Scientists completed a proof-of-principle study on a real-time blood test based on DNA sequencing that can be used to rapidly diagnose Ebola and other acute infections.
A new app gives people the chance to meet like-minded people with similar interests. It aims to fill the social void that often comes from living in a place where pigeons are easier to talk to than people.
A team including the scientist who first harnessed the revolutionary CRISPR-Cas9 system for mammalian genome editing has now identified a different CRISPR system with the potential for even simpler and more precise genome engineering.
A new article discusses how DNA molecules can be assembled into tailored and complex nanostructures, and further, how these structures can find uses in therapeutics and bionanotechnological applications. The researchers outline the superior properties of DNA nanostructures. Moreover, these DNA nanostructures provide new applications in molecular medicine, such as novel approaches in tackling cancer. Tailored DNA structures could find targeted cells and release their molecular payload selectively into the cells.
An international study of nearly 70,000 women has identified more than 40 regions of the human genome involved in governing at what age a woman goes through menopause. The study found that two-thirds of those regions contain genes that act to keep DNA healthy. It also found the first genetic evidence of a link between the timing of menopause and breast cancer, corroborating previous conclusions from observational evidence.
A team including the scientist who first harnessed the revolutionary CRISPR-Cas9 system for mammalian genome editing has now identified a different CRISPR system with the potential for even simpler and more precise genome engineering. In the study researchers describe the unexpected biological features of this new system and demonstrate that it can be engineered to edit the […]...
The first all-optical permanent on-chip memory has been developed. This is an important step on the way towards optical computers. Phase change materials that change their optical properties depending on the arrangement of the atoms allow for the storage of several bits in a single cell.
The Dutch government is now pushing to have the Open Document Format mandatory in all the administration, a move that would make Microsoft very unhappy.
Urinary tract infections could be treated more quickly and efficiently using a DNA sequencing device the size of a USB stick -- according to new research. Researchers used a new device called MinION to perform nanopore sequencing to characterize bacteria from urine samples four times more quickly than using traditional methods of culturing bacteria. The new method can also detect antibiotic resistance -- allowing patients to be treated more effectively and improving stewardship of diminishing antibiotic reserves.
If you go back far enough, all people share a common ancestry. But some populations are more closely related than others based on events in the past that brought them together. Now, researchers have shown that it's possible to use DNA evidence as a means to reconstruct and date those significant past events. The findings suggest that evidence in our genomes can help to recover lost bits of history.
This week’s highlighted item will apparently answer all the questions in the future, rendering my weekly foray moot. Ok, kidding aside, I think this is a great idea. A sort of “living” better-than-textbook project that will really be the only way to keep up with a field that changes as fast as bioinformatics does. If they […]...
Parnell, L., Lindenbaum, P., Shameer, K., Dall'Olio, G., Swan, D., Jensen, L., Cockell, S., Pedersen, B., Mangan, M., Miller, C.... (2011) BioStar: An Online Question . PLoS Computational Biology, 7(10). DOI: 10.1371/journal.pcbi.1002216
You have more in common with your mom than you might think. Microchimerism means that an individual has cells with two different genetic profiles; some are yours and some are your mom’s. They live in your body for more than 40 years and can affect your health. Some of your cells moved into mom too – and they may help her live longer and avoid breast cancer....
Het ongevraagd en op de achtergrond zetten van Windows 10-installatiebestanden op Windows 7- en 8-systemen, zoals Microsoft doet, valt onder de cookiewet, stelt de Autoriteit Consument & Markt. De softwaregigant zou dan nadrukkelijk toestemming moeten vragen.
Prenatal testing business Sequenom is the first company to buy the technology, which has applications in any setting in which genetic data needs mapping, sorting and deduplicating.
HudsonAlpha has rejigged its operation to cope with the torrent of genomes it unleashed when it installed an Illumina HiSeq X Ten. The new model is underpinned by Dragen, the processor Edico Genome has designed specifically to deal with the demands of sequencing data analysis.
Forensic biomedical scientists have developed a test to predict individuals' age on the basis of blood or teeth samples. This test may be particularly useful for the police, as it can help track down criminals or identify human remains.
Because I write nonfiction, I love to read fiction. But I avoid crime novels, especially about serial killers who carry out gruesome rituals on innocent young women. When a book publicist sent me info about a new book, “The Ripper Gene,” however, I couldn’t resist. The book is published by Forge, Tom Doherty Associates, which is part of Macmillan.
