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Exome sequencing gets to the root of rare diseases

Exome sequencing gets to the root of rare diseases | Amazing Science |

Sequencing the protein-coding portion of the genome has helped diagnose the cause of rare disorders and could even predict diseases.


IT'S not quite the long-heralded $1000 genome, but it is getting close. For the first time, doctors have begun rolling out large-scale sequencing of the protein-coding portion of people's genome. This could help to identify the causes of conditions such as congenital deafness and some learning disabilities. More common diseases are expected to follow. The hope is that such sequencing will improve treatments, determine how a person might respond to a drug and possibly even predict disease before it starts.


In an ideal world, people's entire genomes would be mapped to find a potential root cause of a particular disease, but that is very expensive and the technology isn't ready for the clinic. Instead, doctors are turning to the exome - the 1.5 per cent of the genome that encodes proteins. Sequencing takes about 10 days, and some companies already offer it for just $1000.


Last year, a clinic in the Netherlands became the first to start offering clinical exome sequencing to people on a large scale. So far they have examined 262 exomes from people with conditions including intellectual disabilities, blindness and cancer. They were able to match a genetic cause to a diagnosis in about half of the cases of blindness, and in 15 to 25 per cent of the other diseases studied.

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Mapping Every Single U.S. Road Fatality From 2004 to 2013

Mapping Every Single U.S. Road Fatality From 2004 to 2013 | Amazing Science |
The death toll amounts to 373,377 lost lives.


Max Galka of Metrocosm has made some lovely maps in 2015—tracking everything from obesity trends to property values to UFO sightings—but his latest effort may be the most powerful yet. Using data from the federal Fatality Analysis Reporting System, Galka maps every single U.S. road fatality from 2004 to 2013. The death toll amounts to 373,377 lost lives.


At the national level, Galka’s map almost looks like an electricity grid stretching across America’s road network—with bright orange clusters in metro areas connected via dim red threads across remote regions. Here’s a wide view of the whole country:

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Mars' Moon Deimos

Mars' Moon Deimos | Amazing Science |

Mars and Earth have several things in common. Like Earth, Mars is a terrestrial planet (i.e. composed of silicate rock and minerals). It also has polar ice caps, a tilted axis, and evidence of liquid water on its surface. On top of that, Mars and Earth are the only terrestrial planets in the Solar System to have natural satellites.

In fact, Mars has two satellites, which are appropriately named Phobos and Deimos (named after the Greek gods of horror and terror, respectively). Of the two, Deimos is the smaller moon and orbits at a greater distance from the planet. It has the characteristics of an asteroid, which is a strong indication of where it may have come from.

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Physicists find atomic nucleus with a proton ‘bubble’ in the middle

Physicists find atomic nucleus with a proton ‘bubble’ in the middle | Amazing Science |

Scientists have found the first experimental evidence that an atomic nucleus can harbor bubbles. The unstable isotope silicon-34 has a bubble-like center with a paucity of protons, scientists report October 24 inNature Physics. This unusual “bubble nucleus” could help scientists understand how heavy elements are born in the universe, and help scientists find new, ultraheavy stable isotopes.


In their quirky quantum way, protons and neutrons in a nucleus refuse to exist in only one place at a time. Instead, they are spread out across the nucleus in nuclear orbitals, which describe the probability that each proton or neutron will be found in a particular spot. Normally, due to the strong nuclear force that holds the two types of particles together, nuclei have a fairly constant density in their centers, regardless of the number of protons and neutrons they contain. In silicon-34, however, some scientists predicted that one of the proton orbitals that fills the center of the nucleus would be almost empty, creating a bubble nucleus. But not all theories agreed. “This was the reason for doing the experiment,” says coauthor Olivier Sorlin, a nuclear physicist at the National Large Heavy Ion Accelerator, GANIL, in Caen, France. “Some people didn’t believe that it would exist.”


In pursuit of the bubble nucleus, the scientists smashed silicon-34 nuclei into a beryllium target, which knocked single protons out of the nuclei to create aluminum-33. The resulting aluminum-33 nuclei were in excited, or high-energy, states and quickly dropped down to a lower energy by emitting photons, or light particles. By observing the energy of those photons, Sorlin and colleagues could reconstruct the orbital of the proton that had been kicked out of the nucleus.


The scientists found that they ejected few protons from the central orbital that theorists had predicted would be empty. While the orbital can theoretically hold up to two protons, it held only 0.17 protons on average. In silicon-34, the central proton density is about half that of a comparable nucleus, the scientists calculated, after taking into account other central orbitals that contain normal numbers of protons. The density of neutrons in silicon-34’s center, however, is normal.

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The universe is expanding at an accelerating rate – or is it?

