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Cloaked DNA nanodevices evade immune system detection

Cloaked DNA nanodevices evade immune system detection | Amazing Science | Scoop.it

An enveloped virus (left) coats itself with lipid as part of its life cycle. New lipid-coated DNA nanodevices (right) closely resemble those viruses and evade.


Scientists at Harvard’s Wyss Institute for Biologically Inspired Engineering have built the first DNA nanodevices that survive the body’s immune defenses.


The results pave the way for smart DNA nanorobots that could use logic to diagnose cancer earlier and more accurately than doctors can today, target drugs to tumors, or even manufacture drugs on the spot to cripple cancer, the researchers report in the April 22 online issue of ACS Nano.


“We’re mimicking virus functionality to eventually build therapeutics that specifically target cells,” said Wyss Institute Core Faculty member William Shih, Ph.D., the paper’s senior author. Shih is also an Associate Professor of Biological Chemistry and Molecular Pharmacology at Harvard Medical School and Associate Professor of Cancer Biology at the Dana-Farber Cancer Institute.


The same cloaking strategy could also be used to make artificial microscopic containers called protocells that could act as biosensors to detect pathogens in food or toxic chemicals in drinking water.


DNA is well known for carrying genetic information, but Shih and other bioengineers are using it instead as a building material. To do this, they use DNA origami — a method Shih helped extend from 2D to 3D. In this method, scientists take a long strand of DNA and program it to fold into specific shapes, much as a single sheet of paper is folded to create various shapes in the traditional Japanese art.


Shih’s team assembles these shapes to build DNA nanoscale devices that might one day be as complex as the molecular machinery found in cells. For example, they are developing methods to build DNA into tiny robots that sense their environment, calculate how to respond, then carry out a useful task, such as performing a chemical reaction or generating mechanical force or movement.


In 2012 Wyss Institute researchers reported in Science that they had built a nanorobot that uses logic to detect a target cell, then reveals an antibody that activates a “suicide switch” in leukemia or lymphoma cells.

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Carlos Garcia Pando's comment, April 26, 2014 4:10 AM
This might also be used as a powerful and controlled weapon against individuals or groups (ethnic selection, or just other type of genetic or environmental factors). Very dangerous.
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Using static electricity, RoboBees can land and stick to surfaces | Harvard John A. Paulson School of Engineering and Applied Sciences

Using static electricity, RoboBees can land and stick to surfaces | Harvard John A. Paulson School of Engineering and Applied Sciences | Amazing Science | Scoop.it

New system extends the lives of flying microrobots.

 

Call them the RoboBats. In a recent article in Science, Harvard roboticists demonstrate that their flying microrobots, nicknamed the RoboBees, can now perch during flight to save energy -- like bats, birds or butterflies.

 

"Many applications for small drones require them to stay in the air for extended periods," said Moritz Graule, first author of the paper who conducted this research as a student at the Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS) and Wyss Institute for Biologically Inspired Engineering at Harvard University. "Unfortunately, smaller drones run out of energy quickly. We want to keep them aloft longer without requiring too much additional energy." The team found inspiration in nature and simple science.

 

"A lot of different animals use perching to conserve energy," said Kevin Ma, a post-doc at SEAS and the Wyss Institute and coauthor. "But the methods they use to perch, like sticky adhesives or latching with talons, are inappropriate for a paperclip-size microrobot, as they either require intricate systems with moving parts or high forces for detachment."

 

Instead, the team turned to electrostatic adhesion -- the same basic science that causes a static-charged sock to cling to a pants leg or a balloon to stick to a wall.

 

When you rub a balloon on a wool sweater, the balloon becomes negatively charged. If the charged balloon is brought close to a wall, that negative charge forces some of the wall's electrons away, leaving the surface positively charged. The attraction between opposite charges then causes the balloon to stick to the wall.

 

"In the case of the balloon, however, the charges dissipate over time, and the balloon will eventually fall down," said Graule. "In our system, a small amount of energy is constantly supplied to maintain the attraction."

 

The RoboBee, pioneered at the Harvard Microrobotics Lab, uses an electrode patch and a foam mount that absorbs shock. The entire mechanism weighs 13.4 mg, bringing the total weight of the robot to about 100mg -- similar to the weight of a real bee. The robot takes off and flies normally. When the electrode patch is supplied with a charge, it can stick to almost any surface, from glass to wood to a leaf. To detach, the power supply is simply switched off.

 

"One of the biggest advantages of this system is that it doesn't cause destabilizing forces during disengagement, which is crucial for a robot as small and delicate as ours," said Graule.

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Icy objects in our solar system have large oceans under their surfaces

Icy objects in our solar system have large oceans under their surfaces | Amazing Science | Scoop.it

Icy objects in our solar system have large oceans under their surfaces and here life could evolve and flourish. So says a new thesis by Jesper Lindkvist, PhD student at the Swedish Institute of Space Physics and Umeå University. The thesis will be defended on Tuesday 31 May at the Swedish Institute of Space Physics in Kiruna, Sweden.

 

There has long been speculation as to whether Jupiter's large, icy moon Callisto has an ocean beneath its surface. Observations of Callisto's near-space environment by instruments on board the spacecraft Galileo, which is orbiting Jupiter, lead us to believe that there is such a sub-surface ocean. Computer simulations of the space plasma interactions support this belief. "If you find an ocean beneath the surface of one moon, perhaps the same is true of other icy objects in space," says Jesper Lindkvist.

 

Outflow of water vapor has been detected from the surface of the dwarf planet Ceres, which is in the asteroid belt between Mars and Jupiter. This could indicate a reservoir of water, also related to a large sea beneath the surface. The spacecraft Dawn is at Ceres right now, trying to answer this question. "If someone was planning to build a future space base on one of these Solar System objects, for example to seek after signs of life, I would suggest they take an extra long ice bore and their fishing equipment," jokes Jesper Lindkvist.

 

The outflow of water vapor from moons and dwarf planets is similar to that we see from comets. The icy comet 67/Churyumov-Gerasimenko which rounded the sun in the summer of 2015 has been followed closely by the European spacecraft Rosetta. Measurements of the space environment round it show that the water flowing out from the comet's nucleus forms a prominent atmosphere which interacts with the constant flow of ionized particles from the sun, the so-called solar wind.

