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Posts Tagged ‘DNA sequencing

Science Policy Around the Web – February 22, 2019

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By: Janani Prabhakar, Ph.D.

Source: Pixabay

China Uses DNA to Track Its People, With the Help of American Expertise

Recently, global attention fell on China and its treatment of its Uighur people, a predominately Muslim ethnic group who live in the far west region of China and have enjoyed a fair degree of self-autonomy from the Chinese government. In an attempt take control of this ethnic group and region, the Chinese government has used intense surveillance, oppression, and detainment through “re-education” camps. In addition, the Government has been collecting DNA samples from this ethnic group to generate a comprehensive database of Chinese Uighurs. What is unknown is how the Chinese government intends to use this database in its oppression of Chinese Uighurs. To complicate matters, collection of DNA samples has been bolstered by equipment and data from US-based companies and researchers. For example, Thermo Fisher supplies technology to support DNA data collection and analysis. Yale geneticist, Dr. Kenneth Kidd, provided genetic material from global populations to Chinese researchers. In both cases, the US parties were unaware of how their contributions were used. This brings to bear larger questions about culpability, adherence to scientific norms, and the role of scientific collaborations at a global scale. China has included these DNA samples in global databases, but it does not seem that proper consent was received for these samples. In some reports, individuals were called by police for mandatory health screening and medical checkup, suggesting that the samples were obtained through coercion. It is unclear whether inclusion of these samples in databases or during collaborations reflects tacit acceptance of China’s surveillance program of Uighurs.

Researchers including Dr. Kidd have hosted Chinese researchers in their labs to gain techniques in analyzing DNA material. The output of these collaborations has resulted in publications that provide methods to distinguish between ethnic groups, wherein Chinese researchers utilize DNA samples obtained from collaborators as a comparison group to Uighurs. Chinese officials state that this would be useful to identify individuals at a crime scene, which on the surface, is not an incorrect application or use of the data. However, in light of the allegations on the Chinese government in their use of this technology to oppress certain minority groups, the role of scientific collaboration becomes murky. In addition to collaboration is the question about US corporate involvement. Thermo Fisher recently announced that they would stop selling their products that have been integral to forensic DNA analyses in Xinjiang, where the campaign to suppress Uighurs has been most intense. This is striking given that 10 percent of Thermo Fisher’s $21.9 billion-dollar revenue comes from China. While this is a big step, monitoring how technology and science is being used in this global environment must be a central focus given the large human rights implications.

(Sui-Lee Wee, New York Times

The Energy 202: One of world’s biggest coal miners caps production amid climate 

In response to increasing public pressure, Glencore, one of the world’s largest mining companies, has announced that it will cap the amount of coal it mines. Evidence of private companies responding to this global pressure to reduce greenhouse gases has emerged around the world. Most recently, the Tennessee Valley Authority voted to shut down two aging coal-fired power plants. These actions reflect big shifts in an industry that has largely debunked climate change theories, particularly when President Trump has promised to bring back coal.  The pressure on private companies came from more than 200 institutions worldwide that targeted the world’s largest emitters. This has led to a wave of corporations like Glencore to make similar reduction pledges. These commitments are multi-pronged. Glencore has agreed to limit coal production (and not increase it) annually, in a shift away from its original production trends. In addition, the company has considered tying executive pay with meeting these goals as well as ending partnerships with coal lobbies.

This move towards reduction has also come from a waning coal market and its economic promise for companies like Glencore. While many countries like the United States and other advanced economies have reduced their coal use, Asian countries like India and China have increased it. Glencore exports most of its coal to coal-using countries in Asia. As a result, it is actually in the economic interest of private coal companies to reduce coal production:  restricting supply as demand wanes will increase coal prices and increase Glencore’s revenue. Important to climate change activists, increase in coal prices would lead over time to a reduction in coal use. In this way, private companies can work in partnership with efforts to reduce greenhouse gases without compromising their own interests.

