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Museum of Natural History

Museum of Natural History | WWWBiology | Scoop.it

The Smithsonian Museum of Natural History is a fabulous resource in Washington D.C., but now this museum available virtually.  Teachers can now bring the museums to the classroom with these fantastic Smithsonian virtual tours.   

 

Tags: biogeography, virtual tours, environment, ecology, historical, physical.


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Humans toss 8 million metric tons of plastic into the ocean pro year, study shows

Humans toss 8 million metric tons of plastic into the ocean pro year, study shows | WWWBiology | Scoop.it

Scientists for decades have been worried about plastic clogging up our oceans, but now they finally know just how bad the problem is. We dump about five shopping bags full of plastic for every foot of coastline in the world every year, according to a new study. The numbers are orders of magnitude higher than prior estimates.


If we continue to produce large amounts of plastic—and can’t find a better way to dispose of them—the amount of plastic in our oceans will double over the next decade, according to Jenna Jambeck, an environmental engineer at the University of Georgia and lead author on the study.

 

She says these numbers actually undercount the problem because they account for only floating plastic. As much as 50 percent of the plastic produced in North America probably sinks to the ocean floor, she says.

The 8 million metric tons of plastic that litters our oceans every year consists of not only the usual suspects (like six-pack plastic rings, which are the bane of sea turtles), but also microplastics, tiny bits of debris smaller than your fingernail. Microplastics endanger marine life of all sizes, from whales to barnacles, as they are easy to swallow and may contain dangerous chemicals.

 

Jambeck and her team noticed at least one recurring theme within the data. Middle-income countries, especially those that have begun to industrialize but have not yet figured out how to manage their waste, end up tossing a lot of garbage in their oceans. One outlier is the United States, a rich country that would seem to have its waste management act together but still dumps a lot of plastic into the oceans.



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Parasite creating deformed frogs with up to 10 legs in the Western U.S.

Parasite creating deformed frogs with up to 10 legs in the Western U.S. | WWWBiology | Scoop.it
A flatworm parasite called Ribeiroia ondatrae infects several species of frogs just as they're developing their limbs, causing an assortment of defects such as no legs or even multiple legs that jut out at weird angles from the frogs' bodies scientists say.

 

Watch a video of the deformed frogs.

 

The deformed frogs are often unable to move and either die or quickly get eaten by predators. Scientists already knew that the parasite was the culprit in the frog malformations, but the researchers wanted to find out whether known hot spots of Ribeiroia populations in four western states had changed since they were last surveyed in 1999. So in 2010 Pieter Johnson, an ecologist at the University of Colorado at Boulder, and colleagues gathered data on frogs and parasites in 48 wetlands in California, Oregon, Washington, and Montana.


The Ribeiroia parasite has a complex, multihost life cycle, which begins with the ramshorn snail, a creature common to many western U.S wetlands. The flatworm asexually clones itself inside the snail, stripping the mollusk of its gonads and converting it into a "parasite machine," Johnson said. Each night the snail releases hundreds of free-swimmingRibeiroia larvae, which seek out their next hosts—tadpoles—with "remarkable precision."


The parasite larvae penetrate the tadpoles' tissue and zero in on the developing limb buds, so that when a tadpole begins to metamorphose into a frog, its "primary system of locomotion doesn't work—it can't jump, can't swim," he said. "That's when the birds"—the parasite's final host—"zoom in and eat the young mutated frogs up like popcorn."


The parasite then reproduces sexually inside the birds, and when the birds defecate, their feces contain parasite eggs that eventually make their way back into the snails.


Though the Ribeiroia parasite occurs naturally in North America, human activities likely have something to do with its prevalence, Johnson noted. For instance, the snails feed on algae, and runoff from agriculture and industry into wetlands contains nutrients that act as fertilizer, boosting algae growth. With more snails in the wetlands, the parasites have more initial hosts to infect, Johnson noted.


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Why are 10% of the world population left-handed? What are the advantages / disadvantages?

Why are 10% of the world population left-handed? What are the advantages / disadvantages? | WWWBiology | Scoop.it

Today, about one-tenth of the world’s population are southpaws. Why are such a small proportion of people left-handed -- and why does the trait exist in the first place? Daniel M. Abrams investigates how the uneven ratio of lefties and righties gives insight into a balance between competitive and cooperative pressures on human evolution.


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New silicone infused with silicone oil: Super-slippery, and proven to keep bacteria from growing on medical tubing

New silicone infused with silicone oil: Super-slippery, and proven to keep bacteria from growing on medical tubing | WWWBiology | Scoop.it

Infusing liquids into polymers makes long lasting, self-replenishing material that repels deadly bacterial build-up. Harvard researchers have demonstrated a powerful, long-lasting, repellent surface technology that can be used with medical materials to prevent infections caused by microbial biofilms.

 

More than 80 percent of microbial infections in the human body are caused by a build-up of bacteria, according to the National Institutes of Health (NIH). Bacteria cells gain a foothold in the body by accumulating and forming into adhesive colonies called biofilms, which help them to thrive and survive but cause often serious infections and associated life-threatening risks to their human hosts. These biofilms commonly form on medical surfaces including those of mechanical heart valves, urinary catheters, intravenous catheters, and other implants. But a new study reported a powerful, long-lasting repellent surface technology that can be used with medical material to prevent these kind of infections caused by biofilms. The new approach, which its inventors are calling "liquid-infused polymers", joins an arsenal of slippery and hydrophobic surface coatings that have been developed at Harvard's School of Engineering and Applied Sciences (SEAS) and the Wyss Institute for Biologically Inspired Engineering.


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ViaCyte Starts Stem-Cell Clinical Trial of Bioartificial Pancreas

ViaCyte Starts Stem-Cell Clinical Trial of Bioartificial Pancreas | WWWBiology | Scoop.it

Fourteen years ago, during the darkest moments of the “stem-cell wars” pitting American scientists against the White House of George W. Bush, one group of advocates could be counted on to urge research using cells from human embryos: parents of children with type 1 diabetes. Motivated by scientists who told them these cells would lead to amazing cures, they spent millions on TV ads, lobbying, and countless phone calls to Congress.


