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The bacteria that make insects digest their own brains

The bacteria that make insects digest their own brains | Amazing Science | Scoop.it

As far as bacteria are concerned, other living creatures are just another niche to exploit, which means that pretty much every animal and plant has a set of bacterial pathogens that come along with it. These bacteria have made the animal in question their speciality, and are highly adapted to live inside their hosts. While these bacteria often make the host ill, or less fit, or sometimes dead, the longer they live with their host, overall, the less they damage it. After all, it’s no help to the bacteria if their home drops down dead right after they’ve moved in.

 

A great example of this is the bacteria Wolbachia, which infect insects and other arthropods and causes them to stop producing male offspring (so only female survive to pass on the bacterial genome). As well as passing from females onto their offspring, Wolbachia can also be transmitted horizontally, that is between insects in the same generation. In its normal host the Wolbachia is not hugely damaging (apart from removing all males from the population) but when transmitted to a new species it causes various unpleasant nervous system complications, often leading to death. It turns out, the reason Wolbachia are more dangerous in new species isn’t because the bacteria go wild in the unexplored territory, rather it’s because the new host doesn’t know how to deal with them.

 

As the bacteria are found inside cells, the best way for an insect immune system to get rid of them, is by destroying the cells that house the bacteria. Which, as previously mentioned, are mainly the gonads and the central nervous system. When the Wolbachia get into a new species, the first response of the insect is to quickly and efficiently destroy any cells which have bacteria inside them. As a consequence the unfortunate insect basically destroys its own brain, leading to various unpleasant symptoms and death.

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The next step in DNA computing: GPS mapping?

The next step in DNA computing: GPS mapping? | Amazing Science | Scoop.it

Conventional silicon-based computing, which has advanced by leaps and bounds in recent decades, is pushing against its practical limits. DNA computing could help take the digital era to the next level. Scientists are now reporting progress toward that goal with the development of a novel DNA-based GPS. They describe their advance in ACS' The Journal of Physical Chemistry B.

 

Jian-Jun Shu and colleagues note that Moore's law, which marked its 50thanniversary in April, posited that the number of transistors on a computer chip would double every year. This doubling has enabled smartphone and tablet technology that has revolutionized computing, but continuing the pattern will come with high costs. In search of a more affordable way forward, scientists are exploring the use of DNA for its programmability, fast processing speeds and tiny size. So far, they have been able to store and process information with the genetic material and perform basic computing tasks. Shu's team set out to take the next step.

 

The researchers built a programmable DNA-based processor that performs two computing tasks at the same time. On a map of six locations and multiple possible paths, it calculated the shortest routes between two different starting points and two destinations. The researchers say that in addition to cost- and time-savings over other DNA-based computers, their system could help scientists understand how the brain's "internal GPS" works.

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Atoms placed precisely in silicon can act as quantum simulator

Atoms placed precisely in silicon can act as quantum simulator | Amazing Science | Scoop.it

In a proof-of-principle experiment, researchers at UNSW Australia have demonstrated that a small group of individual atoms placed very precisely in silicon can act as a quantum simulator, mimicking nature -- in this case, the weird quantum interactions of electrons in materials.

 

"Previously this kind of exact quantum simulation could not be performed without interference from the environment, which typically destroys the quantum state," says senior author Professor Sven Rogge, Head of the UNSW School of Physics and program manager with the ARC Centre of Excellence for Quantum Computation and Communication Technology (CQC2T).

 

"Our success provides a route to developing new ways to test fundamental aspects of quantum physics and to design new, exotic materials -- problems that would be impossible to solve even using today's fastest supercomputers."

 

The study is published in the journal Nature Communications. The lead author was UNSW's Dr Joe Salfi and the team included CQC2T director Professor Michelle Simmons, other CQC2T researchers from UNSW and the University of Melbourne, as well as researchers from Purdue University in the US.

 

Two dopant atoms of boron only a few nanometres from each other in a silicon crystal were studied. They behaved like valence bonds, the "glue" that holds matter together when atoms with unpaired electrons in their outer orbitals overlap and bond.

The team's major advance was in being able to directly measure the electron "clouds" around the atoms and the energy of the interactions of the spin, or tiny magnetic orientation, of these electrons.