The universe is expanding at an accelerating rate – or is it? | Amazing Science |

Five years ago, the Nobel Prize in Physics was awarded to three astronomers for their discovery, in the late 1990s, that the universe is expanding at an accelerating pace. Their conclusions were based on analysis of Type Ia supernovae – the spectacular thermonuclear explosions of dying stars – picked up by the Hubble space telescope and large ground-based telescopes. It led to the widespread acceptance of the idea that the universe is dominated by a mysterious substance named 'dark energy' that drives this accelerating expansion.


Now, a team of scientists led by Professor Subir Sarkar of Oxford University's Department of Physics has cast doubt on this standard cosmological concept. Making use of a vastly increased data set – a catalogue of 740 Type Ia supernovae, more than ten times the original sample size – the researchers have found that the evidence for acceleration may be flimsier than previously thought, with the data being consistent with a constant rate of expansion.


The study is published in the Nature journal Scientific Reports. Professor Sarkar, who also holds a position at the Niels Bohr Institute in Copenhagen, said: 'The discovery of the accelerating expansion of the universe won the Nobel Prize, the Gruber Cosmology Prize, and the Breakthrough Prize in Fundamental Physics. It led to the widespread acceptance of the idea that the universe is dominated by "dark energy" that behaves like a cosmological constant – this is now the "standard model" of cosmology.


'However, there now exists a much bigger database of supernovae on which to perform rigorous and detailed statistical analyses. We analysed the latest catalogue of 740 Type Ia supernovae – over ten times bigger than the original samples on which the discovery claim was based – and found that the evidence for accelerated expansion is, at most, what physicists call "3 sigma". This is far short of the 5 sigma standard required to claim a discovery of fundamental significance.


'An analogous example in this context would be the recent suggestion for a new particle weighing 750 GeV based on data from the Large Hadron Collider at CERN. It initially had even higher significance – 3.9 and 3.4 sigma in December last year – and stimulated over 500 theoretical papers. However, it was announced in August that new data shows that the significance has dropped to less than 1 sigma. It was just a statistical fluctuation, and there is no such particle.'

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The limits to human lifespan must be respected

The limits to human lifespan must be respected | Amazing Science |
Lengthening our lives will come at a cost.


A study published online in Nature uses demographic data to reveal a lifespan that human beings cannot exceed, simply by virtue of being human. It’s like running, as an accompanying News and Views article points out. Elite athletes might shave a few milliseconds off the world record for the 100-meter sprint, but they’ll never run the same distance in, say, five seconds, or two. Human beings are simply not made that way. The same is true for longevity. The consequences of myriad factors related to our genetics, metabolism, reproduction and development, all shaped over millions of years of evolution, means that few humans will make it past their 120th birthdays. The name of Jeanne Calment, who died in 1997 at the age of 122, is likely to remain as long in the memory in the Methuselah stakes as that of Usain Bolt on the Olympic track.


Maximum lifespan is a bald measure of years accumulated. It is not the same as life expectancy, which is an actuarial measure of how long one is expected to live from birth, or indeed from any given age. Life expectancy at birth has increased in most countries over the past century, not because people have longer lifespans, but mainly because infectious disease does not kill as many infants as it once did. Factors such as poverty and warfare conspire to decrease life expectancy. Although life expectancy at birth has risen steadily for both men and women in France since 1900, for example, there are dramatic and poignant drops that coincide with the two world wars.


In Britain in the early twentieth century, many children still died from infectious diseases, and men would die shortly after retiring from physically demanding jobs. The National Health Service was the political response. It has become, in some ways, the victim of its own success. People live longer than they did even a few decades ago, and die (eventually) of different (and more expensive) complaints. As any beginning medical student is soon taught, gerontology is far from a dying discipline. So if we owe our increases in life expectancy to better public health, nutrition, sanitation and vaccination, is it not fair to ask whether more-effective treatments for diseases such as cancer, Parkinson’s disease and Alzheimer’s might also yield dividends in maximum lifespan? Will 120th birthday parties become routine, outmatched by a small yet increasing number of sesquicentenarians? The demographic data say no. People are living longer, and the population as a whole is greying, but the rate of increase in the number of centenarians is slowing, and might even have peaked.

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Gene-edited CRISPR-Cas9 mushroom escapes US regulation

Gene-edited CRISPR-Cas9 mushroom escapes US regulation | Amazing Science |

The US Department of Agriculture (USDA) will not regulate a mushroom genetically modified withthe gene-editing tool CRISPR–Cas9. The long-awaited decision means that the mushroom can be cultivated and sold without passing through the agency's regulatory process — making it the first CRISPR-edited organism to receive a green light from the US government.


“The research community will be very happy with the news,” says Caixia Gao, a plant biologist at the Chinese Academy of Sciences’s Institute of Genetics and Developmental Biology in Beijing, who was not involved in developing the mushroom. “I am confident we'll see more gene-edited crops falling outside of regulatory authority.”


