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Alcohol-Induced Histone Acetylation Reveals a Gene Network Involved in Alcohol Tolerance

Alcohol-Induced Histone Acetylation Reveals a Gene Network Involved in Alcohol Tolerance | Amazing Science |

Sustained or repeated exposure to sedating drugs such as alcohol, triggers homeostatic adaptations in the brain that lead to the development of drug tolerance and dependence. These adaptations involve long-term changes in the transcription of drug-responsive genes as well as an epigenetic restructuring of chromosomal regions that is thought to signal and maintain the altered transcriptional state.

Alcohol-induced epigenetic changes have been shown to be important in the long-term adaptation that leads to alcohol tolerance and dependence endophenotypes. A major constraint impeding progress is that alcohol produces a surfeit of changes in gene expression, most of which may not make any meaningful contribution to the ethanol response under study.

A research team now used a novel genomic epigenetic approach to find genes relevant for functional alcohol tolerance by exploiting the commonalities of two chemically distinct alcohols. In Drosophila melanogaster, ethanol and benzyl alcohol induce mutual cross-tolerance, indicating that they share a common mechanism for producing tolerance. They surveyed the genome-wide changes in histone acetylation that occur in response to these drugs. Each drug induces modifications in a large number of genes. The genes that respond similarly to either treatment, however, represent a subgroup enriched for genes important for the common tolerance response. Genes were functionally tested for behavioral tolerance to the sedative effects of ethanol and benzyl alcohol using mutant and inducible RNAi stocks. The identified a network of genes that are essential for the development of tolerance to sedation by alcohol.

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Research Teams Use DNA To Make High-Precision 3-D Nanoparticle Structures

Research Teams Use DNA To Make High-Precision 3-D Nanoparticle Structures | Amazing Science |

DNA strands anchored to the surface of nanoparticles allow researchers to assemble the particles into three-dimensional crystalline lattices. Such control allows researchers to make new materials with desirable properties. In two recent studies, independent teams adapted this approach to gain even more control over assembly.

One team, led by Chad A. Mirkin of Northwestern University, designed “transmutable” DNA-coated nanoparticles that can switch from one lattice structure to another on demand in response to chemical cues (Science 2016, DOI: 10.1126/science.aad2212).

To do that, Mirkin’s team coats the nanoparticle surface with DNA that folds back on itself in hairpin loops. The addition of short oligonucleotides complementary to the loops disrupts the hairpins and exposes a DNA recognition sequence that can bind to sequences on other nanoparticles. By using multiple hairpins that bind to different sequences, the researchers can cycle a given nanoparticle mixture between lattice structures by changing which hairpins are opened or closed.

“Until now, all DNA-programmable nanoparticles have been designed to build one particular structure. To get another structure, you must make a whole new batch of nanoparticles with different DNA linkers attached,” says Sharon C. Glotzer, a materials scientist at the University of Michigan. “With this breakthrough, one can embed multiple potential structures into a single batch of identical nanoparticles and then select the desired structure on demand. The nanoparticles are now transmutable.”

The other team, led by Oleg Gang of Brookhaven National Laboratory, made DNA nanoparticle structures with the same crystal lattice as diamond (Science 2016, DOI: 10.1126/science.aad2080). Scientists have been trying to make this structure for decades, Gang says. His team succeeded by combining DNA-coated nanoparticles with tetrahedral cages made with DNA origami. Short, single-stranded DNA sequences on the tetrahedron bind to the DNA coating on the particles. One nanoparticle is trapped inside each tetrahedron; four others are attached to the vertices of the tetrahedron, mimicking the geometry of carbon in diamond.

Gang’s strategy marks the first time DNA origami has been combined with DNA-mediated nanoparticle assembly, Glotzer notes. Such an approach will lead to more complex assemblies than are accessible by more traditional approaches alone, she says.

Via Integrated DNA Technologies
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Man-made global warming effects will play out over next 10,000 years

Man-made global warming effects will play out over next 10,000 years | Amazing Science |

A large group of climate scientists has made a bracing statement in the journal Nature Climate Change, arguing that we are mistaken if we think global warming is only a matter of the next 100 years or so — in fact, they say, we are locking in changes that will play out over as many as 10,000 years.

“The next few decades offer a brief window of opportunity to minimize large-scale and potentially catastrophic climate change that will extend longer than the entire history of human civilization thus far,” write the 22 climate researchers, led by Peter Clark, from Oregon State University.

The author names include not only a number of very influential climate scientists in general but several key leaders behind major reports from the United Nations’ Intergovernmental Panel on Climate Change, including MIT’s Susan Solomon and Thomas Stocker of the University of Bern in Switzerland.

The researchers’ key contention is that we have been thinking about climate change far too narrowly by only projecting outward to the year 2100, which the research says “was originally driven by past computational capabilities.” Rather, we should consider that the long-term consequences of human emissions for global temperatures and sea level will play out over many millennia.

“It’s a statement of worry,” said Raymond Pierrehumbert, a geoscientist at Oxford University and one of the study’s authors. “And actually, most of us who have worked both on paleoclimate and the future have been terrified by the idea of doubling or quadrupling CO2 right from the get-go.”

“In hundreds of years from now, people will look back and say, yeah, the sea level is rising, it will continue to rise, we live with a constant rise of sea level because of these people 200 years ago that used coal, and oil, and gas,” said Anders Levermann, a sea level rise expert at the Potsdam Institute for Climate Impact Research and one of the paper’s authors. “If you just look at this, it’s stunning that we can make such a long-lasting impact that has the same magnitude as the ice ages.”

The key reason for this is that carbon dioxide stays in the atmosphere for a very long time before being slowly removed again by natural processes. “A considerable fraction of the carbon emitted to date and in the next 100 years will remain in the atmosphere for tens to hundreds of thousands of years,” the study noted. Meanwhile, the planet’s sea levels adjust gradually to its rising temperature over thousands of years.

So what will the world look like in 10,000 years, thanks to us? That really depends on what we do in the next few hundred years with the fossil fuels to which we have relatively easy access. It also depends on whether or not we develop technologies that are capable of pulling carbon dioxide out of the air on a massive scale, comparable to the amount that we’re currently emitting.

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Room-temperature lithium metal battery closer to reality

Room-temperature lithium metal battery closer to reality | Amazing Science |

Rechargeable lithium metal batteries have been known for four decades to offer energy storage capabilities far superior to today's workhorse lithium-ion technology that powers our smartphones and laptops. But these batteries are not in common use today because, when recharged, they spontaneously grow treelike bumps called dendrites on the surface of the negative electrode.

Over many hours of operation, these dendrites grow to span the space between the negative and positive electrode, causing short-circuiting and a potential safety hazard.

Current technology focuses on managing these dendrites by putting up a mechanically strong barrier, normally a ceramic separator, between the negative and the positive electrodes to restrict the movement of the dendrite. The relative non-conductivity and brittleness of such barriers, however, means the battery must be operated at high temperature and are prone to failure when the barrier cracks.