"Understanding their origin and how icy bodies evolve is one more piece of the puzzle we need to lay in order to explain the origin of our Solar System and its eventual fate," says Jesper Lindkvist.

 

Jesper Lindkvist comes from the town of Vidsel in Northern Sweden. He has a Masters degree in engineering physics from Luleå University of Technology.

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Scientists create 'rewritable magnetic charge ice'

Scientists create 'rewritable magnetic charge ice' | Amazing Science | Scoop.it

A team of scientists working at the U.S. Department of Energy's (DOE) Argonne National Laboratory and led by Northern Illinois University physicist and Argonne materials scientist Zhili Xiao has created a new material, called "rewritable magnetic charge ice," that permits an unprecedented degree of control over local magnetic fields and could pave the way for new computing technologies.

 

The scientists' research report on development of magnetic charge ice is published in the May 20, 2016 issue of the journal Science. With potential applications involving data storage, memory and logic devices, magnetic charge ice could someday lead to smaller and more powerful computers or even play a role in quantum computing, Xiao said. Current magnetic storage and recording devices, such as computer hard disks, contain nanomagnets with two polarities, each of which is used to represent either 0 or 1 -- the binary digits, or bits, used in computers. A magnetic charge ice system could have eight possible configurations instead of two, resulting in denser storage capabilities or added functionality unavailable in current technologies.

 

"Our work is the first success achieving an artificial ice of magnetic charges with controllable energy states," said Xiao, who holds a joint appointment between Argonne and NIU. "Our realization of tunable artificial magnetic charge ices is similar to the synthesis of a dreamed material. It provides versatile platforms to advance our knowledge about artificial spin ices, to discover new physics phenomena and to achieve desired functionalities for applications."

 

Over the past decade, scientists have been highly interested in creating, investigating and attempting to manipulate the unusual properties of "artificial spin ices," so-called because the spins have a lattice structure that follows the proton positioning ordering found in water ice.

 

Scientists consider artificial spin ices to be scientific playgrounds, where the mysteries of magnetism might be explored and revealed. However, in the past, researchers have been frustrated in their attempts to achieve global and local control of spin-ice magnetic charges.

 

To overcome this challenge, Xiao and his colleagues decoupled the lattice structure of magnetic spins and the magnetic charges. The scientists used a bi-axis vector magnet to precisely and conveniently tune the magnetic charge ice to any of eight possible charge configurations. They then used a magnetic force microscope to demonstrate the material's local write-read-erase multi-functionality at room temperature. For example, using a specially developed patterning technique, they wrote the word, "ICE," on the material in a physical space 10 times smaller than the diameter of a human hair.

 

Magnetic charge ice is two-dimensional, meaning it consists of a very thin layer of atoms, and could be applied to other thin materials, such as graphene. Xiao said the material also is environmentally friendly and relatively inexpensive to produce.

 

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Making Virus Sensors Cheap and Simple: New Method Detects Single Viruses

Making Virus Sensors Cheap and Simple: New Method Detects Single Viruses | Amazing Science | Scoop.it

Although the technique presently works on just one virus, scientists say it could be adapted to detect a range of viruses that plague humans including Ebola, Zika and HIV.

 

"The ultimate goal is to build a cheap, easy-to-use device to take into the field and measure the presence of a virus like Ebola in people on the spot," says Jeffrey Dick, a chemistry graduate student and co-lead author of the study. "While we are still pretty far from this, this work is a leap in the right direction."

 

The new method is highly specific, meaning it is only sensitive to one type of virus, filtering out possible false negatives caused by other viruses or contaminants. There are two other commonly used methods for detecting viruses in biological samples, but they have drawbacks. One requires a much higher concentration of viruses, and the other requires samples to be purified to remove contaminants. The new method, however, can be used with urine straight from a person or animal.

 

The researchers demonstrated their new technique on a virus that belongs to the herpesvirus family, called murine cytomegalovirus (MCMV). To detect individual viruses, the team places an electrode — a wire that conducts electricity, in this case, one that is thinner than a human cell — in a sample of mouse urine. They then add to the urine some special molecules made up of enzymes and antibodies that naturally stick to the virus of interest. When all three stick together and then bump into the electrode, there's a spike in electric current that can be easily detected.

 

The researchers say their new method still needs refinement. For example, the electrodes become less sensitive over time because a host of other naturally occurring compounds stick to them, leaving less surface area for viruses to interact with them. To be practical, the process will also need to be engineered into a compact and rugged device that can operate in a range of real-world environments.

 

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ppGpp preserves DNA integrity in bacteria despite assault from antibiotics

ppGpp preserves DNA integrity in bacteria despite assault from antibiotics | Amazing Science | Scoop.it

A key biochemical enables bacteria to repair otherwise fatal damage to their DNA, including that caused by antibiotics. That is the finding of a study.

 

Adjusting the action of a molecule called ppGpp (guanosine-3',5'-(bis)pyrophosphate), with future treatments may disable DNA repair in microbes to make them many times more vulnerable to existing antibiotics, say the study authors. Bacteria repeatedly exposed to the same drugs become resistant to treatment, according to the Centers for Disease Control and Prevention, with related infections linked to 23,000 deaths and 2 million illnesses each year in the United States.

 

"Most antibiotics have their effect, directly or indirectly, by causing damage to bacterial DNA, so finding ways to cripple DNA repair would represent a significant advance in the treatment of resistant infections," says senior study author Evgeny Nudler, PhD, the Julie Wilson Anderson Professor of Biochemistry, Department of Biochemistry and Molecular Pharmacology, NYU Langone.

 

"While reducing DNA repair in bacteria could help to overcome antibiotic resistance, we're also excited about the prospect of boosting DNA repair in human cells," says Nudler, also an investigator with the Howard Hughes Medical Institute. "DNA damage accumulates with age and creates risk for degenerative diseases from Alzheimer's to cancer."

 

The study results revolve around the delicacy of DNA molecules, the letters making up the genetic code. Experts estimate that DNA is damaged thousands of times an hour in each bacterial cell, and perhaps a million times a day in a human cell with larger, more complicated DNA chains. Sunlight and toxins do much of the damage, but the biggest culprit may be highly reactive byproducts created as cells use oxygen to turn sugar into energy.

 

Given that damaged DNA can result in lethal mistakes in the building of proteins that comprise vital structures and messages, cells evolved early on to have overlapping, split-second DNA repair mechanisms.