(Dino Grandino, New York Times

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February 22, 2019 at 2:08 pm

Science Policy Around the Web – October 12, 2018

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By: Allison Dennis B.S.


source: pixabay

The power of genetics

We will find you: DNA search used to nab Golden State Killer can home in on about 60% of white Americans

In April, the worlds of law enforcement and personal DNA sequencing collided to forever change the game of forensics when detectives were able to identify a California man now charged with thirteen murders using a public database intended for connecting relatives through genetic ancestry. For almost 40 years, an unprocessed rape-kit from the case remained in storage, preserving the perpetrator’s DNA until forensic technology emerged that allowed investigators to profile thousands of DNA markers contained in the genetic material extracted from the kit. The markers used were part of the expansive panel usually included in direct to consumer DNA tests rather than those routinely included in law enforcement DNA databases. After submitting the complete DNA profile to the ancestry website GEDmatch, law enforcement agents found hits for several people genetically third-cousins to the killer, massively narrowing the list of suspects.

Since April, this so called “genetic genealogy” technique has been used by Parabon Nanolabs to identify about twenty other perpetrators from DNA queried from a hundred other cold cases using the 1 million profiles available through the GEDmatch database. While the science and methods behind this company’s success remain private, scientists have gotten curious about how realistic it is to use these types of searches.

Yaniv Elright, a computational geneticist at Columbia University, used a similar database of 1.28 million DNA profiles, MyHeritage, to find out. Searches revealed that for someone of European ancestry living in the United States the odds are as high as 60% that a genetic relative can be identified. This drops to 40% for someone of sub-Saharan ancestry, most likely due to 75% of the database being primarily of North European genetic background and therefore offering fewer potential matches.

As a further exercise, the researchers sought to use this approach to explore the feasibility of re-identify an anonymous DNA donor included in a public collection. While the process took a full day and was “time consuming and not trivial” according to the authors of the study, they were able to re-identify the individual. This finding calls into question the assumption baked into US federal research rules that removing identifying information is enough to anonymize DNA profiles. Just this week, half a million de-identified genomic profiles were made publicly available through the UK Biobank resource, which could be queried by “genetic genealogy.”

It is clear that DNA profiles when combined with genetically defined family trees represent a tremendous opportunity for identification. Already, ethicists and law experts are calling for legislative bodies to draw the line defining in what types of criminal cases these techniques can reasonably be used.

(Jocelyn Kaiser, Science)


Dietary Supplements

Dietary Supplements Can Contain Viagra, Steroids, or Worse

More than half of the adults living in the US report taking dietary supplements, an industry that is only regulated once products hit the shelves. It has been estimated that supplement use is responsible for more than 23,000 emergency room visits each year in the US, stemming from symptoms including heart palpitations, chest pain, and choking. The FDA maintains a list of Tainted Products Marketed as Dietary Supplements, whose disclaimer warns that it “only includes a small fraction of the potentially hazardous products with hidden ingredients marketed to consumers.” Testing is usually only pursued by the FDA once a consumer or physician has issued an alert.

Between 2007 and 2016, the FDA discovered that 776 tested dietary supplements contained unapproved pharmaceutical ingredients. Of these, 360 were voluntarily recalled by the manufacturer. For others on the list, the FDA issued warnings about 342, news releases for 58, consumer updates for eight, direct warning letters for seven, and a suggestion to the US Justice Department to investigate one for criminal wrongdoing. Although the FDA was granted the power to do so as early as 2011, the only mandatory recall that has been issued by the agency came in April of 2018 when a batch of Kratom capsules was discovered to contain salmonella, a known bacterial cause of diarrhea, fever and abdominal cramps.

Sexual enhancement, weight loss, and muscle building seem to be the common ailments targeted by the adulterated supplements, which were laced with sildenafil, sibutramine, and synthetic steroids. Sildenafil is the active pharmaceutical ingredient in Viagra, which is closely regulated by the FDA and requires a prescription. Sibutramine, which has been used for the medical treatment of obesity, was withdrawn from use in 2010 due to an increase risk of cardiovascular events. Short-term synthetic steroid use can lead to mental problems including paranoid jealousy, irritability, delusions, and impaired judgment. Long-term, they can lead to kidney problems, liver damage, and high blood pressure.

To what extent consumers perceive these over-the-counter supplements to be safer than regulated pharmaceuticals is unknown. Advocates for visible regulation, suggest that firms register all supplements before they are sold, which would give the FDA the opportunity to step in before customers risk injury.