Yinong Yang, a plant pathologist at Pennsylvania State University (Penn State) in University Park, engineered the common white button (Agaricus bisporus) mushroom to resist browning. The effect is achieved by targeting the family of genes that encodes polyphenol oxidase (PPO) — an enzyme that causes browning. By deleting just a handful of base pairs in the mushroom’s genome, Yang knocked out one of six PPO genes — reducing the enzyme’s activity by 30%.


The mushroom is one of about 30 genetically modified organisms (GMOs) to sidestep the USDA regulatory system in the past five years. In each case, the agency's Animal and Plant Health Inspection Service (APHIS) has said that the organisms — mostly plants — do not qualify as something the agency must regulate. Once a crop passes the USDA reviews, it may still undergo a voluntary review by the US Food and Drug Administration.


Several of the plants that bypassed the USDA were made using gene-editing techniques such as the zinc-finger nuclease (ZFN) and transcription activator-like effector nuclease (TALEN) systems. But until now, it was not clear whether the USDA would give the same pass to organisms engineered with science’s hottest new tool, CRISPR–Cas9.

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Was Venus the first habitable planet in our solar system?

Was Venus the first habitable planet in our solar system? | Amazing Science |

Its surface is hot enough to melt lead and its skies are darkened by toxic clouds of sulphuric acid. Venus is often referred to as Earth’s evil twin, but conditions on the planet were not always so hellish, according to research that suggests it may have been the first place in the solar system to have become habitable.


The study, due to be presented this week at the at the American Astronomical Society Meeting in Pasadena, concludes that at a time when primitive bacteria were emerging on Earth, Venus may have had a balmy climate and vast oceans up to 2,000 meters (6,562 feet) deep. Michael Way, who led the work at the Nasa Goddard Institute for Space Studies in New York City, said: “If you lived three billion years ago at a low latitude and low elevation the surface temperatures would not have been that different from that of a place in the tropics on Earth,” he said.


The Venusian skies would have been cloudy with almost continual rain lashing down in some regions, however. “So while you might get nice sunsets you would have mostly overcast skies during the day and precipitation,” Way added.


Crucially, if the calculations are correct the oceans may have remained until 715m years ago - a long enough period of climate stability for microbial life to have plausibly sprung up. “The oceans of ancient Venus would have had more constant temperatures, and if life begins in the oceans - something which we are not certain of on Earth - then this would be a good starting place,” said Way.


Other planetary scientists agreed that, despite the differing fates of the two planets, early Earth and Venus may have been similar.

Via Kathy Bosiak
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70% Of Earth's Fresh Water Is Frozen

70% Of Earth's Fresh Water Is Frozen | Amazing Science |

About 71% of the Earth is covered in water. Most of that is in oceans, rivers, and lakes, but some is frozen in the Earth's two ice sheets. Those ice sheets, which cover most of Greenland and Antarctica, only contain 2% of the world's total water supply, but a whopping 70% of the Earth's fresh water.


Scientists estimate that if the Antarctic Ice Sheet—the larger of the two—melted, sea level would rise by around 60 meters (200 feet). Not only that, but it could affect the weather: a study showed that less sea ice in the Arctic causes rainier summers in western Europe, and another study suggests that it's causing more extreme heat waves in the United States and elsewhere. And counterintuitively, melting ice also causes more melting ice.


A 2016 study found that a shrinking in the Greenland Ice Sheet causes what are known as "blocking events," where high-pressure systems park themselves on top of one area for days or even weeks. This brings warm, moist air that heats the surface below and causes even more ice to melt. Explore the relationship between polar ice and climate change in the videos below.

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Unsolved math: The moving sofa problem

Unsolved math: The moving sofa problem | Amazing Science |

So you're moving into your new apartment, and you're trying to bring your sofa. The problem is, the hallway turns and you have to fit your sofa around a corner. If it's a small sofa, that might not be a problem, but a really big sofa is sure to get stuck. If you're a mathematician, you ask yourself: What's the largest sofa you could possibly fit around the corner? It doesn't have to be a rectangular sofa either, it can be any shape.


This is the essence of the moving sofa problem. Here are the specifics: the whole problem is in two dimensions, the corner is a 90-degree angle, and the width of the corridor is 1. What is the largest two-dimensional area that can fit around the corner?


The largest area that can fit around a corner is called—I kid you not—the sofa constant. Nobody knows for sure how big it is, but we have some pretty big sofas that do work, so we know it has to be at least as big as them. We also have some sofas that don't work, so it has to be smaller than those. All together, we know the sofa constant has to be between 2.2195 and 2.8284.

