Wednesday, January 27, 2016

A Bioengineered Tree Could Revive America's Once-Vast Chestnut Forests

TakePart.com
A Bioengineered Tree Could Revive America's Once-Vast Chestnut Forests
A Bioengineered Tree Could Revive America's Once-Vast Chestnut Forests
A century ago, towering forests of chestnut trees blanketed the East Coast of the United States. Then a fungus that hitched a ride on imported Asian chestnut trees began to infect entire woodlands.
The result: Where 4 billion chestnut trees once stretched from Georgia to Maine, only about 400 million remain today. Now scientists aim to bring back the American chestnut by bioengineering a tree to contain a gene that can withstand the Cryphonectria parasitica fungus. If they succeed, new forests of chestnuts could rise across the U.S. in the decades to come, absorbing carbon dioxide from the atmosphere and providing food and shelter for wildlife.
“The fungus took out a quarter of all our eastern forests,” said William Powell, codirector of the American Chestnut Research and Restoration Project, who envisions restoring vast Eastern chestnut forests by reclaiming mining lands and other barren areas.
He began working to bring back the chestnut 26 years ago. He and project codirector Charles Maynard combed through more than 30 plant genes to find one that would help stop the blight. They settled on a gene from a cultivated wheat species that produces an enzyme called oxalate oxidase. (Powell points out that the gene has nothing to do with gluten, and the chestnuts will stay gluten-free.) The gene is also found in strawberries and bananas.
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The enzyme detoxifies the oxalate that the fungus uses to form deadly cankers on chestnut stems. “The best thing about this gene is that it does not harm the fungus at all,” said Powell. “The fungus can still survive, but oxalate oxidase takes the weapon away from the fungus.”
Having the fungus survive is important for the safety of both species. Powell explained that the scientists don’t want to put selective pressure on the pathogen to overcome the resistance. “Since the fungus can still grow on the bark of the tree, we’re changing the lifestyle of the fungus,” he said.
Powell, Maynard, and a group of researchers from the State University of New York have published papers on the blight-resistant nature of the transgenic tree and are awaiting approval from the federal government to plant the trees.
The restoration project hopes to grow 10,000 seedlings when it receives government approval. In three to five years, those trees will be available to the public to buy at cost and plant.
Powell cautioned that reviving chestnut forests will take time. “This is a tree that can live a hundred years, not a weed that spreads quickly,” he said. “It’s going to take some time to get them established.”

