Archive for October 2019
Science Policy Around the Web October 29th, 2019
By Allison Cross PhD
Super-precise new CRISPR tool could tackle a plethora of genetic diseases
Since the first adaption of CRISPR-Cas9 for gene editing in eukaryotic cells in 2013, the hopes of using the technique to cure genetic diseases have been high. Despite the ability of current CRISPR–Cas9 gene-editing tools to edit the human genome, successful edits are often accompanied by unintended and unpredictable errors elsewhere in the genome. However, a new method of editing, published this week in Nature, shows potential for greater control over genome editing.
This new method of genome editing, referred to as prime editing, still uses Cas9 to recognize specific DNA sequencing in the genome. However, instead of producing double stranded breaks, a modified Cas9 enzyme is utilized to cut only one strand of the DNA. The cut strand of DNA (called nicked DNA) is then repaired utilizing a prime editing guide RNA, known as a pegRNA.
Prime editing offers several advantages over a similar previously developed editing technique, known as base editing. Base editing, like prime editing, does not result in double stranded DNA breaks; instead it allows researchers to make specific substitutions to the bases that make up DNA (adenine, guanine, thymine, cytosine). However, it only allows for certain subsets of single base changes to be made (C->T, G->A, A->G, and T->C). Prime editing is more versatile, allowing for all 12 possible base-to-base changes and capable of making multi-base changes. There is, however, a limitation to how large the changes can be using the prime editing technique. If large insertions or deletions are desired, traditional CRISPR-Cas9 tools remain necessary.
Researchers are still evaluating how prime editing works in a variety of cells and organisms, but the initial studies published this week show promise for more versatile and precise gene editing with fewer unwanted byproducts.
(Heidi Ledford, Nature)
U.S. Travel Ban Disrupts the World’s Largest Brain Science Meeting
The travel ban implemented by the Trump administration restricts U.S. travel from 7 nations; Iran, Librya, Somalia, Syria, Yemen, North Korea and Venezuela. The ban has been a very controversial issue with wide ranging implications. After its implementation, many in the scientific community feared the ban would hurt the community by resulting in lost potential collaborators, trainees, and recruits.
This year’s Society for Neuroscience meeting drew more than 25,000 brain scientists from around the world to Chicago this week, however, some scientists were unable to attend due to visa issues. Sepiedeh Keshavarzi, a current Australian citizen who holds an Iranian passport, was invited to give an oral presentation during the year’s meeting. Instead of attending the meeting in person, Keshavarzi instead sent a prerecorded PowerPoint presentation to the meeting after her request for a Visa to the U.S. was denied.
With Visa problems becoming increasing common, the Society to Neuroscience created a special program aimed at helping scientists with Visa issues present their work at this year’s meeting. The program, called Science Knows No Borders, did help some scientists, like Keshavarzi, present their work; however, fewer than a dozen scientists participated in the program.
(Jon Hamilton, NPR)
Science Policy Around the Web October 25th, 2019
By Andrew Wright BSc
NIH and Gates Foundation lay out ambitious plan to bring gene-based treatments for HIV and sickle cell disease to Africa
Following the launch of an initiative to boost gene therapy treatments of sickle cell disease last month, the National Institutes of Health (NIH) and the Bill and Melinda Gates foundation have announced a joint funding agreement of at least $100 million over the next four years to expedite a cure for both sickle cell disease and HIV and make it available in Africa.
The current medical intervention for sickle cell disease is a bone marrow transplant, a treatment that is limited by the availability of genetically compatible donors and can be risky for adult patients. This new partnership aims to build on funding towards more effective treatments that are less restricted and more cost effective. While genetic intervention is being used in a limited clinical setting, it is still necessary to destroy a patient’s stem-cells via chemotherapy before reintroducing the patient’s genetically modified ones. Using burgeoning gene-editing techniques such as CRISPR, researchers for this initiative hope to modify targeted genes with a process more similar to a blood transfusion using replication-deficient viruses or nanoparticles to carry the molecular tools to where they need to be. This should theoretically make treatments much less expensive and more available to regions that have limited medical infrastructure and a high incidence of sickle cell disease such as sub-Saharan Africa.