Now the first test of a type 1 diabetes treatment using stem cells has finally begun. In October, a San Diego man had two pouches of lab-grown pancreas cells, derived from human embryonic stem cells, inserted into his body through incisions in his back. Two other patients have since received the stand-in pancreas, engineered by a small San Diego company called ViaCyte.


It’s a significant step, partly because the ViaCyte study is only the third in the United States of any treatment based on embryonic stem cells. These cells, once removed from early-stage human embryos, can be grown in a lab dish and retain the ability to differentiate into any of the cells and tissue types in the body. One other study, since cancelled, treated several patients with spinal-cord injury (see “Geron Shuts Down Pioneering Stem-Cell Program” and “Stem-Cell Gamble”), while tests to transplant lab-grown retina cells into the eyes of people going blind are ongoing (see “Stem Cells Seem Safe in Treating Eye Disease”).


Douglas Melton, a biologist at Harvard University who has two children with type 1 diabetes, worries that the ViaCyte system may not work. He thinks deposits of fibrotic, scarlike tissue will glom onto the capsules, starving the cells inside of oxygen and blocking their ability to sense sugar and release insulin. Melton also thinks it might take immature cells up to three months to become fully functional. And many won’t become beta cells, winding up as other types of pancreatic cells instead.


Melton says the “inefficiency” of the system means the company “would need a device about the size of a DVD player” to have enough beta cells to effectively treat diabetes. ViaCyte says it thinks 300 million of its cells, or about eight of its capsules, would be enough. (Each capsule holds a volume of cells smaller than one M&M candy.)    Last October, Melton’s group announced it had managed to grow fully mature, functional beta cells in the lab, a scientific first that took more than 10 years of trial-and-error research. Melton thinks implanting mature cells would allow a bioartificial pancreas to start working right away.


To encapsulate his cells, Melton has been working with bioengineer Daniel Anderson at MIT to develop their own capsule. Anderson doesn’t want to say exactly how it works, but a recent patent filing from his lab describes a container made of layers of hydrogels, some containing cells and others anti-inflammatory drugs to prevent the capsule from getting covered with fibrotic tissue. Both Melton and Anderson are cagey about discussing their results. “We do have some successes we are very excited about,” Anderson says. “The bottom line is we have reason to believe it is possible to use Doug’s cells in our devices and cure diabetes in animals.”


After the stem-cell wars, and then a decade of trying to turn the technology’s promises into reality, Henry says he feels convinced that “cells in bags” of some kind are going to be the answer to type 1 diabetes. He’s aware that curing rodents doesn’t guarantee the technology will help people, but he says the clinical trial he’s running is another in a series of “small steps” toward much-improved lives for millions of people. “I am just so positive that this is the future,” he says. 


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The best images from 2014 in BMC Evolutionary Biology

The best images from 2014 in BMC Evolutionary Biology | WWWBiology | Scoop.it

Continuing the look back at the best of BMC Evolutionary Biology in 2014, here BMC showcases 12 images that caught their eye over the last 12 months.

Ground plan of wing patterns in Nymphalinae butterflies. From Suzuki et al. “Gradual and contingent evolutionary emergence of leaf mimicry in butterfly wing patterns”

Fossilised leaves of Bauhinia wenshanensis. From Meng et al. “New biogeographic insight intoBauhinia s.l. (Leguminosae): integration from fossil records and molecular analyses”

 

Sectioned bone elements of ostrich dinosaurs. From Cullen et al. “Osteohistological variation in growth marks and osteocyte lacunar density in a theropod dinosaur”

 

Phylogenetic tree of Tenebrionidae beetles and close relatives. From Kergoat et al. “Cretaceous environmental changes led to high extinction rates in a hyperdiverse beetle family”


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New approach may lead to inhalable vaccines for influenza, pneumonia and tuberculosis

New approach may lead to inhalable vaccines for influenza, pneumonia and tuberculosis | WWWBiology | Scoop.it

Researchers at North Carolina State University and the University of North Carolina at Chapel Hill have uncovered a novel approach to creating inhalable vaccines using nanoparticles that shows promise for targeting lung-specific diseases, such as influenza, pneumonia and tuberculosis.


The work, led by Cathy Fromen and Gregory Robbins, members of the DeSimone and Ting labs (see below), reveals that a particle’s surface charge plays a key role in eliciting immune responses in the lung. Using the Particle Replication in Nonwetting Templates (PRINT) technology invented in the DeSimone lab, Fromen and Robbins were able to specifically modify the surface charge of protein-loaded particles while avoiding disruption of other particle features, demonstrating PRINT’s unique ability to modify particle attributes independently from one another.


When delivered through the lung, particles with a positive surface charge were shown to induce antibody responses both locally in the lung and systemically in the body. In contrast, negatively charged particles of the same composition led to weaker, and in some cases undetectable, immune responses, suggesting that particle charge is an important consideration for pulmonary vaccination.


A paper describing the work, “Controlled analysis of nanoparticle charge on mucosal and systemic antibody responses following pulmonary immunization,” was published in the Proceedings of the National Academy of Sciences Dec. 29. The findings also have broad public health implications for improving the accessibility of vaccines. An inhalable vaccine may eliminate the need for refrigeration, which can not only improve shelf life, but also enable distribution of vaccines to low-resource areas, including many developing countries where there is significant need for better access to vaccines.


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Monkeys can learn to recognize themselves in the mirror

Monkeys can learn to recognize themselves in the mirror | WWWBiology | Scoop.it

Unlike humans and great apes, rhesus monkeys don't realize when they look in a mirror that it is their own face looking back at them. But, according to a report in the Cell Press journal Current Biology on January 8, that doesn't mean they can't learn. What's more, once rhesus monkeys in the study developed mirror self-recognition, they continued to use mirrors spontaneously to explore parts of their bodies they normally don't see.

 

The discovery in monkeys sheds light on the neural basis of self-awareness in humans and other animals. "Our findings suggest that the monkey brain has the basic 'hardware' [for mirror self-recognition], but they need appropriate training to acquire the 'software' to achieve self-recognition," says Neng Gong of the Chinese Academy of Sciences.