Thursday, January 21, 2016

Your Neanderthal DNA may help you fight disease, and give you allergies

http://www.latimes.com

If you sneeze when flowers bloom in the spring and tear up in the presence of a cat, your Neanderthal DNA may be to blame.
About 2% of the DNA in most people alive today came from trysts between ancient humans and their Neanderthal neighbors tens of thousands of years ago, recent studies have shown. Now, scientists are trying to determine what, if any, impact that Neanderthal genetic legacy has on our contemporary lives.
In a pair of papers published this week in the American Journal of Human Genetics, two research teams report that in many people, a group of genes that govern the first line of defense against pathogens was probably inherited from Neanderthals.
These same genes appear to play a role in some people’s allergic reaction to things like pollen and pet fur as well, the scientists said.
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“It's a bit speculative, but perhaps this is some kind of trade-off,” said Janet Kelso, a researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and senior author of one of the new studies. “Increased resistance to bacterial infection was advantageous, but may have resulted in some increased sensitivity to non-pathogenic allergens.”
About 50,000 years ago, the modern humans who left Africa encountered Neanderthal settlements somewhere in the Middle East, scientists believe. On some occasions, these meetings led to couplings whose legacy is apparent in the genomes of people with ancestors from Europe and Asia.
Not everyone with Neanderthal DNA inherited the same genes. But the immunity genes appear to be more popular than others.
Among some Asian and European populations, the researchers found that these particular Neanderthal genes can be found in 50% of people.
“That's huge,” said Lluis Quintana-Murci, an evolutionary geneticist at the Pasteur Institute in Paris and senior author of the other study. “It came as a big surprise to us.”
The findings imply that these Neanderthal genes must have served our ancestors well if they are still hanging out in our genome today, and especially at such high frequency, said Peter Parham, a professor of microbiology and immunology at Stanford School of Medicine. If the DNA weren’t valuable, it would have been flushed out of the human gene pool.
“It suggests there was a benefit for the migrating modern human and the archaic human to get together,” said Parham, who wasn’t involved in the research. “What has survived is a hybridization of those populations.”
Both of the research groups report on a cluster of three genes — known collectively as TLR6-TLR1-TLR10 — that make up part of the body's innate immune response to invading bacteria and viruses.
The innate immune response is different from the acquired immune response that we get through exposure to pathogens, either through vaccines or simply getting sick. Innate immunity kicks in first, and if it’s successful, it can destroy a pathogen in a few hours, before we even know we are sick.
Because this innate immune response is so useful, it has been a strong site of positive selection over time, Quintana-Murci said.
Though both groups of researchers came to the same conclusion that Neanderthal DNA plays an important role in immunity, the teams were asking different questions at the outset of their studies.
Quintana-Murci's group is trying to understand how microscopic pathogens have influenced the human genome as our species has evolved.
Because infectious diseases have killed so many people throughout human history, it makes sense that genes involved in immunity would spread through natural selection.
For their new study, Quintana-Murci and his colleagues examined 1,500 innate immunity genes in people and matched them up with a previously published map of the Neanderthal DNA in the human genome.
The team calculated the percentage of Neanderthal DNA in innate immunity genes as well as in other genes. When they compared them, they saw that innate immunity genes had much higher proportions of Neanderthal sequences.
Kelso's group, on the other hand, is interested in ancient genomes like those of Neanderthals. In particular, her team aims to uncover the functional consequences of long-ago interbreeding between modern humans and Neanderthals.
The Max Planck Institute scientists analyzed the genomes of thousands of present-day people from all over the world, looking for evidence of extended regions with high similarity to the DNA of Neanderthals. Then they checked how often they saw those Neanderthal-like DNA sequences in humans alive today.
“What emerged was this region containing three genes involved in the innate immune system,” she said.
Both research groups said there is still much work to be done to determine exactly how this Neanderthal DNA helped humans survive.
However, they are already certain that interbreeding with Neanderthals aided early humans as they faced new dangers after leaving Africa.
“The things we have inherited from Neanderthals are largely things that have allowed us to adapt to our environment,” Kelso said. “This is perhaps not completely surprising.”
Because Neanderthals had lived in Europe and western Asia for about 200,000 years before modern humans got there, they were probably already well adapted to the local climate, foods and pathogens.
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“By interbreeding with these archaic people, modern humans could then acquire some of these adaptations,” Kelso said.
Parham of Stanford said the results are convincing, especially since they were made by two independent groups that essentially confirmed each other.
The results add to a growing body of work that highlights our debt to our Neanderthal relatives.
“We're right in the beginning,” Parham said. “This type of work has really lit a fire beneath archaeologists to try to find more and more samples of Neanderthals so geneticists can do more population studies.”

Tiny Quantum Dots May Spell Doom For Deadly Superbug Infections

Scientists say the light-activated nanoparticles wipe out infectious bacteria without harming healthy cells

