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Sangamo tries to use engineered zinc finger transcriptional repressors to cure Huntington’s disease

Sangamo tries to use engineered zinc finger transcriptional repressors to cure Huntington’s disease | Amazing Science |
At the root of Huntington’s disease is a specific type of mutation, called a trinucleotide repeat expansion, in the Huntingtin (Htt) gene. The normal Htt gene contains up to 28 copies of the nucleotide sequence CAG, but this expands to more than 40 copies in the disease-causing allele. As a result of the expanded repeat, insoluble clumps of the Huntingtin protein accumulate inside neurons, causing cell death that leads to uncontrollable movements, dementia and, ultimately, death. Patients with between 28 and 35 repeats are unaffected, while those with between 36 and 40 have a form of the disease with reduced penetrance.


In animal models, reducing mutant Htt protein levels prevents disease progression and reverses some symptoms. However, most therapeutic approaches in development lower both versions of the huntingtin protein (the one produced by the normal gene, and the one made by the mutated gene). This has raised concerns about their safety for human use, because the normal protein has important, albeit as yet unknown, cellular function. To overcome this, Sangamo researchers have developed zinc finger transcriptional repressors that specifically target the mutant Htt allele and block its expression while preserving near-normal expression levels of the normal allele. Zinc fingers are naturally occurring protein segments that recognize and bind to specific DNA sequences, typically regulating the output of a given gene. Using genetic engineering, the Sangamo researchers designed zinc finger proteins containing a DNA-binding site that recognizes the prolonged tricnucleotide repeat found in the mutant Htt gene. They then fused this binding site to a protein domain that recruits other molecules that zip closed the chromosomal region containing the Htt gene with the expanded repeat—thus hindering production of mutated huntingtin protein.


In a recent experiment in a lab dish, the group added the engineered zinc fingers to fibroblast cells obtained from six people with Huntington’s disease. This lowered production of the mutant protein by more than 90%, while reducing the amount of the normal protein by just 10% or less, the researchers reported at the annual meeting of the Society for Neuroscience, held here this week. “There was very potent discrimination between the mutant and normal alleles in cells from all six patients, even though each contained mutant alleles of different lengths,” explains Phillip Gregory*, chief scientific officer at Sangamo BioSciences. “The next step is to make that sure they operate at a broad range of doses, and then we need to move into animal studies of efficacy and safety.”


This is the first attempt to apply the zinc finger approach to Huntington’s disease, and the researchers eventually aim to deliver genes for the zinc finger proteins directly into the brain using adeno-associated viral vectors*, which are already being used to successfully deliver therapeutic genes into the brains of people with Parkinson’s disease in clinical trials.


“This is very promising and exciting work,” says Sarah Tabrizi, a professor at the Institute of Neurology in London, who was not involved in the study, “but it’s still at a very early and exploratory stage, and it’s a big jump going from cells in culture to the human brain.” One challenge is that targeting viral vectors to specified brain areas and then ensuring their proper distribution is difficult, and this is further complicated by the fact that Huntington’s disease begins in deep brain structures before spreading to the cerebral cortex. “Distributing the vector will be a challenge,” Tabrizi says, “but I don’t think it’s insurmountable.”


Read more about ZFN and TALENs ("Editing the genome, here, there and everywhere"):

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NASA: Saturn moon Titan has chemical that could form bio-like ‘membranes’

NASA: Saturn moon Titan has chemical that could form bio-like ‘membranes’ | Amazing Science |

Molecules of vinyl cyanide reside in the atmosphere of Titan, Saturn's largest moon, says NASA.


Recent simulations have indicated that vinyl cyanide is the best candidate molecule for the formation of cell membranes/vesicle structures in Titan’s hydrocarbon-rich lakes and seas. Although the existence of vinyl cyanide (C2H3CN) on Titan was previously inferred using Cassini mass spectrometry, a definitive detection has been lacking until now. A team of scientists now report the first spectroscopic detection of vinyl cyanide in Titan’s atmosphere, obtained using archival data from the Atacama Large Millimeter/submillimeter Array (ALMA), collected from February to May 2014. They detect the three strongest rotational lines of C2H3CN in the frequency range of 230 to 232 GHz, each with >4σ confidence. Radiative transfer modeling suggests that most of the C2H3CN emission originates at altitudes of ≳200 km, in agreement with recent photochemical models. The vertical column densities implied by our best-fitting models lie in the range of 3.7 × 10^13 to 1.4 × 10^14 cm−2. The corresponding production rate of vinyl cyanide and its saturation mole fraction imply the availability of sufficient dissolved material to form ~10^7 cell membranes/cm^3 in Titan’s sea Ligeia Mare.

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Astrophysicists explain the mysterious behavior of cosmic rays

Astrophysicists explain the mysterious behavior of cosmic rays | Amazing Science |
A team of scientists from Russia and China has developed a model explaining the nature of high-energy cosmic rays (CRs) in our galaxy. These CRs have energies exceeding those produced by supernova explosions by one or two orders of magnitude. The model focuses mainly on the recent discovery of giant structures called Fermi bubbles.

