Human genome decoded with pocket-sized device

Scientists used a portable device no bigger than a cellphone to sequence the most complete human genome ever assembled with a single technology, according to a study .

The breakthrough, detailed in the journal Nature Biotechnology, brings us closer to the day when family doctors will order up genome scans during a regular check-up along with blood work, the authors suggested.

"We are definitely approaching the point where sequencing genomes will become a routine part of advanced clinical exams," lead author Matthew Loose, a professor at the University of Nottingham, told AFP.

The new sequencing method is the first to read long, unbroken strands of DNA, yielding a final result that is 99.88 percent accurate.

"The process of assembling a genome is like piecing together a jigsaw puzzle," said co-author Nicholas Loman, a scientist at the Institute of Microbiology and Infection and the University of Birmingham.

"The ability to produce extremely long sequencing reads is like finding very large pieces of the puzzle."

Critically, the so-called nanopore technology sheds light on poorly understood regions of the genome governing the body's immune responses and tumour growth.

This may help detect cancer DNA in the blood, and "pick up tumours before they are symptomatic or visible through radiological techniques," said Loman.

In the case of a patient with a suspected infection, the sequencing can be used to ferret out the genome of a virus or bacteria, he told AFP.

"We could also simultaneously look at how the patient is responding to that infection," he added, noting that each individual's immune system is different.

Likewise for sequencing a person's microbiome, the vast community of microbes we each host, mostly in the digestive tract.

Like making a cup of tea

"For personalised medicine, we will want to build up a picture of how individuals may respond to antibiotics and anti-cancer drugs," Loman said.

The human genome is composed of more than three billion pairing of building-block molecules, and grouped into some 25,000 genes.

It contains the codes and instructions that tell the body how to grow and develop. Flaws in the instructions can lead to disease.

The first decoding of a human genome -- completed in 2003 -- was a Manhattan Project-like effort: it took 15 years, cost three billion dollars, and marshalled hundreds of scientists and the computing power from 20 major universities and research institutes.

The new sequencing -- carried out by a dozen researchers and half-a-dozen hand-held devices called MinIONs -- cost a few thousand dollars and took three weeks to complete.

"In five to ten years, genetic sequencing will be a ubiquitous as boiling a kettle or making a cup of tea," predicted co-author Andrew Beggs, a professor at the University of Birmingham, one of nine institutions involved in the project.

The researchers pieced together the genome by passing strands of DNA through minuscule tube-like structures -- manufactured by Oxford Nanopore Technologies -- along with electrically charged atoms.

Changes in the electrical current identify DNA molecules, which can then be mapped.

Complete sequencing is not to be confused with the gene kits offered by companies such as 23andMe and deCODEme, which only provide DNA snapshots, not the whole shebang.

There are only four molecular building blocks of DNA: adenine (A), cytosine (C), guanine (G), and thymine (T).

New gene-editing allow for ultra-precise changes and corrections in DNA coding.

Scientists find new type of ice inside diamonds

A rare form of ice has been found inside diamonds that were newly unearthed around the world, according to a study.

The type of ice, known as ice-VII, features a cubic shape and is about 1.5 times as dense as the regular ice -- ice I.

Different from other solids, whose atoms squeeze together under higher forms of pressure, water-based ice rearrange themselves into new structures when subjected to increasing pressure.

For example, if you press down hard enough on ice-I, it will transform into ice-II, which has a rhombohedral structure. Increase the pressure once gain and the atoms will rearrange themselves into ice-III, then IV, V, VI and VII.

Once it reaches the phase of ice-VII, the structure remains fairly stable even as the pressure increases.

The discovery has cheered the scientists, who previously believed that ice- VII only existed on other planets of the solar systems.

"Water in diamonds is not unknown, but finding this very high pressure form of water ice intact, that was really fortuitous," George Rossman, a mineralogist at Caltech, told the Los Angeles Times. "That's what you call discovery."

Thanks to their discovery, ice-VII has been recognized for the first time as a mineral in the International Mineralogical Assn.

Those diamonds with ice-VII inside were collected from mines in Africa and China.

Scientists transplant memories into snail

Memory transfer has been at the heart of science fiction for decades, but it's becoming more like science fact.

A team successfully transplanted memories by transferring a form of genetic information called RNA from one snail into another.

The snails were trained to develop a defensive reaction.

When the RNA was inserted into snails that had not undergone this process, they behaved just as if they had been sensitised.

The research, published in the journal eNeuro, could provide new clues in the search for the physical basis of memory.