 

They were also able to correlate the interference patterns from the electrons, due to their wave-like nature, with their entanglement, or mutual dependence on each other for their properties. "The behavior of the electrons in the silicon chip matched the behaviour of electrons described in one of the most important theoretical models of materials that scientists rely on, called the Hubbard model," says Dr Salfi.

 

"This model describes the unusual interactions of electrons due to their wave-like properties and spins. And on of its main applications is to understand how electrons in a grid flow without resistance, even though they repel each other," he says. The team also made a counterintuitive find -- that the entanglement of the electrons in the silicon chip increased the further they were apart. "This demonstrates a weird behaviour that is typical of quantum systems," says Professor Rogge.

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How EVE Online's Project Discovery is remapping human biology

How EVE Online's Project Discovery is remapping human biology | Amazing Science | Scoop.it

EVE Online isn't just a game about internet spaceships and sci-fi politics. Since March, developer CCP Games has been running Project Discovery – an initiative to help improve scientific understanding of the human body at the tiniest levels. Run in conjunction with the Human Protein Atlas and Massively Multiplayer Online Science, the project taps into EVE Online's greatest resource – its player base – to help categorise millions of proteins.

 

"We show them an image, and they can change the colour of it, putting green or red dyes on it to help them analyse it a little bit better," Linzi Campbell, game designer on Project Discovery, tells WIRED. "Then we also show them examples – cytoplasm is their favourite one! We show them what each of the different images should look like, and just get them to pick a few that they identify within the image. The identifications are scrambled each time, so it's not as simple as going 'ok, every time I just pick the one on the right' – they have to really think about it."

 

The analysis project is worked into EVE Online as a minigame, and works within the context of the game's lore. "We have this NPC organisation called the Drifters – they're like a mysterious entity in New Eden [EVE's interplanetary setting]," Campbell explains. "The players don't know an awful lot about the Drifters at the minute, so we disguised it within the universe as Drifter DNA that they were analysing. I think it just fit perfectly. We branded this as [research being done by] the Sisters of Eve, and they're analysing this Drifter DNA." 

 

The response has been tremendous. "We've had an amazing number of classifications, way over our greatest expectations," says Emma Lundberg, associate professor at the Human Protein Atlas. "Right now, after six weeks, we've had almost eight million classifications, and the players spent 16.2 million minutes playing the minigame. When we did the math, that translated – in Swedish measures – to 163 working years. It's crazy."

 

"We had a little guess, internally. We said if we get 40,000+ classifications a day, we're happy. If we get 100,000 per day, then we're amazed," Lundberg adds. "But when it peaked in the beginning, we had 900,000 classifications in one day. Now it's stabilised, but we're still getting around 200,000 a day, so everyone is mind-blown. We never expected it."

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Signals that make early stem cells identified

Signals that make early stem cells identified | Amazing Science | Scoop.it

Stem cells work throughout our lives as a sort of handyman, repairing damaged tissues and renewing some normal ones, like the skin we shed. Scientists have come to understand much about how stem cells function when we are adults, but less is known about where these stem cells come from to begin with, as an embryo is developing.

 

Now, researchers at The Rockefeller University have identified a new mechanism by which cells are instructed during development to become stem cells. The results, published in Cell on January 14, help explain how communication between cells mediates this process, and may have implications for skin cancer treatments. The researchers traced the cell divisions that occur as hair follicles form in mice to determine where stem cells first emerge. Above, developing hair follicles are shown at various stages.

 

“While adult stem cells are increasingly well-characterized, we know little about their origins. Here, we show that in the skin, stem cell progenitors of the hair follicle are specified as soon as the cells within the single-layered embryonic epidermis begin to divide downward to form an embryonic hair bud,” explains Elaine Fuchs, Rebecca C. Lancefield Professor and head of the Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development. “This timing was much earlier than previously thought, and gives us new insights into the establishment of these very special cells.”

 

Clusters of stem cells receive signals from other nearby cells that instruct them to either stay a stem cell or differentiate into a specific cell type. These instructive groups of cells, called the “niche,” are known to maintain adult stem cell populations. Less well understood is how the niche forms, or when and where stem cells first appear during embryonic development.

 

“Adult stem cells are dependent on the niche for instructions on both how to become a stem cell, and how to control stem cell population size,” says first author Tamara Ouspenskaia. “The question was, does the niche appear first and call other cells over to become stem cells? Or is it the other way around? Stem cells could be appearing elsewhere first and then recruiting the niche.”