One of the key problems in the theory of the origin of cosmic rays, which consist of high-energy protons and atomic nuclei, is their acceleration mechanism. The issue was addressed by Vitaly Ginzburg and Sergei Syrovatsky in the 1960s when they suggested that CRs are generated during supernova (SN) explosions in the galaxy. A specific mechanism of charged particle acceleration by SN shock waves was proposed by Germogen Krymsky and others in 1977. Due to the limited lifetime of the shocks, it is estimated that the maximum energy of the accelerated particles cannot exceed 1014-1015 eV.

Explaining the nature of particles with energies above 1015 eV is key. A major breakthrough in researching the acceleration processes of such particles came when the Fermi Gamma Ray Space Telescope detected two gigantic structures emitting radiation in the gamma-ray band in the central area of the galaxy in November 2010. The structures are elongated and symmetrically located in the galactic plane perpendicular to its center, extending 50,000 light-years, or roughly half of the diameter of the Milky Way disk. These structures became known as Fermi bubbles. Later, the Planck telescope team discovered their emission in the microwave band.

Via Mariaschnee
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Zebrafish implanted with a cancer patient’s tumor could guide cancer treatment

Zebrafish implanted with a cancer patient’s tumor could guide cancer treatment | Amazing Science |

Fish cancer “avatars” may be better than mice at revealing drugs’ effectiveness.


Eight years ago, developmental biologist Rita Fior learned that her mother, who needed cancer treatment at the time, would receive different drugs depending on nothing more than which hospital she chose. Fior was taken aback. “You don’t know if it’s better to take drug A or B,” she says. “This is a big problem.” Now she is addressing the problem—with a fish.


This week, Fior, who is at the Champalimaud Centre for the Unknown in Lisbon, and her colleagues reported growing implanted human tumor cells in zebrafish larvae. Each fish became a minuscule model of a patient’s cancer—and a testbed for treatments. Similar cancer “avatars” have been created with mice, but the piscine approach may be faster and cheaper, making it accessible for more patients. “Zebrafish could have a unique niche [in cancer treatment],” says Leonard Zon of Harvard Medical School in Boston, who has used the fish for more than a decade to study how cancer develops. 

Via Integrated DNA Technologies
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Buildings to generate their own power with innovative glass blocks

Buildings to generate their own power with innovative glass blocks | Amazing Science |
Buildings could soon be able to convert the sun's energy into electricity without the need for solar panels, thanks to innovative new technology.


Renewable Energy experts from the University of Exeter are developing a pioneering new technique that could accelerate the widespread introduction of net-zero energy buildings through the latest Building Integrated Photovoltaics (BIPV). These products, similar to the solar tile created by Tesla, can become a part of a building's architecture to generate electricity. The team have created an innovative glass block, which can be incorporated into the fabric of a building and is designed to collect solar energy and convert it to electricity.


It is thought that buildings consume more than forty percent of the electricity produced across the globe. This new technology would allow electricity to be produced at the site of use, whilst being seamlessly integrated into the building.


The blocks, called Solar Squared, are designed to fit seamlessly into either new buildings, or as part of renovations in existing properties. They are similar to existing glass blocks by allowing daylight to resonate around a property by replacing traditional bricks and mortar with transparent glass bricks.

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2.7-million-year-old ice core pulled from Antarctica

2.7-million-year-old ice core pulled from Antarctica | Amazing Science |

A team of researchers from Princeton University, the Scripps Institution of Oceanography, the University of Maine and Oregon State University has drilled and retrieved a 2.7-million-year-old ice core from a spot in Antarctica.


Until recently, scientists believed that ice core samples taken from either pole had an age limit of approximately 800,000 years—this was because ice at the bottom melted due to heat from inside the Earth. But a team at Princeton discovered a few year ago that another type of ice could hold much older ice known as blue ice. It forms on glaciers due to snowfall which, over time, becomes compressed, squeezing out air bubbles, making the ice look blue. But it also has another characteristic—over time, the ice at the bottom is pushed upwards, protecting it from melting. In this new effort, the team drilled at a site called the Allan Hills, near McMurdo Station.


Ice cores taken from glaciers present problems because they are more difficult to date—cores from other places are dated by counting their layers. The older ice, it was found, could be dated by studying trace amounts of potassium and argon—though not as precise as layer counting, the researchers believe it is accurate to within 100,000 years. One of the first teams to take a core sample from the older ice drilled to a depth of 128 meters. In this latest effort, the team drilled to 205 meters and found ice that was nearly twice as old.


Ice cores are important because they contain very small air bubbles that are samples of atmospheric conditions. Air bubbles from 2.7 million years ago offer evidence of climactic conditions during the time before the ice ages began, perhaps offering clues as to why they occurred. Already, the team has found that atmospheric carbon dioxide levels were at approximately 300 ppm, which is considerably lower than today's 400 ppm. But the team notes that the core sample represents something perhaps even more exciting—the possibility of finding core samples that are much older, perhaps as old as 5 million years.