Since there is also a high incidence of HIV in sub-Saharan Africa, this initiative also aims to tackle HIV in the region using similar techniques. The current standard for treating HIV is anti-retroviral therapy, which can allow patients to live a normal life, but also must be taken every day, is expensive ($429-$10,896 per month), and does not eliminate the disease. The drive behind genetic intervention strategies comes from serendipitous case-studies when two men were cured of HIV following stem cell transplants that intentionally had white-blood cells with a weakened protein to treat their blood cancers. The NIH-Gates funding initiative will focus on strategies to weaken these proteins (called CCR5 receptors) and to directly destroy HIV genetic material.
(Jon Cohen, Science)
Evidence links poliolike disease in children to a common type of virus
Since 2014 more than 570 children have experienced a condition known as acute flaccid myelitis (AFM) where some suddenly lost limb control, had trouble swallowing or breathing, or ended up paralyzed. These symptoms routinely followed symptoms of a common cold, like a runny nose or fever. Up until now, the route cause behind AFM was not well understood, but recent studies of patients’ spinal fluid suggest the culprit is enterovirus. Infections from enteroviruses are common and rarely cause severe symptoms (although they can cause respiratory illness in asthmatic populations).
Previous studies into the cause of AFM had examined enterovirus but found no trace of it in the central nervous system, where it would need to be in order to lead to loss of motor control. In the most recent study conducted by the University of California San Francisco, researchers sampled for elevated levels of antibodies in the central nervous system rather than the virus itself. They found that 69% of AFM patients had elevated antibodies against enteroviruses. There are still questions as to why only some children experience AFM when infected by enterovirus when most only experience typical symptoms.
Unfortunately, enterovirus-AFM is currently untreatable beyond post-infection physical therapy, although the lead author of the study suggests that immunoglobin therapy may help reduce the worst symptoms. Ultimately, the only way to completely prevent enterovirus-AFM infections, referred to by some as ”the new polio“, will be a vaccine.
(Kelly Servick, Science)
Science Policy Around the Web October 22nd, 2019
By Mohor Sengupta PhD
What’s Behind The Research Funding Gap For Black Scientists?
A recently published study by a group of NIH investigators has found possible reasons for the funding gap that exists between grant proposals submitted by black and white researchers. This gap was first revealed in a report published in 2011 that found that black applicants to NIH grants were awarded funding at a significantly lower rate than white applicants to the same grant. These data prompted the NIH to investigate the grant funding process.
In this paper, the authors analyzed keywords in grant application topics and found that some topics were four times more likely to get funded than others. Broadly, topics dealing with the mechanistic basis of science on a micro-level, such as genetics, or cellular mechanisms were more likely to grab the attention of grant reviewers than grants involving population sciences and community-oriented research. Grants on these subjects are more commonly proposed by African American applicants.
The authors find that black researchers tend to pursue studies on topics that are more connected with their communities. Such topics include health disparities research, which unfortunately don’t figure as priority in grant reviewers’ radar, possibly because they don’t see things through the same lens when evaluating proposals. This may be because the grant reviewers didn’t have similar life experiences while growing up as a person belonging to a minority community might have. In the present study, only 2.4% of grant reviewers was black.
In the study, self-reported demographic data of applicants was not visible to grant reviewers. As a next step, the authors will investigate if applicant anonymity decreases the existing funding gap.
(Emily Vaughn, NPR)
Marijuana and Vaping: Shadowy Past, Dangerous Present
A severe lung disease has been affecting users of e-cigarettes with marijuana. So far nearly 1500 people have become sick, and 33 have died of the mysterious disease. Residents of 49 states and the District of Columbia have reported the vaping-related illness. While the cause of the disease remains unknown, experts say that THC, the chemical in marijuana that makes people feel high, produces different components when burned in rolled joints versus when aerosolized in vaping devices. The latter may have unknown harmful chemicals.
However in addition to THC, vaping oils contain additives, solvents and flavor enhancers. It is unclear which of these ingredients is the culprit, but vitamin E acetate is a likely candidate for the illness. The obscurity surrounding illness-causing vaping components in part exists because of restrictions imposed on cannabis research by the federal government. The reason behind this is the high abuse potential of cannabis, which classifies it as a controlled substance not available for research.