 

In both humans and the bacteria, a key protein complex called RNA polymerase clamps onto and ticks down the DNA chain, reading the code of DNA "letters" as it translates genetic instructions into intermediary RNA molecules on the way to building proteins. Studies in recent years have revealed that the RNA polymerase in bacteria also inspects the DNA chain for damage as it reads.

 

In 1997, Nudler and colleagues published a paper in Cell that found bacterial RNA polymerase, which moves down the DNA chain in one direction during normal reading, instead stops and slips backward in some instances - a process Nudler called backtracking. If RNA polymerase encounters a lesion in DNA, the theory went, backtracking could make room for repair enzymes to fly in, cut out the damaged section, and rebuild a normal chain in a process called nucleotide excision DNA repair (NER).

 

Indeed, in 2014, Nudler's team published work in Nature that found the NER enzyme UvrD causes RNA polymerase to backtrack in the bacterial species E. coli. The newly published paper identifies ppGpp (guanosine-3',5'-(bis)pyrophosphate), a compound related in structure to the guanine building block of DNA, as the central controller of UvrD-driven backtracking in the NER pathway. Levels of ppGpp rise rapidly as bacterial RNA polymerase encounters damage and backtracks, then drop as soon as the chain is repaired to return RNA polymerase to normal transcription. The study authors conclude that ppGpp is the sensor that enables RNA polymerase to shift back and forth between DNA transcription and repair, coupling the two processes in bacteria.

 

Bacteria must be able to repair DNA and preserve their genomic integrity to survive, so targeting this ability is sound strategy for drug development, says Nudler. In seeking to translate this work into new treatments that defeat antibiotic resistance, he says, the field needs to determine whether or not RNA polymerase directly communicates with enzymes that produce ppGpp, and if they do, to design specific inhibitors against them.

 

Researchers also hope to soon confirm that RNA polymerase backtracking enables related forms of DNA repair in human cells as theorized, an important step toward boosting human DNA repair in the future.

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Duke's Poliovirus Oncolytic Therapy Wins "Breakthrough" Status

Duke's Poliovirus Oncolytic Therapy Wins "Breakthrough" Status | Amazing Science | Scoop.it

The recombinant poliovirus therapy developed at the Preston Robert Tisch Brain Tumor Center at Duke Health has been granted “breakthrough therapy designation” from the U.S. Food and Drug Administration.

 

Duke’s poliovirus therapy is an immunotherapy developed in the laboratory of Matthias Gromeier, M.D., a professor in the departments of Neurosurgery, Molecular Genetics and Microbiology, and Medicine at Duke University School of Medicine. 

 

Using a modified form of poliovirus that has been altered to eliminate harm, the therapy preferentially attacks cancer cells, which have an abundance of receptors that work like magnets to attract the poliovirus. The modified poliovirus then kills the infected tumor cells while also igniting an additional immune response.

 

A phase I clinical trial using the therapy was launched in 2012 to determine an optimal dose of the novel treatment among adult patients with glioblastoma whose cancer had returned after receiving traditional therapy.

 

Early testing found that lower doses of the treatment were superior to higher doses. Of 23 glioblastoma patients enrolled at the optimal dose level, 15 are still alive and enrollment is ongoing. Three patients treated early using different dosages are still alive more than 36 months after treatment. With current standard therapy, the median survival time for people with glioblastoma is 14.6 months. 

 

The Duke team is moving to expand its work and open a clinical trial for children with brain tumors, which is expected to begin enrollment before year’s end. The researchers have also received federal grants to explore the therapy’s effect on solid tumors. Laboratory studies are already underway in breast cancer models.


Via Krishan Maggon
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Genome Sequencing Reveals Differences Between Giraffes and Ocapi

Genome Sequencing Reveals Differences Between Giraffes and Ocapi | Amazing Science | Scoop.it

Scientists spot mutations that could explain how giraffes became the world’s tallest living mammals.

 

Call it a tall task: researchers have decoded the genomes of the giraffe and its closest relative, the okapi. The sequences, published on May 17 in Nature Communications, reveal clues to the age-old mystery of how the giraffe evolved its unusually long neck and legs.

 

Researchers in the United States and Tanzania analyzed the genetic material of two Masai giraffes (Giraffa camelopardalis tippelskirchi) from the Masai Mara National Reserve in Kenya, one at the Nashville Zoo in Tennessee and an okapi fetus (Okapia johnstoni) from the White Oak Conservation Center in Yulee, Florida.

 

“This is one more wonderful demonstration of the power of comparative genomics to connect the evolution of animal species on this planet to molecular events that we know must underpin the extraordinary diversity of life on this planet,” says David Haussler, director of the Genomics Institute at the University of California, Santa Cruz.

 

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The gene hunters 

The gene hunters  | Amazing Science | Scoop.it

Criss-crossing the globe on a quest for unusual DNA, researchers have discovered a rare mutation that promises insights into both epilepsy and autism — and points to a treatment.


Via Integrated DNA Technologies
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Disney’s VertiGo Combines Car, Helicopter to Seemingly Defy Gravity

Disney’s VertiGo Combines Car, Helicopter to Seemingly Defy Gravity | Amazing Science | Scoop.it

From Disney and ETH Zurich, this steam-punkish robot can transition from ground to wall and back again.

 

VertiGo is a wall-climbing robot that is capable of transitioning from the ground to the wall, created in collaboration between Disney Research Zurich and ETH. The robot has two tiltable propellers that provide thrust onto the wall, and four wheels. One pair of wheels is steerable, and each propeller has two degrees of freedom for adjusting the direction of thrust. By transitioning from the ground to a wall and back again, VertiGo extends the ability of robots to travel through urban and indoor environments. The robot is able to move on a wall quickly and with agility. The use of propellers to provide thrust onto the wall ensures that the robot is able to traverse over indentations such as masonry. The choice of two propellers rather than one enables a floor-to-wall transition – thrust is applied both towards the wall using the rear propeller, and in an upward direction using the front propeller, resulting in a flip onto the wall.