RNA stands for ribonucleic acid; it's a large molecule involved in various essential roles within biological organisms - including the assembly of proteins and the way that genes are expressed more generally.

The scientists gave mild electric shocks to the tails of a species of marine snail called Aplysia californica. After these shocks were administered. the snail's defensive withdrawal reflex - where the snails contract in order to protect themselves from harm.

When the researchers subsequently tapped the snails, they found those that had been given the shocks displayed a defensive contraction lasting about 50 seconds, while those that had not received the shocks contracted for only about one second.

The shocked snails had been "sensitised" to the stimulus.

Purple ink

Scientists extracted RNA from the nervous systems of the snails that received the shocks and injected it into a small number of marine snails that had not been sensitised in this way.

The non-sensitised snails injected with the RNA from the shocked animals behaved as if they had themselves received the tail shocks, displaying a defensive contraction of about 40 seconds.

They saw a similar effect when they did the same thing to sensory nerve cells being studied in petri dishes.

Prof David Glanzman, one of the authors, from the University of California, Los Angeles (UCLA), said the result was "as though we transferred the memory".

He also stressed that the snails did not get hurt: "These are marine snails and when they are alarmed they release a beautiful purple ink to hide themselves from predators. So these snails are alarmed and release ink, but they aren't physically damaged by the shocks," he said.

Traditionally, long-term memories were thought to be stored at the brain's synapses, the junctions between nerve cells. Each neuron has several thousand synapses.

But Prof Glanzman said: "If memories were stored at synapses, there is no way our experiment would have worked."

The UCLA professor of integrative biology holds a different view, believing that memories are stored in the nuclei of neurons. The paper might support hints from studies conducted decades ago that RNA was involved in memory.

The type of RNA relevant to these findings is believed to regulate a variety functions in the cell involved with the development and disease.

The researchers said that the cells and molecular processes in the marine snails are similar to those in humans, despite the fact that the snail has about 20,000 neurons in its central nervous system and humans are thought to have about 100 billion.

The researchers see this result as a step towards alleviating the effects of diseases such as Alzheimer's or post traumatic stress disorder (PTSD).

When asked if this process would be conducive to the transplant of memories laid down through life experiences, Prof Glanzman was uncertain, but he expressed optimism that the greater understanding of memory storage would lead to a greater opportunity to explore different aspects of memory.

Sweeping gene survey reveals new facets of evolution

Who would have suspected that a handheld genetic test used to unmask sushi bars pawning off tilapia for tuna could deliver deep insights into evolution, including how new species emerge?

And who would have thought to trawl through five million of these gene snapshots -- called "DNA barcodes" -- collected from 100,000 animal species by hundreds of researchers around the world and deposited in the US government-run GenBank database?

That would be Mark Stoeckle from The Rockefeller University in New York and David Thaler at the University of Basel in Switzerland, who together published findings last week sure to jostle, if not overturn, more than one settled idea about how evolution unfolds.

It is textbook biology, for example, that species with large, far-flung populations -- think ants, rats, humans -- will become more genetically diverse over time.

But is that true?

"The answer is no," said Stoeckle, lead author of the study, published in the journal Human Evolution.

For the planet's 7.6 billion people, 500 million house sparrows, or 100,000 sandpipers, genetic diversity "is about the same," he told AFP.

The study's most startling result, perhaps, is that nine out of 10 species on Earth today, including humans, came into being 100,000 to 200,000 years ago.

"This conclusion is very surprising, and I fought against it as hard as I could," Thaler told AFP.

That reaction is understandable: How does one explain the fact that 90 percent of animal life, genetically speaking, is roughly the same age?

Was there some catastrophic event 200,000 years ago that nearly wiped the slate clean?

- Simpler, cheaper -

To understand the answer, one has to understand DNA barcoding. Animals have two kinds of DNA.

The one we are most familiar with, nuclear DNA, is passed down in most animals by male and female parents and contains the genetic blueprint for each individual.

The genome -- made up of DNA -- is constructed with four types of molecules arranged in pairs. In humans, there are three billion of these pairs, grouped into about 20,000 genes.

But all animals also have DNA in their mitochondria, which are the tiny structures inside each cell that convert energy from food into a form that cells can use.

Mitochondria contain 37 genes, and one of them, known as COI, is used to do DNA barcoding.

Unlike the genes in nuclear DNA, which can differ greatly from species to species, all animals have the same set of mitochondrial DNA, providing a common basis for comparison.

Mitochondrial DNA is also a lot simpler, and cheaper, to isolate.

Around 2002, Canadian molecular biologist Paul Hebert -- who coined the term "DNA barcode" -- figured out a way to identify species by analysing the COI gene.

