Tag Archive: Genes


dna-repair-machinery

When it comes to genetic engineering, we’re amateurs. Sure, we’ve known about DNA’s structure for more than 60 years, we first sequenced every A, T, C, and G in our bodies more than a decade ago, and we’re becoming increasingly adept at modifying the genes of a growing number of organisms.

But compared with what’s coming next, all that will seem like child’s play. A new technology just announced today has the potential to wipe out diseases, turn back evolutionary clocks, and reengineer entire ecosystems, for better or worse. Because of how deeply this could affect us all, the scientists behind it want to start a discussion now, before all the pieces come together over the next few months or years. This is a scientific discovery being played out in real time.

Today, researchers aren’t just dropping in new genes, they’re deftly adding, subtracting, and rewriting them using a series of tools that have become ever more versatile and easier to use. In the last few years, our ability to edit genomes has improved at a shockingly rapid clip. So rapid, in fact, that one of the easiest and most popular tools, known as CRISPR-Cas9, is just two years old. Researchers once spent months, even years, attempting to rewrite an organism’s DNA. Now they spend days.

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If scientists can clone sheep and 3D-print human ears, surely they can figure out how to make our bodies heal themselves like Wolverine’s does.

Thanks to a curious accidental discovery from Harvard Medical School and Boston Children’s Hospital researcher George Daley, we may be closer than we previously thought.

While conducting cancer research, Daley clipped holes in ears of mice that were genetically engineered with the Lin28a gene so he could quickly tell them apart from the control group. But the holes kept healing. So he clipped their toes, but they grew back. He then waxed their backs, but their fur grew back more quickly than usual. It appeared that Lin28a — a gene that scientists think regulates the self-renewal of stem cells — gave the mice special regeneration abilities.

“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,” said Daley.

Aside from any “Rats of NIMH” flashbacks many of us might be having from this description, it’s worth considering the scientific significance of Daley’s accidental discovery.

The team “found they could replicate the healing abilities of the engineered mice by giving non-genetically altered ones drugs that help activate certain metabolic processes — the same pathway Lin28a stimulates — revving up and energizing cells as if they were much younger,” Scientific American explains.

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Patented Fertility Calculator Could Create The Perfect Baby

23andMe, a company that analyzes customers’ DNA and provides info about their health and ancestry, has recently received a U.S. patent for a system that can help future parents choose the traits they want for their would-be children.

The patent, titled Gamete Donor Selection Based On Genetic Calculations, describes a system of computing the likely genetic outcomes of the combinations of the customer and the donor and then identifying which combinations would most likely result in the desired traits. In effect, the technology can be used to identify the donor who matches the desired genetic profile and in turn create a baby with the traits that the parents had in mind. The system is more specific than the general or broad kind of selection that is being done in fertility clinics.

Some of the traits mentioned as examples in the patent include height, weight, hair color, risks of congenital heart defects, estimated life span, among others. The technology raises several ethical concerns, but it can potentially help future parents have healthier babies by screening out donors with genes predisposed to specific illnesses.

According to an article on the company’s website, 23andMe applied for the patent some five years ago to cover the technology that supports one of the company’s existing tools, the Family Traits Inheritance Calculator, a tool that tells customers the potential traits that their child may inherit from them. At the time of the filing, the company was already aware of the potential applications of the technology in fertility clinics, but 23andMe claims that it has no plans of using the patent in that way.

The term “survival of the fittest” refers to natural selection in biological systems, but Darwin’s theory may apply more broadly than that. New research from the U.S. Department of Energy’s Brookhaven National Laboratory shows that this evolutionary theory also applies to technological systems.

Computational biologist Sergei Maslov of Brookhaven National Laboratory worked with graduate student Tin Yau Pang from Stony Brook University to compare the frequency with which components “survive” in two complex systems: bacterial genomes and operating systems on Linux computers.

Their work is published in the Proceedings of the National Academy of Sciences. Maslov and Pang set out to determine not only why some specialized genes or computer programs are very common while others are fairly rare, but to see how many components in any system are so important that they can’t be eliminated. “If a bacteria genome doesn’t have a particular gene, it will be dead on arrival,” Maslov said. “How many of those genes are there? The same goes for large software systems. They have multiple components that work together and the systems require just the right components working together to thrive.’”

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Researchers have long known that the gene, p16INK4a (p16), plays a role in aging and cancer suppression by activating an important tumor defense mechanism called “cellular senescence.”

A team led by Norman Sharpless, Professor of Cancer Research at University of North Carolina, has developed a strain of mice that turns on a gene from fireflies when the normal p16 gene is activated. In cells undergoing senescence, the p16 gene is switched on, activating the firefly gene and causing the affected tissue to glow.