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Scientists create first 'diamond rain' that forms inside of icy giant planets

Scientists create first 'diamond rain' that forms inside of icy giant planets | Amazing Science |

In an experiment designed to mimic the conditions deep inside the icy giant planets of our solar system, scientists were able to observe "diamond rain" for the first time as it formed in high-pressure conditions.


The glittering precipitation has long been hypothesized to arise more than 5,000 miles below the surface of Uranus and Neptune, created from commonly found mixtures of just hydrogen and carbon. The interiors of these planets are similar—both contain solid cores surrounded by a dense slush of different ices. With the icy planets in our solar system, "ice" refers to hydrogen molecules connected to lighter elements, such as carbon, oxygen and/or nitrogen.


Researchers simulated the environment found inside these planets by creating shock waves in plastic with an intense optical laser at the Matter in Extreme Conditions (MEC) instrument at SLAC National Accelerator Laboratory's X-ray free-electron laser, the Linac Coherent Light Source (LCLS).


In the experiment, they were able to see that nearly every carbon atom of the original plastic was incorporated into small diamond structures up to a few nanometers wide. On Uranus and Neptune, the study authors predict that diamonds would become much larger, maybe millions of carats in weight. Researchers also think it's possible that over thousands of years, the diamonds slowly sink through the planets' ice layers and assemble into a thick layer around the core.


The research was published in Nature Astronomy on August 21, 2017.

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WIRED: A Total Solar Eclipse Feels Really Really Weird

WIRED: A Total Solar Eclipse Feels Really Really Weird | Amazing Science |
During the minutes during which the sun is completely blocked, observers experience the exquisitely odd and wondrous sensation of solar emissions, both visible and invisible, vanishing right in the middle of the day.
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Stunning 100-Million-Year-Old Flowers Found Perfectly Preserved In Amber

Stunning 100-Million-Year-Old Flowers Found Perfectly Preserved In Amber | Amazing Science |

Seven flowers have been found perfectly preserved in amber, from 100 million years ago. The flowers, discovered in Myanmar, were encased in amber in the Cretaceous period in what would have been a pine forest.


The authors of a paper studying the flowers, which are in stunning condition, speculated that they could have been dislodged from their trees by a passing dinosaur. “Dinosaurs may have knocked the branches that dropped the flowers into resin deposits on the bark of an araucaria tree, which is thought to have produced the resin that fossilized into the amber." George Poinar Jr, professor emeritus of Oregon State University’s College of Science said in a statement.


"Araucaria trees are related to kauri pines found today in New Zealand and Australia, and kauri pines produce a special resin that resists weathering.”

Via Neelima Sinha
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A Speedier Way to Catalog Human Cells (All 37 Trillion of Them)

A Speedier Way to Catalog Human Cells (All 37 Trillion of Them) | Amazing Science |

Many types of cells remain unknown, but researchers have discovered a faster way to group cells by function, paving the way for a complete census.


There are some questions in biology that you’d think were settled long ago. For instance: How many types of cells are there in the human body? “If you just Google this, the number everyone uses is 200,” said Jay Shendure, a geneticist at the University of Washington. “But to me that seems absurdly low.” A number of scientists like him want to build a more complete catalog.


Yet there are an estimated 37 trillion cells in the human body. The traditional ways to identify cell types — such as carefully tracing the shape of individual cells under a microscope — are too slow and crude for the job.


Dr. Shendure and his colleagues recently published a report describing a speedy new method for taking such a cell census. Instead of inspecting one cell at a time, they measured the activity of genes inside 42,035 cells at once. Although still at an experimental stage, the method may become an essential tool for cataloging every cell type in the human body, experts said.

Via Integrated DNA Technologies
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This Mercury Atomic Clock neither gains nor loses one second in about 300 million years

This Mercury Atomic Clock neither gains nor loses one second in about 300 million years | Amazing Science |

National Institute of Standards and Technology has officially launched a new atomic clock, called NIST-F2, to serve as a new US civilian time and frequency standard, along with the current NIST-F1 standard. NIST-F2 would neither gain nor lose one second in about 300 million years, making it about three times as accurate as NIST-F1, which has served as the standard since 1999. Both clocks use a 'fountain' of cesium atoms to determine the exact length of a second.


NIST-F1 uses a tiny, cigar-shaped cloud of cesium atoms that is tossed in the air to determine the length of a second (see Atoms in different parts of the cloud are subject to slight variations in electric and magnetic fields that affect clock accuracy. By contrast, single ions such as mercury can be isolated at a point in space for better control. The ion is created inside an electromagnetic trap, which holds the ion in one place with electric fields oscillating at radio frequencies. Once trapped, the ion is cooled with lasers until it is nearly motionless. The ticks are generated by the oscillations of the ultraviolet light used to induce the ion's transition between two energy levels. These oscillations are about 100,000 times faster than the corresponding oscillations in NIST-F1, which also improves the precision of the mercury ion clock.