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'Virtual partner' elicits emotional responses from a human partner in real-time

'Virtual partner' elicits emotional responses from a human partner in real-time | Amazing Science | Scoop.it

Can machines think? That's what renowned mathematician Alan Turing sought to understand back in the 1950s when he created an imitation game to find out if a human interrogator could tell a human from a machine based solely on conversation deprived of physical cues. The Turing test was introduced to determine a machine's ability to show intelligent behavior that is equivalent to or even indistinguishable from that of a human. Turing mainly cared about whether machines could match up to humans' intellectual capacities.

 

But there is more to being human than intellectual prowess, so researchers from the Center for Complex Systems and Brain Sciences (CCSBS) in the Charles E. Schmidt College of Science at Florida Atlantic University set out to answer the question: "How does it 'feel' to interact behaviorally with a machine?"

 

They created the equivalent of an "emotional" Turing test, and developed a virtual partner that is able to elicit emotional responses from its human partner while the pair engages in behavioral coordination in real-time.

 

Results of the study, titled "Enhanced Emotional Responses during Social Coordination with a Virtual Partner," are recently published in the International Journal of Psychophysiology. The researchers designed the virtual partner so that its behavior is governed by mathematical models of human-to-human interactions in a way that enables humans to interact with the mathematical description of their social selves.

 

"Our study shows that humans exhibited greater emotional arousal when they thought the virtual partner was a human and not a machine, even though in all cases, it was a machine that they were interacting with," said Mengsen Zhang, lead author and a Ph.D. student in FAU's CCSBS. "Maybe we can think of intelligence in terms of coordinated motion within and between brains."

 

The virtual partner is a key part of a paradigm developed at FAU called the Human Dynamic Clamp -- a state-of-the-art human machine interface technology that allows humans to interact with a computational model that behaves very much like humans themselves. In simple experiments, the model -- on receiving input from human movement -- drives an image of a moving hand which is displayed on a video screen. To complete the reciprocal coupling, the subject sees and coordinates with the moving image as if it were a real person observed through a video circuit. This social "surrogate" can be precisely tuned and controlled -- both by the experimenter and by the input from the human subject.

 

"The behaviors that gave rise to that distinctive emotional arousal were simple finger movements, not events like facial expressions for example, known to convey emotion," said Emmanuelle Tognoli, Ph.D., co-author and associate research professor in FAU's CCSBS. "So the findings are rather startling at first."

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Hunting for hidden life on worlds orbiting old, red stars

Hunting for hidden life on worlds orbiting old, red stars | Amazing Science | Scoop.it

All throughout the universe, there are stars in varying phases and ages. The oldest detected Kepler planets (exoplanets found using NASA's Kepler telescope) are about 11 billion years old, and the planetary diversity suggests that around other stars, such initially frozen worlds could be the size of Earth and could even provide habitable conditions once the star becomes older. Astronomers usually looked at middle-aged stars like our sun, but to find habitable worlds, one needs to look around stars of all ages.

 

In their work, Ramses M. Ramirez, research associate at Cornell's Carl Sagan Institute and Lisa Kaltenegger, associate professor of astronomy and director of the Carl Sagan Institute, have modeled the locations of the habitable zones for aging stars and how long planets can stay in it. Their research, "Habitable Zones of Post-Main Sequence Stars," is published in the Astrophysical Journal May 16.

 

The "habitable zone" is the region around a star in which water on a planet's surface is liquid and signs of life can be remotely detected by telescopes.

 

"When a star ages and brightens, the habitable zone moves outward and you're basically giving a second wind to a planetary system," said Ramirez. "Currently objects in these outer regions are frozen in our own solar system, and Europa and Enceladus -- moons orbiting Jupiter and Saturn -- are icy for now."

 

Dependent upon the mass (weight) of the original star, planets and their moons loiter in this red giant habitable zone up to 9 billion years. Earth, for example, has been in our sun's habitable zone so far for about 4.5 billion years, and it has teemed with changing iterations of life. However, in a few billion years our sun will become a red giant, engulfing Mercury and Venus, turning Earth and Mars into sizzling rocky planets, and warming distant worlds like Jupiter, Saturn and Neptune -- and their moons -- in a newly established red giant habitable zone.

 

"Long after our own plain yellow sun expands to become a red giant star and turns Earth into a sizzling hot wasteland, there are still regions in our solar system -- and other solar systems as well -- where life might thrive," says Kaltenegger.

 

"For stars that are like our sun, but older, such thawed planets could stay warm up to half a billion years in the red giant habitable zone. That's no small amount of time," said Ramirez, who is the lead author of the study.

"In the far future, such worlds could become habitable around small red suns for billions of years, maybe even starting life, just like Earth. That makes me very optimistic for the chances for life in the long run," said Kaltenegger.

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This AI can recreate Nobel Prize-winning experiments

This AI can recreate Nobel Prize-winning experiments | Amazing Science | Scoop.it

Artificial intelligence developed by a group of Australian research teams has replicated a complex experiment which won the Nobel Prize for Physics in 2001. The intelligent machine learned how to run a Bose-Einstein condensation – isolating an extremely cold gas inside a beam of laser light – in under an hour, something the team "didn't expect". Results have been published in the Scientific Reports journal. The algorithm has also been uploaded to GitHub for other researchers working on "quantum experiments".

 

"A simple computer program would have taken longer than the age of the universe to run through all the combinations and work this out," said Paul Wigley, co-lead researcher of the study and professor at the School of Physics and Engineering at the Australian National University.

 

The gas was cooled to 1 microkelvin before the artificial intelligence was "handed control" of three laser beams in which to trap the gas. It also did things that "surprised" the team.

 

"It did things a person wouldn't guess – such as changing one laser's power up and down and compensating with another," said Wigley. "It may be able to come up with complicated ways humans haven't thought of to get experiments colder and more precise".

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Most compelling climate change visualization

Most compelling climate change visualization | Amazing Science | Scoop.it
Ed Hawkins, a climate scientist at the National Center for Atmospheric Science at the University of Reading, devised the spiral animation to show how global average surface temperatures are increasing relative to the average temperature during preindustrial times.
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No sex gene triggers asexual reproduction in moss

No sex gene triggers asexual reproduction in moss | Amazing Science | Scoop.it

When a sperm and an egg cell merge a new life begins. This is the case in humans and in animals, but in principle also in plants. A German-Israeli team led by the biologists Professor Ralf Reski from Freiburg and Professor Nir Ohad from Tel-Aviv has discovered a gene trigger in the moss Physcomitrella patens which leads to offspring without fertilization. The researchers assume that this mechanism is conserved in evolution and holds the key to answer fundamental questions in biology. The study is published in the journal “Nature Plants”.