In earlier studies, scientists had offered monkeys mirrors of different sizes and shapes for years, even beginning at a young age, Gong explains. While the monkeys could learn to use the mirrors as tools for observing other objects, they never showed any signs of self-recognition. When researchers marked the monkeys' faces and presented them with mirrors, they didn't touch or examine the spot or show any other self-directed behaviors in front of those mirrors in the way that even a very young person would do.


In the new study, Gong and his colleagues tried something else. They sat the monkeys in front of a mirror and shined a mildly irritating laser light on the monkeys' faces. After 2 to 5 weeks of the training, those monkeys had learned to touch face areas marked by a spot they couldn't feel in front of a mirror. They also noticed virtual face marks in mirroring video images on a screen. They had learned to pass the standard mark test for mirror self-recognition.


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Lin28A Accelerates Wound Healing, Hair Regrowth, and Turns Back The Aging Clock A Little

Lin28A Accelerates Wound Healing, Hair Regrowth, and Turns Back The Aging Clock A Little | WWWBiology | Scoop.it

For centuries, biologists have wondered why an organism’s capacity for tissue repair and wound healing tends to decline as it gets older. The new study, which is published in the journal Cell, submits that this strange phenomenon may be the result of Lin28a – a gene whose protein product plays a crucial role in the early growth and development of a wide variety of animals. According to senior author George Daley, our gradual loss of regenerative powers may be symptomatic of a decline in Lin28a protein levels.


"It sounds like science fiction, but Lin28a could be part of a healing cocktail that gives adults the superior tissue repair seen in juvenile animals," he said in a press release.


To investigate the “fountain-of-youth” gene, the researchers reactivated it in adult mice. They found that the Lin28a protein accelerated the regeneration of cartilage, bone, and mesenchyme in a variety of injury models. Intriguingly, the gene also promoted faster regrowth of hair by stimulating anagen in the test subject’s hair follicles. Daley and his colleagues believe that Lin28a achieves these rejuvenating effects by stimulating metabolic processes otherwise associated with an organism’s embryo stage.


Study author Shyh-Chang Ng believes that the “fountain-of-youth” gene could be integrated into a number of different therapies. "We were surprised that what was previously believed to be a mundane cellular 'housekeeping' function would be so important for tissue repair," he told reporters. "One of our experiments showed that bypassing Lin28a and directly activating mitochondrial metabolism with a small-molecule compound also had the effect of enhancing wound healing, suggesting that it could be possible to use drugs to promote tissue repair in humans."


The current study is the latest in a growing series of inquiries into regeneration – a fascinating biological phenomenon that is observed across the entire evolutionary spectrum of organisms. Earlier this year, researchers at the Max Planck Institute of Molecular Cell Biology and Genetics showed that a single knocked-out gene allows planarian flatworms to regenerate their head and brain. A more recent study describes a so-called bio patch thatpromotes and sustains local bone growth in weakened and damaged areas. Like the current study, these research efforts remind us that when it comes to biotechnology and medicine, the line between science fiction and reality is not always clear.  

 
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UCSC Ebola genome browser now online to aid researchers' response to crisis

UCSC Ebola genome browser now online to aid researchers' response to crisis | WWWBiology | Scoop.it

The UC Santa Cruz Genomics Institute late Tuesday (September 30) released a new Ebola genome browser to assist global efforts to develop a vaccine and antiserum to help stop the spread of the Ebola virus.

The team led by University of California, Santa Cruz researcher Jim Kent worked around the clock for the past week, communicating with international partners to gather and present the most current data. The Ebola virus browser aligns five strains of Ebola with two strains of the related Marburg virus. Within these strains, Kent and other members of the UC Santa Cruz Genome Browser team have aligned 148 individual viral genomes, including 102 from the current West Africa outbreak.

UC Santa Cruz has established the UCSC Ebola Genome Portal, with links to the new Ebola genome browser as well as links to all the relevant scientific literature on the virus. 

“Ebola has been one of my biggest fears ever since I learned about it in my first microbiology class in 1997," said Kent, who 14 years ago created the first working draft of the human genome.  "We need a heroic worldwide effort to contain Ebola. Making an informatics resource like the genome browser for Ebola researchers is the least we could do.”

Scientists around the world can access the open-source browser to compare genetic changes in the virus genome and areas where it remains the same. The browser allows scientists and researchers from drug companies, other universities, and governments to study the virus and its genomic changes as they seek a solution to halt the epidemic. 


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Bio-Inspired ‘Nano-Cocoons’ Offer Targeted Drug Delivery Against Cancer Cells

Bio-Inspired ‘Nano-Cocoons’ Offer Targeted Drug Delivery Against Cancer Cells | WWWBiology | Scoop.it

Biomedical engineering researchers have developed a drug delivery system consisting of nanoscale “cocoons” made of DNA that target cancer cells and trick the cells into absorbing the cocoon before unleashing anticancer drugs. The work was done by researchers at North Carolina State University and the University of North Carolina at Chapel Hill.


“This drug delivery system is DNA-based, which means it is biocompatible and less toxic to patients than systems that use synthetic materials,” says Dr. Zhen Gu, senior author of a paper on the work and an assistant professor in the joint biomedical engineering program at NC State and UNC Chapel Hill.


“This technique also specifically targets cancer cells, can carry a large drug load and releases the drugs very quickly once inside the cancer cell,” Gu says. “In addition, because we used self-assembling DNA techniques, it is relatively easy to manufacture,” says Wujin Sun, lead author of the paper and a Ph.D. student in Gu’s lab.


Each nano-cocoon is made of a single strand of DNA that self-assembles into what looks like a cocoon, or ball of yarn, that measures 150 nanometers across. The core of the nano-cocoon contains the anticancer drug doxorubicin (DOX) and a protein called DNase. The DNase, an enzyme that would normally cut up the DNA cocoon, is coated in a thin polymer that traps the DNase like a sword in a sheath.