But a Cornell team, led by chemical and biomolecular engineering professor Lynden Archer and graduate student Snehashis Choudhury, proposed in a recent study that by designing nanostructured membranes with pore dimensions below a critical value, it is possible to stop growth of dendrites in lithium batteries at room temperature. "The problem with ceramics is that this brute-force solution compromises conductivity," said Archer, the William C. Hooey Director and James A. Friend Family Distinguished Professor of Engineering and director of the Robert Frederick Smith School of Chemical and Biomolecular Engineering.

"This means that batteries that use ceramics must be operated at very high temperatures – 300 to 400 degrees Celsius [572 to 752 degrees Fahrenheit], in some cases," Archer said. "And the obvious challenge that brings is, how do I put that in my iPhone?" You don't, of course, but with the technology that the Archer group has put forth, creating a highly efficient lithium metal battery for a cellphone or other device could be reality in the not-too-distant future.

Archer credits Choudhury with identifying the polymer polyethylene oxide as particularly promising. The idea was to take advantage of "hairy" nanoparticles, created by grafting polyethylene oxide onto silica to form nanoscale organic hybrid materials (NOHMs), materials Archer and his colleagues have been studying for several years, to create nanoporous membranes.

To screen out dendrites, the nanoparticle-tethered PEO is cross-linked with another polymer, polypropylene oxide, to yield mechanically robust membranes that are easily infiltrated with liquid electrolytes. This produces structures with good conductivity at room temperature while still preventing dendrite growth. "Instead of a 'wall' to block the dendrites' proliferation, the membranes provided a porous media through which the ions pass, with the pore-gaps being small enough to restrict dendrite penetration," Choudhury said. "With this nanostructured electrolyte, we have created materials with good mechanical strength and good ionic conductivity at room temperature."

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What people and their domesticated animals ate 30,000 years ago

What people and their domesticated animals ate 30,000 years ago | Amazing Science |

Biogeologists have shown how Gravettian people shared their food 30,000 years ago. Around 30,000 years ago Predmosti was inhabited by people of the pan-European Gravettian culture, who used the bones of more than 1000 mammoths to build their settlement and to ivory sculptures. Did prehistoric people collect this precious raw material from carcasses -- easy to spot on the big cold steppe -- or were they the direct result of hunting for food?

Předmostí I is an exceptional prehistoric site located near Brno in the Czech Republic. Around 30,000 years ago it was inhabited by people of the pan-European Gravettian culture, who used the bones of more than 1,000 mammoths to build their settlement and to ivory sculptures. Did prehistoric people collect this precious raw material from carcasses -- easy to spot on the big cold steppe -- or were they the direct result of hunting for food? This year-round settlement also yielded a large number of canids remains, some of them with characteristics of Palaeolithic dogs. Were these animals used to help hunt mammoths?

To answer these two questions, Tübingen researcher Hervé Bocherens and his international team carried out an analysis of carbon and nitrogen stable isotopes in human and animal fossil bones from the site. Working with researchers from Brno and Brussels, the researchers were able to test whether the Gravettian people of Předmostí ate mammoth meat and how the "palaeolithic dogs" fit into this subsistence picture.

They found that humans did consume mammoth -- and in large quantities. Other carnivores, such as brown bears, wolves and wolverines, also had access to mammoth meat, indicating the high availability of fresh mammoth carcasses, most likely left behind by human hunters. Surprisingly, the dogs did not show a high level of mammoth consumption, but rather consumed essentially reindeer meat that was not the staple food of their owners. A similar situation is observed in traditional populations from northern regions, who often feed their dogs with the food that they do not like. These results also suggest that these early dogs were restrained, and were probably used as transportation helpers.

These new results provide clear evidence that mammoth was a key component of prehistoric life in Europe 30,000 years ago, and that dogs were already there to help.

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AI: Machine learning helps discover the most luminous supernova in history

AI: Machine learning helps discover the most luminous supernova in history | Amazing Science |
Machine-learning technology developed at Los Alamos National Laboratory played a key role in the discovery of supernova ASASSN-15lh, an exceptionally powerful explosion that was 570 billion times brighter than the sun and more than twice as luminous as the previous record-holding supernova. This extraordinary event marking the death of a star was identified by the All Sky Automated Survey for SuperNovae (ASAS-SN) and is described in a new study published today in Science.

"This is a golden age for studying changes in astronomical objects thanks to rapid growth in imaging and computing technology," said Przemek Wozniak, the principal investigator of the project that created the software system used to spot ASASSN-15lh. "ASAS-SN is a leader in wide-area searches for supernovae using small robotic telescopes that repeatedly observe the same areas of the sky looking for interesting changes."

ASASSN-15lh was first observed in June 2015 by twin ASAS-SN telescopes¾just 14 centimeters in diameter¾located in Cerro Tololo, Chile. While supernovae already rank among the most energetic explosions in the universe, this one was 200 times more powerful than a typical supernova. The event appears to be an extreme example of a "superluminous supernova," a recently discovered class of rare cosmic explosions, most likely associated with gravitational collapse of dying massive stars. However, the record-breaking properties of ASASSN-15lh stretch even the most exotic theoretical models based on rapidly spinning neutron stars called magnetars.

"The grand challenge in this work is to select rare transient events from a deluge of imaging data in time to collect detailed follow-up observations with larger, more powerful telescopes," said Wozniak. "We developed an automated software system based on machine-learning algorithms to reliably separate real transients from bogus detections." This new technology will soon enable scientists to find ten or perhaps even hundred times more supernovae and explore truly rare cases in great detail. Since January 2015 this capability has been deployed on a live data stream from ASAS-SN.

Los Alamos is also developing high-fidelity computer simulations of shock waves and radiation generated in supernova explosions. As explained by Chris Fryer, a computational scientist at Los Alamos who leads the supernova simulation and modeling group, "By comparing our models with measurements collected during the onset of a supernova, we will learn about the progenitors of these violent events, the end stages of stellar evolution leading up to the explosion, and the explosion mechanism itself."

The next generation of massive sky monitoring surveys is poised to deliver a steady stream of high-impact discoveries like ASASSN-15lh. The Large Synoptic Survey Telescope (LSST) expected to go on sky in 2022 will collect 100 Petabytes (100 million Gigabytes) of imaging data. The Zwicky Transient Facility (ZTF) planned to begin operations in 2017 is designed to routinely catch supernovae in the act of exploding. However, even with LSST and ZTF up and running, ASAS-SN will have a unique advantage of observing the entire visible sky on daily cadence. Los Alamos is at the forefront of this field and well prepared to make important contributions in the future.

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Looking back: Biomedicine 2015 - Baby Engineering, Spray-On GMOs, and Cancer Cures

Looking back: Biomedicine 2015 - Baby Engineering, Spray-On GMOs, and Cancer Cures | Amazing Science |
During 2015, the combination of potent biotechnologies solved problems and created new ones.

Biologists often emphasize how little anyone really knows about the brain, the genome, and the mechanisms behind effective drugs. But this year their tune changed as diverse technologies–gene editing, stem cells, cloning, and DNA databases–coalesced into an immensely powerful toolkit for manipulating life. The message in 2015 seemed to be: “We can do anything.” The technology that stole the headlines was CRISPR, the versatile genetic scissors that make it easy to cut and edit DNA of living cells.

