that although the situation is being closely monitored, the IOC is committed to continuing with the Olympic games this summer.

In their statement, WHO urged athletes and anyone traveling to Brazil to attend the Olympic games to take steps to protect against Zika, including wearing insect repellent and clothing that covers as much of the body as possible. The WHO statement also cautions against sexual transmission of the virus and suggested practicing safe sex or abstaining from sex during their stay and for at least four weeks after returning from the epidemic zone. This recommendation contrasts those issued by the Centers for Disease Control (CDC) that recommend abstaining from sex for eight weeks after returning, further highlighting how little is known about transmission of the virus. There have been few documented cases of sexual transmission and many questions regarding sexual transmission of the virus remain, including if an asymptomatic infected person can transmit the virus sexually. WHO also recommended that Olympic visitors stay in air-conditioned accommodations and avoid areas where there is increased risk of being bitten by a mosquito such as “impoverished and overcrowded areas in cities and towns with no piped water and poor sanitation.” (Pam Belluck, New York Times)

Genetic Engineering

Secret Harvard meeting on synthetic human genomes incites ethics debate

The ability to modify the genome is rapidly advancing the medical field, but a private meeting of scientists has brought intrigue and concern to the field of genetics. Nearly 150 Scientists gathered at Harvard Medical School last week to discuss how to create a complete genome from scratch. The project has been described as a follow-up to the human genome project, but rather than aiming to read all of the base pairs of the human genome, the goal is to synthesize a “complete human genome.” Although scientists already have the capability to synthesize DNA chemically, significant focus is being given to improving these techniques with the goal to construct complete genomes that could be implanted in cells for research purposes.

However, the meeting has drawn criticism because the organizers of the event asked attendees not to contact the media or post to Twitter during the meeting. Researchers Drew Endy and Laurie Zoloth published an essay questioning the decision to keep the meeting private. In their joint statement they questioned whether the organizers gave full consideration to potential ethical issues by asking “how many Einstein genomes should be made and installed in cells, and who would get to make them?”

George Church, the Harvard geneticist who oversaw the meeting, explained that the project was aimed at creating cells, not people. He further explained that the project is not restricted to the human genome, and that these techniques could be applied to other animals, plants, and microbes. The meeting was originally intended to be open with video streaming and numerous invited journalists, but attendees were asked not to publicly discuss the event since there were also plans to pair the meeting with a peer-reviewed article. Church commented that “there was nothing secret about it” that a video of the meeting will be released with their soon-to-be published peer-reviewed article. (Joel Achenbach, Washington Post)

Federal Science Initiatives

Earth’s microbes get their own White House Initiative

With months left in Obama’s presidency, the White House Office of Science and Technology has announced yet another scientific endeavor, the National Microbiome Initiative (NMI). This latest initiative will join numerous other efforts in the Obama administration’s scientific legacy including: the BRAIN Initiative, the Antibiotic Resistance Solutions Initiative, the Precision Medicine Initiative (PMI), and the Cancer Moonshot Initiative. The human “microbiome” is the collection of microbes that inhabit our bodies, and variations in its composition has been found to correlate with many diseases including autoimmune diseases, diabetes, and obesity.

The NMI however includes many governmental departments to study the microbiome of many ecosystems such as “those that help plants pull nutrients from soil, to those that capture and release carbon dioxide in the ocean.” Because these environments contain many species of bacteria, viruses, and fungi, determining the role of any one species is nearly impossible. Reaching the lofty goals set by this initiative will require better tools to dissect individual species within the microbiome, and to address these shortcomings, the NMI has set forth 3 goals:  supporting interdisciplinary research, developing platform technologies, and expanding the microbiome workforce. To support these goals, the NMI will receive an investment of $121 million dollars from federal 2016 fiscal appropriations and 2017 fiscal proposals, as well as commitments of $400 million dollars from stakeholder and institutions in different sectors. (Kelly Servick, ScienceInsider)

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May 17, 2016 at 9:00 am

Science Policy Around the Web – November 6, 2015

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By: Sylvina Raver, Ph.D.

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Education and Mental Health

Sesame Street’s new brand of autism education

There’s a new Muppet on the block: her name is Julia, she’s in preschool, and she has autism. Julia’s arrival on Sesame Street is part of a coordinated effort by the Sesame Workshop – the nonprofit organization behind the long-running educational children’s program – to reduce the stigma associated with autism and to normalize the disorder among preschool children. The initiative, called Sesame Street and Autism: See Amazing in All Children, is a web-based project with resources for parents that include videos aimed at educating kids ages 2-5 about their peers with autism, a storybook featuring Julia and her friends, and free daily routine cards that parents can use to teach their autistic children basic skills like teeth brushing.