(Emily Dreyfuss, Wired Magazine)

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October 12, 2018 at 4:19 pm

Science Policy Around the Web – July 6, 2018

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By: Kelly Tomins, BSc


source: pixabay

Genetic privacy

Could DNA Testing Reunite Immigrant Families? Get the Facts.

Since the enactment of the Trump administration’s “zero tolerance” immigration policy, over 2300 children have been separated from their families at the border. The policy caused widespread outrage throughout the US, and over 400,000 people protested the policy at the “Families Belong Together” march last week. Although the policy has since been redacted, the government has shown little transparency on how they plan to reunite families. Could DNA testing be a solution?

DNA testing companies, MyHeritage and 23andMe, seem to think so. They have offered thousands of testing kits to help reunite migrant children to their families. Scientifically, these tests are very reliable, and can detect direct relations by 99.9% accuracy. However, the science is the least complicated aspect of this situation.

Consent and privacy are several of the most troubling aspects of the use of these tests. Due to medical privacy rules, children would need a designated legal guardian or representative to have their DNA tested, which is clearly a problem. In addition, adults likely cannot give informed consent, especially since they are in distressing conditions and many do not speak English. Migrants may feel pressured to have the sequencing done if they believe it is the only way to be reunited with their children. DNA sequencing reveals private information about health and paternity, and sequencing data stored in databases has been used to genetically track criminals. It is difficult to imagine that detainees would be given enough information about DNA sequencing and its’ implications to make an informed decision.

Despite these concerns, according to an unnamed federal official, DNA testing has already begun. Jennifer K. Falcon, communications director for RAICES, a nonprofit in Texas that offers free and low-cost legal services to immigrants and refugees, is extremely against DNA testing in this context. In addition to her concerns regarding consent, she argues that the government will have access to extremely personal data that could be used for future surveillance. Although 23andMe and MyHeritage have assured that the genetic data will only be used for reunification, it is unclear what will happen to the DNA samples and data afterwards.

Beyond the ethical and logistical hurdles in this case, DNA sequencing is not a quick fix. 23andMe state on their website that sample processing takes 6-8 weeks. It would also be a logistical nightmare to obtain and match DNA samples from all the detainees currently in custody, especially when matching results from two different genetic testing companies. Critics point out that registering the identity and locations of migrant parents and children would have circumvented the need for such invasive testing. Although genetic tests are cheaper and more accessible than ever, they require unique consideration to address issues of privacy and consent.

(Maya Wei-Haas, National Geographic)

Endangered species

Rhino Embryos Made in Lab to Save Nearly Extinct Subspecies

Thousands of northern white rhinos once inhabited the grasslands of east and central Africa, but habitat loss and poaching led to the population’s swift demise. All hope for the survival of the rhino subspecies seemed lost when the its’ last remaining male, Sudan, died earlier this year.  There are now only two surviving individuals of the subspecies, a mother-daughter pair named Najin and Fatu, both of whom are infertile. Remarkably, a new breakthrough in reproductive technology has reignited the possibility of saving this subspecies.

In a recent study published in Nature Communications, Dr. Thomas Hildebrant, a wildlife reproductive biologist, and his team show for the first time that rhino embryos can be created using in vitro fertilization (IVF). Although there are no remaining living males of the subspecies, there are four samples of frozen sperm that could potentially be used for reproduction. The research group created four hybrid embryos by combining frozen northern white rhino sperm and eggs from southern white rhinos. The scientists plan on implanting these hybrid embryos into surrogates, to see if they survive to birth. If that is successful, the scientists aim to extract eggs from the remaining female northern white rhinos and create pure-blood northern white rhinos in the lab.

Since there is a limited supply of northern white rhino gametes (only four sperm samples and two egg samples), Hildebrant and his team are also pursuing a technology called induced pluripotent stem cells (iPSC). iPSC are a type of stem cell that can be created from adult cells, such as skin or blood. These iPSC can then be reprogrammed into various cell types. iPSC have already been created from northern white rhinos, and scientists are now figuring out how to convert them to sperm and eggs. Since the San Diego zoo has skin cells from 12 northern white rhinos, the future conversion of these cells into gametes could provide more genetic diversity to any future population.