For the year, the number of scientific publications involving the technique doubled to more than 1,200, as scientists use gene editing to engineer extra-muscular dogs, create mosquitoes that can’t spread malaria, and alter plants so easily that companies predict it’s just a matter of years before gene-edited foods hit our dinner plates.

We can do these things, but should we? Social and ethical questions began dogging the CRISPR breakthrough early in the year, when MITTechnology Review toured readers through one emerging debate: the possibility of genetically modifying human embryos in IVF clinics to spare children from inherited disease. With an April publication from China disclosing the first edited human embryos, the debate over whether the technology is a slippery slope to eugenics exploded, and by December many of the world’s top gene-editing scientists had gathered in Washington for a will-we-or-won’t-we debate.

They concluded that we shouldn’t, not yet. It would be “irresponsible” to use CRISPR to make customized babies, the experts declared. In fact, one participant felt that our power to engineer life had outstripped our wisdom. “We are becoming masters of manipulating genes, but our understanding of their function is very limited,” said Klaus Rajewsky of the Max Delbrück Center for Molecular Medicine, in Berlin.

Yet we might know enough to cure some cancers, or solve the shortage of organs for transplant. Companies including Juno Therapeutics this year raised billions to start treating patients with genetically engineered immune cells that they have crafted into a lifesaving new treatment for leukemia. Surgeons in the U.S. smashed records for so-called “xenotransplantation” (transplants between species) by keeping a monkey alive nearly six months with a gene-modified pig kidney.

Gene technology isn’t just more powerful. It’s easier to access. Entrepreneurs started selling do-it-yourself DNA engineering kits to modify bacteria, and in October we told the story of a startup founder, Elizabeth Parrish, who claimed to be the first person to thumb her nose at the U.S. Food and Drug Administration and treat herself with anti-aging genes. “I am patient zero,” she declared.

It’s a sign that we are deep into the second generation of biotechnology. That also means some pioneering inventions are being retired. This year, Monsanto’s patents on its original herbicide-resistant soybeans expired (pound for pound, the beans are easily the most important product of the biotech era), allowing farmers to plant “generic GMOs” for the first time. But  Monsanto has new ideas in its pipeline, like genetic sprays that can kill bugs or even change the behavior of plants on contact. Those products rely on RNA interference, which was also used to create the world’s first biotech apple.

A different trend that gained traction was the use of electricity to heal the mind or treat the body. Some call these therapies “electroceuticals.” Doctors began using brain stimulation to treat cocaine addiction,obsessive-compulsive disorder, and other problems once “considered too complex and mysterious” to cure with a simple jolt of electricity. In Cleveland, meanwhile, specialists at Case Western ran wires between the brain of a paralyzed man and the muscles of his arm, allowing him to move the arm with his thoughts. We didn’t forget to check in with the brave volunteers who got us here. We learned how patients who received a previous generation of implants at Case were left without tech support, rendering the devices useless inside their bodies. One far-out scientific pioneer even decided to put an implant in his own brain.

That role Silicon Valley might play in biotechnology is also worth watching. For that, we checked in several times this year with famed Facebook investor Peter Thiel to learn about a cancer-fighting startup he funded and get his views on how drug development could be more efficient if only biotech companies acted a little more like computer startups. Thiel, who thinks there shouldn’t be so much trial and error going on, told us his goal is to “get rid of randomness.”

We also tracked tech companies attempting to disrupt the huge, unhealthy U.S. health-care system. It’s not going too well: consumers don’t trust tech companies with their health data, and wrist-worn devices aren’t too accurate. But tech companies won’t be dissuaded. This year we learned that Apple was in discussions with researchers tocollect people’s DNA data, and a San Francisco startup called Helix, bankrolled with $100 million, said it would launch the first DNA app store for consumers in 2016.

These ideas were part of an emerging boom in consumer use of genomics, which drew in figures like J. Craig Venter. Yet the economics of consumer DNA services remain unclear, partly because DNA predictions aren’t always foolproof or useful. This year, a $699 direct-to-consumer blood test for cancer got a very chilly reception, while pregnancy tests expanded into uncharted territory and sometimesfound cancer by accident. Even better-established cancer tests aren’t proven to really help patients. The leader in tumor DNA testing in the U.S., Foundation Medicine, sold a majority of its shares to Roche, a sign that its future was uncertain.

Making DNA data more useful is the goal of President Obama’s “precision medicine initiative,” a $215 million effort that includes a planned study of the health records and DNA of one million people. Only with big numbers, the government says, will the next wave of links between genes and disease be discovered. Yet big studies could cause big, unexpected problems. In March, the CEO of DeCode Genetics, a subsidiary of Amgen that runs a nationwide gene bank in Iceland, said its database was now so big that it could pinpoint each and every Icelandic woman with a dangerous breast cancer mutation. Yet because of privacy laws, DeCode complained, it is unable to tell them. 
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Americans are ten times more likely to die from firearms than citizens of other nations

Americans are ten times more likely to die from firearms than citizens of other nations | Amazing Science |

Gun deaths are a serious public health issue in the United States and the scope of the problem is often difficult to illustrate. A new study published in The American Journal of Medicine lays out the risk in concrete terms. When compared to 22 other high-income nations, Americans are ten times more likely to be killed by a gun than their counterparts in the developed world. Specifically, gun homicide rates are 25 times higher in the U.S. and, while the overall suicide rate is on par with other high-income nations, the U.S. gun suicide rate is eight times higher.

In order to help put America's relationship with guns into perspective, researchers from the University of Nevada-Reno and the Harvard T.H. Chan School of Public Health analyzed mortality data gathered by the World Health Organization in 2010. Investigators found that despite having similar rates of nonlethal crimes as other high-income countries, the U.S. has much higher rates of lethal violence, mostly driven by extremely higher rates of gun-related homicides.

The study reveals some stark truths about living and dying in the United States. When compared to other high-income nations, as an American you are:

• Seven times more likely to be violently killed

• Twenty-five times more likely to be violently killed with a gun

• Six times more likely to be accidentally killed with a gun

• Eight times more likely to commit suicide using a gun

• Ten times more likely to die from a firearm death overall

Homicide is the second leading cause of death for Americans 15 to 24 years of age, and the third leading cause of death among those 25 to 34 years of age. Investigators found that for these two groups, the risk relative to their counterparts in other developed nations is alarmingly elevated. Americans 15 to 24 years of age are 49 times more likely to die from firearm homicide compared to similarly aged young people in other high-income nations. For those aged 25 to 34, the risk is 32 times higher.

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Largest rocky exoplanet found (half the size of Neptune)

Largest rocky exoplanet found (half the size of Neptune) | Amazing Science |
A planet roughly half the size of Neptune might be 100 percent rock, making it the largest known rocky world.

When it comes to big balls of rock, exoplanet BD+20594b might have all other known worlds beat. At roughly half the diameter of Neptune, BD+20594b is 100 percent rock, researchers suggest online January 28 at The planet seems to defy recent calculations that indicate a planet this large should be gassy (SN: 8/22/15, p. 32).

BD+20594b sits about 500 light-years away in the constellation Aries. The planet is about 16 times as massive as Earth but just a little over twice as wide, making its density about 8 grams per cubic centimeter, Néstor Espinoza, an astrophysicist at the Pontifical Catholic University of Chile in Santiago, and colleagues report. Earth’s density, by comparison, is 5.5 grams per cubic centimeter. The new rocky planet was discovered in 2015 with the Kepler space telescope, which looks for the silhouettes of planets passing in front of their stars.