The surface of the nano-cocoon is studded with folic acid ligands. When the nano-cocoon encounters a cancer cell, the ligands bind the nano-cocoon to receptors on the surface of the cell – causing the cell to suck in the nano-cocoon.


Once inside the cancer cell, the cell’s acidic environment destroys the polymer sheath containing the DNase. Freed from its sheath, the DNase rapidly slices through the DNA cocoon, spilling DOX into the cancer cell and killing it.



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Bacteria Make Drug-Like Molecules in Humans: Over 14,000 biosynthetic Gene Clusters for Small Molecules Identified

Bacteria Make Drug-Like Molecules in Humans: Over 14,000 biosynthetic Gene Clusters for Small Molecules Identified | WWWBiology | Scoop.it

Small molecules encoded by biosynthetic gene clusters are widely used in the clinic and constitute much of the chemical language of interspecies interactions. In a recent study, researchers used a systematic approach to identify more than 3,000 small-molecule biosynthetic gene clusters in the genomes of human-associated bacteria. As reported in Cell, they discovered that biosynthetic gene clusters for thiopeptides—a class of antibiotics—are widely distributed in the genomes of the human microbiota.


“This study shows for the first time that our microbiota—the good microbes that live with humans—produce drug-like molecules to protect us from pathogens,” said lead study author Mohamed Donia of the University of California, San Francisco (UCSF). “For a long time, scientists used to go to remote and exotic places to find bacteria that produce novel chemical entities with drug-like properties. Who knew we could find similar ones in our own bodies?”


Donia and his collaborators used an algorithm they recently developed to systematically analyze about 2,400 reference genomes of the human microbiota from various body sites. They detected more than 14,000 biosynthetic gene clusters for a broad range of small-molecule classes. Reasoning that the products of these gene clusters are most likely to mediate conserved microbe-host and microbe-microbe interactions, they set out to identify the subset of gene clusters commonly found in healthy individuals by analyzing 752 metagenomic samples from the National Institutes of Health Human Microbiome Project.


Remarkably, nearly all of these gene clusters had never before been studied or even described, illustrating how little is known about their small-molecule products. “We need to study every single one of these molecules and understand what they are doing,” Donia said. “We have published the list of the small molecule-encoding genes that we identified, and we are reaching out to the scientific community to help us characterize them.”


Thiopeptides are perhaps the most interesting of these molecules because they have potent antibacterial activity against Gram-positive species. Currently, one semisynthetic member of this class is undergoing clinical trials for treating bacterial infections. But according to the authors, no thiopeptide biosynthetic gene cluster or small-molecule product from the human microbiome had ever been experimentally characterized. Surprisingly, their analysis revealed thiopeptide-like biosynthetic gene clusters in isolates from every human body site.

 

Donia and his collaborators went on to purify and solve the structure of a thiopeptide named lactocillin, which showed potent antibacterial activity against a range of Gram-positive vaginal pathogens. By analyzing human metatranscriptomic sequencing data, they showed that lactocillin and other thiopeptide biosynthetic gene clusters were expressed in vivo, suggesting a potential role in mediating microbe-microbe interactions.


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Shang Zhuo's curator insight, October 25, 2014 9:04 AM

We can find antibiotics from our own body! It is really fascinating news. Perhaps the microbiota in our gut is a good source of bioactive molecules but is ignored by scientists for a long time.

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From decisions to disorders: how neuroscience is changing what we know about ourselves

From decisions to disorders: how neuroscience is changing what we know about ourselves | WWWBiology | Scoop.it

People have wanted to understand our motivations, thoughts and behaviors since the ancient Greeks inscribed “know thyself” on the Temple of Apollo at Delphi. And understanding the brain’s place in health and disease is one of this century’s greatest challenges – take Alzheimer’s, dementia and depression for example.


There are many exciting contributions from neuroscience that have given insight into our thoughts and actions. Three neuroscientists have just been awarded the 2014 Nobel Prize for their discoveries of cells that act as a positioning system in the brain – in other words, the mechanism that allows us to navigate spaces using spatial information and memory at a cellular level.


There are many exciting contributions from neuroscience that have given insight into our thoughts and actions. For example, the neural basis of how we make fast and slow decisions and decision-making under conditions of uncertainty. There is also an understanding how the brain is affected by stress and how these stresses might switch our brains into habit mode, for example operating on “automatic pilot” and forgetting to carry out planned tasks, or the opposite goal-directed system, which would see you going out of your usual routine, for example, popping into a different supermarket to get special ingredients for a recipe.


Disruption in the balance between the two is evident in neuro-psychiatric disorders, such as obsessive compulsive disorder, and recent evidence suggests that lower grey matter volumes in the brain can bias towards habit formation. Neuroscience is also demonstrating commonalities in disorders of compulsivity, methamphetamine abuse and obese subjects with eating disorders.


Neuroscience can challenge previously accepted views. For example, major abnormalities in dopamine function were thought the main cause of adult attention deficit hyperactivity disorder (ADHD). However, recent work suggests that the main cause of the disorder may instead be associated with structural differences in grey matter in the brain.


What neuroscience has made evidently clear is that changes in the brain cause changes in your thinking and actions, but the relationship is two-way. Environmental stressors, including psychological and substance abuse, can also change the brain. We also now know our brains continue developing into late adolescence or early young adulthood, it is not surprising that these environmental influences are particularly potent in a number of disorders during childhood and adolescence including autism.



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Is whole-genome sequencing for newborns coming?

Is whole-genome sequencing for newborns coming? | WWWBiology | Scoop.it

The advent and refinement of sequencing technologies has resulted in a decrease in both the cost and time needed to generate data on the entire sequence of the human genome. This has increased the accessibility of using whole-genome sequencing and whole-exome sequencing approaches for analysis in both the research and clinical contexts. The expectation is that more services based on these and other high-throughput technologies will become available to patients and the wider population. Some authors predict that sequencing will be performed once in a lifetime, namely, shortly after birth. The Public and Professional Policy Committee of the European Society of Human Genetics, the Human Genome Organization Committee on Ethics, Law and Society, the PHG Foundation and the P3G International Pediatric Platform address herein the important issues and challenges surrounding the potential use of sequencing technologies in publicly funded newborn screening (NBS) programs. This statement presents the relevant issues and culminates in a set of recommendations to help inform and guide scientists and clinicians, as well as policy makers regarding the necessary considerations for the use of genome sequencing technologies and approaches in NBS programs. The primary objective of NBS should be the targeted analysis and identification of gene variants conferring a high risk of preventable or treatable conditions, for which treatment has to start in the newborn period or in early childhood.


