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Science Policy Around the Web – March 06, 2017

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By: Liu-Ya Tang, PhD

Source: pixabay

Technology and Health

Is That Smartphone Making Your Teenager’s Shyness Worse?

The development of new technologies, especially computers and smartphones, has greatly changed people’s lifestyles. People can telework without going to offices, and shop online without wandering in stores. While this has brought about convenience, it has also generated many adverse effects. People tend to spend more time with their devices than with their peers. Parents of shy teenagers ask, “Is that smartphone making my teenager’s shyness worse?”

Professor Joe Moran, in his article in the Washington Post, says that the parents’ concern is reasonable. The Stanford Shyness Survey, which was started by Professor Philip Zimbardo in the 1970s, found that “the number of people who said they were shy had risen from 40 percent to 60 percent” in about 20 years. He attributed this to new technology like email, cell phones and even ATMs. He even described such phenomena of non-communication as the arrival of “a new ice age”.

Contrary to Professor Zimbardo’s claims, other findings showed that the new technology provided a different social method. As an example, teenagers often use texting to express their love without running into awkward situations. Texting actually gives them time and space to digest and ponder a response. Further, Professor Moran said that the claim of Professor Zimardo was made before the rise of social networks;  shy teenagers can share their personal life online even if they don’t talk in public. He also talks about the paradox of shyness, where shyness is caused by “our strange capacity for self-attention”, while “we are also social animals that crave the support and approval of the tribe.” Therefore, new technologies are not making the shyness worse, in contrast social networks and smartphones can help shy teenagers find new ways to express that contradiction. (Joe Moran, Washington Post)

Genomics

Biologists Propose to Sequence the DNA of All Life on Earth

You may think that it is impossible to sequence the DNA of all life on Earth, but at a meeting organized by the Smithsonian Initiative on Biodiversity Genomics and the Shenzhen, China-based sequencing powerhouse BGI, researchers announced their intent to start the Earth BioGenome Project (EBP). The news was reported in Science. There are other ongoing big sequencing projects such as the UK Biobank, which aims to sequence the genomes of 500,000 individuals.

The significance of the EBP will greatly help “understand how life evolves”, says Oliver Ryder, a conservation biologist at the San Diego Zoo Institute for Conservation Research in California. Though the EBP researchers are still working on many details, they propose to carry out this project in three steps. Firstly, they plan to sequence the genome of a member of each eukaryotic family (about 9000 in all) in great detail as reference genomes. Secondly, they would sequence species from each of the 150,000 to 200,000 genera to a lesser degree. Finally, the sequencing task will be expanded to the 1.5 million remaining known eukaryotic species with a lower resolution, which can be improved if needed. As suggested by EBP researchers, the eukaryotic work might be completed in a decade.

There are many challenges to starting this project. One significant challenge is sampling, which requires international efforts from developing countries, particularly those with high biodiversity. The Global Genome Biodiversity Network could supply much of the DNA needed, as it is compiling lists and images of specimens at museums and other biorepositories around the world. As not all DNA samples in museum specimens are good enough for high-quality genomes, getting samples from the wild would be the biggest challenge and the highest cost. The EBP researchers also need to develop standards to ensure high-quality genome sequences and to record associated information for each species sequenced. (Elizabeth Pennisi, ScienceInsider)

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March 6, 2017 at 8:41 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.

Written by sciencepolicyforall

June 1, 2016 at 9:00 am

Science Policy Around the Web – March 1, 2016

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By: Melissa Pegues, Ph.D.

Photo source: pixabay.com

European Science

Exit from European Union Could impact British Research

As Britain considers its future with the European Union (EU), academics worry that an exit could jeopardize British research. Scientists in the United Kingdom (UK) are concerned that acquiring funding for their work may become more difficult. There is also concern that collaborations between British scientists and researchers in other member states that have been fostered through the EU could be disrupted. Nobel Prize winner Professor Sir Paul Nurse has indicated that because ideas and people are easily shared, all EU scientists have benefited from the union. Science Minister Jo Johnson also believes it would be detrimental to the future of British research if the UK were to secede, and during remarks from an event hosted by the Royal Society stated that “the risks to valuable institutional partnerships, to flows of bright students and to a rich source of science funding mean the Leave campaign has serious questions to answer.”