An optical atomic clock has three components: an atom that switches from one energy level to another when probed by a laser at a well-defined optical frequency; the laser used to induce this transition; and a counter that faithfully records each oscillation per unit time (the ticks) of the probe laser.


The latest version of the NIST mercury clock incorporates several improvements over the original design. Most importantly, it compensates for the irregular shape of mercury's electron cloud, which causes a frequency shift that was not previously measured or corrected. NIST developed a method for nullifying the shift by applying a magnetic field on three different axes of the trap, measuring the frequencies at each axis, and calculating the average. The researchers also reduced the frequency shift caused by magnetic fields by reducing the strength of the field used to hold the ion in the trap.


The NIST mercury clock is unusual in part because of the method for stabilizing the ultraviolet laser used to probe the clock transition. The laser light is locked to an ultra-stable reference cavity that sits on an isolation platform suspended from the ceiling by latex tubing, essentially a set of huge rubber bands. The suspended platform offers passive isolation against vibration to very low frequency, according to Bergquist, the system designer. Better vibration isolation improves laser frequency stability and that leads to higher resolution when probing the laser's clock transition.


"You only want the atom to respond at precisely one frequency," Bergquist says. "An acoustical analogy is the resonant response of a tuning fork to an exquisitely pure musical note, either sung or played."


NIST also built the optical "frequency comb" used to convert the optical ticks to microwave frequencies so they can be counted. (No electronics exist that are fast enough to directly count optical frequencies.) A frequency comb is a very precise tool for measuring different frequencies, or colors, of light (see comb was used to compare the mercury and cesium clocks, serving as the gears, or clockworks, for converting the stable and accurate optical frequency of the mercury clock transition to a stable microwave frequency. The accuracy of the optical frequency measurement is made possible largely by the high accuracy of the NIST-F1 standard.  

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NASA - Earth-Size Planets: The Newest and Weirdest Generation

NASA - Earth-Size Planets: The Newest and Weirdest Generation | Amazing Science |

A bumper crop of Earth-size planets huddled around an ultra-cool, red dwarf star could be little more than chunks of rock blasted by radiation, or cloud-covered worlds as broiling hot as Venus.


Or they could harbor exotic lifeforms, thriving under skies of ruddy twilight.


Scientists are pondering the possibilities after this week’s announcement: the discovery of seven worlds orbiting a small, cool star some 40 light-years away, all of them in the ballpark of our home planet in terms of their heft (mass) and size (diameter). Three of the planets reside in the “habitable zone” around their star, TRAPPIST-1, where calculations suggest that conditions might be right for liquid water to exist on their surfaces—though follow-up observations are needed to be sure.


All seven are early ambassadors of a new generation of planet-hunting targets.


Red dwarf stars -- also called “M-dwarfs” -- outnumber others, including yellow stars like our sun, by a factor of three to one, comprising nearly 75 percent of the stars in our galaxy. They also last far longer. And their planets are proportionally larger compared to the small stars they orbit. That means small, rocky worlds orbiting the nearest red dwarfs will be primary targets for new, powerful telescopes coming online in the years ahead, both in space and on the ground.


“The majority of stars are M-dwarfs, which are faint and small and not very luminous,” said Martin Still, program scientist at NASA headquarters in Washington. “So the majority of places where you would look for planets are around these cool, small stars. We are interested in the nearest stars, and the nearest stars are mostly M-dwarfs.”


But these are sure to be perplexing planets, with strange properties that must be teased out by careful observation as well as computer simulations. Finding out whether they can support some form of life, and what kind, likely will keep astrobiologists working overtime, perhaps attempting to recreate in the laboratory some of the conditions on these red-tinged worlds.


“We’re definitely all working overtime now,” said Nancy Kiang, an astrobiologist at NASA’s Goddard Institute for Space Studies in New York City.

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Brain Training Has No Effect on Decision-making or Cognitive Function

Brain Training Has No Effect on Decision-making or Cognitive Function | Amazing Science |

During the last decade, commercial brain-training programs have risen in popularity, offering people the hope of improving their cognitive abilities through the routine performance of various “brain games” that tap cognitive functions such as memory, attention and cognitive flexibility.


But a recent study at the University of Pennsylvania found that, not only did commercial brain training with Lumosity™ have no effect on decision-making, it also had no effect on cognitive function beyond practice effects on the training tasks.


The findings were published in the Journal of Neuroscience.


Seeking evidence for an intervention that could reduce the likelihood that people will engage in unhealthy behaviors such as smoking or overeating, a team of researchers at Penn, co-led by Joseph Kable, PhD, the Baird Term associate professor in the department of Psychology in the School of Arts & Sciences, and Caryn Lerman, PhD, the vice dean for Strategic Initiatives and the John H. Glick professor in Cancer Research in the Perelman School of Medicine, examined whether, through the claimed beneficial effect on cognitive function, commercial brain training regimes could reduce individuals’ propensity to make risky or impulsive choices.