Throughout the entire lifespan of these mice, the researchers followed p16 activation by simply tracking the brightness of each animal. They found that old mice are brighter than young mice, and that sites of cancer formation become extremely bright, allowing for the early identification of developing cancers.

“With these mice, we can visualize in real-time the activation of cellular senescence, which prevents cancer but causes aging. We can literally see the earliest molecular stages of cancer and aging in living mice,” says Sharpless, who is also the Deputy Cancer Center Director.

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A team of Scottish researchers say that they have made a breakthrough discovery, locating the moment in evolutionary history when intelligence and the ability to reason first appeared in our earliest ancestors. They also say that the root cause of many brain disorders can also be traced back to the same genetic events.

According to Seth Grant, the lead researcher on the study and a professor of molecular neuroscience at University of Edinburgh: “One of the greatest scientific problems is to explain how intelligence and complex behaviours arose during evolution.”

Grant and his colleagues say this happened around 500 million years ago as a result of a sudden increase in the number of brain genes possessed by our early invertebrate ancestors. The researchers say that these simple ocean-dwelling animals experienced a ‘genetic accident’ that resulted in an unintended multiplication in the number of brain genes that they possessed. In the millions of years that followed, these extra intelligence genes provided survival benefits to the animals that inherited them and gave rise to increasingly sophisticated behaviors. In humans, these abilities reached their peak with our unique abilities to analyze situations, understand abstract concepts and learn complicated skills.

The study results, which have been published as two papers in the journal Nature Neuroscience, also point to a direct link between the evolution of complex behavior and the origins of a number of brain disorders. The scientists say that the same genes that gave us our enhanced cognitive abilities are also to blame for a variety of common brain diseases.

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The justices’ decision will likely resolve an ongoing battle between scientists who believe that genes carrying the secrets of life should not be exploited for commercial gain and companies that argue that a patent is a reward for years of expensive research that moves science forward. The current case involves Myriad Genetics Inc. of Salt Lake City, which has patents on two genes linked to increased risk of breast and ovarian cancer.

Myriad’s BRACAnalysis test looks for mutations on the breast cancer predisposition gene, or BRCA. Those mutations are associated with much greater risks of breast and ovarian cancer. But the American Civil Liberties Union challenged those patents, arguing that genes couldn’t be patented, and in March 2010, a New York district court agreed. But the U.S. Court of Appeals for the Federal Circuit has now twice ruled that genes can be patented, in Myriad’s case because the isolated DNA has a “markedly different chemical structure” from DNA within the body. Among the ACLU’s plaintiffs are geneticists who said they were not able to continue their work because of Myriad’s patents, as well as breast cancer and women’s health groups, patients and groups of researchers, pathologists and laboratory professionals.

“It’s wrong to think that something as naturally occurring as DNA can be patented by a single company that limits scientific research and the free exchange of ideas,” said Chris Hansen, staff attorney with the ACLU Speech, Privacy and Technology Project. A call to a Myriad spokeswoman was not immediately returned, but in court papers the company’s lawyers said without being able to patent and profit from their work, they would not be able to fund the type of medical breakthroughs doctors depend on. The company also said that deciding now that genes can’t be patented would throw into chaos current research and profits structures for drug-makers and medical research companies, who have gotten more than 40,000 DNA-related patents from the Patent and Trademark Office for almost 30 years, according to court papers.

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Scientists have discovered for the first time how humans – and other mammals – have evolved to have intelligence.

Researchers have identified the moment in history when the genes that enabled us to think and reason evolved.

This point 500 million years ago provided our ability to learn complex skills, analyse situations and have flexibility in the way in which we think.

Professor Seth Grant, of the University of Edinburgh, who led the research, said: “One of the greatest scientific problems is to explain how intelligence and complex behaviours arose during evolution.”

The research, which is detailed in two papers in Nature Neuroscience, also shows a direct link between the evolution of behaviour and the origins of brain diseases.

Scientists believe that the same genes that improved our mental capacity are also responsible for a number of brain disorders.

“This ground breaking work has implications for how we understand the emergence of psychiatric disorders and will offer new avenues for the development of new treatments,” said John Williams, Head of Neuroscience and Mental Health at the Wellcome Trust, one of the study funders.

The study shows that intelligence in humans developed as the result of an increase in the number of brain genes in our evolutionary ancestors.

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The completion of human and primate genome sequences (including some close, extinct relatives) reveals a great deal about the evolutionary innovations behind modern humans. All indications are a large collection of relatively subtle genetic changes added up to considerable differences in our brains and anatomy.

So, it was a bit shocking to see a headline claiming a single gene separated us from our fellow apes. The article behind the headline turned out to be wrong, of course. But there was an additional research paper behind that article. The story this told turned out to be rather interesting, even after the hype was stripped away.