BD+20594b is comparable to Kepler 10c, a rocky “mega Earth” reported in 2014 (SN: 7/12/14, p. 10) to be 2.4 times as wide as Earth with a hefty mass (equal to about 17 Earths). Recent measurements indicate, however, that Kepler 10c isn’t quite as “mega” or as rocky as thought — only 14 times as massive as Earth — which means that the planet is probably encased in shell of gas or water. 

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Future of drug delivery in a crystal ball 100 times stronger than liposomes

Future of drug delivery in a crystal ball 100 times stronger than liposomes | Amazing Science |

A Drexel University materials scientist has discovered a way to encapsulate medication to deliver it more effectively inside the body. Until now, crystals have grown in rigid, structured formations (like the snowflake) — with a web of straight lines connecting to making a grid that grows into the crystalline flake.*

But the formation of a crystal is affected by the environment in which it forms. And Christopher Li, PhD, a professor in the College of Engineering and head of the Soft Materials Lab in the Department of Materials Science & Engineering, uses this workaround to engineer hollow crystal spheres. He recently reported his finding in Nature Communications(open access).

Li was able to overcome crystal’s edge-forming tendencies by creating a tiny bubble of oil to encase water molecules. When the surfactant bubble was cooled to the appropriate temperature, the molecules inside began to crystalize. But rather than forming an angular web of connections, the molecules, instead, lined up along the interior of the oil bubble — crystallizing in a hollow, spherical shape.

Early tests indicate that Li’s “crystalsome” (named for their similarity to liposomes — tiny bubbles with the same membrane as cells that are being explored for use as biological packages for delivering drug treatments) is a few hundred times stronger than liposomes, making them a sturdier option for medicine encapsulation.

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Ravens might possess a Theory of Mind, say scientists

Ravens might possess a Theory of Mind, say scientists | Amazing Science |
A new study of ravens' behavior when they think they're being 'spied on' suggests they possess building blocks of humans' own ability to interpret others' thoughts, hopes, and fears.

Recent studies purported to demonstrate that chimpanzees, monkeys and corvids possess a basic Theory of Mind, the ability to attribute mental states like seeing to others. However, these studies remain controversial because they share a common confound: the conspecific’s line of gaze, which could serve as an associative cue. Here, we show that ravens Corvus corax take into account the visual access of others, even when they cannot see a conspecific.

Specifically, we find that ravens guard their caches against discovery in response to the sounds of conspecifics when a peephole is open but not when it is closed. Our results suggest that ravens can generalize from their own perceptual experience to infer the possibility of being seen. These findings confirm and unite previous work, providing strong evidence that ravens are more than mere behavior-readers.

Ravens do spy on each other, it turns out, and they can infer when other birds are snooping on them. New findings, released Tuesday in a study inNature Communications, highlight just how sophisticated – and human-like – ravens' cognitive abilities are.

Rescooped by Dr. Stefan Gruenwald from Medical Science!

Cancer Spread Tracked From A Single Cell In A Live Animal

Cancer Spread Tracked From A Single Cell In A Live Animal | Amazing Science |

Researchers at Harvard-affiliated Boston Children’s Hospital have, for the first time, visualized the origins of cancer from the first affected cell and watched its spread in a live animal. Their work, published in the Jan. 29 issue of Science, could change the way scientists understand melanoma and other cancers and lead to new, early treatments before the cancer has taken hold.

“An important mystery has been why some cells in the body already have mutations seen in cancer, but do not yet fully behave like the cancer,” says the paper’s first author, Charles Kaufman, a postdoctoral fellow in the Zon Laboratory at Boston Children’s Hospital. “We found that the beginning of cancer occurs after activation of an oncogene or loss of a tumor suppressor, and involves a change that takes a single cell back to a stem cell state.”

That change, Kaufman and colleagues found, involves a set of genes that could be targeted to stop cancer from ever starting. The study imaged live zebrafish over time to track the development of melanoma. All the fish had the human cancer mutation BRAFV600E — found in most benign moles — and had also lost the tumor suppressor gene p53.

Kaufman and colleagues engineered the fish to light up in fluorescent green if a gene called crestin was turned on — a “beacon” indicating activation of a genetic program characteristic of stem cells. This program normally shuts off after embryonic development, but occasionally, in certain cells and for reasons not yet known, crestin and other genes in the program turn back on.

“Every so often we would see a green spot on a fish,” said Leonard Zon, director of the Stem Cell Research Program at Boston Children’s and senior investigator on the study. “When we followed them, they became tumors 100 percent of the time.”

When Kaufman, Zon, and colleagues looked to see what was different about these early cancer cells, they found that crestin and the other activated genes were the same ones turned on during zebrafish embryonic development — specifically, in the stem cells that give rise to the pigment cells known as melanocytes, within a structure called the neural crest.

“What’s amazing about this group of genes is that they also get turned on in human melanoma,” said Zon, who is also a member of the Harvard Stem Cell Instituteand a Howard Hughes Medical Institute investigator. “It’s a change in cell fate, back to neural crest status.”

Finding these cancer-originating cells was tedious. Wearing goggles and using a microscope with a fluorescent filter, Kaufman examined the fish as they swam around, shooting video with his iPhone. Scanning 50 fish could take two to three hours. In 30 fish, Kaufman spotted a small cluster of green-glowing cells about the size of the head of a Sharpie marker — and in all 30 cases, these spots grew into melanomas. In two cases, he was able to see on a single green-glowing cell and watch it divide and ultimately become a tumor mass.

Via Steven Krohn
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Visualizing Cross-Sectional Data in a Real-World Context

Visualizing Cross-Sectional Data in a Real-World Context | Amazing Science |
Combining the capabilities of an open-source drawing tool with Google Earth maps allows researchers to visualize real-world cross-sectional data in three dimensions.

If you could fly around your research results in three dimensions, wouldn’t you like to do it? Visualizing research results properly during scientific presentations already does half the job of informing the public on the geographic framework of your research. Many scientists use Google Earth™ mapping service (V7.1.2.2041) because it’s a great interactive mapping tool for assigning geographic coordinates to individual data points, localizing a research area, and draping maps of results over Earth’s surface for displaying the results in three dimensions. Yet scientists often do not fully explore the Google Earth™ platform.

Visualizations of research results in vertical cross sections through these maps are often not shown at the same time as the maps. However, a few tutorials to display cross-sectional data in Google Earth™ do exist, and the workflow is rather simple. By importing cross-sectional data into in the open software SketchUp Make [Trimble Navigation Limited, 2016], any spatial model displaying research results can be exported to a vertical figure in Google Earth™. A website now explains an easy workflow including tips, and discusses some of the endless applications of the method. This workflow will give researchers better spatial visibility of their results and will allow for more dynamic scientific presentations.

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Tick genome reveals secrets of a successful bloodsucker

Tick genome reveals secrets of a successful bloodsucker | Amazing Science |

With tenacity befitting their subject, an international team of nearly 100 researchers toiled for a decade and overcame tough technical challenges to decipher the genome of the blacklegged tick (Ixodes scapularis)The National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, contributed primary support to the research, which appears in the online, open-access journal Nature Communications.