01/20/2016 02:49 pm ET
iLexx via Getty Images 
 
Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterium responsible for several difficult-to-treat infections in humans.
Does nanotechnology hold the key to stopping antibiotic-resistant bacteria and the deadly infections they cause?
Scientists in Colorado think it just might. They've developed light-activated nanoparticles -- each roughly 20,000 times smaller than the thickness of a single human hair -- and shown in lab tests that these "quantum dots" are more than 90 percent effective at wiping out antibiotic-resistant germs like Salmonella, E. coli and Staphylococcus.
"In our study, we tailored these quantum dots so they can selectively kill these 'superbugs' without affecting other host mammalian cells (or human cells)," Dr. Prashant Nagpal, assistant professor of chemical and biological engineering at the University of Colorado at Boulder and a leader of the research, told The Huffington Post in an email. "This means, after more careful clinical trials, we can simply administer these dots to patients with infections and it can cure the infection without potential effects (or side effects) for healthy host cells."
If Nagpal is right, that would be a very big deal.
Antibiotic-resistant bacterial infections, fueled in part by doctors' improper use of common antibiotics, represent an enormous public health problem. In the U.S. alone, infections caused by germs that can't be eradicated with antibiotics sicken 2 million people and cause at least 23,000 deaths a year. And new, more effective antibiotics have proven very hard to develop.
(Story continues below image.)
courtesy Dr. Prashant Nagpal
High-resolution electron micrograph of a cadmium telluride nanoparticle. Scale bar is 2 nanometers.
Previous research on nanoparticles showed that those made of metals like gold and silver can be harmful to healthy tissue as well as the target bacteria, according to a written statement released by the university.
But that kind of collateral damage doesn't seem to be a problem with the new quantum dots.
Made of semiconducting materials like cadmium telluride instead of metal, they can be tailored to specific infections, slipping inside the disease-causing germs and, when activated by light, triggering chemical reactions that destroy them.
"We don't use any special light, and a typical weak light source (a lamp, well-lighted room, sunlight, etc.) is enough to activate these quantum dots," Nagpal said in the email.
Nagpal foresees several applications for quantum dots, depending on the nature of the infection. Infected cuts might simply be covered with nanoparticle-impregnated bandages. Patients with systemic infections might receive injections of quantum dots.
In addition, hospital rooms and medical instruments might be treated with a dot-containing disinfectant in order to reduce the risk of spreading infections from patient to patient.
But more research, including clinical trials, will be needed to develop quantum dot therapy and prove its safety and effectiveness in humans. Nagpal said he was seeking funding from federal agencies or private donors to make that happen.
Once tested, there is a chance that bacteria might adapt to the therapy. But even so, Nagpal said, it should be easy to then tune nanoparticles to "keep up in this evolutionary race" between bacteria and measures to eradicate them.
A paper describing the research was published online on Monday in the journal Nature Materials

Monday, January 4, 2016

Why Don’t People Eat Turtle Soup Anymore?

http://www.slate.com/

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Alligator snapping turtles were the main ingredient in soups and stews.
Courtesy of Sean Sterrett.