Lerman’s prior work had shown that engagement of brain circuits involved in self-control predicts whether people can refrain from smoking. This work provided the foundation for examining whether modulating these circuits through brain training could lead to behavior change. 


“Our motivation,” Kable said, “was that there are enough hints in the literature that cognitive training deserved a real, rigorous, full-scale test. Especially given the addiction angle, we're looking for things that will help people make the changes in their lives that they want to make, one of which is being more future-oriented.”

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Fertile offspring from sterile sex chromosome trisomic mice

Fertile offspring from sterile sex chromosome trisomic mice | Amazing Science |

Having the correct number of chromosomes is vital for normal development and health. Sex chromosome trisomy (SCT) affects 0.1% of the human population and is associated with infertility. Scientists now show that during reprogramming to induced pluripotent stem cells (iPSC), fibroblasts from sterile trisomic XXY and XYY mice lose the extra sex chromosome, by a phenomenon we term trisomy-biased chromosome loss (TCL). Resulting euploid XY iPSCs can be differentiated into the male germ cell lineage and functional sperm that can be used in intracytoplasmic sperm injection to produce chromosomally normal, fertile offspring. Sex chromosome loss is comparatively infrequent during mouse XX and XY iPSC generation. TCL also applies to other chromosomes, generating euploid iPSCs from cells of a Down syndrome mouse model. It can also create euploid iPSCs from human trisomic patient fibroblasts. The findings have relevance to overcoming infertility and other trisomic phenotypes.

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A breakthrough new method for 3D-printing living tissues

A breakthrough new method for 3D-printing living tissues | Amazing Science |

Scientists at the University of Oxford have developed a radical new method of 3D-printing laboratory-grown cells that can form complex living tissues and cartilage to potentially support, repair, or augment diseased and damaged areas of the body.


Printing high-resolution living tissues is currently difficult because the cells often move within printed structures and can collapse on themselves. So the team devised a new way to produce tissues in protective nanoliter droplets wrapped in a lipid (oil-compatible) coating that is assembled, layer-by-layer, into living cellular structures.


This new method improves the survival rate of the individual cells and allows for building each tissue one drop at a time to mimic the behaviors and functions of the human body. The patterned cellular constructs, once fully grown, can mimic or potentially enhance natural tissues.


“We were aiming to fabricate three-dimensional living tissues that could display the basic behaviors and physiology found in natural organisms,” explained Alexander Graham, PhD, lead author and 3D Bioprinting Scientist at OxSyBio (Oxford Synthetic Biology).


“To date, there are limited examples of printed tissues [that] have the complex cellular architecture of native tissues. Hence, we focused on designing a high-resolution cell printing platform, from relatively inexpensive components, that could be used to reproducibly produce artificial tissues with appropriate complexity from a range of cells, including stem cells.”


The researchers hope that with further development, the materials could have a wide impact on healthcare worldwide and bypass clinical animal testing. The scientists plan to develop new complementary printing techniques that allow for a wider range of living and hybrid materials, producing tissues at industrial scale.

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Electrons flowing like liquid in graphene start a new wave of physics

Electrons flowing like liquid in graphene start a new wave of physics | Amazing Science |
A new understanding of the physics of conductive materials has been uncovered by scientists observing the unusual movement of electrons in graphene.


Graphene is many times more conductive than copper thanks, in part, to its two-dimensional structure. In most metals, conductivity is limited by crystal imperfections which cause electrons to frequently scatter like billiard balls when they move through the material.


Now, observations in experiments at the National Graphene Institute have provided essential understanding as to the peculiar behavior of electron flows in graphene, which need to be considered in the design of future Nano-electronic circuits.

In some high-quality materials, like graphene, electrons can travel micron distances without scattering, improving the conductivity by orders of magnitude. This so-called ballistic regime, imposes the maximum possible conductance for any normal metal, which is defined by the Landauer-Buttiker formalism.


Appearing in Nature Physics, researchers at The University of Manchester, in collaboration with theoretical physicists led by Professor Marco Polini and Professor Leonid Levitov, show that Landauer's fundamental limit can be breached in graphene. Even more fascinating is the mechanism responsible for this.


Last year, a new field in solid-state physics termed 'electron hydrodynamics' generated huge scientific interest. Three different experiments, including one performed by The University of Manchester, demonstrated that at certain temperatures, electrons collide with each other so frequently they start to flow collectively like a viscous fluid.

Via CineversityTV
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We share the Milky Way with 100 million black holes

We share the Milky Way with 100 million black holes | Amazing Science |
New census calculates black hole populations in galaxies big and small.


The Milky Way teems with black holes — about 100 million of them. But there’s no reason to fear. “It may sound like a big number, but by astronomical standards, it’s a pretty small number,” says physicist Daniel Holz of the University of Chicago. The number of stars in the Milky Way, for example, is about a thousand times larger.