"The mitochondrial sequence has proved perfect for this all-animal approach because it has just the right balance of two conflicting properties," said Thaler.

- 'Neutral' mutations -

On the one hand, the COI gene sequence is similar across all animals, making it easy to pick out and compare.

On the other hand, these mitochondrial snippets are different enough to be able to distinguish between each species.

"It coincides almost perfectly with species designations made by specialist experts in each animal domain," Thaler said.

In analysing the barcodes across 100,000 species, the researchers found a telltale sign showing that almost all the animals emerged about the same time as humans.

What they saw was a lack of variation in so-called "neutral" mutations, which are the slight changes in DNA across generations that neither help nor hurt an individual's chances of survival.

In other words, they were irrelevant in terms of the natural and sexual drivers of evolution.

How similar or not these "neutral" mutations are to each other is like tree rings -- they reveal the approximate age of a species.

Which brings us back to our question: why did the overwhelming majority of species in existence today emerge at about the same time?

- Darwin perplexed -

Environmental trauma is one possibility, explained Jesse Ausubel, director of the Program for the Human Environment at The Rockefeller University.

"Viruses, ice ages, successful new competitors, loss of prey -- all these may cause periods when the population of an animal drops sharply," he told AFP, commenting on the study.

"In these periods, it is easier for a genetic innovation to sweep the population and contribute to the emergence of a new species."

But the last true mass extinction event was 65.5 million years ago when a likely asteroid strike wiped out land-bound dinosaurs and half of all species on Earth. This means a population "bottleneck" is only a partial explanation at best.

"The simplest interpretation is that life is always evolving," said Stoeckle.

"It is more likely that -- at all times in evolution -- the animals alive at that point arose relatively recently."

In this view, a species only lasts a certain amount of time before it either evolves into something new or goes extinct.

And yet -- another unexpected finding from the study -- species have very clear genetic boundaries, and there's nothing much in between.

"If individuals are stars, then species are galaxies," said Thaler. "They are compact clusters in the vastness of empty sequence space."

The absence of "in-between" species is something that also perplexed Darwin, he said. 

FBI issues malware warning

The Federal Bureau of Investigation (FBI) has recommended businesses and individuals worldwide to reboot the routers at office or home to counter a malware known as "VPNFilter" that is spreading fast.

The malware affects routers and collect users' information or shut down network traffic.

According to a FBI statement, foreign cyber actors have compromised hundreds of thousands of home and office routers and other networked devices worldwide.

The actors used "VPNFilter" malware to target small office and home office routers.

"The FBI recommends any owner of small office and home office routers power cycle (reboot) the devices," the FBI said.

The malware targets routers produced by several manufacturers and network-attached storage devices by at least one manufacturer. The initial infection vector for this malware is currently unknown.

"VPNFilter is able to render small office and home office routers inoperable. The malware can potentially also collect information passing through the router. Detection and analysis of the malware's network activity is complicated by its use of encryption and misattributable networks," the FBI said.

The FBI recommended people to reboot the routers to temporarily disrupt the malware and aid the potential identification of infected devices.

"Owners are advised to consider disabling remote management settings on devices and secure with strong passwords and encryption when enabled. Network devices should be upgraded to the latest available versions of firmware," the US agency noted.

Earlier, Iran's Computer Emergency Response Team Coordination Centre issued a warning about the fast-spreading malware attack.

The attack is not limited to Iran and has impacted many computer users across the world, the centre warned.

It said it has advised the owners of many brands of routers to turn them off and on again, and download updates from the manufacturer to protect themselves.

The malware was initially detected by Cisco Systems Inc.

New material found to eliminate organic pollutants in water

A group of researchers has developed a material capable of the absorption of organic pollutants present in water. According to a study conducted by the University of Seville, two new absorbent materials have shown the capability of eliminating organic pollutants in solution in less than 24 hours.

The appearance of criteria and emerging pollutants in water is a modern theme that has caused the scientific community to research new solutions and alternatives.

Specifically, they have evaluated two types of phyllosilicates: a highly-charged expandable synthetic mica (Na-Mica-4), and one obtained from cation exchange with an organo-functionalised mica (C18-Mica-4). Phyllosilicates are a subclass of silicates and include common mineral in very different environments.

The results show that the material C18-Mica-4 is capable of eliminating the majority of pollutants that were evaluated in urban waste water, as well as surface water and potable water.

The study, also, provided data on the adsorption mechanism and establishes a significant correlation between the physical-chemical properties of the selected criteria and emerging pollutants and the adsorption to the material.