The development of next-generation sequencing (NGS) technologies has substantially reduced both the cost and the time required to sequence an entire human genome. The prospect of the availability of NGS technologies and consequently the greater facility to conduct whole-genome sequencing (WGS) have led some to predict that the use of this technology will change the current practice of medicine and public health by enabling more accurate, sophisticated and cost-effective genetic testing.1 It is anticipated that in the short term, the implementation of WGS in the clinic will improve diagnosis and management of some disorders with a strong heritable component,2 as well as improve personalized diagnosis and personalized drug therapy and treatment.


Presently, NGS is being used for targeted sequencing of sets of genes to help guide cancer treatment, and a number of cancer centers are considering using WGS or whole-exome sequencing (WES) in the future. During pregnancy, noninvasive prenatal testing for aneuploidy is also being done using NGS.3 In the clinic, WGS and WES are also being used to identify the causes of rare genetic diseases especially in children4 and in individuals with ‘atypical manifestations, (that) are difficult to confirm using clinical or laboratory criteria alone, or otherwise require extensive or costly evaluation’.5 Disorders for which WGS has been used as a diagnostic tool are usually genetically heterogeneous and have variable phenotypic expression such as intellectual disability, congenital malformations and mitochondrial dysfunctions.5 Other foreseen applications include tissue matching, disease risk predictions, reproductive risk information, forensics or even recreational genomic information (such as genealogy or nonmedically related traits).

 

Nonetheless, Goldenberg and Sharp6 predict that ‘it is likely that the earliest applications of whole-genome sequencing will be restricted to settings in which genetic testing is already a routine part of clinical or public health practice, such as state newborn screening (NBS) programs’.6 In truth, it should be noted that DNA testing, per se, is not a routine part of NBS and that only a very small proportion of babies, depending on the country, have a DNA test (as opposed to a biochemical test).7


Furthermore, the above prediction could be criticized as the routine nature of NBS with its often implied consent, together with its public health context, and the particular vulnerability of the population tested, would make it an unsuitable context into which to first welcome a WGS approach.


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Researchers Produce First Map of New York City Subway System Microbes

Researchers Produce First Map of New York City Subway System Microbes | WWWBiology | Scoop.it

The microbes that call the New York City subway system home are mostly harmless, but include samples of disease-causing bacteria that are resistant to drugs — and even DNA fragments associated with anthrax and Bubonic plague — according to a citywide microbiome map published today by Weill Cornell Medical College investigators.


The study, published in Cell Systems, demonstrates that it is possible and useful to develop a "pathogen map" — dubbed a "PathoMap" — of a city, with the heavily traveled subway a proxy for New York's population. It is a baseline assessment, and repeated sampling could be used for long-term, accurate disease surveillance, bioterrorism threat mitigation, and large scale health management for New York, says the study's senior investigator, Dr. Christopher E. Mason, an assistant professor in Weill Cornell's Department of Physiology and Biophysics and in the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine (ICB).

 

The PathoMap findings are generally reassuring, indicating no need to avoid the subway system or use protective gloves, Dr. Mason says. The majority of the 637 known bacterial, viral, fungal and animal species he and his co-authors detected were non-pathogenic and represent normal bacteria present on human skin and human body. Culture experiments revealed that all subway sites tested possess live bacteria.


Strikingly, about half of the sequences of DNA they collected could not be identified — they did not match any organism known to the National Center for Biotechnology Information or the Centers for Disease Control and Prevention. These represent organisms that New Yorkers touch every day, but were uncharacterized and undiscovered until this study. The findings underscore the vast potential for scientific exploration that is still largely untapped and yet right under scientists' fingertips.


"Our data show evidence that most bacteria in these densely populated, highly trafficked transit areas are neutral to human health, and much of it is commonly found on the skin or in the gastrointestinal tract," Dr. Mason says. "These bacteria may even be helpful, since they can out-compete any dangerous bacteria."

 

But the researchers also say that 12 percent of the bacteria species they sampled showed some association with disease. For example, live, antibiotic-resistant bacteria were present in 27 percent of the samples they collected. And they detected two samples with DNA fragments of Bacillus anthracis (anthrax), and three samples with a plasmid associated with Yersinia pestis (Bubonic plague) — both at very low levels. Notably, the presence of these DNA fragments do not indicate that they are alive, and culture experiments showed no evidence of them being alive.

 

Yet these apparently virulent organisms are not linked to widespread sickness or disease, Dr. Mason says. "They are instead likely just the co-habitants of any shared urban infrastructure and city, but wider testing is needed to confirm this."



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Glassed-in DNA data storage makes the ultimate time capsule, up to 2 million years storage time

Glassed-in DNA data storage makes the ultimate time capsule, up to 2 million years storage time | WWWBiology | Scoop.it

IF YOU must preserve messages for people in the far future to read, Blu-ray discs and USB sticks are no good. For real long-term storage, you want a DNA time capsule. Just 1 gram of DNA is theoretically capable of holding 455 exabytes – enough for all the data held by Google, Facebook and every other major tech company, with room to spare. It's also incredibly durable: DNA has been extracted and sequenced from 700,000-year-old horse bones. But conditions have to be right for it to last.


"We know that if you just store it lying around, you lose information," saysRobert Grass of the Swiss Federal Institute of Technology in Zurich. So he and colleagues are working on ways to increase DNA's longevity, with the aim of storing data for thousands or millions of years.


They began by looking at the way information is encoded on a DNA strand. The simplest method treats the DNA bases A and C as a "0" and G and T as a "1". Of course, any damage to the DNA leaves holes in the data, so the team used an error-correcting technique called a Reed-Solomon code. This includes redundant blocks that can be used to reconstruct garbled bits of data.