Scientists from the University of California, Irvine calculated the galaxy’s black hole population as part of a new census that estimates the numbers of cosmic chasms in galaxies big and small. The analysis, in press in Monthly Notices of the Royal Astronomical Society, quantified stellar-mass black holes, which form when a star collapses. Such objects can have masses tens of times that of the sun.


To draw up the celestial inventory, the researchers combined a variety of information about stars and galaxies. A star’s size and composition — the proportion of heavy elements it contains — determine whether it can form a black hole, and how big the black hole will be. And given a galaxy‘s size, scientists can estimate the number and properties of stars within, allowing researchers to deduce the number of black holes and their sizes.


Such stellar-mass black holes are a target of the Advanced Laser Interferometer Gravitational-Wave Observatory, LIGO, which has detected three sets of gravitational waves from colliding black holes (SN: 6/24/17, p. 6). When LIGO made its first detection, some physicists thought the coalescing black holes were surprisingly large; each was about 30 times the mass of the sun (SN: 3/5/16, p. 6). This puzzle led scientists to propose exotic origins for LIGO’s black holes — for example, that they formed during the universe’s infancy, instead of from collapsing stars (SN: 9/3/16, p. 8).

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Unconventional quantum systems may lead to novel optical devices

Unconventional quantum systems may lead to novel optical devices | Amazing Science |

Physicists have experimentally demonstrated an optical system based on an unconventional class of quantum mechanical systems that could lead to the development of new quantum optical devices. The system is called a "PT-symmetric quantum walk," since it consists of single photons that occupy a superposition of states, called quantum walks, that obey parity-time (PT) symmetry—the property in which a system's coordinates in space and time can have their signs reversed without inherently changing the system.

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Dinosaur-killing asteroid could have thrown Earth into two years of darkness

Dinosaur-killing asteroid could have thrown Earth into two years of darkness | Amazing Science |

Tremendous amounts of soot, lofted into the air from global wildfires following a massive asteroid strike 66 million years ago, would have plunged Earth into darkness for nearly two years, new research finds. This would have shut down photosynthesis, drastically cooled the planet, and contributed to the mass extinction that marked the end of the age of dinosaurs.


 These new details about how the climate could have dramatically changed following the impact of a 10-kilometer-wide asteroid will be published Aug. 21 in the Proceedings of the National Academy of Sciences. The study, led by the National Center for Atmospheric Research (NCAR) with support from NASA and the University of Colorado Boulder, used a world-class computer model to paint a rich picture of how Earth's conditions might have looked at the end of the Cretaceous Period, information that paleobiologists may be able to use to better understand why some species died, especially in the oceans, while others survived.


Scientists estimate that more than three-quarters of all species on Earth, including all non-avian dinosaurs, disappeared at the boundary of the Cretaceous-Paleogene periods, an event known as the K-Pg extinction. Evidence shows that the extinction occurred at the same time that a large asteroid hit Earth in what is now the Yucatán Peninsula. The collision would have triggered earthquakes, tsunamis, and even volcanic eruptions.


Scientists also calculate that the force of the impact would have launched vaporized rock high above Earth's surface, where it would have condensed into small particles known as spherules. As the spherules fell back to Earth, they would have been heated by friction to temperatures high enough to spark global fires and broil Earth's surface. A thin layer of spherules can be found worldwide in the geologic record.


"The extinction of many of the large animals on land could have been caused by the immediate aftermath of the impact, but animals that lived in the oceans or those that could burrow underground or slip underwater temporarily could have survived," said NCAR scientist Charles Bardeen, who led the study. "Our study picks up the story after the initial effects—after the earthquakes and the tsunamis and the broiling. We wanted to look at the long-term consequences of the amount of soot we think was created and what those consequences might have meant for the animals that were left."

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Theorem of the Day

Theorem of the Day | Amazing Science |

250+ math theorems. Can you solve some of them?

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Scientists Develop Blood Test That Spots Tumor-Derived DNA in People With Early-Stage Cancers 

Scientists Develop Blood Test That Spots Tumor-Derived DNA in People With Early-Stage Cancers  | Amazing Science |

In a bid to detect cancers early and in a noninvasive way, scientists at the Johns Hopkins Kimmel Cancer Center report they have developed a test that spots tiny amounts of cancer-specific DNA in blood and have used it to accurately identify more than half of 138 people with relatively early-stage colorectal, breast, lung and ovarian cancers. The test, the scientists say, is novel in that it can distinguish between DNA shed from tumors and other altered DNA that can be mistaken for cancer biomarkers.

Via Integrated DNA Technologies
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A new “atlas” of cancer genes could help personalize therapies for patients

A new “atlas” of cancer genes could help personalize therapies for patients | Amazing Science |

Researchers use a big-data approach to find links between different genes and patient survival.


Understanding the genetic changes in tumors that distinguish the most lethal cancers from more benign ones could help doctors better treat patients. Recently, Swedish researchers launched a new open-access catalog that maps many of those genetic changes. This “atlas” links thousands of specific genes involved in numerous cancers to patient survival and also reveals potential new drug targets.