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Innovative technique for shaping light could solve bandwidth crunch

Innovative technique for shaping light could solve bandwidth crunch | Amazing Science |

As data demands continue to grow, scientists predict that it's only a matter of time before today's telecommunication networks reach capacity unless new technologies are developed for transporting data. A new technique could help avert this bandwidth crunch by allowing light-based optical networks to carry more than one hundred times more data than is possible with current technologies.


Laser light comes in many different shapes, or spatial modes. However, today's optical networks use just one spatial mode to carry information, limiting the amount of data that can be transmitted at one time. Researchers led by Andrew Forbes, a professor at the University of Witwatersrand, South Africa, developed a technique known as spatial multiplexing that reshapes a laser beam into many spatial modes that can each carry information.


In a paper presented at the OSA Laser Congress in Boston, the researchers demonstrate optical communication with more than 100 spatial modes by combining their new spatial multiplexing approach with wavelength division multiplexing (WDM), which uses different wavelengths of light to carry information.


"We created 35 spatial modes encoded in three different wavelengths, producing 105 total modes," said Carmelo Rosales-Guzmán, research fellow and first author of the paper. "Our new method might serve as the basis for future communication technologies."


The researchers demonstrated that their technique can transmit data with 98 percent efficiency in a laboratory free-space optical network, which uses light to transmit information over the air. The scientists say the approach should also work in optical fibers, the basis for fiber-optic communications.

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Quantum computers: 10-fold boost in stability achieved

Quantum computers: 10-fold boost in stability achieved | Amazing Science |

Australian engineers have created a new quantum bit which remains in a stable superposition for 10 times longer than previously achieved, dramatically expanding the time during which calculations could be performed in a future silicon quantum computer. 


The new quantum bit, made up of the spin of a single atom in silicon and merged with an electromagnetic field - known as 'dressed qubit' - retains quantum information for much longer that an 'undressed' atom, opening up new avenues to build and operate the superpowerful quantum computers of the future. The result by a team at Australia's University of New South Wales (UNSW), appears today in the online version of the international journal, Nature Nanotechnology.


"We have created a new quantum bit where the spin of a single electron is merged together with a strong electromagnetic field," said Arne Laucht, a Research Fellow at the School of Electrical Engineering & Telecommunications at UNSW, and lead author of the paper. "This quantum bit is more versatile and more long-lived than the electron alone, and will allow us to build more reliable quantum computers."


Building a quantum computer has been called the 'space race of the 21st century' - a difficult and ambitious challenge with the potential to deliver revolutionary tools for tackling otherwise impossible calculations, such as the design of complex drugs and advanced materials, or the rapid search of massive, unsorted databases.


Its speed and power lie in the fact that quantum systems can host multiple 'superpositions' of different initial states, which in a computer are treated as inputs which, in turn, all get processed at the same time.


"The greatest hurdle in using quantum objects for computing is to preserve their delicate superpositions long enough to allow us to perform useful calculations," said Andrea Morello, leader of the research team and a Program Manager in the Centre for Quantum Computation & Communication Technology (CQC2T) at UNSW.

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Mice share each other's pain through the sense of smell

Mice share each other's pain through the sense of smell | Amazing Science |
Pain can jump from one mouse to another, presumably through chemicals detected by the nose.


Pain is contagious, at least for mice. After encountering bedding where mice in pain had slept, other mice became more sensitive to pain themselves. The experiment, described online October 19 in Science Advances, shows that pain can move from one animal to another — no injury or illness required.  


The results “add to a growing body of research showing that animals communicate distress and are affected by the distress of others,” says neuroscientist Inbal Ben-Ami Bartal of the University of California, Berkeley.


Neuroscientist Andrey Ryabinin and colleagues didn’t set out to study pain transfer. But the researchers noticed something curious during their experiments on mice who were undergoing alcohol withdrawal. Mice in the throes of withdrawal have a higher sensitivity to pokes on the foot. And surprisingly, so did these mice’s perfectly healthy cagemates. “We realized that there was some transfer of information about pain” from injured mouse to bystander, says Ryabinin, of Oregon Health & Sciences University in Portland.


When mice suffered from alcohol withdrawal, morphine withdrawal or an inflaming injection, they become more sensitive to a poke in the paw with a thin fiber — a touchy reaction that signals a decreased pain tolerance. Mice that had been housed in the same cage with the mice in pain also grew more sensitive to the poke, Ryabinin and colleagues found. These bystander mice showed other signs of heightened pain sensitivity, such as quickly pulling their tails out of hot water and licking a paw after an irritating shot.


The results are compelling evidence for the social transmission of pain, says neuroscientist Christian Keysers of the Netherlands Institute for Neuroscience in Amsterdam.