In total, 18 organic pollutants were studied, among which were industrial pollutants, personal care products, and the pharmacologically active ingredients such as anti-inflammatories, antibiotics, anti-epileptics, central nervous system stimulants and lipid-lowering agents, among others.

Within the industrial pollutants, several compounds frequently used as cleaning products were analysed, as well as others used as water- and oil-repellents. With the personal care products, two synthetic preservatives were analysed (methylparaben and propylparaben), both widely used in cosmetic and pharmaceutical products.

Lastly, nine active pharmacological ingredients were also tested (diclofenac, ibuprofen, salicylic acid, trimethoprim, carbamazepine, propranolol, caffeine, clofibric acid and gemfibrozil). Taken to achieve different therapeutic effects, these all end up polluting our waters, essentially, via human excretion. The study was carried out on untreated urban wastewater, treated urban wastewater, surface water from rivers and potable water.

"Studies like this, and others in the same line, are showing the potential of certain adsorbent materials for use in the industrial treatment of water affected by different types of pollution. Obtaining universal materials with a high elimination capacity and which can be used for a wide range of pollutants is the main goal in this area of investigation," said Esteban Alonso, the head of the research project.

The study appears in the journal Environmental Research.

New rare black holes spotted in space, evidence suggests

In a first, scientists have spotted the evidence of a rare intermediate-mass black hole - an elusive object whose existence has been hotly debated.

Scientists have been able to prove the existence of small black holes and those that are super-massive, but the existence of intermediate-mass black holes (IMBHs) was never proven.

Researchers from the University of New Hampshire (UNH) in the US found the strongest evidence to date that such middle-of-the-road black holes exist, by serendipitously capturing one in action devouring an encountering star.

"We feel very lucky to have spotted this object with a significant amount of high-quality data, which helps pinpoint the mass of the black hole and understand the nature of this spectacular event," said Dacheng Lin, a research assistant professor at UNH.

"Earlier research, including our own work, saw similar events, but they were either caught too late or were too far away," Lin said.

In the study, published in the journal Nature Astronomy, researchers used satellite imaging to detect for the first time this significant telltale sign of activity.

They found an enormous multiwavelength radiation flare from the outskirts of a distant galaxy. The brightness of the flare decayed over time exactly as expected by a star disrupting, or being devoured, by the black hole.

In this case, the star was disrupted in October 2003 and the radiation it created decayed over the next decade. The distribution of emitted photons over the energy depends on the size of the black hole.

This data provides one of the very few robust ways to weight, or determine the size of, the black hole.

Researchers used data from a trio of orbiting X-ray telescopes, NASA's Chandra X-ray Observatory and Swift Satellite as well as European Space Agency (ESA)'s XMM-Newton, to find the multiwavelength radiation flares that helped identify the otherwise uncommon IMBHs.

The characteristic of a long flare offers evidence of a star being torn apart and is known as a tidal disruption event (TDE).

Tidal forces, due to the intense gravity from the black hole, can destroy an object - such as a star - that wanders too close. During a TDE, some of the stellar debris is flung outward at high speeds, while the rest falls toward the black hole.

As it travels inward and is ingested by the black hole, the material heats up to millions of degrees and generates a distinct X-ray flare.

According to the researchers, these types of flares can easily reach the maximum luminosity and are one of the most effective ways to detect IMBHs.

"From the theory of galaxy formation, we expect a lot of wandering intermediate-mass black holes in star clusters," said Lin.

"But there are very, very few that we know of because they are normally unbelievably quiet and very hard to detect and energy bursts from encountering stars being shredded happen so rarely," he said.

Due to the very low occurrence rate of such star-triggered outbursts for an IMBH, the scientists believe that their discovery implies that there could be many IMBHs lurking in a dormant state in galaxy peripheries across the local universe.

Microplastics may enter foodchain through mosquitoes

Mosquito larvae have been observed ingesting microplastics that can be passed up the food chain, researchers said, potentially uncovering a new way that the polluting particles could damage the environment.

Microplastics — tiny plastic shards broken down from man-made products such as synthetic clothing, car tyres and contact lenses — litter much of the world’s oceans.

Hard to spot and harder to collect, they can seriously harm marine wildlife and are believed to pose a significant risk to human health as they move through the food chain and contaminate water supplies.

Now researchers of the University of Reading believe they have proof for the first time that microplastics can enter our ecosystem by air via mosquitoes and other flying insects.

The team observed mosquito larvae ingesting microscopic plastic beads — similar to the tiny plastic balls found in everyday cosmetic products — before monitoring them through their life cycle.