They also tried to mimic the way fossils keep a DNA sequence intact. Excluding all water from the environment was key, so they encapsulated the DNA in microscopic spheres of glass.


To test how long this storage system might last, they encoded two venerable documents, totalling 83 kilobytes: the Swiss federal charter from 1291, and the Archimedes Palimpsest, a 10th-century version of ancient Greek texts. DNA versions of these texts were kept at 60, 65 and 70 °C for a week to simulate ageing. They remained readable without any errors (Angewandte Chemie,doi.org/f23gmf).


The results suggest that data in DNA form could last 2000 years if kept at a temperature of around 10 °C. The Global Seed Vault in the Arctic could preserve it for over 2 million years at a chilly -18 °C, offering truly long-term storage.


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Oil Eating Microbes Have Worldwide Underground Connections With Each Other

Oil Eating Microbes Have Worldwide Underground Connections With Each Other | WWWBiology | Scoop.it

Living deep underground ain't easy. In addition to hellish temperatures and pressures, there's not a lot to eat. Which is why oil reservoirs are the microbes’ cornucopia in this hidden realm. 

Microbes feast on many oil reservoirs, but it has been unclear how the micro-organisms got to those locales. One proposal has been that the microbes colonize a pool of dead algae corpses and then go along for the ride as the pool gets buried deeper and deeper and the algae slowly become oil. That’s the so-called "burial and isolation" hypothesis.

But under that set of rules each pool of oil should have its own unique microbes—and that's not the case, according to a recent study in the Journal of the International Society for Microbial Ecology. [Camilla L. Nesbø et al, Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments]

Researchers surveyed the genetics of oil-eating microbes from around the world. They found that populations from Nevada to the North Sea matched up almost exactly. They also determined that microbes in the North Sea appear to have swapped genes with Japanese microbes despite the locations being more than 8,000 kilometers apart on the Earth’s surface. 

These findings suggest that the deep biosphere is actually filled with connections, and that microbes move from one oil reservoir to another, colonizing them almost as soon as they form in some cases. Or it could also be that marine microbes migrate down and then evolutionary selection pressure causes a convergence in the genetics that make it possible to survive under these extreme conditions. 


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Scientists Discover Potent Antibiotic, A Potential Weapon Against a Range of Diseases

Scientists Discover Potent Antibiotic, A Potential Weapon Against a Range of Diseases | WWWBiology | Scoop.it

Scientists have discovered a powerful new antibiotic they say can kill an array of germs without the bugs easily becoming resistant to it, a potential weapon against a range of diseases.


The discovery is a rare—and much-needed—breakthrough in the quest for new antibiotics to overcome the problem of growing resistance to existing drugs. While the new compound was shown to be safe and effective in mice, scientists need to determine whether this is the case for people.


The discovery of the new class of antibiotic, called teixobactin, was reported Wednesday in the journal Nature. It was uncovered by screening 10,000 bacterial strains from soil. Teixobactin will be investigated further in animals before being tested in people.

If all goes well, “we’ll be in clinical trials two years from now,” said Kim Lewis, a professorat Northeastern University in Boston and lead author of the study. Human trials could take two to three years, he added.


Because of widespread and indiscriminate use of antibiotics, bacteria in recent years have acquired mutations and new genes that render them more resistant to drugs. At the same time, antibiotic research at pharmaceutical companies stalled. This dual problem—the rise of resistant bacterial strains and the lack of new antibiotics—threatens to undermine many advances of modern medicine. Infections are becoming harder to control; standard treatments are less effective; illness and hospital stays are getting longer; and there are more deaths from infection.

 
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New 'cyborg' spinal implant attaches directly to the spine and could help paralysed to walk again

New 'cyborg' spinal implant attaches directly to the spine and could help paralysed to walk again | WWWBiology | Scoop.it

Paralysed patients have been given new hope of recovery after rats with severe spinal injuries walked again through a ‘groundbreaking’ new cyborg-style implant. In technology which could have come straight out of a science fiction novel or Hollwood movie, French scientists have created a thin prosthetic ribbon, embedded with electrodes, which lies along the spinal cord and delivers electrical impulses and drugs.

The prosthetic, described by British experts as ‘quite remarkable’, is soft enough to bend with tissue surrounding the backbone to avoid discomfort.


Paralysed rats who were fitted with the implant were able to walk on their own again after just a few weeks of training. Researchers at the Ecole Polytechnique Fédérale de Lausanne are hoping to move to clinical trials in humans soon. They believe that a device could last 10 years in humans before needing to be replaced. 


The implant, called ‘e-Dura’, is so effective because it mimics the soft tissue around the spine – known as the dura mater – so that the body does not reject its presence. “Our e-Dura implant can remain for a long period of time on the spinal cord or cortex,” said Professor Stéphanie Lacour.


“This opens up new therapeutic possibilities for patients suffering from neurological trauma or disorders, particularly individuals who have become paralyzed following spinal cord injury.” Previous experiments had shown that chemicals and electrodes implanted in the spine could take on the role of the brain and stimulate nerves, causing the rats' legs to move involuntarily when they were placed on a treadmill.


However the new gadget is flexible and stretchy enough that it can be placed directly onto the spinal cord. It closely imitates the mechanical properties of living tissue, and can simultaneously deliver electric impulses and drugs which activate cells. The implant is made of silicon and covered with gold electric conducting tracks that can be pulled and stretched. The electrodes are made of silicon and platinum microbeads which can also bend in any direction without breaking.



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Most MS Patients Who Received Stem Cell Transplants Are Still in Remission Years Later

Most MS Patients Who Received Stem Cell Transplants Are Still in Remission Years Later | WWWBiology | Scoop.it

Most of the multiple sclerosis (MS) patients who took part in the cutting-edge stem cell study HALT-MS are still in remission years later. The phase 2 study has demonstrated impressive results by rebuilding the immune system using a patient’s own stem cells.