„Just like humans and animals, mosses possess egg cells and motile sperm. That is why they are particularly well-suited to answer fundamental questions in biology”, Reski says. After fusion of sperm and egg cell, a network of genes is activated. That leads to the development of an embryo which grows into a new living being. Until now it was unclear whether a central genetic switch for this gene activation exists. In their latest publication the team describes the gene BELL1 as a master regulator for the formation of embryos and their development in Physcomitrella. After the researchers activated this gene in the plants by genetic engineering, embryos developed spontaneously on a specific cell type. These embryos grew to fully functional moss sporophytes. These spore capsules could even form spores, which grew into new moss plants. Thus, the team identified BELL1 as a master regulator for embryo development in mosses.

The protein encoded by this gene belongs to the class of so-called homeobox transcription factors. Similar homeotic genes are also present in humans and animals, where they also control pivotal developmental processes. Whether a congener of BELL1 is a master regulator of embryo development in humans is not yet known. “Our results are important beyond mosses”, Reski says. “On the one hand they can explain how algae developed into land plants and thus shaped our current ecosystems. Secondly, they may help to revive the concept of genetic master regulators in the development of plants, animals and humans.” Ohad explains, “Moreover, our results may help to modernize agriculture through the creation of genetically identical offspring from high-yielding crop plants. In seed plants such offsprings are formed by parthenogenesis or apomixis.”

Ralf Reski from the University of Freiburg is a specialist in moss research and has helped to develop Physcomitrella as a model organism for biology and biotechnology at a world-wide scale. Nir Ohad from Tel-Aviv University is a specialist in the epigenetic regulation of reproductive development. He helped to identify the first BELL genes in seed plants about 20 years ago as member of a team led by Professor Robert Fischer from UC Berkeley. Research was supported by the German-Israeli Foundation GIF, the Freiburg Excellence Cluster BIOSS and the Freiburg Institute for Advanced Studies.

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Robots Get Creative To Cut Through Clutter

Robots Get Creative To Cut Through Clutter | Amazing Science | Scoop.it

Clutter is a special challenge for robots, but new Carnegie Mellon University software is helping robots cope, whether they're beating a path across the Moon or grabbing a milk jug from the back of the refrigerator.

 

The software not only helped a robot deal efficiently with clutter, it surprisingly revealed the robot's creativity in solving problems.

"It was exploiting sort of superhuman capabilities," Siddhartha Srinivasa, associate professor of robotics, said of his lab's two-armed mobile robot, the Home Exploring Robot Butler, or HERB. "The robot's wrist has a 270-degree range, which led to behaviors we didn't expect. Sometimes, we're blinded by our own anthropomorphism." In one case, the robot used the crook of its arm to cradle an object to be moved. "We never taught it that," Srinivasa added.

 

The rearrangement planner software was developed in Srinivasa's lab by Jennifer King, a Ph.D. student in robotics, and Marco Cognetti, a Ph.D. student at Sapienza University of Rome who spent six months in Srinivasa's lab. They will present their findings May 19 at the IEEE International Conference on Robotics and Automation in Stockholm, Sweden. In addition to HERB, the software was tested on NASA's KRex robot, which is being designed to traverse the lunar surface. While HERB focused on clutter typical of a home, KRex used the software to find traversable paths across an obstacle-filled landscape while pushing an object.

 

Robots are adept at "pick-and-place" (P&P) processes, picking up an object in a specified place and putting it down at another specified place. Srinivasa said this has great applications in places where clutter isn't a problem, such as factory production lines. But that's not what robots encounter when they land on distant planets or, when "helpmate" robots eventually land in people's homes.

 

P&P simply doesn't scale up in a world full of clutter. When a person reaches for a milk carton in a refrigerator, he doesn't necessarily move every other item out of the way. Rather, a person might move an item or two, while shoving others out of the way as the carton is pulled out.

 

The rearrangement planner automatically finds a balance between the two strategies, Srinivasa said, based on the robot's progress on its task. The robot is programmed to understand the basic physics of its world, so it has some idea of what can be pushed, lifted or stepped on. And it can be taught to pay attention to items that might be valuable or delicate, in case it must extricate a bull from a china shop.

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Astronomers confirm faintest early-universe galaxy ever seen

Astronomers confirm faintest early-universe galaxy ever seen | Amazing Science | Scoop.it

An international team of scientists, including two professors and three graduate students from UCLA, has detected and confirmed the faintest early-universe galaxy ever. Using the W. M. Keck Observatory on the summit on Mauna Kea in Hawaii, the researchers detected the galaxy as it was 13 billion years ago. The results were published in the Astrophysical Journal Letters.

 

Tommaso Treu, a professor of physics and astronomy in the UCLA College and a co-author of the research, said the discovery could be a step toward unraveling one of the biggest mysteries in astronomy: how a period known as the "cosmic dark ages" ended.

 

The researchers made the discovery using an effect called gravitational lensing to see the incredibly faint object, which was born just after the Big Bang. Gravitational lensing was first predicted by Albert Einstein almost a century ago; the effect is similar to that of an image behind a glass lens appearing distorted because of how the lens bends light. The detected galaxy was behind a galaxy cluster known as MACS2129.4-0741, which is massive enough to create three different images of the galaxy.

 

According to the Big Bang theory, the universe cooled as it expanded. As that happened, Treu said, protons captured electrons to form hydrogen atoms, which in turn made the universe opaque to radiation -- giving rise to the cosmic dark ages.

 

"At some point, a few hundred million years later, the first stars formed and they started to produce ultraviolet light capable of ionizing hydrogen," Treu said. "Eventually, when there were enough stars, they might have been able to ionize all of the intergalactic hydrogen and create the universe as we see it now."

 

That process, called cosmic reionization, happened about 13 billion years ago, but scientists have so far been unable to determine whether there were enough stars to do it or whether more exotic sources, like gas falling onto supermassive black holes, might have been responsible.

 

"Currently, the most likely suspect is stars within faint galaxies that are too faint to see with our telescopes without gravitational lensing magnification," Treu said. "This study exploits gravitational lensing to demonstrate that such galaxies exist, and is thus an important step toward solving this mystery."