While many conservation scientists applaud the use of technology to save the subspecies, many wonder whether the resources should rather be spent protecting habitats for remaining rhinos on-the-ground. In a study in Nature Ecology and Evolution, scientists show that de-extinction efforts can lead to a net biodiversity loss, since resources could be spent on endangered species. As Dr. Bennett, a conservation scientist at Carleton University, puts it “if the person is couching de-extinction in terms of conservation, then she or he needs to have a very sober look at what one could do with those millions of dollars with living species — there’s already plenty to do.”

(Steph Yin, New York Times)

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July 6, 2018 at 3:11 pm

Science Policy Around the Web – June 6, 2018

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By: Leopold Kong, PhD


source: pixabay

Research funding

China increasingly challenges American dominance of science

Earlier this year, China’s science minister announced that China’s total spending on research and development in 2017 was estimated to be US$279 billion, which is up 70.9% since 2012 and represents 2.1% GDP. In comparison, the United States devoted 2.8% GDP to research and development that same year.  In terms of scientific research, the United States spends half a trillion dollars, more than any other country, but China has pulled into second place and is on track to surpass the U.S. by the end of this year, according to the National Science Board.  In fact, China surpassed the US in terms of scientific publications in 2016. According to Pastor-Pareja, a geneticist who gave up Yale for Bejing, there are now 30 fly genetics laboratories in Beijing, more than in either Boston or San Francisco. Furthermore, China has 202 of the world’s 500 most powerful supercomputers, 60 more than the U.S., and the largest radio telescope ever built, a US$180 million dish used to hunt for black holes.

The increased investment in science has enabled Chinese scientists to make more cutting edge discoveries.  For example, last year, biologists in China were the first to clone a monkey, which may speed medical research. Chinese physicists developed the proof of concept for a quantum communications system that is theoretically instant and secure. Much of this growth is driven by aggressive recruiting programs such as the Thousand Talents, which targets Chinese citizens who have studied science in the United States or elsewhere, driving a “reverse brain drain”.  The program has recruited more than 7,000 scientists, who are given a US$160,000 signing bonus and guaranteed research funding for many years.  Foreign-born scientists may get additional perks such as subsidies for housing, meals, relocation and additional bonuses.

Despite the massive growth in science, Chinese research faces challenges in quality control.  For example, last year, 107 scientific papers involving over 400 Chinese authors were retracted in a major publication fraud.  In fact since 2012, China has retracted more scientific papers because of faked peer-reviews than all other countries and territories put together, according to Retraction Watch.  In 2013, Science had exposed a thriving academic black market in China involving corrupt scientists and editors operating in plain view.  Poor quality Chinese research may be exacerbated by lack of stringent regulatory systems. “In America, if you purposely falsify data, then your career in academia is over.  But in China, the cost of cheating is very low. They won’t fire you. You might not get promoted immediately, but once people forget, then you might have a chance to move up”, said Zhang Lei, a professor of applied physics at Xi’an Jiaotong University in an interview with the New York Times.  Still, China has much to offer as collaborators according to experts. Denis Simon, executive chancellor of Duke Kunshan University noted, “The Chinese, for the first time, really have something to offer us. It is vitally in the U.S. interest to plug in.”

(Ben Guarino, Emily Rauhala and William Wan, The Washington Post)


Took an ancestry DNA test? You might be a ‘genetic informant’ unleashing secrets about your relatives

Last Friday, police revealed parts of the arrest warrant for Joseph DeAngelo, the 72 year old former police officer accused of being the Golden State Killer who committed at least 12 murders, more than 50 rapes and over 100 burglaries from 1974 to 1986. Until recently, DeAngelo had eluded capture until DNA from a genealogical website was found to match the DNA found at one of the killer’s crime scenes. The lead from the website belonged to a distant relative of the suspect which helped lead the authorities to focus their investigation on DeAngelo.  Supplemented with other evidence, such as saliva collected from the suspect’s garbage can for a more direct DNA match, the authorities arrested DeAngelo in April of this year.