It remains unclear whether or not scientific funding would be adversely affected by a British exit. Between 2007 and 2013 the UK has supplied over 78 billion Euros to the EU with 5.4 billion Euros specified for research and development. In that same time period, UK researchers have received 8.8 billion Euros from the EU for research. This amounts to approximately 16% of total research funding. However, it is unknown if the UK could still submit applications for funding if they chose to secede. Norway and Switzerland, non-EU members, do receive funding for scientific research through the EU, demonstrating that it may be possible for the UK as well. An exit would also raise questions as to how current large-scale, international collaborative efforts such as CERN and the European Space Agency will proceed. Additionally, the UK has worked with other EU member states to reform policies pertaining to clinical trials that would ease the bureaucratic burden through measures such as simplified reporting and lighter regulations where medicines are already authorized and promote sharing of data, while still protecting clinical trial volunteers. Opponents to staying in the EU, including Scientists for Britain, counter that the UK is not reliant on the EU for funding or participation in collaborative projects. Still, British researchers may lose priority to EU members when trying to access funds, and will lose their political voice in discussion of the future of these projects.

While the potential effects of a British exit from the EU remain under debate, Britons will have much to consider. A referendum has been set for June 23rd. (, BBC News)

Biotech and Intellectual Property

Illumina files suit over DNA sequencing technology

Illumina has recently filed a lawsuit against rival Oxford Nanopore Technologies arguing that technology used in Oxford Nanopore’s devices infringe upon patents held by Illumina for sequencing technology produced by researchers at the University of Washington and the University of Alabama at Birmingham. California-based Illumina, a leader in the development of technologies used for next generation sequencing (NGS), was once an investor in UK-based Oxford Nanopore Technologies, but that relationship ended in 2013 when Oxford Nanopore turned their focus towards technologies not covered by their agreement.

The suit is centered on Oxford Nanopore’s palm-sized MinION sequencer that has been hailed for its size, speed, and low cost. Although the device’s accuracy is not high enough for use in studying human genomics, the device is well-suited for reading smaller sequences and applications where data needs to be read in real time, such as diagnosing infections during epidemics. Indeed, the device was used to identify new infections during the recent Ebola epidemic in Western Africa. Although Illumina does not currently market a similar device, they argue that they have made “substantial investments” in nanopores, and that the pore used in the MinION infringes upon patents that Illumina holds for pores used to read DNA.

Oxford Nanopore was the first to commercialize nanopore technology for sequencing DNA and have planned the release of a higher-throughput device, PromethION, for later this year. If successful, Illumina’s suit could prevent Oxford Nanopore from selling their devices in the US. Some researchers, including Opinionomics author Mick Watson, worry that this could threaten the development of innovative sequencing methods.

Oxford Nanopore’s CEO, Dr. Gordon Sanghera responded to the litigation by stating that “[i]t is gratifying to have the commercial relevance of Oxford Nanopore proucts so public acknowledged by the market monopolist for NGS.” (Erika Check Hayden, Nature News)