 

The research team was led by Marusa Bradac, a professor at UC Davis. Co-authors include Matthew Malkan, a UCLA professor of physics and astronomy, and UCLA graduate students Charlotte Mason, Takahiro Morishita and Xin Wang.

The galaxy's magnified spectra were detected independently by both Keck Observatory and Hubble Space Telescope data.

 

 

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Shedding light on the 'dark matter' of the genome

Shedding light on the 'dark matter' of the genome | Amazing Science | Scoop.it

What used to be dismissed by many as "junk DNA" is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs)—genome's messages that do not code for proteins—in development and disease formation. But our progress in understanding these molecules has been slow because of the lack of technologies that allow the systematic mapping of their functions.

 

Now, Professor Benjamin Blencowe's team at the University of Toronto's Donnelly Centre, including lead authors Eesha Sharma and Tim Sterne-Weiler, have developed a method, described in May 19, 2016 issue of Molecular Cell, that enables scientists to explore in depth what ncRNAs do in human cells. The study is published on the same day with two other papers in Molecular Cell and Cell, respectively, from Dr. Yue Wan's group at the Genome Institute of Singapore and Dr. Howard Chang's group at Stanford University in California, who developed similar methods to study RNAs in different organisms.

 

Of the 3 billion letters in the human genome, only two per cent make up the protein-coding genes. The genes are copied, or transcribed, into messenger RNA (mRNA) molecules, which provide templates for building proteins that do most of the work in the cell. Much of the remaining 98 per cent of the genome was initially considered by some as lacking in functional importance. However, large swaths of the non coding genome—between half and three quarters of it—are also copied into RNA.

 

What the resulting ncRNAs might do depends on whom you ask. Some researchers believe that most ncRNAs have no function, that they are just a by-product of the genome's powerful transcription machinery that makes mRNA. However, it is emerging that many ncRNAs have important roles in gene regulation. This view is supported in that some ncRNAs act as carriages for shuttling the mRNAs around the cell, or provide a scaffold for other proteins and RNAs to attach to and do their jobs.

 

But the majority of available data has trickled in piecemeal or through serendipitous discovery. And with emerging evidence that ncRNAs could drive disease progression, such as cancer metastasis, there was a great need for a technology that would allow a systematic functional analysis of ncRNAs.

 

"Up until now, with existing methods, you had to know what you are looking for because they all require you to have some information about the RNA of interest. The power of our method is that you don't need to preselect your candidates, you can see what's occurring globally in cells, and use that information to look at interesting things we have not seen before and how they are affecting biology," says Eesha Sharma, a PhD candidate in Blencowe's group who, along with postdoctoral fellow Tim Sterne-Weiler, co-developed the method.

 

The new tool, called 'LIGR-Seq', captures interactions between different RNA molecules. When two RNA molecules have matching sequences - strings of letters copied from the DNA blueprint - they will stick together like Velcro. The paired RNA structures are then removed from cells and analyzed by state-of-the-art sequencing methods to precisely identify the RNAs that are stuck together. "Most researchers in the life sciences agree that there's an urgent need to understand what ncRNAs do. This technology will open the door to developing a new understanding of ncRNA function," says Blencowe, who is also a professor in the Department of Molecular Genetics.

 

Not having to rely on pre-existing knowledge is one strength of the method that will boost the discovery of RNA pairs that have never been seen before. The other is that scientists can for the first time look at RNA interactions as they occur in living cells, in all their complexity, unlike in the juices of mashed up cells that they had to rely on before. This is a bit like moving on to explore marine biology from collecting shells on the beach to scuba-diving among the coral reefs where the scope for discovery is so much bigger.

ncRNAs come in multiple flavours: there's rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA's place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control what goes on in the cell, nor how they do this. The new technology developed by Blencowe's group has been able to pick up new interactions involving all classes of RNAs and has already revealed some unexpected findings.

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With a few skin cells, scientists can make mini, thinking version of your brain

With a few skin cells, scientists can make mini, thinking version of your brain | Amazing Science | Scoop.it

Tiny, rolling balls of brain cells knocking around in a lab may one day help keep you from losing your marbles—among other things.

The small cellular balls act like mini-brains, mimicking aspects of the real thing, including forming noggin-like structures and pulsing with electrical signals like a thinking mind, researchers reported Friday at the annual meeting of the American Association for the Advancement of Science in Washington. The mini-brains, which can be personalized based on whose cells they’re made from, may soon help scientists study a wide variety of diseases and health problems—from autism and Parkinson’s to multiple sclerosis and Alzheimer’s, as well as stroke, brain trauma, and infections, such as Zika virus.

 

“There are a variety of places where a mini brain could be useful,” said Wayne Drevets of Janssen Pharmaceuticals Inc., who was not involved with the research. In some cases, they may offer a cheaper, more ethical, and more realistic model for human health than mice and other animals, he and other researchers said at the conference.

 

Researchers who developed the wee noodles, led by Thomas Hartung, of Johns Hopkins University Bloomberg School of Public Health, hope to have the mini-brains commercially available this year.


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Biochemistry and Cell Biology of Tau in Neurofibrillary Degeneration

Biochemistry and Cell Biology of Tau in Neurofibrillary Degeneration | Amazing Science | Scoop.it

The tau protein is a subunit of one of the major hallmarks of Alzheimer disease (AD), the neurofibrillary tangles, and is therefore of major interest as an indicator of disease mechanisms. Many of the unusual properties of Tau can be explained by its nature as a natively unfolded protein. Examples are the large number of structural conformations and biochemical modifications (phosphorylation, proteolysis, glycosylation, and others), the multitude of interaction partners (mainly microtubules, but also other cytoskeletal proteins, kinases, and phosphatases, motor proteins, chaperones, and membrane proteins). The pathological aggregation of Tau is counterintuitive, given its high solubility, but can be rationalized by short hydrophobic motifs forming β structures. The aggregation of Tau is toxic in cell and animal models, but can be reversed by suppressing expression or by aggregation inhibitors. This review summarizes some of the structural, biochemical, and cell biological properties of Tau and Tau fibers. Further aspects of Tau as a diagnostic marker and therapeutic target, its involvement in other Tau-based diseases, and its histopathology are covered by other chapters in this volume.