Written by Michael Ransom – known in biotech circles as molecular pharmacologist Michael Burczynski, PhD – The Ripper Gene is a cleverly-crafted, tightly unfolding thriller based on solid science. And that’s why it’s scary.
The Ripper Gene is a case study in genetic determinism, the idea that our DNA dictates who we are and how we behave. The protagonist, neuroscientist and FBI profiler Lucas Madden, has discovered a “damnation algorithm” genotype that predisposes those who have two copies of it to violence.
Early in the book, Madden/Ransom takes pains to explain that the damnation algorithm is more complicated than a lone serial killer gene, in jargon and then in plain English:
Michael Ransom, author of “The Ripper Gene”
“Importantly, we don’t just look at single nucleotide polymorphisms, as scientists did in the past. We can now investigate many different aspects of human DNA – its methylation patterns, microRNA binding sites, copy number variants, insertions and deletions, just to name a few. When we examined the totality of genetic differences that can be observed, we found that key differences between violent offenders mapped to several dozen human genes … all of which are linked in one way or another to neurochemical signaling in the brain.”
But the focus indeed becomes a single gene, “ripper,” that encodes a subunit of a dopamine receptor, expressed in the amygdala. It’s a plausible set-up for the biology of violence.
XYY Revisited
We had a preview of the risks of attributing violent behavior to genetic information half a century ago. In 1961, a tall, healthy man, known for his boisterous behavior, had his chromosomes checked after fathering a child with Down syndrome. The man had an extra Y chromosome. Could that have caused his aggression?
A few other cases of aggressive men with extra Y’s were reported. Then in 1965, British geneticist Patricia Jacobs surveyed 197 inmates at a high-security prison in Scotland. Of twelve men with unusual chromosomes, seven had an extra Y. After Jacobs’s findings were repeated for mental institutions, Newsweek ran a cover story on “congenital criminals.” An extra Y became a legal defense for committing a violent crime, a connection that eventually became a plot on Law and Order and other programs.
In the early 1970s, newborn screens began in hospital nurseries in England, Canada, Denmark, and Boston, with social workers and psychologists visiting parents of XYY boys to offer “anticipatory guidance” for dealing with their toddling future criminals. By 1974, geneticists and others halted the program, recognizing that the well-meant intervention could invite a self-fulfilling prophecy.
In fact, 96 percent of the one in a thousand males with an extra Y can blame their extra chromosome for only great height, acne, and learning disabilities. But might the large size of such boys lead teachers, employers, parents, or others to expect more of them, because they appear older, especially given the learning disabilities? Might that stress of expectation provoke some individuals with an extra Y to respond with aggression?
XYY syndrome continues to be a harbinger of what may happen when we all know our genome sequences. At Bioethics TodayI addressed a 2012 study by criminologists reawakening the “blame the extra Y” theme: “These simple conclusions based on fuzzy data from non-geneticists feed the genetic determinism mindset that we are our genes. And that can lead to making excuses for antisocial behavior, or losing hope of changing it, for if a trait is encoded in our DNA sequences, then we can’t control it.”
That’s eerily like what Lucas Madden says when confronting the killer at the end of The Ripper Gene: “You kill because you think you have the right to kill. And it’s a conscious decision on your part. Your genetics had precious little to do with it, you piece of shit.”
MAOA Revisited
A second historic example of blaming genes is the monoamine oxidase A (MAOA) gene, aka the “psycho” or “warrior” gene. The association of certain variants of this gene with violent behavior dates to a study of a Dutch family published in 1993, with 13 males who had “X-linked borderline mental retardation with prominent behavioral disturbance.”
The family members who had committed arson, attempted rape, and engaged in exhibitionism shared a mutation in a gene on the X chromosome that encodes MAOA, the enzyme that oversees metabolism of the neurotransmitters dopamine, serotonin, and norepinephrine. Like the XYY scenario, the MAOA-violence connection spread beyond the genetics community. An attorney used the “MAOA deficiency defense’ to attempt to free a client from impending execution for murder, and an appeals court in Italy reduced a convicted killer’s sentence by a year because of his MAOA status. A talk-show host joked that people with the “mean gene” should be sterilized.
Online Mendelian Inheritance in Man, my favorite source for all things human genetics, is more polite. It lists “susceptibility to antisocial behavior following childhood maltreatment” for men with certain variants of the MAOA gene.