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A smart ‘bionic’ cardiac patch that doubles as advanced pacemaker/arrhythmia detector

A smart ‘bionic’ cardiac patch that doubles as advanced pacemaker/arrhythmia detector | Amazing Science |

Harvard researchers have designed nanoscale electronic scaffolds (support structures) that can be seeded with cardiac cells to produce a new “bionic” cardiac patch (for replacing damaged cardiac tissue with pre-formed tissue patches). It also functions as a more sophisticated pacemaker: In addition to electrically stimulating the heart, the new design can change the pacemaker stimulation frequency and direction of signal propagation.


In addition, because because its electronic components are integrated throughout the tissue (instead of being located on the surface of the skin), it could detect arrhythmia far sooner, and “operate at far lower (safer) voltages than a normal pacemaker, [which] because it’s on the surface, has to use relatively high voltages,” according to Charles Lieber, the Mark Hyman, Jr. Professor of Chemistry and Chair of the Department of Chemistry and Chemical Biology.


“Even before a person started to go into large-scale arrhythmia that frequently causes irreversible damage or other heart problems, this could detect the early-stage instabilities and intervene sooner,” he said. “It can also continuously monitor the feedback from the tissue and actively respond.”


The patch might also find use, Lieber said, as a tool to monitor responses to cardiac drugs, or to help pharmaceutical companies screen the effectiveness of drugs under development.

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Long-term, hi-res tracking of eruptions on Jupiter’s moon Io

Long-term, hi-res tracking of eruptions on Jupiter’s moon Io | Amazing Science |

Jupiter’s moon Io continues to be the most volcanically active body in the solar system, as documented by the longest series of frequent, high-resolution observations of the moon’s thermal emission ever obtained.


Using near-infrared adaptive optics on two of the world’s largest telescopes — the 10-meter Keck II and the 8-meter Gemini North, both located near the summit of the dormant volcano Maunakea in Hawaii — UC Berkeley astronomers tracked 48 volcanic hot spots on the surface over a period of 29 months from August 2013 through the end of 2015.

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AI milestone: a new system can match humans in speech recognition

AI milestone: a new system can match humans in speech recognition | Amazing Science |

A team at Microsoft's Artificial Intelligence and Research group has published a study in which they demonstrate a technology that recognizes spoken words in a conversation as well as a real person does.


Last month, the same team achieved a word error rate (WER) of 6.3%. In their new paper this week, they report a WER of just 5.9%, which is equal to that of professional transcriptionists and is the lowest ever recorded against the industry standard Switchboard speech recognition task. “We’ve reached human parity,” said Xuedong Huang, the company’s chief speech scientist. “This is an historic achievement.”


“Even five years ago, I wouldn’t have thought we could have achieved this,” said Harry Shum, the group's executive vice president. “I just wouldn’t have thought it would be possible.”


Microsoft has been involved in speech recognition and speech synthesis research for many years. The company developed Speech API in 1994 and later introduced speech recognition technology in Office XP and Office 2003, as well as Internet Explorer. However, the word error rates for these applications were much higher back then.


In their new paper, the researchers write: "the key to our system's performance is the systematic use of convolutional and LSTM neural networks, combined with a novel spatial smoothing method and lattice-free MMI acoustic training."


The team used Microsoft’s own Computational Network Toolkit – an open source, deep learning framework. This was able to process deep learning algorithms across multiple computers, running a specialized GPU to greatly improve its speed and enhance the quality of research. The team believes their milestone will have broad implications for both consumer and business products, including entertainment devices like the Xbox, accessibility tools such as instant speech-to-text transcription, and personal digital assistants such as Cortana. “This will make Cortana more powerful, making a truly intelligent assistant possible,” Shum said.


“The next frontier is to move from recognition to understanding,” said Geoffrey Zweig, who manages the Speech & Dialog research group. Future improvements may also include speech recognition that works well in more real-life settings – places with lots of background noise, for example, such as at a party or while driving on the highway. The technology will also become better at assigning names to individual speakers when multiple people are talking, as well as working with a wide variety of voices, regardless of age, accent or ability.


The full study – Achieving Human Parity in Conversational Speech Recognition – is available at:

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DNA data offer evidence of unknown extinct human relative

DNA data offer evidence of unknown extinct human relative | Amazing Science |

Traces of long-lost human cousins may be hiding in modern people’s DNA, a new computer analysis suggests. People from Papua New Guinea (shown) and Australia carry small amounts of DNA from extinct human relatives. New research suggests that the DNA may not come from Neandertals or Denisovans, but from a third, previously unknown extinct hominid.