This rule annoys scientists and industry experts alike. Lack of hard science and awareness among the vaping community is made worse by the many cheaper products freely available in black markets, both in states where vaping THC is illegal and legal. As counterfeit cartridges are much cheaper than the tested and taxed licensed products, these have many consumers. Vaping cartridges sold on the black market are not tested.
Considering the recent illnesses taking a toll on people who use e-cigarettes to smoke cannabis, the government should allow investigation into the chemical underpinnings of the disease.
“I’m not able to take products we think are potentially harmful and do analysis. I can buy a vape device around the corner, but I can’t bring it into the lab and test it,” UCSF researcher on nicotine and vaping, Dr. Neal Benowitz said. Benowitz has sent a letter to the congress about the hugely popular and unstudied practice of vaping.
(Matt Richtel, The New York Times)
Science Policy Around the Web October 18th, 2019
By Ben Wolfson PhD
Scientific integrity bill advances in U.S. house with bipartisan support
On Thursday the U.S. House of Representatives Science Committee voted to advance scientific integrity bill H.R. 1709 to the house floor by a vote of 25 to six.
H.R. 1709 would require federal research agencies to develop their own clear principles that would protect scientists and the research they carry out from political influences. The bill originates from a 2010 executive order by then-President Obama instructing Federal departments and agencies to “share tools and good practices to improve the implementation of scientific integrity policies across the Federal government”. While some agencies have adopted these policies already, if passed the bill would turn the order into a law requiring all to do so.
The bill comes two years after the Trump Administration restricted Federal Scientists at U.S. Department of Agriculture and the Environmental Protection Agency (EPA) from discussing agency research with news media in February of 2017. In October 2017 the Administration blocked scientists from the EPA from discussing their research at a conference, and censored Interior Department Biologists from voicing concerns about the impact of the border wall on wildlife in October of 2017. Earlier this month, dismissed EPA science advisors gathered to rebuke the EPA’s handling of pollution standards standards.
House Democrats initially did little to separate H.R. 1709 from these actions, leading Republicans to believe that it was a direct rebuke to the Trump Administration. However, Thursday morning the Science Committee stated that “scientific integrity transcends any one Party.” While the initial bill gave scientists the right to talk to the media without agency clearance, Democrats met their Republican colleagues halfway by removing the language, leaving all media decisions up to the agency.
Now that H.R. 1709 has passed in the Science Committee, it needs to win approval from the House of Representatives before moving to the Senate and eventually for signing by President Trump.
(Jeffrey Mervis, Science)
Science Policy Around the Web October 15th, 2019
By Neetu M. Gulati PhD
Nobel Prize in Chemistry Awarded to Developers of Lithium-Ion Batteries
Three scientists won the Nobel Prize in Chemistry this year for their work developing lithium-ion batteries, a technology that led to a revolution in electronics. John B. Goodenough of the US, M. Stanley Whittingham of the U.K, and Akira Yoshino of Japan were instrumental in making these rechargeable batteries a reality. The Nobel Committee for Chemistry said that lithium batteries have enabled devices to become smaller and more powerful. One member of the Committee, Olof Ramström, explained, “this battery enabled our mobile world… we now have power anywhere we go.”
The winners for the Nobel Prize in Chemistry will share a cash prize of over $900,000 and will each receive a gold medal and diploma in December. Other winners of the Nobel Prize in scientific fields for this year were also recently announced. The Nobel Prize in Physics was awarded to Canadian-American scientist James Peebles and Swiss scientists Michel Mayor and Didier Queloz, for their work in the physical cosmology and discovery of exoplanets orbiting a solar-type star. The Nobel Prize in Physiology or Medicine was awarded to American researchers William Kaelin and Gregg Semenza and British researcher Peter Ratcliffe for their discoveries of how cells sense and adapt to oxygen availability.