(NHGRI)
Exploring Mutations in Fiction
The idea for The Ripper Gene grew out of a grizzly memory from the author’s adolescence, spun into a serial killer thriller with at least four possible characters who could’ve done it. As the plot unfolds, the dopamine receptor subunit gene itself becomes a powerful clue, and its recessive nature part of an eloquent metaphor. Each victim holds an apple that hides an embedded razor blade, like people fear will be handed out to children on Halloween. But it’s also an eerie symbol of the hidden nature of a recessive gene.
I don’t want to spill any spoilers. But the ultimate message of the novel is not so much the degree to which inheriting a genotype that affects a neurotransmitter receptor increases the likelihood of criminal behavior, but more about discrimination based on knowing an individual’s genotype.
Oddly, as soon as I finished reading The Ripper Gene, I picked up Summer Secrets, by Jane Green, a futile attempt to delay the coming of autumn. I was surprised to discover that it’s about a woman coming to terms with her alcoholism when she discovers that the man she thought was her father really wasn’t – and her real dad suffered from alcoholism too.
New technologies fuel the imagination. (PLOS Biology)
I’m glad that the idea of genetic determinism has filtered into crime novels and summer beach reads. It means that the general reading public is already thinking about what may happen once sequencing our genomes becomes routine, albeit one gene per plotline. Peter Donnelly, director of the Wellcome Trust Centre for Human Genetics, recently wrote in PLOS Biology: “Within 15 years, there may be one billion humans whose genomes have been sequenced, in many cases with links to electronic health data.”
Will we use any of that information to excuse deviant behavior? The Ripper Gene provides a compelling look ahead.
A small fluorescent molecule has shed new light on knots of DNA thought to play a role in regulating how genes are switched on and off. DNA is typically arranged in a double helix, where two strands are intertwined like a coiled ladder, but previous research has shown the existence of unusual DNA structures called quadruplexes, where four strands are arranged in the form of little knots.
You have more in common with your mom than you might think. Microchimerism means that an individual has cells with two different genetic profiles; some are yours and some are your mom’s. They live in your body for more than 40 years and can affect your health. Some of your cells moved into mom too – and they may help her live longer and avoid breast cancer....
In April 2015, a paper by Chinese scientists about their attempts to edit the DNA of a human embryo rocked the scientific world and set off a furious debate. Leading scientists warned that altering the human germ line without studying the consequences could have horrific consequences. Geneticists with good intentions could mistakenly engineer changes in DNA that generate dangerous mutations and cause painful deaths. Scientists — and countries — with less noble intentions could again try to build a race of super humans.
Human DNA is, however, merely one of many commercial targets of ethical concern. The DNA of every single organism — every plant, every animal, every bacterium — is now fair game for genetic manipulation. We are entering an age of backyard synthetic biology that should worry everybody. And it is coming about because of CRISPRs: clustered regularly interspaced short palindromic repeats.
Discovered by scientists only a few years ago, CRISPRs are elements of an ancient system that protects bacteria and other single-celled organisms from viruses, acquiring immunity to them by incorporating genetic elements from the virus invaders. CRISPRs evolved over millions of years to trim pieces of genetic information from one genome and insert it into another. And this bacterial antiviral defence serves as an astonishingly cheap, simple, elegant way to quickly edit the DNA of any organism in the lab.
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Until recently, editing DNA required sophisticated labs, years of experience, and many thousands of dollars. The use of CRISPRs has changed all that. CRISPRs work by using an enzyme — Cas9 — that homes in on a specific location in a strand of DNA. The process then edits the DNA to either remove unwanted sequences or insert payload sequences. CRISPRs use an RNA molecule as a guide to the DNA target. To set up a CRISPR editing capability, a lab only needs to order an RNA fragment (costing about $10) and purchase off-the-shelf chemicals and enzymes for $30 or less.
Because CRISPRs are cheap and easy to use, they have both revolutionized and democratized genetic research. Hundreds, if not thousands, of labs are now experimenting with CRISPR-based editing projects. A race is on between the major research institutions to file CRISPR-technique patents. Research dollars, both public and private, are pouring into CRISPR projects. Meanwhile, a panoply of leading geneticists — including one of the developers of the CRISPR technology — has urged for a moratorium on alterations to the human germ line until the implications of messing with human DNA are further studied and safeguards have been put in place.
Changing human DNA creates, for scientists and humanity, a frightening ethical grey zone. On the one hand, for the many millions of poor souls suffering from diseases arising from genetic defects, CRISPRs and the research they fuel could mean finding a cure for their problem in their lifetimes. On the other hand, changing the human germ line is incredibly risky without much better knowledge of how our DNA actually works.