The new atlas is one of several ongoing efforts to make sense of data that’s been collected by public databases—like the National Cancer Institute’s Cancer Genome Atlas—that act as repositories for tumor samples. The goal is to glean practical information, like markers of disease, that can be used to develop cancer drugs and diagnostics.


To generate the atlas, researchers led by Mathias Uhlén, a professor of microbiology at the Royal Institute of Technology in Sweden, used a supercomputer to analyze 17 major types of human cancers from nearly 8,000 tumor samples. Uhlén says his team was looking for “holistic changes across the genome caused by these mutations.”


They then mapped all the genes found in those cancer cells to find out how proteins made by these genes affect patient survival. Genes carry instructions for making proteins, and the level of gene expression increases or decreases the amount of protein that genes make. These resulting proteins can dramatically influence biological processes like cancer.

Via Integrated DNA Technologies
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Single Molecules Can Work as Reproducible Transistors, even at Room Temperature

Single Molecules Can Work as Reproducible Transistors, even at Room Temperature | Amazing Science |

Columbia Engineering researchers are first to reproducibly achieve the current blockade effect using atomically precise molecules at room temperature, a result that could lead to shrinking electrical components and boosting data storage and computing power.

Columbia researchers wired a single molecular cluster to gold electrodes to show that it exhibits a quantized and controllable flow of charge at room temperature.


A major goal in the field of molecular electronics, which aims to use single molecules as electronic components, is to make a device where a quantized, controllable flow of charge can be achieved at room temperature. A first step in this field is for researchers to demonstrate that single molecules can function as reproducible circuit elements such as transistors or diodes that can easily operate at room temperature.


A team led by Latha Venkataraman, professor of applied physics and chemistry at Columbia Engineeringand Xavier Roy, assistant professor of chemistry (Arts & Sciences), published a study (DOI 10.1038/nnano.2017.156) today in Nature Nanotechnology that is the first to reproducibly demonstrate current blockade—the ability to switch a device from the insulating to the conducting state where charge is added and removed one electron at a time—using atomically precise molecular clusters at room temperature.


Bonnie Choi, a graduate student in the Roy group and co-lead author of the work, created a single cluster of geometrically ordered atoms with an inorganic core made of just 14 atoms—resulting in a diameter of about 0.5 nanometers—and positioned linkers that wired the core to two gold electrodes, much as a resistor is soldered to two metal electrodes to form a macroscopic electrical circuit (e.g. the filament in a light bulb).


The researchers used a scanning tunneling microscope technique that they have pioneered to make junctions comprising a single cluster connected to the two gold electrodes, which enabled them to characterize its electrical response as they varied the applied bias voltage. The technique allows them to fabricate and measure thousands of junctions with reproducible transport characteristics. “We found that these clusters can perform very well as room-temperature nanoscale diodes whose electrical response we can tailor by changing their chemical composition,” says Venkataraman.


“Theoretically, a single atom is the smallest limit, but single-atom devices cannot be fabricated and stabilized at room temperature. With these molecular clusters, we have complete control over their structure with atomic precision and can change the elemental composition and structure in a controllable manner to elicit certain electrical response.”

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Algebraic Numbers

Algebraic Numbers | Amazing Science |

This is a picture of the algebraic numbers in the complex plane, made by David Moore based on earlier work by Stephen J. Brooks, and available along with other neat stuff at Moore’s site Math and Code.


Algebraic numbers are roots of polynomials with integer coefficients. The integers 0 and 1 are the big dots near the bottom, while ii is near the top. In this picture, the color of a point indicates the degree of the polynomial of which it’s a root:

• red = roots of linear polynomials, i.e. rational numbers,

• green = roots of quadratic polynomials,

• blue = roots of cubic polynomials,

• yellow = roots of quartic polynomials, and so on.


The size of a point decreases exponentially with the ‘complexity’ of the simplest polynomial with integer coefficient of which it’s a root. Here the complexity is the sum of the absolute values of the coefficients of that polynomial.


There are many patterns in this picture that call for explanation! For example, look near the point ii. Can you describe some of these patterns, formulate some conjectures about them, and prove some theorems? Maybe you can dream up a stronger version of Roth’s theorem, which says roughly that algebraic numbers tend to ‘repel’ rational numbers of low complexity.


David Moore made this image using software created by Stephen J. Brooks on Wikipedia

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Super-heatwaves of 55°C to emerge everywhere if global warming continues

Super-heatwaves of 55°C to emerge everywhere if global warming continues | Amazing Science |
Heatwaves amplified by high humidity can reach above 40°C and may occur as often as every two years, leading to serious risks for human health. If global temperatures rise with 4°C, a new super heatwave of 55°C can hit regularly many parts of the world, including Europe, warn researchers.


A recently published study by the Joint Research Centre (JRC) -- the European Commission's science and knowledge service -- analyses the interaction between humidity and heat. The novelty of this study is that it looks not only at temperature but also relative humidity to estimate the magnitude and impact of heat waves.