“Ticks spread more different kinds of infectious microbes to people and animals than any other arthropod group,” said NIAID Director Anthony S. Fauci, M.D. “The spiral-shaped bacterium that causes Lyme disease is perhaps the best known microbe transmitted by ticks; however, ticks also transmit infectious agents that cause human babesiosis, anaplasmosis, tick-borne encephalitis and other diseases. The newly assembled genome provides insight into what makes ticks such effective disease vectors and may generate new ways to lessen their impact on human and animal health.”

Catherine A. Hill, Ph.D., of Purdue University, headed the team of investigators. Aside from the logistical challenges of coordinating activities of dozens of workers across many time zones, the researchers’ focus was a creature that is extremely difficult to maintain and that lives a long time — up to two years in the wild and nine months in the lab, Dr. Hill noted. Ixodes ticks have three blood-feeding life stages, and during each one, they feed on a different vertebrate animal. During feeding, ticks ingest blood for hours or days at a time. After mating, adult female ticks rapidly imbibe a large blood meal during which they expand hugely. “Because genes may switch on or off depending on the life stage of the tick, we needed to culture and collect ticks at each stage for analysis. This was not easy to do,” said Dr. Hill.

Another challenge was the sheer size of the tick genome — some 2.1 billion DNA base pairs — and expansive regions where sequences are repeated. “The degree of DNA repetition — approximately 70 percent of the total — made assembling the full genome in the correct order very difficult,” Dr. Hill said. In the end, the team determined the order and sequence of about two-thirds of the total genome. “We determined the sequence for 20,486 protein-coding genes,” she said, “of which 20 percent may be unique to ticks. Those tick-specific genes are like guideposts that say ‘start here’ as we look for new ways to counter infectious ticks.”

Although the latest research represents just a first look at the tick genome, the scientists have already identified genes and protein families that shed light on why Ixodes ticks succeed so well as parasites and hint at the reasons they excel at spreading pathogens, Dr. Hill noted. For example, compared with other blood-feeders, ticks have many more proteins devoted to consuming, concentrating and detoxifying their iron-containing food. Although mosquitoes — which quickly siphon up relatively small amounts of blood through a tube-like mouthpiece — have several proteins dedicated to blood digestion, ticks have many more proteins involved in this process. Other genes code for proteins that help ticks concentrate the blood and rapidly excrete excess water that accompanies large blood meals. Still other genes allow ticks to quickly expand their stiff outer coats to accommodate a 100-fold increase in total body size during blood feeding.

Other peculiarities of the tick’s lifestyle reflected in the genome include genes associated with the multifaceted sensory systems that the parasite uses when “questing” for a host during each of its separate blood-feeding stages. Compared with mosquitoes, ticks appear to have fewer genes used to detect hosts, and, unlike a mosquito’s “smell” receptors, ticks may use “taste” receptors to locate their food sources. Each of the newly identified proteins is a potential target for new, tick-specific interventions, explained Dr. Hill. “The genome gives us a code book to the inner workings of ticks. With it, we can now begin to hack their system and write a counter-script against them.”

In an effort to explain variations in Lyme disease prevalence across the United States, the team also examined genetic diversity within and among I. scapularis populations gathered from five states in the Northeast and Midwest and three in the South. Some have speculated that ticks in the Northeast and Midwest spread the bacteria that cause Lyme disease more easily than those in the South, or that the two populations perhaps comprise separate species. The genetic analysis showed that there is only one species of I. scapularis, said Dr. Hill, but subtle genetic differences were detected, and these may help explain some of the variance in the ability of populations to transmit disease and, therefore, affect disease prevalence.

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Cyanobacteria see like tiny little eyeballs

Cyanobacteria see like tiny little eyeballs | Amazing Science |
Biologists discover how bacteria sense light and move towards it: the entire single-cell organism focuses light like a tiny eyeball.

Cyanobacteria, including the Synechocystis species used in the study, are an ancient and abundant lifeform. They live in water and get their energy from photosynthesis - which explains their enthusiasm for bright light. "It has a way of detecting where the light is; we know that because of the direction that it moves. But we were puzzled about this because the cells are very, very small," said study co-author Conrad Mullineaux, from Queen Mary University of London.

The researchers used a laser beam to probe exactly how such focused light affected the bugs' behavior. With the laser beam trained steadily on the centre of a dish, the team shone a bigger, separate light on the Synechocystis cells from one side. This drew the little critters across the surface in the usual way, pulling themselves towards the light with tiny tentacles. The usual bright "image" of the light was visible, focused on their trailing side. But the moment any of the bugs strayed into the laser beam, there was an abrupt about-face. "When they hit it, they bounced off it," Prof Mullineaux said. "As soon as the laser was hitting one side of the cell, the cells moved away. They switched direction."

In other words, bright light focused on one side of the bacterium definitely does drive it to run the other way - which under normal circumstances takes it towards the source of the light. In fact, because some amount of light is hitting the cell from all around, the team says that each microbe will have a "360-degree image" of its surroundings focused on the inside of its cell membrane. That image is very fuzzy - with a resolution of about 21 degrees, compared to the 0.02-degree precision of our eyes - but it is enough for photoreceptor molecules, embedded in the cell membrane, to guide the bug's movement.

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Alcaline ocean on Enceladus - could it harbor life?

Alcaline ocean on Enceladus - could it harbor life? | Amazing Science |
Recently, geochemist Christopher Glein led a team that developed a new approach to estimating the pH of Enceladus' ocean using observational data of the carbonate geochemistry of plume material. This is a classic problem in geochemical studies of Earth (such as rainwater), but scientists can now solve the carbonate problem on an extraterrestrial body thanks to measurements of dissolved inorganic carbon by the Cosmic Dust Analyzer (CDA), and carbon dioxide gas by the Ion and Neutral Mass Spectrometer (INMS) onboard Cassini.
Glein's team tried to create the most comprehensive chemical model to date of the ocean by accounting for compositional constraints from both INMS and CDA, such as the salinity of the plume. Their model suggests that Enceladus has a sodium, chloride and carbonate ocean with an alkaline pH of 11 or 12, close to the equivalent of ammonia or soapy water. The estimated pH is slightly higher by 1 to 2 units than an earlier estimate based on CDA data alone, but the different modeling approaches are consistent in terms of the overall chemistry of an alkaline ocean.
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Energy-friendly chip for mobile devices can perform powerful artificial-intelligence tasks

Energy-friendly chip for mobile devices can perform powerful artificial-intelligence tasks | Amazing Science |
MIT researchers have developed a new chip designed to implement neural networks. It is 10 times as efficient as a mobile GPU, so it could enable mobile devices to run powerful artificial-intelligence algorithms locally, rather than uploading data to the Internet for processing.

In recent years, some of the most exciting advances in artificial intelligence have come courtesy of convolutional neural networks, large virtual networks of simple information-processing units, which are loosely modeled on the anatomy of the human brain.

Neural networks are typically implemented using graphics processing units (GPUs), special-purpose graphics chips found in all computing devices with screens. A mobile GPU, of the type found in a cell phone, might have almost 200 cores, or processing units, making it well suited to simulating a network of distributed processors.