People from Melanesia, a region in the South Pacific encompassing Papua New Guinea and surrounding islands, may carry genetic evidence of a previously unknown extinct hominid species, Ryan Bohlender reported October 20 at the annual meeting of the American Society of Human Genetics. That species is probably not Neandertal or Denisovan, but a different, related hominid group, said Bohlender, a statistical geneticist at the University of Texas MD Anderson Cancer Center in Houston. “We’re missing a population or we’re misunderstanding something about the relationships,” he said.

This mysterious relative was probably from a third branch of the hominid family tree that produced Neandertals and Denisovans, an extinct distant cousin of Neandertals. While many Neandertal fossils have been found in Europe and Asia, Denisovans are known only from DNA from a finger bone and a couple of teeth found in a Siberian cave (SN: 12/12/15, p. 14).


Bohlender isn’t the first to suggest that remnants of archaic human relatives may have been preserved in human DNA even though no fossil remains have been found. In 2012, another group of researchers suggested that some people in Africa carry DNA heirlooms from an extinct hominid species (SN: 9/8/12, p. 9).


Less than a decade ago, scientists discovered that human ancestors mixed with Neandertals. People outside of Africa still carry a small amount of Neandertal DNA, some of which may cause health problems (SN: 3/5/16, p. 18). Bohlender and colleagues calculate that Europeans and Chinese people carry a similar amount of Neandertal ancestry: about 2.8 percent. Europeans have no hint of Denisovan ancestry, and people in China have a tiny amount — 0.1 percent, according to Bohlender’s calculations. But 2.74 percent of the DNA in people in Papua New Guinea comes from Neandertals, and another 3 to 6 percent stems from Denisovans, Bohlender calculated.

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Oldest Known Squawk Box Suggests Dinosaurs Likely Did Not Sing

Oldest Known Squawk Box Suggests Dinosaurs Likely Did Not Sing | Amazing Science |

The oldest known vocal organ of a bird has been found in an Antarctic fossil of a relative of ducks and geese that lived more than 66 million years ago during the age of dinosaurs.


The discovery of the Mesozoic-era vocal organ—called a syrinx—and its apparent absence in non-avian dinosaur fossils of the same age indicate that the organ may have originated late in the evolution of birds and that other dinosaurs may not have been able to make noises similar to the bird calls we hear today, according to findings published in Nature on Oct 12. Birds are direct descendants of dinosaurs and are considered living dinosaurs by scientists.

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Microsoft’s quest for a topological quantum computer

Microsoft’s quest for a topological quantum computer | Amazing Science |

The race is on build a ‘universal’ quantum computer. Such a device could be programmed to speedily solve problems that classical computers cannot crack, potentially revolutionizing fields from pharmaceuticals to cryptography. Many of the world's major technology firms are taking on the challenge, but Microsoft has opted for a more tortuous route than its rivals.


IBM, Google and a number of academic labs have chosen relatively mature hardware, such as loops of superconducting wire, to make quantum bits (qubits). These are the building blocks of a quantum computer: they power its speedy calculations thanks to their ability to be in a mixture (or superposition) of ‘on’ and ‘off’ states at the same time.


Microsoft, however, is hoping to encode its qubits in a kind of quasiparticle: a particle-like object that emerges from the interactions inside matter. Some physicists are not even sure that the particular quasiparticles Microsoft are working with — called non-abelian anyons — actually exist. But the firm hopes to exploit their topological properties, which make quantum states extremely robust to outside interference, to build what are called topological quantum computers. Early theoretical work on topological states of matter won three physicists the Nobel Prize in Physics on 4 October, 2016.


The firm has been developing topological quantum computing for more than a decade and today has researchers  writing software for future machines, and working with academic laboratories to craft devices.

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Mitochondrial diseases

Mitochondrial diseases | Amazing Science |

Mitochondrial diseases are a group of genetic disorders that are characterized by defects in oxidative phosphorylation and caused by mutations in genes in the nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) that encode structural mitochondrial proteins or proteins involved in mitochondrial function.


Mitochondrial diseases are the most common group of inherited metabolic disorders and are among the most common forms of inherited neurological disorders. One of the challenges of mitochondrial diseases is the marked clinical variation seen in patients, which can delay diagnosis. However, advances in next-generation sequencing techniques have substantially improved diagnosis, particularly in children. Establishing a genetic diagnosis allows patients with mitochondrial diseases to have reproductive options, but this is more challenging for women with pathogenetic mtDNA mutations that are strictly maternally inherited.


Recent advances in in vitro fertilization techniques, including mitochondrial donation, will offer a better reproductive choice for these women in the future. The treatment of patients with mitochondrial diseases remains a challenge, but guidelines are available to manage the complications of disease. Moreover, an increasing number of therapeutic options are being considered, and with the development of large cohorts of patients and biomarkers, several clinical trials are in progress.