(Brianna Abbott, Peter Landers and Joanna Sugden, Wall Street Journal)
Prestigious journal pulls paper about chemical attack in Syria after backlash
The journal Science and Global Security (SGS) has chosen not to publish a controversial paper, after previously choosing to accept the paper for publication. The reversal came after backlash from scientists accusing one of the authors of the paper, Ted Postol, a expert on missile defense, of pushing conspiracy theories. The subject of the paper is a sarin gas attack that killed more than 80 people in a rebel-held town in Syria in April 2017. The paper casts doubt on the Syrian government’s responsibility for the chemical attack, despite the fact that two international organizations, the Organisation for the Prohibition of Chemical Weapons (OPCW) and the Joint Investigative Mechanism (JIM) of the United Nations, have concluded that the Syrian government had dropped a sarin-filled bomb on the town.
The authors of the paper used computer modeling to argue that the impact crater where it is believed sarin gas was released was created by an artillery rocket fitted with an explosive rocket, not a bomb. Furthermore, Postol has separately suggested that sarin was not used at all in the attack, and that this attack and two others he examined were not caused by the Syrian regime.
Gregory Koblentz, a biological and chemical weapons expert, argued that the purpose of the paper was “to challenge the impartiality and competence of the OPCW and JIM,” and urged SGS not to publish the manuscript. He argued that the paper would be “misused to cover up the [Assad] regime’s crimes.” The journal’s editors decided to hold off on publishing the manuscript, citing issues with peer-review and the revision process. The journal’s website now states that “The Editors have decided to return this manuscript to the authors without prejudice and not proceed further with considering it for publication.”
(Kai Kupferschmidt, Science)
Science Policy Around the Web October 11th, 2019
By Ben Wolfson PhD
Massive California power outage triggers chaos in science labs
On Wednesday and Thursday of this week, upwards of 600,000 California residents lost power when Pacific Gas & Electric, the state’s largest utility company, instituted rolling blackout. Due to high winds, PG&E worried that keeping power on could result in sparking and increased risk of wildfires.
PG&E has been found to be liable for approximately two dozen wildfires, including the deadly 2018 Camp Fire, and filed for bankruptcy in January of 2018 due to the lawsuits it faced. The weeks rolling blackouts were instituted in an attempt to prevent further wildfires. State Senator Jerry Hill (D-CA), stated that the decision to target such large numbers of people for blackouts demonstrated the serious risk of fire, but also showed that PG&E has so far failed to improve the safety of their power system.
In addition to affecting residential customers, the rolling blackouts have also thrown scientists and research labs into disarray as they struggle to protect valuable reagents and samples. Many labs have limited or no access to backup power, meaning items that must be refrigerated or frozen are at risk of being lost when they increase in temperature. In addition, tissue culture requires a stable environment maintained by a powered incubator, and laboratory animals need filtration and temperature control systems that may be shut off in light of power loss.
While California has always had high risks of wildfires, the warming climate has increased the chance and frequency of deadly fires. California’s annual burned area has increased 5-fold since 1972, and 7/10 of the most destructive fires have occurred in the last decade.
(Jeff Tollefson, Nature)
Science Policy Around the Web October 8th, 2019
By Mary Weston PhD
A single tea bag can leak billions of pieces of microplastic into your brew
A recently published studyfrom McGill University shows that plastic teabags release billions of plastic micro- and nanoparticles into your tea. Researchers steeped plastic tea bags in 95°C (203°F) water for 5 minutes, finding that a single bag released approximately 11.6 billion microplastics and 3.1 billion nanoplastics. This concentration of plastic particles is thousands of times larger than any other reported food/drink item.
Although tea bags contain food-grade, FDA approved plastics, researchers know little about how plastics can degrade or leach toxic substances when heated above 40C (104F). Based on these new results, the study’s authors conclude that more research needs to be done to both determine how microparticles are released in our foods and the impact those substances have on human health.
To gain insight on the effect of plastic particle exposure, researchers grew water fleas, a common environmental toxicology model system, in the brewed solution, discovering they survived but had both behavioral and developmental abnormalities. While the plastic particle exposure levels these fleas experienced are far greater than what humans would be exposed to, it begs the question of what happens to humans with chronic low-dose exposure over time.
Microplastics are being detected everywhere, from the deepest parts of the ocean to regularly consumed bottled water, and their effect on human health have yet to be seen. One study suggests humans are consuming 5 grams of plastic a week, approximately the weight of a credit card. However, In their first review of microplastics in tap and bottled water, the WHO asserts that microplastics “don’t appear to pose a health risk at current levels,” but also state that knowledge is limited and more research is needed to determine their impact on human health.