It finds out that the combinations of the two, and the resulting heatwaves, leave ever more people exposed to significant health risks, especially in East Asia and America's East Coast.


Warm air combined with high humidity can be very dangerous as it prevents the human body from cooling down through sweating, leading to hyperthermia. As a result, if global warming trends continue, many more people are expected to suffer sun strokes, especially in densely populated areas of India, China and the US.


The study analyses changes in yearly probability for a high humidity heatwaves since 1979 under different global warming scenarios. If global temperatures increase up to 2 C above pre-industrial levels the combined effect of heat and humidity (known as apparent temperature or Heat Index) will likely exceed 40°C every year in many parts of Asia, Australia, Northern Africa, South and North America. Europe will be least affected with up to 30% chance of having such strong heat wave annually.


However, if temperatures rise to 4°C a severe scenario is on the horizon. Scientists predict that a new super-heatwave will appear with apparent temperature peaking at above 55°C- a level critical for human survival. It will affect densely populated areas such as USA's East coast, coastal China, large parts of India and South America. Under this global warming scenario Europe is likely to suffer annual heatwaves with apparent temperature of above 40°C regularly while some regions of Eastern Europe may be hit by heatwaves of above 55°C.


The authors highlight that although some urban areas such as Chicago and Shanghai are not considered to have high risk for heatwaves based on temperature only, the probability of extreme weather strongly increased when considering relative humidity.


According to the study, the effect of relative humidity on heatwaves' magnitude and peak might be underestimated in current research. The results of the study support the need for urgent mitigation and adaptation action to address the impacts of heatwaves, and indicate regions where new adaptation measures might be necessary to cope with heat stress.


The study draws on the Apparent Heat Wave Index (AHWI), a composite index for humidity and heat developed by JRC's Competence Centre on Composite Indicators and Scoreboards (

Arturo Pereira's curator insight, August 13, 5:39 PM
We are getting really hot. I am afraid we have already went beyond the tipping point.
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Scientists Record and Replay Movie Encoded in DNA

Scientists Record and Replay Movie Encoded in DNA | Amazing Science |

For the first time, a primitive movie has been encoded in – and then played back from – DNA in living cells. Scientists funded by the National Institutes of Health say it is a major step toward a “molecular recorder” that may someday make it possible to get read-outs, for example, of the changing internal states of neurons as they develop.


“We want to turn cells into historians,” explained neuroscientist Seth Shipman, Ph.D. , a post-doctoral fellow at Harvard Medical School, Boston. “We envision a biological memory system that’s much smaller and more versatile than today’s technologies, which will track many events non-intrusively over time.”


Shipman, Harvard’s Drs. George Church , Jeffrey Macklis  andJeff Nivala  report on their proof-of-concept for a futuristic “molecular ticker tape” online July 12, in the journal Nature. The work was funded by NIH’s National Institute of Mental Health, National Institute of Neurological Disorders and Stroke, and the National Human Genome Research Institute.


The ability to record such sequential events like a movie at the molecular level is key to the idea of reinventing the very concept of recording using molecular engineering, say the researchers. In this scheme, cells themselves could be induced to record molecular events – such as changes in gene expression over time – in their own genomes. Then the information could be retrieved simply by sequencing the genomes of the cells it is stored in.


“If we had those transcriptional steps, we could potentially use them like a recipe to engineer similar cells,” added Shipman. “These could be used to model disease – or even in therapies.”


For starters, the researchers had to show that DNA can be used to encode not just genetic information, but any arbitrary sequential information into a genome. For this they turned to the cutting-edge, NIH-funded gene editing technology CRISPR . They first demonstrated that they could encode and retrieve an image of the human hand in DNA inserted into bacteria. They then similarly encoded and reconstructed frames from a classic 1870s race horse in motion  sequence of photos – an early forerunner of moving pictures.


The researchers had previously shown that they could use CRISPR to store sequences of DNA in bacteria. CRISPR is a group of proteins and DNA that act as an immune system in some bacteria, vaccinating them with genetic memories of viral infections. When a virus infects a bacterium, CRISPR cuts out part of the foreign DNA and stores it in the bacteria’s own genome. The bacterium then uses the stored DNA to recognize the virus and defend against future attacks. “The sequential nature of CRISPR makes it an appealing system for recording events over time,” explained Shipman.


The researchers then similarly translated five frames from the race horse in motion photo sequence into DNA. Over the course of five days, they sequentially treated bacteria with a frame of translated DNA. Afterwards, they were able to reconstruct the movie with 90 percent accuracy by sequencing the bacterial DNA.


Although this technology could be used in a variety of ways, the researchers ultimately hope to use it to study the brain. “We want to use neurons to record a molecular history of the brain through development,” said Shipman. “Such a molecular recorder will allow us to eventually collect data from every cell in the brain at once, without the need to gain access, to observe the cells directly, or disrupt the system to extract genetic material or proteins.”

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