The new initiative was created based on solid academic research thanks to input from multiple universities, professional organizations, and advocacy groups. The Sesame Workshop also worked to ensure that these resources included the viewpoints of individuals with autism. One in 68 children in the US is diagnosed with autism, which ensures that young kids are almost assured to interact with an autistic peer.  Despite the prevalence of the disorder, bullying is still extremely common. One recent study by the Interactive Autism Network found that 63 percent of children with autism have been bullied. The Sesame Street initiative aims to foster tolerance and acceptance with preschool age children in the hope of decreasing bullying among older children, in part by normalizing the features of autism, rather than by exaggerating how they may be disabling to children with the disorder. There’s plenty of room for optimism concerning the effectiveness of using Sesame Street as a platform for this type of education. A 2015 report from the National Bureau of Economic Research found that the program is “the largest and least-costly [early-childhood] intervention that’s ever been implemented” in the US. (Lauren McKenna, The Atlantic; Elizabeth Blair, NPR)

Drug Policy

In heroin crisis, white families seek gentler war on drugs

The nation’s long-running war on drugs has been defined by zero tolerance and stiff prison sentences. It emerged during a crack cocaine epidemic of the mid 1980’s that was primarily concentrated in poor, predominantly black, urban areas. In contrast, the heroin epidemic of the last decade is concentrated in white communities, many of which are suburban and middle-class. This demographic shift in drug use is starting to have profound consequences on how the drug war is being waged. Families who have lost loved ones to heroin are increasingly channeling their anger and grief into efforts to change the language surrounding addiction, and to urge politicians and government to treat drug use as a disease instead of a crime. For example, the derogatory term “junkie” is falling out of favor in lieu of softer and more understanding language. President Obama visited West Virginia recently, a mostly white state with staggering numbers of heroin overdose deaths, to discuss a new proposal to expand access for drug treatment and prevention programs. Presidential hopefuls from both parties have adopted a tone of compassion, rather than punishment: Hillary Clinton has been hosting forums on the issue in New Hampshire, and Jeb Bush is openly discussing his family’s experiences with drug addiction. In a dramatic shift, the Gloucester, Massachusetts police department is employing a new approach to heroin use that at least three dozen other departments have now adopted: users will no longer be arrested if they walk into a police station for help, even if they are in possession of heroin or its associated paraphernalia.

Many people welcome this shift as a needed course correction in light of our scientific understanding of the biology of addiction. However, some black scholars express frustration that similar calls for a more empathetic approach to drug addiction were not heard when they originated from the black community.  Kimberle Williams Crenshaw, a scholar of racial issues at Columbia and UCLA law schools, notes …”had this compassion existed for African-Americans caught up in addiction and the behaviors it produces, the devastating impact of mass incarceration upon entire communities would never have happened.” (Katherine Q. Seelye, The New York Times)


Create a global microbiome effort

In last weeks’ issue of Science magazine, a group of leading scientists in the US called for the creation of a Unified Microbiome Initiative (UMI) which would assemble researchers with representatives from private and public agencies and foundations to study the activities of the Earth’s microbial ecosystems. Nearly every organism and habitat on Earth hosts a unique population of microorganisms, known as its microbiome. These microbial communities are fundamental to nearly all aspects of life on Earth. For example, soil microbes drive the production of usable forms of crucial planetary elements like carbon and nitrogen, and their manipulation shows promise for reducing agricultural use of pesticides, fertilizers, and water use. Ocean microbes produce much of earth’s oxygen, and may be able to be engineered to remove gases from the Earth’s atmosphere that contribute to global warming. Emerging research has revealed the role played by microbes that live within our own bodies in driving overall health and shaping our behavior. This human microbiome is increasingly seen as a target for new drugs, and is an essential tool for precision medicine.

Despite the crucial functions that microorgansms play, and the spectacular promise that they show for addressing challenges to environmental and human health, scientists know very little about how microbes interact with each other, their environments, and their hosts. This is in large part due to an absence of tools currently available that would “enable a mechanistic, predictive, and actionable understanding of global microbiome processes.” Addressing these technical limitations are central to the proposed UMI. The team calling for its formation describes a need for enhanced multi-disciplinary collaboration between physical, life, and biomedical sciences; engineering, and computer science in order to implement hypothesis-driven approaches that can establish causal relationships between microorganisms and their environments.