They found that many of the particles were transferred into the mosquitoes’ adult form, meaning whatever creatures then ate the flying insects in the wild would also ingest the plastic.

“The significance is that this is quite possibly widespread,” Amanda Callaghan, biological scientist at Reading and the lead study author, told AFP.

“We were just looking at mosquitoes as an example but there are lots of insects that live in water and have the same life-cycle with larvae that eat things in water and then emerge as adults.”

The animals known to eat such insects include several species of birds, bats and spiders, all of which are hunted in turn by other animals.

“It’s basically another pathway for pollution that hadn’t been considered previously,” Callaghan said.

Although the team observed the mosquitoes in lab conditions, she said it was “highly possible” the process was already happening in the wild.

Several countries including Britain have banned products containing microbeads, but Callaghan said the scale of the problem was still being discovered.

“It’s a major problem and those plastics already in the environment are going to be with us for a very, very long time,” she said.

Mercury mission to explore origin of Solar System

Is Mercury's core liquid or solid, and why -- on the smallest planet in our solar system -- is it so big? What can the planet closest to the Sun tell us about how our solar system came into being?

An unmanned European-Japanese space mission, dubbed BepiColombo, blasted off early Saturday morning from French Guiana, to probe these and other mysteries.

"BepiColombo is coming like a white knight with better and more precise data," said Alain Doressoundiram, an astronomer at the Paris Observatory.

"To understand how Earth was formed, we need to understand how all rocky planets formed," including Venus and Mars, he told AFP.

"Mercury stands apart and we don't know why."

First, however, the suite of instruments on board the Ariane 5 rocket will have to travel seven years and nine million kilometres (5.6 million miles) to reach their destination.

In a statement after the launch, ArianeGroup said the satellite had successfully escaped Earth's gravity field and was beginning its long journey where it will reach speeds of up to 40,000 kilometres (25,000 miles) an hour.

According to Pierre Bousquet, an engineer at France's National Centre for Space Research and head of the French team contributing to the mission, Mercury is "abnormally small," leading to speculation that it survived a massive collision in its youth.

"A huge crater visible on its surface could be the scar left over from that encounter," Bousquet told AFP. Finding out if this is true is on BepiColombo's "to do" list.

Going hot and cold

This scenario would explain why Mercury's core accounts for a whopping 55 percent of its mass, compared to 30 per cent for Earth.

Mercury is also the only rocky planet orbiting the Sun beside our own to have a magnetic field.

Magnetic fields are generated by a liquid core but given its size, Mercury's should have grown cold and solid by now, as did Mars.

This anomaly might be due to some feature of the core's composition, something BepiColombo's instruments will measure with much greater precision than has been possible so far.

On its surface, Mercury is a planet of extremes, vacillating between hot days of about 430 degrees Celsius (more than 800 degrees Fahrenheit) to super-frosty nights of minus 180C (minus 290F).

Those days and nights last nearly three Earth months each.

Earlier missions have detected evidence of ice in the deepest recesses of the planet's polar craters.

Scientists speculate that this may have accumulated from comets crashing onto Mercury's surface.

"If the presence of ice is confirmed, it means that some of those water samples date back nearly to the origin of the solar system," Doressoundiram said.

Lashed by solar winds

Mercury is 58 million kilometres (36 million miles) from the Sun, nearly three times closer than Earth.

"The planet is whipped by solar winds," a constant torrent of ionised particles bombarding the surface at 500 kilometres per second, said Bousquet.

The scientists will be able to study the impact of these winds -- 10 times stronger than the ones hitting Earth's atmosphere -- on Mercury's magnetic field.

The BepiColombo mission will deploy two spacecraft. The Mercury Planet Orbiter, built by ESA, will investigate planet's surface and interior composition.

The Mercury Magnetospheric Orbiter, made by the Japan Aerospace Exploration Agency, will study the region of space around the planet that is influenced by its magnetic field.

The mission will also look for tectonic activity, and seek to understand why spectroscopic observations show no iron even if it is thought to be one of the planet's major component elements.

Compared to Mars, Venus, and Saturn, Mercury has barely been explored. Only two spacecraft have ever paid it a visit.

NASA's Mariner 10 did three flybys in 1974 and 1975, providing the first up-close images. More than 30 years later, NASA's Messenger did the same, before settling into orbit around Mercury in 2011.

The new mission is named after Giuseppe (Bepi) Colombo, a brilliant Italian mathematician and engineer who first understood the relationship between Mercury's rotation and orbit.