At the International Solid State Circuits Conference in San Francisco this week, MIT researchers presented a new chip designed specifically to implement neural networks. It is 10 times as efficient as a mobile GPU, so it could enable mobile devices to run powerful artificial-intelligence algorithms locally, rather than uploading data to the Internet for processing.

Neural nets were widely studied in the early days of artificial-intelligence research, but by the 1970s, they’d fallen out of favor. In the past decade, however, they’ve enjoyed a revival, under the name “deep learning.”

“Deep learning is useful for many applications, such as object recognition, speech, face detection,” says Vivienne Sze, the Emanuel E. Landsman Career Development Assistant Professor in MIT's Department of Electrical Engineering and Computer Science whose group developed the new chip. “Right now, the networks are pretty complex and are mostly run on high-power GPUs. You can imagine that if you can bring that functionality to your cell phone or embedded devices, you could still operate even if you don’t have a Wi-Fi connection. You might also want to process locally for privacy reasons. Processing it on your phone also avoids any transmission latency, so that you can react much faster for certain applications.”

The new chip, which the researchers dubbed “Eyeriss,” could also help usher in the “Internet of things” — the idea that vehicles, appliances, civil-engineering structures, manufacturing equipment, and even livestock would have sensors that report information directly to networked servers, aiding with maintenance and task coordination. With powerful artificial-intelligence algorithms on board, networked devices could make important decisions locally, entrusting only their conclusions, rather than raw personal data, to the Internet. And, of course, onboard neural networks would be useful to battery-powered autonomous robots.

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'Cannibalism' between stars

'Cannibalism' between stars | Amazing Science |

Stars are born inside a rotating cloud of interstellar gas and dust, which contracts to stellar densities thanks to its own gravity. Before finding itself on the star, however, most of the cloud lands onto a circumstellar disk forming around the star owing to conservation of angular momentum. The manner in which the material is transported through the disk onto the star, causing the star to grow in mass, has recently become a major research topic in astrophysics.

It turned out that stars may not accumulate their final mass steadily, as was previously thought, but in a series of violent events manifesting themselves as sharp stellar brightening. The young FU Orionis star in the constellation of Orion is the prototype example, which showed an increase in brightness by a factor of 250 over a time period of just one year, staying in this high-luminosity state now for almost a century.

One possible mechanism that can explain these brightening events was put forward 10 years ago by Eduard Vorobyov, now working at the Astrophysical Department of the Vienna University, in collaboration with Shantanu Basu from the University of Western Ontario, Canada.

According to their theory, stellar brightening can be caused by fragmentation due to gravitational instabilities in massive gaseous disks surrounding young stars, followed by migration of dense gaseous clumps onto the star. Like the process of throwing logs into a fireplace, these episodes of clump consumption release excess energy which causes the young star to brighten by a factor of hundreds to thousands. During each episode, the star is consuming the equivalent of one Earth mass every ten days. After this, it may take another several thousand years before another event occurs.

Eduard Vorobyov describes the process of clump formation in circumstellar disks followed by their migration onto the star as "cannibalism on astronomical scales". These clumps could have matured into giant planets such as Jupiter, but instead they were swallowed by the parental star. This invokes an interesting analogy with the Greek mythology, wherein Cronus, the leader of the first generation of Titans, ate up his newborn children (though failing to gobble up Zeus, who finally brought death upon his father).

With the advent of advanced observational instruments, such as SUBARU 8.2 meter optical-infrared telescope installed in Mauna Kea (Hawaii), it has become possible for the first time to test the model predictions. Using high-resolution, adaptive optics observations in the polarized light, an international group of astronomers led by Hauyu Liu from European Space Observatory (Garching, Germany) has verified the presence of the key features associated with the disk fragmentation model -- large-scale arms and arcs surrounding four young stars undergoing luminous outbursts, including the prototype FU Orionis star itself. The results of this study were accepted for publication in Science Advances.

"This is a major step towards our understanding of how stars and planets form and evolve", says Vorobyov, "If we can prove that most stars undergo such episodes of brightening caused by disk gravitational instability, this would mean that our own Sun might have experienced several such episodes, implying that the giant planets of the Solar system may in fact be lucky survivors of the Sun's tempestuous past".

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Gloop from the deep sea: The unusual secretions of the hagfish

Gloop from the deep sea: The unusual secretions of the hagfish | Amazing Science |

ETH scientists are researching the unusual secretions of the hagfish. Over the next three years, the researchers will try to find out how this natural hydrogel can be harnessed for human use.

This animal has done everything right. It has been around for 300 million years, outlived the dinosaurs and survived the catastrophic meteorite impact, warm phases and glacial periods. Even today, it continues to populate the sea at depths where it eats carrion and hunts prey. The Atlantic hagfish (Myxine glutinosa) is not really attractive at first glance. In fact, most people probably consider it quite disgusting. Nevertheless, the hagfish – or rather its slime – has caught the attention of a group of ETH researchers at the Laboratory of Food Process Engineering.

The slime of the hagfish is an extraordinary defense mechanism. When a hagfish is attacked by a predator, it secretes a glandular exudate that gels within a split second and forms a massive slime mass – even in cold water. This slime immobilizes vast amounts of water, forming a dilute, viscous and cohesive network. Fish attempting to attack the hagfish may then suffocate on the slime and thus let go of the hagfish.

Preliminary research quickly revealed to the scientists that there had been little examination of the structure of the slime and how it is formed and secreted. The scientific community knows that the natural hydrogel produced by the hagfish has two main components: 15- to 30-cm-long protein threads and mucin, which sits between the threads and makes the slime “slimy”. The protein threads have properties similar to spider silk. According to Kuster, the threads are extremely tear-resistant and elastic, though only when moist.

The slime consists of almost 100 % water and contains just 0.004 % gelling agent. In other words, the weight ratio of gelling agent to water is 26,000-fold, which is over 200 times more than in conventional animal gelatine. Furthermore, very little energy is required for the gelling process.

The ETH researchers were especially fascinated by the fact that the protein filaments have the form of a sphere measuring 150 micrometers in diameter while still in the glands, but once they are part of the slime they extend to threads of several centimeters in length. How the threads unwind from the sphere is not yet understood in depth. "The way the threads coil within the cells is highly specialized and very unusual," says Böni.

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Monstrous high-velocity gas cloud boomerangs back to our galaxy

Monstrous high-velocity gas cloud boomerangs back to our galaxy | Amazing Science |
New Hubble telescope observations suggest that a high-velocity gas cloud was launched from the outer regions of our own galaxy around 70 million years ago. Now, the cloud is on a return collision course and is expected to plow into the Milky Way's disk in about 30 million years. Astronomers believe it will ignite a spectacular burst of star formation then.

Hubble Space Telescope astronomers are finding that the old adage "what goes up must come down" even applies to an immense cloud of hydrogen gas outside our Milky Way galaxy. The invisible cloud is plummeting toward our galaxy at nearly 700,000 miles per hour. Though hundreds of enormous, high-velocity gas clouds whiz around the outskirts of our galaxy, this so-called "Smith Cloud" is unique because its trajectory is well known. New Hubble observations suggest it was launched from the outer regions of the galactic disk, around 70 million years ago. The cloud was discovered in the early 1960s by doctoral astronomy student Gail Smith, who detected the radio waves emitted by its hydrogen.