A second – and equally important – aspect of a UMI involves the need for enhanced collaboration between researchers who study different microbiome populations. Boundaries between scientists who investigate various microorganism communities are artificial and are largely due to historical divides between scientific disciplines, rather than reflecting fundamental differences between microbes that colonize a human mouth or the ocean floor. Furthermore, microbe communities are not limited to national borders but are instead part of a global microbiome. Indeed, the journal Nature contains an accompanying call for the creation of an International Microbiome Initiative to provide universal insight into the microscopic organisms all around and within us. (Alivisatos et al., Science; Dubilier, McFall-Ngai, & Zhao, Nature; Ed Yong, The Atlantic)

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November 6, 2015 at 9:00 am

Science Policy Around the Web – May 22, 2015

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By: Agila Somasundaram, Ph.D.

“Ball-and-stick model of the morphine molecule, C17H19NO3.” by Ben Mills. – Own work. source

Drug Policy and Biotechnology

A Way to Brew Morphine Raises Concerns Over Regulation

Traditionally, heroin has been made from poppy – the opium from poppy seeds yields morphine, which can then be refined to heroin. However, it might soon be possible to convert sugar to morphine using genetically modified yeast. There are several steps in this conversion, and a recent study by scientists from the University of California, Berkeley, and Canada’s Concordia University, published in the journal Nature Chemical Biology, has provided the final missing one. This has triggered a debate on whether synthesis of morphine should be regulated, and if yes, how? Dr. Kenneth A. Oye, a professor of engineering and political science at M.I.T., and other experts argue that this technology could benefit the heroin trade more than the prescription painkiller industry, because drug sellers currently rely on smuggling raw materials from countries like Afghanistan and Laos, and brewing close to home would save them costs. The pharmaceutical industry, on the other hand, has a steady supply of cheap opium from countries like India and Australia, or can synthesize opiates in their own labs. Dr. Oye and others suggest that steps should be taken to prevent abuse of the synthetic approach, including restricting access to the bio-engineered yeast strains and the DNA. Biotech experts who counter these suggestions say that Dr. Oye’s precautions might be overkill, because producing morphine by fermentation using engineered yeasts is a delicate process that may not yet be ready for producing heroin in large quantities. They argue that restricting access to DNA stifles research and may not necessarily succeed in preventing a heroin synthesis epidemic. Robert H. Carlson, the author of “Biology Is Technology,” says, “DNA synthesis is already a democratic, low-cost technology. If you restrict access, you create a black market.” Because the genetically modified yeast strain is not commonly available yet, the Drug Enforcement Administration (DEA) is not too concerned about an imminent threat. But FBI Supervisory Special Agent Edward You is glad that the debate on regulating access has begun before the synthetic technology is ready. He says, “We want the people in the field to be the sentinels, to recognize when someone is trying to abuse or exploit their work and call the FBI.” (Donald G. McNeil Jr., The New York Times)


In unusual move, German scientists lobby for GM labeling

Whether or not to label genetically modified (GM) food is a topic of huge debate, and generally, people who oppose GM food want the food labeled. In a surprising move, German scientists and other supporters of GM crops are lobbying for labeling GM crops because they want the public to know that there is nothing to be afraid of, hoping that this would make it easier for GM products to reach the consumer. This petition requests the German government to draft a law that would require labeling of all products that contain or have been produced using GM organisms. The petition was drafted by Horst Rehberger, leader of the group Forum Grüne Vernunft (Forum Green Reason), and has the support of several prominent scientists and politicians. It requires 50,000 signatures in 4 weeks to be considered by the German parliament. Though GM crops and food derived directly from them are already labeled in Germany, certain products in which genetic engineering plays an indirect role are not required to be labeled. This petition seeks to address the deficiencies in the current system. But environmental organizations like the Greenpeace are concerned that labeling all GM products, irrespective of how much genetic engineering actually went into their making, would negate the differences and could distract the public from the real issue, and make it harder for consumers to make choices. Proponents of the GM labeling say that the labels should be graded differentially, for instance, between products that contain GM organisms versus products that were processed by GM organisms. “I think we just need to be honest and transparent to consumers,” says Wilfried Schwab, a professor of biotechnology of natural products at Technische Universität München. The proposal is a chance to change the conversation about GM organisms, says geneticist Hans-Jörg Jacobsen. Modeling studies have suggested that if GM food was sold at a 15 % discount, and organic food at a 15 % premium, consumers are more likely to choose GM products. With time, a GM label could even become a positive sign, Jacobsen says. (Kai Kupferschmidt, Science Insider)