Though scientists now commonly sequence human DNA, they still struggle to understand how the different pieces of the human genome work together. For example, until recently, scientists thought that much of our genetic material was useless and served no purpose. They called it “junk” DNA. In a previous era, they might have considered editing the junk out of our genes.
Now, research is emerging that shows junk DNA plays a key role in regulating genetic expression (effectively turning various genes on and off), regulation that is fundamental to the biological processes that govern our bodies and our endocrine systems. What if a well-intentioned researcher develops a cure for one of these diseases and shares it with thousands of sufferers before realizing that the cure is far worse than the disease and that the side effects are painful — or even deadly — and easily spread from person to person?
Such a scenario could arise through good intent. But in the hands of evil biohackers, these powerful and simple tools are a cause for alarm. A smart biohacker could alter the influenza genome, for example, to make it more potent, setting off an epidemic that kills hundreds of millions of people. Though a nuclear weapon can cause tremendous long-lasting damage, the ultimate biological doomsday machine is bacteria, because they can spread so quickly and quietly.
No one is prepared for an era when editing DNA is as easy as editing a Microsoft Word document. The government does not have any regulations on editing human DNA. The ethical concerns have not been fleshed out. There is no centralized risk-management inventory, listing which labs are doing what with CRISPR. It’s all rather terrifying.
Rarely do I argue that a moratorium on technological progress is the prudent course. But the stakes in the case of CRISPRs are so high that I believe a blanket moratorium is the only course. Yes, rogue scientists may nonetheless continue working at modifications on the human germ line, which could endow them with a first-mover advantage and unfair knowledge. But such a moratorium could be as effective as the global moratorium on the cloning of humans has been: At the least, scientists such as those who engineered the human embryos in China would become international pariahs rather than being celebrated for publishing papers in prestigious publications.
Vivek Wadhwa is a fellow at Rock Center for Corporate Governance at Stanford University, director of research at Center for Entrepreneurship and Research Commercialization at Duke, and distinguished fellow at Singularity University. His past appointments include Harvard Law School, University of California Berkeley, and Emory University.
Motherboard: A software package reproducibly built should be byte for byte identical to the publicly-available package. Any difference would be evidence of tampering.
The Scottish whisky that spent three years ageing aboard the International Space Station has finally been tasted. The result, according to the Ardbeg distillery and aerospace company NanoRacks, is a whisky with a "noticeably different" flavour profile to one matured on earth.
Ardbeg, a distillery from the Isle of Islay in Scotland, and NanoRacks hoped to determine what effect microgravity conditions would have on terpene, a set of organic compounds found in whisky and other foods that give them a distinct flavour. By sending unmatured whisky into space along with charred oak wood shavings—which were only brought together inside a sealed vial once in space—they also hoped to reveal the effect of microgravity on the extraction of certain flavour compounds from the oak. A control sample was left back on Earth for comparison.
Three distinct analyses were conducted upon the whisky's return to Earth: chromatography for volatile congener analysis (substances other than alcohol produced during fermentation that give it its flavour); high-pressure liquid chromatography (HPLC) for maturation-related congener analysis; and "organoleptic assessment," which is an incredibly fancy way of describing a simple taste test.
Scientists have found that current school and university start times are damaging the learning and health of students. Drawing on the latest sleep research, the authors conclude students start times should be 8:30 or later at age 10; 10:00 or later at 16; and 11:00 or later at 18. Implementing these start times should protect students from short sleep duration and chronic sleep deprivation, which are linked to poor learning and health problems.
Exercise improves health in overweight and obese adults but can be hard to incorporate into a daily routine. New findings show that taking vitamin C supplements daily instead can have similar cardiovascular benefits as regular exercise in these adults.
Because I write nonfiction, I love to read fiction. But I avoid crime novels, especially about serial killers who carry out gruesome rituals on innocent young women. When a book publicist sent me info about a new book, “The Ripper Gene,” however, I couldn’t resist. The book is published by Forge, Tom Doherty Associates, which is part of Macmillan.
In the early 1970s, newborn screens began in hospital nurseries in England, Canada, Denmark, and Boston, with social workers and psychologists visiting parents of XYY boys to offer “anticipatory guidance” for dealing with their toddling future criminals. By 1974, geneticists and others halted the program, recognizing that the well-meant intervention could invite a self-fulfilling prophecy.
MAOA Revisited
Ars Technica.