The second paper was the product of a research group studying the evolution of human micro RNAs. These are short pieces of RNA that form a “hairpin” structure: two stretches of complementary sequence that can base pair to form a double helix, separated by a short loop that lets the RNA fold back on itself.

Micro RNAs, unlike messenger RNAs, don’t code for other proteins. Instead, they help control which messenger RNAs do get made into proteins. The hairpin structure is recognized by a complex of proteins inside the cell, which process it in a way that leaves a short guide sequence exposed. The guide sequence can then base pair with sequences on messenger RNAs, leading the protein complex to them. The complex will typically either block the messenger RNA from being translated into protein or cause it to be destroyed altogether.

The net result of this: a single micro RNA can determine whether a much larger number of genes are made into proteins. In that sense, they act a lot like the proteins that bind to DNA and regulate the activity of large collections of genes.

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Scientists have genetically modified mice in hopes of increasing their ability to smell TNT with 500 times the sensitivity of normal mice. If successful, the mice could provide a cheap and effective way to sniff out landmines and other explosive devices that haunt nations all over the world.

There are an estimated 45 to 100 million landmines buried around the world, according to the Red Cross, many of which are remnants of wars long since ended. The mines kill thousands each year and hamper development and economic growth. For many-war torn countries the cost of removing the mines is simply too much, and they’re left to suffer the occasional but inevitable consequences.

But a group of scientists at Hunter College in New York are trying to give them a lifesaving biosensor alternative. The group, led by Paul Feinstein, inserted a gene into odor sensing neurons in mice that could drastically increase their ability to smell TNT. Detecting an odor involves small molecules, called odorants, entering the nose and binding to receptors that sit on the ends of neurons there. Each neuron has a single type of receptor that binds to a specific odorant molecule, and when different odorant molecules bind to their receptors, they combine to generate the smells we’ve come to love, like coffee, and hate, like…decaf coffee.

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Spending long periods at low gravity may alter genes, suggests a new experiment involving a magnet-powered trick used on Earth to simulate weightlessness in space.

Subjected to magnetic levitation that generated an effect similar to microgravity experienced by astronauts orbiting Earth, fruit flies experienced changes in crucial genes.

Humans won’t necessarily respond like fruit flies, but the system is considered an useful model for probing the effects of permanent free-fall on biology. However, it’s also possible that the gene disruption was caused by magnetism, not low gravity.

“We have tried to separate the effects of microgravity and magnetism, but we’ve learned it’s not so easy,” said molecular biologist Raul Herranz of Centro de Investigaciones Biológicas in Spain, leader of the upcoming study in BMC Genomics. “We don’t know yet what is causing what — the magnetism or the microgravity?”

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Food We Eat Might Control Our Genes

“You are what you eat.” The old adage has for decades weighed on the minds of consumers who fret over responsible food choices. Yet what if it was literally true? What if material from our food actually made its way into the innermost control centers of our cells, taking charge of fundamental gene expression?

That is in fact what happens, according to a recent study of plant-animal micro­RNA transfer led by Chen-Yu Zhang of Nanjing University in China. MicroRNAs are short sequences of nucleotides—the building blocks of genetic material. Although microRNAs do not code for proteins, they prevent specific genes from giving rise to the proteins they encode. Blood samples from 21 volunteers were tested for the presence of microRNAs from crop plants, such as rice, wheat, potatoes and cabbage.

The results, published in the journal Cell Research, showed that the subjects’ bloodstream contained approximately 30 different microRNAs from commonly eaten plants. It appears that they can also alter cell function: a specific rice microRNA was shown to bind to and inhibit the activity of receptors controlling the removal of LDL—“bad” cholesterol—from the bloodstream. Like vitamins and minerals, microRNA may represent a previously unrecognized type of functional molecule obtained from food.

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There is a vast, unseen marketplace that connects us all. The traders are the trillions of bacteria that live on or within our bodies; the commodities they exchange are genes. This flow of genes around our bodies allows bacteria to rapidly evolve new skills, including the abilities to resist antibiotics, cause disease, or break down environmental chemicals. In the past, scientists have caught glimpses of individual deals, but now the full size of the marketplace is becoming clear.

The human body is home to 100 trillion microbes, whose cells outnumber ours by ten to one, and whose genes outnumber ours by a hundred to one. These genes are not only more numerous than ours, but they operate under different rules. While we can only pass down our DNA to our children, bacteria and other microbes can swap genes between one another. For example, the gut bacteria of Japanese people have a gene that helps them to digest seaweed. They borrowed it from an oceanic species that hitched its way into Japanese bowels, aboard uncooked pieces of sushi. Continue reading

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