(Rob Picheta, CNN)
Science Policy Around the Web September 30th, 2019
By Allison Dennis B.S.
23andMe, moving beyond consumer DNA tests, is building a clinical trial recruitment business
Clinical trials are often criticized for poor patient recruitment that inadequately represents patients from minorities, e.g., women of reproductive age, racial minorities, underserved patient populations and people with rare genetic diseases. To fight this, 23andMe feels that its vast database of patients comfortable enough to trade their genetic information and a small bit of spit to learn more about their genetic predisposition to disease and heritage could be a much-needed recruiting tool for those enrolling patients in clinical trials, and one they would be willing to pay for.
23andMe can mine the database of their 8 million potential research participants to identify which customers fit the needed demographics and genetic profiles relevant for studying a particular drug. For example, 23andMe found about 7,500 carriers of a rare mutation in the gene LRRK2, a potential target being pursued by GlaxoSmithKline to prevent the progression of Parkinson’s disease. In patient populations, this mutation is only found in one in a thousand people, meaning it would take years to identify enough participants to enroll in a trial. With enough potential participants to choose from trial managers are hoping to to recruit local patients, allowing them to overcome the costs of paying for patient travel and ease the stress patients experience by spending extended time away from home.
To augment the diversity of their database, 23andMe has launched programs to provide free genetic analysis to people whose four grandparents were born in the same country. The Global Genetics Project focuses on underrepresented countries like Mali, Tajikistan, and Paraguay, while the African Genetics Project focuses on the ethnic and tribal groups of countries such as Cameroon, Ghana, Libera, and Senegal. By starting with the genomes of people with clearly known ancestry to better define the genetic differences common to them, 23andMe is hoping it will be able to improve its unravelling of more complicated genetic lineages. A greater diversity of enrollees is sure to appeal to clinical trial recruiters, who are trying to meet FDA guidelines designed to enhance the diversity of clinical trial populations.
It remains to be seen how receptive 23andMe customers will be to being targeted for participation in clinical trials. Many of the 8 million may not have fully realized that consenting to genetic research would potentially extend to drug companies paying for their data. However, for many people, the possibility of playing a role in the discovery of cures for genetic diseases may outweigh privacy concerns and any initial discomfort from being singled-out.
(Rebecca Robbins, STAT News)
NIH reveals its formula for tracking foreign influences
NIH’s extramural research program is struggling to find the balance between curbing inappropriate information sharing, fostering the international collaboration recognized as necessary for the global pursuit of science and maintaining some level of ease in the grant application process. The grants that are distributed by NIH are won following review by a panel of experts, composed of about 27,000 reviewers recruited to serve on committees by NIH each year. It is believed that some reviewers have violated NIH policy by sharing the confidential contents of grant applications with international colleagues. The data and research approaches described in grant applications is proprietary and often has the potential to result in patents in addition to publications.
A more complicated scheme concerning officials involves international researchers setting up labs in parallel, one in the US to win grant money, and one in a foreign country where the grant winner wishes to benefit from any emerging intellectual properties stemming from the funded research. Such an arrangement allows US funded discoveries to be transferred to another country without any oversight from the US government.
It is difficult to clearly spot scientists unfairly leveraging their role in NIH grant giving activities. While grant reviewers are not supposed to share any parts of the application, it is common for researchers to share grants with trainees in their lab, sometimes seeking relief from the burden of review by having junior researchers take the first look, other times viewing it as a needed opportunity for future grant-seekers to become familiar with the process. Grant applicants routinely have joint appointments with international institutions. This is acceptable if clearly disclosed when they seek funding from NIH.
In the past the issue has been treated as a regulatory hot potato, NIH requires grant seeking institutions certify the grantee listed on the application, institutions rely on the assumption that foreign scientists would be denied visas by the US Department of state if they were thought to have improper ties to their home countries. Of course, citizens that are US citizens are at risk of behaving improperly as well. NIH is taking the next sixth months to develop a risk-based approach to flag potential conflicts with reviewers. As a first step they are considering moving grant reviews to a read-only online portal to prevent any untracked distribution of downloaded applications.
(Jeffrey Mervis, Science)
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