The cloud is on a return collision course and is expected to plow into the Milky Way's disk in about 30 million years. When it does, astronomers believe it will ignite a spectacular burst of star formation, perhaps providing enough gas to make 2 million suns.

"The cloud is an example of how the galaxy is changing with time," explained team leader Andrew Fox of the Space Telescope Science Institute in Baltimore, Maryland. "It's telling us that the Milky Way is a bubbling, very active place where gas can be thrown out of one part of the disk and then return back down into another."

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Removing senescent cells makes mice live longer and prosper

Removing senescent cells makes mice live longer and prosper | Amazing Science |

Killing worn-out cells helps middle-aged mice live longer, healthier lives, a new study suggests. Removing those worn-out or “senescent” cells increased the median life span of mice from 24 to 27 percent over that of rodents in which senescent cells built up normally with age, Mayo Clinic researchers report online February 3 in Nature. Clearing senescent cells also improved heart and kidney function, the researchers found.

If the results hold up in people, they could lead to an entirely new way to treat aging, says gerontology and cancer researcher Norman Sharpless at the University of North Carolina School of Medicine in Chapel Hill. Most prospective antiaging treatments would require people to take a drug for decades. Periodically zapping senescent cells might temporarily turn back the clock and improve health for people who are already aging, he says. “If this paper is right, I believe it will be one of the most important aging papers ever,” Sharpless says.

Senescent cells are ones that have ceased to divide and do their usual jobs. Instead, they hunker down and pump out inflammatory chemicals that may damage surrounding tissues and promote further aging. “They’re zombie cells,” says Steven Austad, a biogerontologist at the University of Alabama at Birmingham. ”They’ve outlived their usefulness. They’re bad.”

Cancer biologist Jan van Deursen of the Mayo Clinic in Rochester, Minn., and colleagues devised the strategy for eliminating senescent cells by making the cells commit suicide. A protein called p16 builds up in senescent cells, the researchers had previously discovered. The team hooked up a gene for a protein that causes cells to kill themselves to DNA that helps turn on p16 production, so that whenever p16 was made the suicide protein was also made.

The suicide protein needs a partner chemical to actually kill cells, though. Once mice were a year old — 40 to 60 years old in human terms — the researchers started injecting them with the partner chemical. Mice got injections about every three days for six months. Mice that got the cell-suicide cocktail were compared with genetically engineered mice that were injected with a placebo mix.

Senescent cells were easier to kill in some organs than others, the researchers found. Colon and liver senescent cells weren’t killed, for instance. But age-related declines in the function of organs in which the treatment worked — eyes, fat, heart and kidney —were slowed.

Genetic engineering and regular shots would not be feasible for use in people, but several companies are developing drugs that might clear the zombie cells from humans, Austad says. Some side effects to the treatment in mice also would be important to consider if those drugs are ever used in people. Senescent cells have previously been shown to be needed for wound healing, and mice that got the killing cocktail couldn’t repair wounds as well as those that didn’t get the treatment. Once treatment stopped, the mice were able to heal normally again. That result suggests that people undergoing senescent-cell therapy might need to stop temporarily to heal wounds from surgery or accidents.

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Rapid loss of phytoplankton in the Indian Ocean

Rapid loss of phytoplankton in the Indian Ocean | Amazing Science |

A rapid loss of phytoplankton threatens to turn the western Indian Ocean into an “ecological desert,” a new study warns. The research reveals that phytoplankton populations in the region fell an alarming 30 percent over the last 16 years.

A decline in ocean mixing due to warming surface waters is to blame for that phytoplankton plummet, researchers propose online January 19 in Geophysical Research Letters. The mixing of the ocean’s layers ferries phytoplankton nutrients from the ocean’s dark depths up into the sunlit layers that the mini plants inhabit.

The loss of these microbes, which form the foundation of the ocean food web, may undermine the region’s ecosystem, warns study coauthor Raghu Murtugudde, an oceanographer at the University of Maryland in College Park.

“If you reduce the bottom of the food chain, it’s going to cascade,” Murtugudde says. The phytoplankton decline may be partially responsible for a 50 to 90 percent decline in tuna catch rates over the last half-century in the Indian Ocean, he says. “This is a wake-up call to look if similar things are happening elsewhere.”

In the 20th century, surface temperatures in the Indian Ocean rose about 50 percent more than the global average. Previous investigations into this ocean warming’s impact on phytoplankton suggested that populations had increased. But those studies looked at only a few years of data — not long enough to clearly identify any long-term trend.

Roxy Mathew Koll, a climate scientist at the Indian Institute of Tropical Meteorology in Pune, Murtugudde and colleagues tracked the microscopic phytoplankton from space. Phytoplankton, like land plants, are tinted green. When the sea surface is filled with phytoplankton, the water takes on a lighter, greener tinge. As the phytoplankton population thins, the water turns darker and bluer.

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Twenty-four new beetle species discovered in Australian rain forests

Twenty-four new beetle species discovered in Australian rain forests | Amazing Science |

As many as twenty-four new species from Australian rainforests are added to the weevil genus Trigonopterus. Museum scientists Dr. Alexander Riedel, State Museum of Natural History Karlsruhe, Germany, and Rene Tanzler, Zoological State Collection Munich, Germany, have first discovered them among unidentified specimens in different beetle collections. The study is published in the open-access journal ZooKeys.

Australia is well known for its extensive deserts and savanna habitats. However, a great number of native Australian species are restricted to the wet tropical forests along the east coast of northern Queensland. These forests are also the home of the recent discoveries.

Most of the weevil species now recognised as new have already been collected in the 80s and 90s of the past century. Since then they had been resting in museum collections until German researcher Alexander Riedel had the opportunity to study them.

“Usually a delay of decades or even centuries occurs between the encounter of a new species in the field and its thorough scientific study and formal naming,” he explains. “This is due to the small number of experts who focus on species discovery,” he elaborates. “There are millions of unidentified insect specimens stored in collections around the world but only few people have the training necessary to identify those of special interest.”

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How specialized enzymes remodel condensed chromatin in order to control genes

How specialized enzymes remodel condensed chromatin in order to control genes | Amazing Science |

An international team of biologists has discovered how specialized enzymes remodel the extremely condensed genetic material in the nucleus of cells in order to control which genes can be used. The discovery will be published in the print edition of the journal Nature on Feb. 4, 2016.

It was known that the DNA in cells is wrapped around proteins in structures called nucleosomes that resemble beads on a string, which allow the genetic material to be folded and compacted into a structure called chromatin. "We knew that the compaction into chromatin makes genes inaccessible to the cellular machinery necessary for gene expression, and we also knew that enzymes opened up the chromatin to specify which genes were accessible and could be expressed in a cell, but until now, we didn't know the mechanism by which these enzymes functioned," said B. Franklin Pugh, Evan Pugh Professor, Willaman Chair in Molecular Biology, and professor of biochemistry and molecular biology at Penn State University and one of the two corresponding authors of the paper along with Matthieu Gérard of the University of Paris-Sud in France.