Privacy and Genomic Data

Microbiomes raise privacy concerns

The human body harbors many types of bacteria, collectively called the microbiome. The microbiome’s influence on our health has become an important topic of research. A recent study published in the Proceedings of the National Academy of Sciences suggests that it would be possible to uniquely identify an individual based on information contained in their microbiome DNA. This information could also reveal details about their health, diet or ethnicity, raising privacy concerns. Curtis Huttenhower, a computational biologist at the Harvard T. H. Chan School of Public Health in Boston, Massachusetts, and lead author of the study, says, “As the field develops, we need to make sure there’s a realization that our microbiomes are highly unique.” Huttenhower’s team investigated if microbiomes lasted long enough in humans to help identify individuals over time. They used the microbiome data publicly available through the National Institutes of Health (NIH) Microbiome Project (HMP). Though the HMP does not identify individuals by name, a participant’s first sample could be compared with a second one donated much later. The researchers found that the microbiome in a person’s stool sample offered the best signature – a person’s first sample could be linked to their second sample using microbial DNA 86% of the time, whereas skin samples could be match only about 25% of the time. But Huttenhower concludes that it would be “exceptionally challenging to do anything with the microbiome data in a single study,” and that privacy risks would come when a person participated in two different microbiome studies that each contained different pieces of identifiable information. Publicly available microbiome data poses privacy risks also because of the presence of potentially identifiable human DNA, suggests another study published recently in the journal Genome Research. A team lead by computational biologist Jonathan Allen of Lawrence Livermore National Laboratory in California has found that the HMP database has stretches of human DNA called short tandem repeats that are used in forensics to distinguish between individuals (even though NIH took measures to eliminate human DNA from the HMP as much as possible). Even if this information per se does not help form a precise DNA signature of an individual, the increase in publicly available DNA databases increases the risk. Amy McGuire, a bioethicist at Baylor College of Medicine in Houston, Texas, says that those who participated in the HMP study were advised of the risk, and that there should not be premature panic over this. Laura Rodriguez, director of policy at the NIH’s National Human Genome Research Institute, says that an overreaction could slow understanding of the microbiome, and that as long as precautions are taken to eliminate privacy concerns (such as removing human DNA from the HMP) “we would want to keep it in open access because of the value it adds to science.” (Ellen Callaway, Nature)

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May 22, 2015 at 11:00 am

Science Policy Around the Web – November 28, 2014

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By: Varun Sethi, Ph.D

photo credit: El Bibliomata via photopin cc

Interdisciplinary Science

Gut-brain link grabs neuroscientists

Gut bacteria benefit mental health. Do they? This is what companies selling probiotics have long claimed. Though traditionally skeptical to the theory, many neuroscientists are becoming interested in the clinical implications of the gut microbiome. The National Institute of Mental Health spent more then US$ 1 million this year, on research aimed at studying the microbiome-brain connection. Studies presented at the recent SFN meeting in DC reported this as a paradigm shift in neuroscience. Bifidobacterium and Lactobacillus are genera that have been reported to show beneficial effects on anxiety and depression related behavior. Gut bacteria and bacterial waste products may regulate stress, anxiety and cognition, especially in early life. Mechanisms and therapeutic potential of these associations are the focus of research in the field. The interaction between the gut associated immune system, enteric nervous system and gut based endocrine system has led to intriguing speculations about the impact of the bi-directional signaling between the mind, brain and gut. Are psychobiotics and melancholic microbes going to be the prescription to happiness? Though majority of the studies are in rodent models, the implications of microbiota in our intestines is being increasingly looked at with interest. There maybe some science in the use of the term ‘gut feeling’ after all! (Sara Reardon, Nature)


Health Care Policy

Medicare’s Chronic Care Management Payment — Payment Reform for Primary Care

A fee-for-service system, wherein payments for primary care are restricted to office based visits, is unable to provide good support for the core activities of primary care outside the office visit. These include tasks such as patient care co-ordination, patient communication, medication refill and care provided via electronic or telephonic channels. In 2015, the Centers for Medicare and Medicaid Services (CMS) will be introducing a non-visit-based payment for chronic care management (CCM). This is an important and broadly applicable change to primary care payment and reflects an investment in creating a value-oriented healthcare system. The system will allow a practices to receive a monthly fee of $40 for beneficiaries with two or more chronic conditions, that are expected to last at least 12 months and confer a significant risk of death, decompensation or functional decline. Practices will have to use electronic health records (EHR), provide round the clock availability to staff able to access EHR and maintain a designated practitioner amongst other things. The implementation of this policy will, however, have to deal with many challenges. Beneficiaries will be expected to pay a 20% co-insurance for CCM, a fee for a service they have so far received free. They will have the choice to consent, and in the event that they refuse, how will the practice continue to care for such patients ? Smaller practices with limited resources may have trouble meeting the requirements and may perhaps be rendered ineligible. The details of the implementation are unclear as yet. While the payment will provide additional resources to the primary care system, it may not achieve the transformation in practice as per the patient-centered medical home (PCMH) initiatives. (Samuel T. Edwards, Bruce E. Landon, New England Journal of Medicine)