Studying 24 study volunteers who underwent stem cell transplants between 2006 and 2010, Dr. Richard A. Nash of the Colorado Blood Cancer Institute in Denver and his colleagues recently published their findings in JAMA Neurology. Researchers found that more than 86 percent of the patients remained relapse free after three years, and nearly 91 percent showed no sign of disease progression.


The goal was to reboot the patients’ immune systems. The researchers gauged success based on how long the patients remained relapse-free. The study involved patients with relapsing-remitting MS whose disease did not respond to at least one FDA-approved disease-modifying drug. Patients also had to score between 3.0 and 5.5 on the Expanded Disability Status Scale (EDSS), a set of tests to measure walking, cognition, dexterity, and quality of life in MS patients. People who fall into this range typically have mild to moderate disability.


 

Patients were given high-dose immunosuppressive therapy, or HDIT, to erase their native immune system. Then, researchers reintroduced blood-forming stem cells that had been harvested from the patients’ own blood.

 

“On average patients were hospitalized for three to four weeks,” said Nash in an interview with Healthline. That allowed enough time for the immune system to regenerate so patients could safely return home. “Patients are immunosuppressed, so they are on prophylactic antimicrobial medications. They are also educated regarding how to reduce the risk of infections after transplant,” explained Nash.


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‘Text neck’ is becoming an ‘epidemic’ and could wreck your spine

‘Text neck’ is becoming an ‘epidemic’ and could wreck your spine | WWWBiology | Scoop.it

The human head weighs about a dozen pounds. But as the neck bends forward and down, the weight on the cervical spine begins to increase. At a 15-degree angle, this weight is about 27 pounds, at 30 degrees it’s 40 pounds, at 45 degrees it’s 49 pounds, and at 60 degrees it’s 60 pounds.


That’s the burden that comes with staring at a smartphone — the way millions do for hours every day, according to research published by Kenneth Hansraj in the National Library of Medicine. The study will appear next month in Surgical Technology International. Over time, researchers say, this poor posture, sometimes called “text neck,” can lead to early wear-and-tear on the spine, degeneration and even surgery.


“It is an epidemic or, at least, it’s very common,” Hansraj, chief of spine surgery at New York Spine Surgery and Rehabilitation Medicine, told The Washington Post. “Just look around you, everyone has their heads down.”


Can’t grasp the significance of 60 pounds? Imagine carrying an 8-year-old around your neck several hours per day. Smartphone users spend an average of two to four hours per day hunched over, reading e-mails, sending texts or checking social media sites. That’s 700 to 1,400 hours per year people are putting stress on their spines, according to the research. And high-schoolers might be the worst. They could conceivably spend an additional 5,000 hours in this position, Hansraj said.


“The problem is really profound in young people,” he said. “With this excessive stress in the neck, we might start seeing young people needing spine care. I would really like to see parents showing more guidance.”


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Miloš Bajčetić's curator insight, January 13, 1:38 AM

Hansraj gave smartphone users tips to avoid pain:

 

- Look down at your device with your eyes. No need to bend your neck.

 

- Exercise: Move your head from left to right several times. Use your hands to provide resistance and push your head against them, first forward and then backward. Stand in a doorway with your arms extended and push your chest forward to strengthen “the muscles of good posture,” Hansraj said.

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Algae deliver hydrogen at a 5 times higher efficiency

Algae deliver hydrogen at a 5 times higher efficiency | WWWBiology | Scoop.it
Hydrogen as a regenerative fuel produced in gigantic water tanks full of algae, which need nothing more than sunlight to produce the promising green energy carrier: a great idea in theory, but one that fails due to the vast amount of space required for the production process. Scientists from the Max Planck Institutes for Chemical Energy Conversion and Coal Research) in Mülheim an der Ruhr, and from the research group Photobiotechnology at Ruhr-Universität Bochum (RUB) have now discovered a way of increasing the efficiency of hydrogen production in microalgae by a factor of five. If the algae can generate the fuel more efficiently, it can be produced in a smaller area and in quantities suitable for practical use. This approach also dispenses with the need for rare and expensive precious metals, which are used to split the energy-rich gas is technically from water.
Living organisms need electrons in many places, as they use them to form chemical compounds. Algae and other organisms which carry out photosynthesis release electrons from water with the help of sunlight and then distribute them in the cell. The ferrous protein PETF is responsible for this: It transports the electrons in particular to ferredoxin-NADP+ oxidoreductase (FNR), so that NADPH is formed and carbohydrates are finally synthesised from carbon dioxide. The production of hydrogen through hydrogenases is among the many other processes, for which PETF provides the necessary electrons.
Hydrogenases are very efficient enzymes that contain a unique active centre comprising six iron atoms, where the electrons supplied by PETF are bound to protons. Molecular hydrogen is produced in this way.

With the help of nuclear magnetic resonance spectroscopy, on which magnetic resonance imaging in medicine is also based, the scientists working with Sigrun Rumpel, a post doc at the Max Planck Institute for Chemical Energy Conversion in Mülheim, investigated the components of PETF – or more precisely amino acids – that interact with the hydrogenase and those that interact with FNR. It emerged that only two amino acids of PETF are important for binding FNR. When the researchers modified these two amino acids and the enzyme FNR, PETF was no longer able to bind FNR as efficiently. Thus, the enzyme transferred less electrons to FNR and more to the hydrogenase. In this way, the scientists increased the hydrogen production by a factor of five.


“For a technically feasible hydrogen production with the help of algae, its efficiency must be increased by a factor of 10 to 100 compared to the natural process,” says Sigrun Rumpel. “Through the targeted modification of PETF and FNR we have taken a step towards achieving this objective.” Up to now, the production of hydrogen from renewable energy carriers involved the electrolytic splitting of water. Expensive and rare precious metals like platinum are currently required for this purpose. Sigrun Rumpel and other researchers are therefore working on finding a way of enabling algae to efficiently produce the fuel. Microalgae produce the gas naturally, but in very small volumes. Thus, if cars were to be powered one day using hydrogen rather than petrol or diesel, to come anywhere near covering Germany’s fuel requirements, gigantic areas with tanks full of algal cultures would have to be set up.