The DNA match was found on GEDmatch, a Florida- based website that pools raw genetic profiles, which now number more than a million genomes.  In at least eight states, authorities can search law enforcement databases for possible genetic matches.  Genetic family searching has been used numerous times in the past.  For example, in 2003, Craig Harman was identified as the individual who threw a brick through a windshield of a passing vehicle that caused the driver to suffer a fatal heart attack via a DNA match to Harman’s brother. In 2011, the serial killer Lonnie Franklin, charged on 10 counts of murder, was identified through DNA of Franklin’s son.

While genomics searching may provide valuable leads, some critics say it infringes on privacy. “When you put your information into a database voluntarily, and law enforcement has access to it, you may be unwittingly exposing your relatives — some you know, some you don’t know — to scrutiny by law enforcement. Even though they may have done nothing wrong,” said Andrea Roth, assistant professor of law at UC Berkeley Boalt School of Law and an expert on of forensic science in criminal trials.  Genomics searching failed in 2014 when Micheal Usry, a New Orleans filmmaker was falsely accused of murder using evidence from AncestryDNA after authorities asked for access to the data through a court order. “…even though it is easy to think of this technology as something that is used just to track down serial killers,” says Roth, “If we allow the government to use it with no accountability or no further safeguards, then all of our genetic information might be at risk for being used for things we don’t want it to be used for.”

(Ashley May, USA Today)

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June 5, 2018 at 10:00 pm

Science Policy Around the Web – April 14, 2017

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By: Leopold Kong, PhD

Fatty foods: By Lucasmartin2 (Own work) [CC BY-SA 4.0], via Wikimedia Commons

Health Policy

Banning Trans Fats in New York Prevented Thousands of Heart Attacks

In an effort to lower the incidence of heart disease, the leading cause of death in the United States, the FDA will prohibit food manufacturers from using trans fats next summer. FDA’s decision was based on decades of research linking trans fat consumption with increased risk of heart disease. A study published this Wednesday in JAMA Cardiology provided further support for the ban. Using data from the New York State Department of Public Health, collected from 11 counties where trans fats restriction was recently implemented, the researchers showed a statistically significant decline in heart attack (7.8%) and stroke (3.6%) events since then. “The most important message from these data is that they confirm what we predicted — benefit in the reduction of heart attacks and strokes,” said the lead author, Dr. Eric J. Brandt, a fellow in cardiovascular medicine at Yale. “This is a well-planned and well-executed public policy.” With the rising cost of health care in the United States, the FDA’s long awaited trans fat ban is urgently needed to lighten the public health burden. (Leah Samuel, STATNews)

Vaccine Research

The Human Vaccines Project, Vanderbilt and Illumina Join Forces to Decode the Human Immunome

Rapidly evolving viruses such as HIV and Hepatitis C have been difficult targets for traditional vaccine development, in which inactivated viruses or viral proteins are used as vaccine components. Despite the success of small molecule therapeutics against HIV and Hepatitis C, an effective vaccine remains the most cost effective solution to curb the global pandemics caused by these viruses. Scientists now seek to optimize vaccine candidates based on a deeper understanding of host-pathogen interactions using multidisciplinary approaches, ranging from protein engineering and evolutionary biology to immunology and genetics. To facilitate these sophisticated efforts, the Human Vaccines Project, an international public-private collaboration, was established. A major initiative of the project, the Human Immunome Program, is led by Vanderbilt University Medical Center. Now, Illumina has joined the collaboration to help decipher the genetic features of the immune system, or the “immunome,” using cutting edge sequencing technology. DNA sequences from immune cells during infection may capture how the immune system adapts to viruses, providing guidelines for vaccine design. “Successfully defining the human immunome will provide the foundational knowledge to usher in a new era of vaccine, diagnostic, and therapeutic development,” says Gary Schroth, vice president for product development at Illumina. Greater understanding of the immunome may also lead to more effective cancer vaccines. (Human Vaccines Project)


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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)


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.

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June 1, 2016 at 9:00 am

Science Policy Around the Web – March 1, 2016

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By: Melissa Pegues, Ph.D.

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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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Written by sciencepolicyforall

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


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



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



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