Public Heath and Infectious Disease

Japanese encephalitis virus could have a new transmission route in pigs

Mosquitoes have recently been in the news for being potent disease vectors in diseases like Zika. However, many questions remain as to how these mosquito-borne diseases are maintained when their vectors die out over temperate months. A recent study assessing Japanese encephalitis virus (JEV) transmission, a mosquito-borne virus that is distantly related to the Zika virus, provided a surprising answer: pigs. According to the World Health Organization (WHO), the JEV causes approximately 68,000 clinical cases per year. While progression to encephalitis is rare, it can cause lifelong neurological damage or even death. It is well established that pigs act as a reservoir from which uninfected mosquitoes can acquire the virus before spreading the virus to other animals. Although this cycle was well-accepted, a natural question that arose from this paradigm is how the virus is maintained when mosquitoes are absent. The study identified that during the colder months, pigs can pass JEV to other pigs, where “the virus lingered for weeks in the pigs’ lymphatic tissue and tonsils.” This is the first time mosquito-free transmission of the virus has been documented in pigs, but remains to be further validated on the farms where natural transmission occurs. Interestingly, a vaccine does exist for this virus for both humans and pigs. Implementation of this vaccine has proven difficult, since “it’s not cost-effective to vaccinate pigs because they breed and turn over so quickly.” As such, the WHO suggests on their site “that JE vaccination be integrated into national immunization schedules in all areas where JE disease is recognized as a public health issue.” (Laurel Hamers, Science News)

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March 1, 2016 at 9:00 am

Science Policy Around the Web – October 24, 2014

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By: Amie D. Moody, Ph.D.

photo credit: MJ/TR (´・ω・) via photo pin cc

Congress

Congressman continues inquiry into National Science Foundation grant decisions

Members of Congress have been known to call out specific grants awarded by government funding agencies that they deem unworthy of the hard-earned tax payers’ dollars. On August 27th of this year, Congressman Lamar Smith (R-TX), who is the House Science, Space, and Technology Committee Chairman, wrote a letter to the National Science Foundation (NSF) requesting “all official documents pertaining to 20 NSF-approved research projects.” Although the Committee has the authority to oversee government appropriations, he cited no specific reason for the inquiry. In a letter responding to Mr. Smith, the senior Democrat on the Committee, Eddie Bernice (D-TX), argued that this is a “fishing expedition, pure and simple.” Her letter voiced concern that the inquiry is jeopardizing the NSF’s merit-review process and mentioned that a media report contained confidential material that should have only been known to Committee members. In response, Mr. Smith stated, “Our efforts will continue until NSF agrees to only award grants that are in the national interest.” But, to what end? Richard M. Jones, American Institute of Physics

 

Health

To beat once more – surgeons successfully transplant “dead hearts”

Historically, the heart was the only organ not used after it has stopped beating. But now a team of surgeons at St. Vincent’s Hospital in Sydney, Australia, has successfully transplanted three hearts that had stopped beating for up to 20 minutes. The doctors utilized a machine known as a “heart-in-a-box” to revive a stopped heart, and then flush the organ with a nourishing fluid. Similar tactics are used to improve the success of liver and lung transplants. Although the exact data to estimate how many more lives could be saved with these new protocols, one estimate places that number around 30%. No matter what the exact number is, the ability to save even more lives each year is a great achievement. James Gallagher, BBC News Health

 

Genetics

The oldest man

This week, Nature published an article reporting on the completed sequence from a man who lived 45,000 years ago in Siberia. It is the oldest reconstructed sequence from a modern human. A Russian fossil collector, Nikolai V. Peristov, found the bone in 2008 while looking for mammoth tusks in Siberia. He took it to the Russian Academy of Sciences, where researchers dated the thighbone. They ran the tests twice to ensure they were right. Next, a team of scientists led by Dr. Svate Paabo at the Max Planck Institute for Evolutionary Anthropology took samples of the bone and found enough DNA for sequencing. Dr. Paabo’s group has made a name for themselves by deriving highly refined sequencing methods, specifically designed to sequence ancient DNA. They published an entire Neanderthal genome in December 2013. These findings add amazing new insight into modern human migration out of Africa, and place a more precise time frame for how long ago Neanderthals and humans interbred (roughly 50K-60K years ago). Carl Zimmer, New York Times

 

 

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Written by sciencepolicyforall

October 24, 2014 at 2:16 pm