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Cold Spring Harb Perspect Med. 2012 Jul; 2(7): a006247. 
doi: 10.1101/cshperspect.a006247 PMCID: PMC3385935 

Biochemistry and Cell Biology of Tau Protein in Neurofibrillary Degeneration 

Eva-Maria Mandelkow and Eckhard Mandelkow

Image   Visualization of Tau and kinesin bound to microtubules.
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Self-healing, flexible electronic material restores functions after many breaks

Self-healing, flexible electronic material restores functions after many breaks | Amazing Science | Scoop.it

Electronic materials have been a major stumbling block for the advance of flexible electronics because existing materials do not function well after breaking and healing. A new electronic material created by an international team, however, can heal all its functions automatically even after breaking multiple times. This material could improve the durability of wearable electronics.

 

"Wearable and bendable electronics are subject to mechanical deformation over time, which could destroy or break them," said Qing Wang, professor of materials science and engineering, Penn State. "We wanted to find an electronic material that would repair itself to restore all of its functionality, and do so after multiple breaks."

 

Self-healable materials are those that, after withstanding physical deformation such as being cut in half, naturally repair themselves with little to no external influence.

 

In the past, researchers have been able to create self-healable materials that can restore one function after breaking, but restoring a suite of functions is critical for creating effective wearable electronics. For example, if a dielectric material retains its electrical resistivity after self-healing but not its thermal conductivity, that could put electronics at risk of overheating.

 

The material that Wang and his team created restores all properties needed for use as a dielectric in wearable electronics -- mechanical strength, breakdown strength to protect against surges, electrical resistivity, thermal conductivity and dielectric, or insulating, properties. They published their findings online in Advanced Functional Materials.

 

Most self-healable materials are soft or "gum-like," said Wang, but the material he and his colleagues created is very tough in comparison. His team added boron nitride nanosheets to a base material of plastic polymer. Like graphene, boron nitride nanosheets are two dimensional, but instead of conducting electricity like graphene they resist and insulate against it.

 


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Autonomous Mini Rally Car Teaches Itself to Powerslide

Autonomous Mini Rally Car Teaches Itself to Powerslide | Amazing Science | Scoop.it

Most autonomous vehicle control software is deliberately designed for well-constrained driving that's nice, calm, and under control. Not only is this a little bit boring, it's also potentially less safe: If your car autonomous vehicle has no experience driving aggressively, it won't know how to manage itself if something goes wrong. 

 

At Georgia Tech, researchers are developing control algorithms that allow small-scale autonomous cars to power around dirt tracks at ludicrous speeds. They presented some this week at the 2016 IEEE International Conference on Robotics and Automation in Stockholm, Sweden. Using real-time onboard sensing and processing, the little cars maximize their speed while keeping themselves stable and under control. Mostly.

 

The electrically powered research platform pictured above, which is a scale model one-fifth the size of a vehicle meant for human occupants, is called AutoRally. It's about a meter long, weighs 21kg, and has a top speed of nearly 100 kilometers per hour. It's based on an R/C truck chassis, with some largely 3D-printed modifications to support a payload that includes a GPS, IMU, wheel encoders, a pair of fast video cameras, and a beefy quad-core i7 computer with a Nvidia GTX 750ti GPU and 32 gigs of RAM. All of this stuff is protected inside of an aluminum enclosure that makes crashing (even crashing badly) not that big of a deal.

 

The researchers attest that most of the crashes in the video happened due to either software crashes (as opposed to failures of the algorithm itself), or the vehicle having trouble adapting to changes in the track surface. Since that video was made, they've upgraded the software to make it able to handle a more realistically dynamic environment. The result: AutoRally is now able to drive continuously on a track that, because of temperature changes, goes from, say, partially frozen to a huge puddle of mud over the course of a couple of hours.

They’ve placed all of AutoRally’s specs online (and made the software available on Github) in the hopes that other vehicle autonomy researchers will be able to take advantage of the platform’s robust, high-performance capabilities. The code is open source and ROS compatible, with an accompanying Gazebo-based simulation.

We're hoping that this algorithm will eventually be mature enough to be tried out on a full-size rally car (maybe in a little friendly competition with a human driver). But if that does ever happen, crashing will be a much bigger deal than it is now.

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Printing metal in midair with laser-assisted direct-ink 3D printing

Printing metal in midair with laser-assisted direct-ink 3D printing | Amazing Science | Scoop.it

"Flat" and "rigid" are terms typically used to describe electronic devices. But the increasing demand for flexible, wearable electronics, sensors, antennas and biomedical devices has led a team at Harvard's Wyss Institute for Biologically Inspired Engineering and the John A. Paulson School of Engineering and Applied Sciences (SEAS) to innovate an eye-popping new way of printing complex metallic architectures -- as though they are seemingly suspended in midair.

 

Reported online May 16, 2016 in the Proceedings of the National Academy of Sciences, this laser-assisted direct ink writing method allows microscopic metallic, free-standing 3D structures to be printed in one step without auxiliary support material. The research was led by Wyss Core Faculty member Jennifer Lewis, Sc.D., who is also the Hansjörg Wyss Professor of Biologically Inspired Engineering at SEAS.

 

"I am truly excited by this latest advance from our lab, which allows one to 3D print and anneal flexible metal electrodes and complex architectures 'on-the-fly,' " said Lewis.

 

Lewis' team used an ink composed of silver nanoparticles, sending it through a printing nozzle and then annealing it using a precisely programmed laser that applies just the right amount of energy to drive the ink's solidification. The printing nozzle moves along x, y, and z axes and is combined with a rotary print stage to enable freeform curvature. In this way, tiny hemispherical shapes, spiral motifs, even a butterfly made of silver wires less than the width of a hair can be printed in free space within seconds. The printed wires exhibit excellent electrical conductivity, almost matching that of bulk silver.

 

When compared to conventional 3D printing techniques used to fabricate conductive metallic features, laser-assisted direct ink writing is not only superior in its ability to produce curvilinear, complex wire patterns in one step, but also in the sense that localized laser heating enables electrically conductive silver wires to be printed directly on low-cost plastic substrates.

According to the study's first author, Wyss Institute Postdoctoral Fellow Mark Skylar-Scott, Ph.D., the most challenging aspect of honing the technique was optimizing the nozzle-to-laser separation distance.