They say you can get seven different kinds of meat from butchering a turtle. Depending on what part of the turtle you’re chewing on, the taste may be reminiscent of pork, or chicken, or veal, or fish, or whatever … you get the picture. Perhaps this variability can partly explain why turtle has been such a popular menu item throughout the history of the United States. At least, it used to be. Not so long ago you could find Campbell’s turtle soup sitting alongside minestrone and tomato in grocery stores throughout the country. So what happened? How and why did an American staple virtually vanish?
It’s a question Saveur magazine recently tried to tackle. Now, if you ask me or anyone else who knows much about turtles and turtle conservation, the answer is quite simple: There are not enough turtles left to eat. For example, a picture of a few chefs hovering over the carcass of a green sea turtle (Chelonia mydas) leads off the Saveur article. Today green sea turtles, like all other species of sea turtles, are federally protected under the Endangered Species Act. If you ate one in the United States, you would be committing a felony.
Turtles are one of the most imperiled groups of animals on the planet. Habitat loss is probably their biggest threat; when a wetland is drained, a field paved over, or a nesting beach overrun with condominiums, there is simply no space left for turtles. But harvesting too many for food has played a key role in driving down turtle populations in this country and across the world. In fact, the market for turtle soup was so intensive in the United States that many of our turtle populations are still recovering from trapping and harvesting that occurred decades ago. Ironically, the Saveur article exploring the loss of turtle soup did not even consider that the meal’s popularity played an important role in its own vanishing act. As turtles disappeared, so did turtle soup.
The Saveur article unwittingly demonstrates why so many species have become threatened or gone extinct in the past few hundred years. When we have a limited understanding of an animal’s natural history and care only about its meat or feathers or shells, we may overlook how our actions could be killing them off for good.
Turtle populations have an interesting survival strategy. Most young turtles and eggs are eaten by predators like raccoons, herons, and big fish. This wasn’t historically a problem, because turtles that do survive to adulthood typically live for many, many years. They produce so many eggs over their lifetime that chances are good at least a few will survive long enough to replace their aging parents. The strategy works quite well as long as we don’t take the adult turtles out of the population—particularly the females—before they’ve had their many years of reproduction. That is why even individual turtles are so important (and why I have been known to go to great lengths to help them).
There are many different species of turtles, and we have different relationships with (and recipes for) each of them. During the Great Depression, gopher tortoises became such an important source of meat for rural Southerners that they earned a new nickname, “Hoover chicken” that honored, so to speak, our president at the time, Herbert Hoover. That species is now federally threatened in Louisiana, Mississippi, and western Alabama, and is under protection everywhere it occurs. Diamondback terrapins, the beautifully patterned turtles inhabiting brackish waters along the East Coast, were harvested so heavily for food that the U.S. government started to get concerned about their vastly depleted populations more than 100 years ago.
Any species could end up in soup or stew, but in this country turtle soup is synonymous with the alligator snapping turtle. Interestingly, you would never know of our long history with alligator snapping turtles from reading the Saveur magazine piece, because it never even mentioned the species. That’s like writing an entire article about cheeseburgers and never mentioning beef … or cows.
Alligator snapping turtles are the largest freshwater turtle in North America. Formerly considered one species, there are now two or three different kinds of alligator snapping turtle, depending on whom you ask. They are quite impressive: Big old alligator snappers can reach well over 100 pounds. And old is right, these turtles can live past 50 years, if not a century; they don’t even become sexually mature and able to reproduce until after their first decade of life. In the 1960s and 1970s we almost wiped out alligator snapping turtles because so many adults were harvested for soup. One former collector reported that he and his colleagues removed several tons of these animals from one river in Georgia every day during the 1970s and only stopped when they weren’t catching enough anymore to make it worthwhile.
That river is the Flint River, which I lived next to from 2004 to 2007. Despite having lived near excellent alligator snapping turtle habitat, I have seen only a few of these animals in my life. It is hard to imagine the Flint River crawling with literally tons of giant alligator snapping turtles. Maybe someday our streams and rivers will again be chock-full of these beasts, but it won’t be during my lifetime.
Fortunately, alligator snapping turtles are now afforded some protection in every state in which they occur, and at this very moment the federal government is under pressure to protect them under the Endangered Species Act. Even Louisiana, once the hub of the turtle soup industry, outlawed commercial collection of this species in 2004. Given that these animals received protection only recently, it will be a long time before populations rebound to their historic levels, if ever. In some restaurants you can still find traditional turtle soup that contains alligator snapping turtle, but these days the animals come from farms and were not collected from wild populations.

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Even if you can legally eat a snapping turtle, there's another good reason why you shouldn't.
Courtesy of Sean Sterrett.

The turtle hunters from the Saveur article were in Virginia, and their quarry was a different kind of snapping turtle, Chelydra serpentina. This species is still relatively abundant in Virginia, but commercial collection is illegal. Commercial collection of even relatively common turtle species has recently been outlawed throughout much the southeastern United States in response to an increasing demand from Asia. This alarming and increasing demand had started to put an unsustainable strain on our turtle populations. But in some states, depending on the species, you can still take a couple for personal use.
Even if people are allowed to eat a few turtles every once in a while, there is another important reason why we may not want to: It’s not just bad for the turtles; it’s bad for us. Remember how turtles can live for decades? Well, if that turtle is sitting in polluted water, it is going to be absorbing and consuming contaminants for many years. This unfortunate habit has made the snapping turtle (Chelydra serpentina)—the same species that features heavily in the Saveur article—a model organism for studying how pollutants persist in wetlands. For example, despite a ban since 1979 on the manufacture of polychlorinated biphenyls, turtles in some areas still have alarmingly high concentrations of PCBs in their blood and their meat. PCBs can cause a wide range of serious health problems in people. And forget tuna—if you want to avoid mercury, you should cut snapping turtle out of your diet. Patterns of pollutants differ depending on which swamp the turtle has been sitting in for the past 50 years, but I think I’ll pass either way.
Turtle soup in the United States did not fade away simply because our palates changed. Our taste for turtle soup exploded to unsustainable levels and caused the turtles to disappear first. They still haven’t come back.

Dr. David A. Steen researches wildlife ecology and conservation biology, and blogs about his work at www.livingalongsidewildlife.com. Follow him on Twitter.