“These results represent a path to the economically-viable regenerative production of fuels with the help of microalgae,” says Sigrun Rumpel. The change of electron transfer pathways could further improve hydrogen production in future. The researchers therefore now want to combine different modifications with each other.


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World first: Man paralyzed from the chest down walks again after cell transplant from his nasal cavity

World first: Man paralyzed from the chest down walks again after cell transplant from his nasal cavity | WWWBiology | Scoop.it

A paralysed man has been able to walk again after a pioneering therapy that involved transplanting cells from his nasal cavity into his spinal cord. Darek Fidyka, who was paralyzed from the chest down in a knife attack in 2010, can now walk using a frame. The treatment, a world first, was carried out by surgeons in Poland in collaboration with scientists in London.


Details of the research are published in the journal Cell Transplantation. BBC One's Panorama program had unique access to the project and spent a year charting the patient's rehabilitation. Darek Fidyka, 40, from Poland, was paralyzed after being stabbed repeatedly in the back in the 2010 attack. He said walking again - with the support of a frame - was "an incredible feeling", adding: "When you can't feel almost half your body, you are helpless, but when it starts coming back it's like you were born again."


Prof Geoff Raisman, chair of neural regeneration at University College London's Institute of Neurology, led the UK research team. He said what had been achieved was "more impressive than man walking on the moon".


 

The treatment used olfactory ensheathing cells (OECs) - specialist cells that form part of the sense of smell. OECs act as pathway cells that enable nerve fibers in the olfactory system to be continually renewed. In the first of two operations, surgeons removed one of the patient's olfactory bulbs and grew the cells in culture. Two weeks later they transplanted the OECs into the spinal cord, which had been cut through in the knife attack apart from a thin strip of scar tissue on the right. They had just a drop of material to work with - about 500,000 cells. About 100 micro-injections of OECs were made above and below the injury.


Four thin strips of nerve tissue were taken from the patient's ankle and placed across an 8mm (0.3in) gap on the left side of the cord.

 

The scientists believe the OECs provided a pathway to enable fibers above and below the injury to reconnect, using the nerve grafts to bridge the gap in the cord.


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Tarantula toxin is used to report electrical activity inside live cells

Tarantula toxin is used to report electrical activity inside live cells | WWWBiology | Scoop.it

Crucial experiments to develop a novel probe of cellular electrical activity were conducted in the Neurobiology course at the Marine Biological Laboratory (MBL) in 2013. Now, that optical probe, which combines a tarantula toxin with a fluorescent compound, is introduced in a paper in the Proceedings of the National Academy of Sciences.

The lead authors of the paper are Drew C. Tilley of UC-Davis and the late Kenneth Eum, a Ph.D. candidate at UC-Davis and teaching assistant in the MBL Neurobiology course. The probe takes advantage of the potent ability of tarantula toxin to bind to electrically active cells, such as neurons, while the cells are in a resting state. The team discovered that a trace amount of toxin combined with a fluorescent compound would bind to a specific subset of voltage-activated proteins (Kv2-type potassium ion channels) in live cells. The probe lights up cell surfaces with this ion channel, and the fluorescent signal dims when the channel is activated by electrical signals.

 

This is the first time that researchers have been able to visually observe these ion channels "turning on" without first genetically modifying them. All that is required is a means to detect probe location, suggesting that related probes could potentially one day be used to map neural activity in the human brain.


"This is a demonstration, a prototype probe. But the promise is that we could use it to measure the activity state of the electrical system in an organism that has not been genetically compromised," says senior author Jon Sack, an assistant professor in the departments of Physiology and Membrane Biology at UC-Davis. Sack is a faculty member in the MBL Neurobiology course.


Since the probe binds selectively to one of the many different kinds of ion channels, it can help scientists disentangle the function of those specific channels in neuronal signaling. This can, in turn, lead to the identification of drug targets for neurological diseases and disorders.


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Brain barrier opened for first time to treat cancer

Brain barrier opened for first time to treat cancer | WWWBiology | Scoop.it

For the first time, doctors have opened and closed the brain's protector – the blood-brain barrier – on demand. The breakthrough will allow drugs to reach diseased areas of the brain that are otherwise out of bounds. Ultimately, it could make it easier to treat conditions such as Alzheimer's and brain cancer.


The blood-brain barrier (BBB) is a sheath of cells that wraps around blood vessels (in black) throughout the brain. It protects precious brain tissue from toxins in the bloodstream, but it is a major obstacle for treating brain disorders because it also blocks the passage of drugs.


Several teams have opened the barrier in animals to sneak drugs through. Now Michael Canney at Paris-based medical start-up CarThera, and his colleagues have managed it in people using an ultrasound brain implant and an injection of microbubbles.

When ultrasound waves meet microbubbles in the blood, they make the bubbles vibrate. This pushes apart the cells of the BBB.


With surgeon Alexandre Carpentier at Pitié-Salpêtrière Hospital in Paris, Canney tested the approach in people with a recurrence of glioblastoma, the most aggressive type of brain tumour. People with this cancer have surgery to remove the tumours and then chemotherapy drugs, such as Carboplatin, are used to try to kill any remaining tumour cells. Tumours make the BBB leaky, allowing in a tiny amount of chemo drugs: if more could get through, their impact would be greater, says Canney.


The team tested the idea on four patients by implanting an ultrasound transducer through a hole already made in their skulls during tumour-removal surgery. They were then given an injection of microbubbles and had the transducer switched on for 2 minutes. This sent low-intensity pulses of ultrasound into a region of the brain just 10 millimetres by 4 mm. Canney reckons this makes the BBB in this region more permeable for about 6 hours. In this time window, each person received normal chemotherapy.


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Warwick Raverty's curator insight, October 22, 2014 7:48 PM

Hope at last for people with inoperable brain tumours!

Nicole Masureik's curator insight, October 23, 2014 2:41 AM

What an amazing advance! This could open doors for all sorts of things. However, there is so much about the functioning of the brain that we don't understand, that we will need to watch the long term effects carefully.