Via MBN Comunicación
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Zika Virus Infection Alters Human and Viral RNA

Zika Virus Infection Alters Human and Viral RNA | Amazing Science |

Researchers at University of California San Diego School of Medicine have discovered that Zika virus infection leads to modifications of both viral and human genetic material. These modifications — chemical tags known as methyl groups — influence viral replication and the human immune response. The study is published October 20 by Cell Host & Microbe.


“I’m excited about this study because it teaches us something new about the human immune system,” said senior author Tariq Rana, PhD, professor of pediatrics at UC San Diego School of Medicine. “But these findings are also something researchers should keep in mind as they are designing new Zika virus vaccines and treatments that target the viral genome — some approaches won’t work unless they take methylation into account.”


In human cells, RNA is the genetic material that carries instructions from the DNA in a cell’s nucleus out to the cytoplasm, where molecular machinery uses those instructions to build proteins. Cells can chemically modify RNA to influence protein production. One of these modifications is the addition of methyl groups to adenosine, one of the building blocks that make up RNA. Known as N6-methyladenosine (m6A), this modification is common in humans and other organisms.


In contrast to humans, the entire genomes of some viruses, including Zika and HIV, are made up of RNA instead of DNA. These viruses hijack the host’s cellular machinery to translate its RNA to proteins. Rana and his team previously discovered that m6A plays an important role in HIV infection. “After that, we decided to investigate m6A RNA in Zika virus as well, since we didn’t want to miss out on this important information the way we missed it for 30 years of HIV research,” Rana said.


When Zika virus infects a human cell, Rana’s team found, the cell modifies viral RNA with m6A as a means to get rid of the infection. RNA tagged with m6A is a beacon for human enzymes that come along and destabilize it. In addition, they found that this host response to Zika viral infection also induced specific m6A modifications on human RNA. These human RNA changes were not present in the absence of Zika virus.

Via Integrated DNA Technologies
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Space oddity: Group claims to have created nation in space

Space oddity: Group claims to have created nation in space | Amazing Science |

Welcome to Asgardia! Today, an international group of researchers, engineers, lawyers, and entrepreneurs announced the creation of a nation in space, named after the city of the skies ruled over by Odin in Norse mythology. Although Asgardia does not yet have any land, it is attracting citizens. Anyone can sign up on the nation’s website. Asgardia would allow space entrepreneurs to flourish, and protect Earth, too.


The idea behind the initiative, organizers say, is to create a new legal framework for the peaceful exploitation of space free of the control of Earth-bound nations (governance by Norse deities being preferable, obviously). The nation-building effort is led by Igor Ashurbeyli, a Russian space scientist and engineer who in 2013 founded the Aerospace International Research Center (AIRC) in Vienna, known mostly for publishing the space journal Room. Ashurbeyli told a press conference in Paris today: “The scientific and technological component of the project can be explained in just three words—peace, access, and protection.”


The protection component comes in the form of a satellite, scheduled to be launched in 2017, which will provide a “state-of-the-art protective shield for all humankind from cosmic manmade and natural threats to life on Earth such as space debris, coronal mass ejections, and asteroid collisions.” A bold plan, because the combined might of the world’s space agencies and military have yet to figure out how to prevent their own satellites colliding with each other, let alone protect Earth from a rock the size of a city. And it is not clear whether the organizers have the financing or technical capability to launch their own satellite.


The initiative appears to be an effort to sidestep the oversight of the United Nations’s Outer Space Treaty, which gives nations the duty of overseeing any space activities undertaken from its territory, whether by government bodies, commercial companies, or nonprofit organizations. The nation then takes responsibility for any damage that launchers and satellites may cause both in space and anywhere on Earth. “By creating a new Space Nation, private enterprise, innovation and the further development of space technology to support humanity will flourish free from the tight restrictions of state control that currently exist,” the project said in a statement. It’s not yet clear, however, what kind of governmental oversight, democratic or otherwise, is provided for in the Asgardian constitution—or whether the nation even has one.


Asgardia is not yet recognized by any other nation, nor by the United Nations, and it is not clear how, not having its own territory to launch from, it will be able to loft a satellite without it coming under some other nation’s control as described by the Outer Space Treaty. 

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‘On-the-fly’ 3-D printing system prints what you design, as you design it

‘On-the-fly’ 3-D printing system prints what you design, as you design it | Amazing Science |

Cornell researchers have developed an interactive prototyping system that prints a wire frame of your design as you design it. You can pause anywhere in the process to test or measure and make needed changes, which will be added to the physical model still in the printer.


In conventional 3-D printing, a nozzle scans across a stage depositing drops of plastic, rising slightly after each pass to build an object in a series of layers. With the On-the-Fly-Print system, the nozzle instead extrudes a rope of quick-hardening plastic to create a wire frame that represents the surface of the solid object described in a computer-aided design (CAD) file and allows the designer to make refinements while printing is in progress.