The discovery was achieved by an international collaboration of scientists from the Alternative Energies and Atomic Energy Commission in France (Commissariat à l'énergie atomique et aux énergies alternatives), the National Center for Scientific Research in France (Centre national de la recherche scientifique), the University of Paris-Sud in France, Southern Medical University in Guangzhou in China, and Penn State University in the United States.

The researchers first mapped the location of several "chromatin-remodeller enzymes" across the entire genome of the embryonic stem cells of the mouse. The mapping showed that remodeller enzymes bind to particular nucleosomes "beads" at the sites along the wrapped-up DNA that are located just before the gene sequence begins. These sites are important because they are the location where the process of expressing genes begins -- where other proteins required for gene expression team up for the process of turning a gene on.

The researchers then tested how the chromatin-remodeller enzymes impact gene expression by reducing the amount of each of these enzymes in embryonic stem cells. The scientists found that some chromatin-remodeller enzymes promote gene expression, some repress gene expression, and some can do both.

"The correct expression of genes is necessary to define the identity and function of different types of cells in the course of embryonic development and adult life," said Pugh. "Chromatin-remodeller enzymes help each cell type accurately express the proper set of genes by allowing or blocking access to the critical section of DNA at the beginning of genes."

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Evidence that life once existed on Mars may have been discovered, scientists suggest

Evidence that life once existed on Mars may have been discovered, scientists suggest | Amazing Science |

Unusual silica formations spotted by a NASA rover look a lot like structures formed by microbes around geysers on Earth.

The hunt for signs of life on Mars has been on for decades, and so far scientists have found only barren dirt and rocks. Now a pair of astronomers thinks that strangely shaped minerals inside a Martian crater could be the clue everyone has been waiting for.

In 2008, scientists announced that NASA’s Spirit rover had discovered deposits of a mineral called opaline silica inside Mars's Gusev crater. That on its own is not as noteworthy as the silica’s shape: Its outer layers are covered in tiny nodules that look like heads of cauliflower sprouting from the red dirt.

No one knows for sure how those shapes—affectionately called “micro-digitate silica protrusions”—formed. But based on recent discoveries in a Chilean desert, Steven Ruff and Jack Farmer, both of Arizona State University in Tempe, think the silica might have been sculpted by microbes. At a meeting of the American Geophysical Union in December, they made the case that these weird minerals might be our best targets for identifying evidence of past life on Mars.

If the logic holds, the silica cauliflower could go down in history as arguably the biggest discovery ever in astronomy. But biology is hard to prove, especially from millions of miles away, and Ruff and Farmer aren’t claiming victory yet. All they’re saying is that maybe these enigmatic growths are mineral greetings from ancient aliens, and someone should investigate.

Spirit found the silica protrusions near the “Home Plate” region of Gusev crater, where geologists think hot springs or geysers once scorched the red planet's surface. To understand what that long-dormant landscape used to be like, we have to look closer to home: hydrothermal regions of modern Earth that resemble Mars in its ancient past.

To that end, Ruff has twice in the past year trekked to Chile’s Atacama Desert, a high plateau west of the Andes cited as the driest non-polar place on Earth. Scientists often compare this desert to Mars, and not just poetically. It’s actually like Mars. The soil is similar, as is the extreme desert climate.

In this part of the Atacama, it rains less than 100 millimeters per year, and temperatures swing from -13°F to 113°F. With an average elevation of 13,000 feet above sea level, lots of ultraviolet radiation makes it through the thin atmosphere to the ground, akin to the punishing radiation that reaches the surface of Mars.

Just as we interpret others’ behavior and emotions by peering into our own psychology, scientists look around our planet to help them interpret Mars, find its most habitable spots and look for signs of life. While the Atacama does have breathable oxygen and evolutionarily clever foxes (which Mars does not), its environment mimics Mars’s pretty well and makes a good standin for what the red planet may have been like when it was warmer and wetter.

So when geologists see something in the Atacama or another Mars analog that matches a feature on the red planet, they reasonably conclude that the two could have formed the same way. It’s not a perfect method, but it’s the best we’ve got. “I don't think there is any way around using modern Earth analogs to test where Martian microbes may be found,” says Kurt Konhauser of the University of Alberta, who is the editor-in-chief of the journal Geobiology.

But the comparison goes further: When Ruff peered closely at El Tatio’s silica formations, he saw shapes remarkably similar to those that Spirit had seen on Mars. Fraternal cauliflower twins also exist in Yellowstone National Park in Wyoming and the Taupo Volcanic Zone in New Zealand. In both of those places, the silica bears the fossilized fingerprints of microbial life.

Since microbes sculpted the silica features in Wyoming and New Zealand, it's possible they also helped make the formations at El Tatio. And if microbes were involved with the cauliflower at El Tatio, maybe they made it grow on Mars, too.

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Same Switches Program Taste and Smell in Fruit Flies

Same Switches Program Taste and Smell in Fruit Flies | Amazing Science |

A new study sheds light on how fruit flies get their keen sense of smell.

Duke University biologist Pelin Volkan and colleagues have identified a set of genetic control switches that interact early in a fly’s development to generate dozens of types of olfactory neurons, specialized nerve cells for smell. 

The same gene network also plays a role in programming the fly neurons responsible for taste, the researchers report in the journal PLOS Genetics.

The findings do more than merely explain how a household pest distinguishes rotting vegetables from ripening fruit, the authors say. The research could be a key to understanding how the nervous systems of other animals -- including humans, whose brains have billions of neurons -- produce such a dazzling array of cell types from a modest number of genes.

Fruit flies rely on their keen sense of smell to tell the difference between good food and bad, safety and danger, potential mates and those off-limits. The tiny insects perceive this wide range of chemical cues through a diverse set of olfactory sensory neurons along their antennae. More than 2000 such neurons are organized into 50 types, each of which transmits information to a specific region of the fly’s poppy seed-sized brain.

“Each neuron type detects a very specific range of odors,” Volkan said. Certain odors from fermenting fruit, for example, activate one class of neurons, and carbon dioxide activates another.

Volkan is interested in how the many types of smell neurons come to be as a fruit fly develops from egg to an adult.  Smell neurons begin as identical precursor cells, immature cells that have not yet “decided” which type of nerve cell they will become. All precursor cells have the same DNA, and how they produce one neuron type versus another was unknown.

One way to get many types of cells or proteins from the same genetic starting material is by mixing and matching different parts of one gene to produce multiple gene readouts, a phenomenon known as alternative splicing. The team’s results point to another strategy, however: using the same genes in different combinations, or “combinatorial coding.”

By tweaking different fly genes and counting how many neuron types were produced as the flies matured, the team identified a network of five genes that work together like coordinated control switches to guide the precursor cells’ transformation to mature neurons. The genes regulate each other’s activity, interacting in unique combinations to set each precursor cell on a distinct path by turning on different olfactory receptors in each cell.

The researchers found that manipulating the network had similar effects in the legs, which flies use not only to walk but also to taste. “The same basic toolkit gives rise to diverse types of neurons in completely different tissues,” said Volkan, who is also a member of the Duke Institute for Brain Sciences.

Via Integrated DNA Technologies
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