 

"If the laser gets too close to the nozzle during printing, heat is conducted upstream which clogs the nozzle with solidified ink," said Skylar-Scott. "To address this, we devised a heat transfer model to account for temperature distribution along a given silver wire pattern, allowing us to modulate the printing speed and distance between the nozzle and laser to elegantly control the laser annealing process 'on the fly.' "

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Combining nanotextured surfaces with the Leidenfrost effect for extreme water repellency

Combining nanotextured surfaces with the Leidenfrost effect for extreme water repellency | Amazing Science | Scoop.it

Combining superhydrophobic surfaces with Leidenfrost levitation--picture a water droplet hovering over a hot surface rather than making physical contact with it--has been explored extensively for the past decade by researchers hoping to uncover the holy grail of water-repellent surfaces.

 

In a new twist, a group of South Korean researchers from Seoul National University and Dankook University report an anomalous water droplet-bouncing phenomenon generated by Leidenfrost levitation on nano-textured surfaces in Applied Physics Letters.

 

"Wettability plays a key role in determining the equilibrium contact angles, contact angle hysteresis, and adhesion between a solid surface and liquid, as well as the retraction process of a liquid droplet impinged on the surface," explained Doo Jin Lee, lead author, and a postdoctoral researcher in the Department of Materials and Engineering at Seoul National University.

 

Non-wetting surfaces tend to be created by one of two methods. "First, textured surfaces enable non-wettability because a liquid can't penetrate into the micro- or nano-features, thanks to air entrapment between asperities on the textured materials," Lee said.

 

Or, second, the Leidenfrost effect "can help produce a liquid droplet dancing on a hot surface by floating it on a cushion of its own vapor," he added. "The vapor film between the droplet and heated surface allows the droplet to bounce off the surface--also known as the 'dynamic Leidenfrost phenomenon.'"

 

Lee and colleagues developed a special "non-wetting, nano-textured surface" so they could delve into the dynamic Leidenfrost effect's impact on the material.

 

"Our nano-textured surface was verified to be 'non-wetting' via thermodynamic analysis," Lee elaborated. "This analytical approach shows that the water droplet isn't likely to penetrate into the surface's nanoholes, which is advantageous for designing non-wetting, water-repellant systems. And the water droplet bouncing was powered by the synergetic combination of the non-wetting surface--often called a 'Cassie surface'--and the Leidenfrost effect."

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Jupiter's moon: Europa's ocean may have an Earthlike chemical balance

Jupiter's moon: Europa's ocean may have an Earthlike chemical balance | Amazing Science | Scoop.it
The ocean of Jupiter's moon Europa could have the necessary balance of chemical energy for life, even if the moon lacks volcanic hydrothermal activity, finds a new study.

 

Europa is strongly believed to hide a deep ocean of salty liquid water beneath its icy shell. Whether the Jovian moon has the raw materials and chemical energy in the right proportions to support biology is a topic of intense scientific interest. The answer may hinge on whether Europa has environments where chemicals are matched in the right proportions to power biological processes. Life on Earth exploits such niches.

 

In the new study published in Geophysical Research Letters, a journal of the American Geophysical Union, scientists at NASA's Jet Propulsion Laboratory (JPL), Pasadena, California, compared Europa's potential for producing hydrogen and oxygen with that of Earth, through processes that do not directly involve volcanism. The balance of these two elements is a key indicator of the energy available for life. The study found that the amounts would be comparable in scale; on both worlds, oxygen production is about 10 times higher than hydrogen production.

 

The work draws attention to the ways that Europa's rocky interior may be much more complex and possibly Earthlike than people typically think, according to Steve Vance, a planetary scientist at JPL and lead author of the new study. "We're studying an alien ocean using methods developed to understand the movement of energy and nutrients in Earth's own systems. The cycling of oxygen and hydrogen in Europa's ocean will be a major driver for Europa's ocean chemistry and any life there, just it is on Earth."

 

Ultimately, Vance and colleagues want to also understand the cycling of life's other major elements in the ocean: carbon, nitrogen, phosphorus and sulfur.

 

As part of their study, the researchers calculated how much hydrogen could potentially be produced in Europa's ocean as seawater reacts with rock in a process called serpentinization. In this process, water percolates into spaces between mineral grains and reacts with the rock to form new minerals, releasing hydrogen in the process. The researchers considered how cracks in Europa's seafloor likely open up over time, as the moon's rocky interior continues to cool following its formation billions of years ago. New cracks expose fresh rock to seawater, where more hydrogen-producing reactions can take place.

In Earth's oceanic crust, such fractures are believed to penetrate to a depth of 5 to 6 kilometers (3 to 4 miles). On present-day Europa, the researchers expect water could reach as deep as 25 kilometers (15 miles) into the rocky interior, driving these key chemical reactions throughout a deeper fraction of Europa's seafloor.

 

The other half of Europa's chemical-energy-for-life equation would be provided by oxidants -- oxygen and other compounds that could react with the hydrogen -- being cycled into the Europan ocean from the icy surface above. Europa is bathed in radiation from Jupiter, which splits apart water ice molecules to create these materials. Scientists have inferred that Europa's surface is being cycled back into its interior, which could carry oxidants into the ocean.

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Complex life on Earth began a billion years earlier than previously thought, study argues

Complex life on Earth began a billion years earlier than previously thought, study argues | Amazing Science | Scoop.it

A claim by researchers that complex life on Earth may have evolved a billion years earlier than previously thought has immediately divided scientists in the field, with some hailing the evidence as rock-solid and others unconvinced.

The researchers, writing in the journal Nature Communications, said they had uncovered fossils showing that complex life on Earth began more than 1.5bn years ago.

After first emerging from the primordial soup, life remained primitive and single-celled for billions of years, but some of those cells eventually congregated like clones in a colony. Scientists took to calling the later part of this period the “boring billion” because evolution seemed to have stalled.

But at some point there was a leap – arguably second in importance only to the appearance of life itself – towards complex organisms with multiple cells.

This transition progressively gave rise to all the plants and animals that have ever existed.

Exactly when multi-celled “eukaryotes” – organisms in which differentiated cells each contain a membrane-bound nucleus with genetic material – showed up has inflamed scientific passions for many decades.

“Our discovery pushes back nearly one billion years the appearance of macroscopic, multi-cellular eukaryotes compared to previous research,” said Maoyan Zhu, a professor at the Nanjing Institute of Geology and Palaeontology.

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