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Biologists first to observe direct inheritance of gene-silencing RNA

Biologists first to observe direct inheritance of gene-silencing RNA | Amazing Science |

The basics of genetic inheritance are well known: parents each pass half of their DNA to their offspring during reproduction. This genetic recipe is thought to contain all of the information that a new organism needs to build its body. But recent research has shown that, in some species, parents' life experiences can alter their offspring. Being underfed, exposed to toxins or stricken by disease can cause changes in a parent's gene expression patterns, and in some cases, these changes can be passed down to the next generation. However, the mechanisms that cause this effect—known as non-genetic inheritance—are a mystery.


New research from the University of Maryland provides a surprising possible explanation. For the first time, developmental biologists have observed molecules of double-stranded RNA (dsRNA)—a close cousin of DNA that can silence genes within cells—being passed directly from parent to offspring in the roundworm Caenorhabditis elegans. Importantly, the gene silencing effect created by dsRNA molecules in parents also persisted in their offspring.


The work, published October 17, 2016 in the online early edition of the Proceedings of the National Academy of Sciences, suggests that the mechanisms for non-genetic inheritance might be simpler than anyone had suspected. "This is the first time we've seen a dsRNA molecule passing from one generation to the next," said Antony Jose, an assistant professor in the UMD Department of Cell Biology and Molecular Genetics and senior author on the study. "The assumption has been that dsRNA changes the parent's genetic material and this altered genetic material is transmitted to the next generation. But our observations suggest that RNA is cutting out the middle man."


Jose and his team, including graduate student and lead author Julia Marré and former research technician Edward Traver, introduced dsRNA marked with a fluorescent label into the circulatory system of C. elegans worms. They then watched as these fluorescent RNA molecules physically moved from the parent's circulatory system into an egg cell waiting to be fertilized.

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In a scientific first, mouse eggs grown from skin cells

In a scientific first, mouse eggs grown from skin cells | Amazing Science |

For the first time, researchers have grown eggs entirely in a lab dish. Skin-producing cells called fibroblasts from the tip of an adult mouse’s tail have been reprogrammed to make eggs, Japanese researchers report online October 17 in Nature. Those eggs were fertilized and grew into six healthy mice.


The accomplishment could make it possible to study the formation of gametes — eggs and sperm — a mysterious process that takes place inside fetuses. If the feat can be repeated with human cells, it could make eggs easily available for research and may eventually lead to infertility treatments.

“This is very solid work, and an important step in the field,” says developmental biologist Diana Laird of the University of California, San Francisco, who was not involved in the study. But, she cautions, “I wouldn’t want patients who have infertility to think this can be done in humans next year,” or even in the near future.


Stem cells reprogrammed from adult body cells have been coaxed into becoming a wide variety of cells. But producing eggs, the primordial cells of life, is far trickier. Egg cells are the ultimate in flexibility, able to create all the bits and parts of an organism from raw genetic instructions. They are far more flexible, or potent, than even the embryonic-like stem cells from which the researchers created them.


Making eggs in a dish is such a difficult task that it required a little help from ovary cells that support egg growth, stem cell researcher Katsuhiko Hayashi of Kyushu University in Fukuoka, Japan, and colleagues found. The team had previously reprogrammed stem cells to produce primordial germ cells, the cells that give rise to eggs. But they had to put those cells into mice to finish developing into eggs in the ovary (SN: 11/3/12, p. 14).

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“Singing” fish rely on circadian rhythm and melatonin for for nocturnal courtship vocalization

“Singing” fish rely on circadian rhythm and melatonin for for nocturnal courtship vocalization | Amazing Science |
For widemouthed, musical midshipman fish, melatonin is not a sleep hormone — it’s a serenade starter.

In breeding season, male plainfin midshipman fish (Porichthys notatus) spend their nights singing — if that’s the word for hours of sustained foghorn hums. Males dig trysting nests under rocks along much of North America’s Pacific coast, then await females drawn in by the crooning.

New lab tests show that melatonin, familiar to humans as a possible sleep aid, is a serenade “go” signal, says behavioral neurobiologist Ni Feng of Yale University.

From fish to folks, nighttime release of melatonin helps coordinate bodily timekeeping and orchestrate after-dark biology. The fish courtship chorus, however, is the first example of the hormone prompting a launch into song, according to Andrew Bass of Cornell University. And what remarkable vocalizing it is.

The plainfin midshipman male creates a steady “mmm” by quick-twitching specialized muscles around its air-filled swim bladder up to 100 times per second in chilly water. A fish can extend a single hum for about two hours, Feng and Bass report October 10 in Current Biology. That same kind of super-fast muscle shakes rattle-snake tails and trills vocal structures in songbirds and bats.
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