Translational Science

Changing the Mindset in Life Sciences Toward Translation: A Consensus

Basic discoveries in biomedical science continue to a fast pace, however, the translation of this knowledge into clinical use lags behind significantly. Biomedical translation is challenged with scientific, financial and political speed-breakers. In May 2014, Translate, a meeting in Berlin, brought together stakeholders from around the world with the common goal of improving biomedical translation. Infrastructure, funding and de-risking issues in biomedical technology were major factors identified as barriers in biomedical translations. An appalling 80 to 90% research projects fail before they are tested in humans, and those that do proceed require up to 15 years to find a clinical use. A multidisciplinary approach involving clinical scientists, researchers, patent agents, industrial partners and regulatory authorities is required to create expert professional translators, who have the expertise to capture those discoveries that have the potential to make it to the clinical market. A change in academic funding and education is warranted. Academic reward systems should focus on not only the publication quality, number and journal impact factor, but also on tangible impacts of research on medical treatments and patient benefits. Cross-talk between scientists from different specialties, with different ideas, perspectives and expertise needs to encouraged and facilitated. The importance of professionalizing translation was emphasized at the meeting. Adequate economic incentives and market forces are essential in driving and directing successful translation. While industry is eager to take over projects beyond phase 2, funding for early phase development is complicated by larger risks and remains an uphill task. This paper discusses the role of a translational researcher in recognizing these challenges and invoking the industry, networking to form partnerships that are essential to collect market data and find solutions. A change in scientific mindset with a greater emphasis on interactive and collaborative relationships is needed. In future articles of this series, funding barriers and derisking will be discussed. Biomedical translation, is not a passive process and is a very crucial step in improving the value of health care, health outcomes and the quality of patient life. (Duda et al., Science Translational Medicine)



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Written by sciencepolicyforall

November 28, 2014 at 3:50 pm

Science Policy Around the Web – November 14, 2014

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By: Nicholas Jury, Ph.D

Photo Credit: Lester V. Bergman/Corbis


Mental Health

Recent evidence linking gut microbes and mental disorders grab neuroscientists’ attention

Dietary supplement companies selling “probiotics” have often claimed that adding them to a diet can enhance the overall mental health of an individual. Even though these gut-derived microbes are readily available over-the-counter, neuroscientists are not completely sold on their utility. However, recent pre-clinical studies have provided some evidence linking mental conditions such as autism and depression to the gut microbiome. These studies have spurred new interest in the potential connection between the “gut-brain axis.”

More than $1 million has been spent this year by the National Institute of Mental Health on research projects investigating the connection between the gut microbiome and the brain. Furthermore, John Cryan at the University of College Cork in Ireland will present evidence linking gut microbes to depression-like behavior in mice at the Society for Neuroscience Annual Meeting in Washington, D.C. His study demonstrated that mice that were born via caesarean section acted in a more depressed-like manner when compared to mice that were born vaginally. “The microbiome is likely to have its greatest impact on early life,” said Cryan.

Another study conducted in mice demonstrated a potential link between autism-like symptoms and the gut microbe Bacteroides fragilis. Mice with autism-like symptoms were fed these gut bacteria and symptoms ceased. Furthermore, this same group found that the mice with autism-like symptoms had high levels of a bacterial metabolite, and that injecting this metabolite into normal mice caused them to exhibit autism-like symptoms.

These pre-clinical studies provide some evidence of the interaction between our gut microbiome and the brain, and the potential therapeutic utility of probiotics in mental health disorders.

(Sara Reardon, Nature)


Federal Science Policy – Regulatory

The 21st century cures initiative drums up bipartisan support on Capitol Hill

Amidst the partisan rancor and gridlock on Capitol Hill, there appears to be some resemblance of bipartisanship with a new biomedical legislative priority. The 21st Century Cures Initiative aims to reduce unnecessary regulation and decrease the time to bring new biological and pharmacological treatments to market. Specifically, the initiative could address regulation regarding clinical trials and institutional review boards. The initiative was conceived by two unlikely bedfellows on the House Energy and Commerce Committee: a conservative, Representative Fred Upton (R-MI), chairman, and a liberal Representative Diana DeGette (D-CO). The first draft of the legislation is expected to be announced at the beginning of the 114th Congress.

(Kelly Servick,  ScienceInsider)


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Written by sciencepolicyforall

November 14, 2014 at 11:12 pm