 

Working in the mouse hair follicle, a region that contains active stem cells, Fuchs and colleagues investigated the cell divisions that occur as a hair follicle is first forming. The hair follicle begins as a small bud called a placode, and develops into a tissue of multiple layers, comprised of different cell types. By labeling cells within the placode and tracing their progeny, the researchers determined that from each division, one daughter cell stayed put, while the other escaped to a different layer.

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Researchers create 1-step graphene patterning method

Researchers create 1-step graphene patterning method | Amazing Science | Scoop.it

Researchers from the University of Illinois at Urbana-Champaign have developed a one-step, facile method to pattern graphene by using stencil mask and oxygen plasma reactive-ion etching, and subsequent polymer-free direct transfer to flexible substrates.

 

Graphene, a two-dimensional carbon allotrope, has received immense scientific and technological interest. Combining exceptional mechanical properties, superior carrier mobility, high thermal conductivity, hydrophobicity, and potentially low manufacturing cost, graphene provides a superior base material for next generation bioelectrical, electromechanical, optoelectronic, and thermal management applications.

 

"Significant progress has been made in the direct synthesis of large-area, uniform, high quality graphene films using chemical vapor deposition (CVD) with various precursors and catalyst substrates," explained SungWoo Nam, an assistant professor of mechanical science and engineering at Illinois. "However, to date, the infrastructure requirements on post-synthesis processing--patterning and transfer--for creating interconnects, transistor channels, or device terminals have slowed the implementation of graphene in a wider range of applications."

 

"In conjunction with the recent evolution of additive and subtractive manufacturing techniques such as 3D printing and computer numerical control milling, we developed a simple and scalable graphene patterning technique using a stencil mask fabricated via a laser cutter," stated Keong Yong, a graduate student and first author of the paper, "Rapid Stencil Mask Fabrication Enabled One-Step Polymer-Free Graphene Patterning and Direct Transfer for Flexible Graphene Devices appearing in Scientific Reports.

 

"Our approach to patterning graphene is based on a shadow mask technique that has been employed for contact metal deposition," Yong added. "Not only are these stencil masks easily and rapidly manufactured for iterative rapid prototyping, they are also reusable, enabling cost-effective pattern replication. And since our approach involves neither a polymeric transfer layer nor organic solvents, we are able to obtain contamination-free graphene patterns directly on various flexible substrates."

 

Nam stated that this approach demonstrates a new possibility to overcome limitations imposed by existing post-synthesis processes to achieve graphene micro-patterning. Yong envisions this facile approach to graphene patterning sets forth transformative changes in "do It yourself" (DIY) graphene-based device development for broad applications including flexible circuits/devices and wearable electronics.

 

"This method allows rapid design iterations and pattern replications, and the polymer-free patterning technique promotes graphene of cleaner quality than other fabrication techniques," Nam said. "We have shown that graphene can be patterned into varying geometrical shapes and sizes, and we have explored various substrates for the direct transfer of the patterned graphene."

 

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MicroRNA Pathway Could Lead to New Avenues for Leukemia Treatment

MicroRNA Pathway Could Lead to New Avenues for Leukemia Treatment | Amazing Science | Scoop.it

Cancer researchers at the University of Cincinnati have found a particular signaling route in microRNA (miR-22) that could lead to targets for acute myeloid leukemia, the most common type of fast-growing cancer of the blood and bone marrow. These findings are being published in the April 26 issue of the online journal Nature Communications.  

 
Acute myeloid leukemia (AML) is the most common type of acute leukemia and occurs when the bone marrow begins to make blasts, cells that have not yet completely matured. These blasts normally develop into white blood cells. However, in AML, these cells do not develop and are unable to ward off infections.
 
Jianjun Chen, PhD, associate professor in the Department of Cancer Biology at the UC College of Medicine, member of the UC Cancer Institute and lead author on the study, says that microRNAs are sophistically controlled and play key roles in the development of cancer.
 
"MicroRNAs make up a class of small, non-coding internal RNAs that control a gene’s job, or expression, by directing their target messaging RNAs, or mRNAs, to inhibit or stop. Cellular organisms use mRNA to convey genetic information,” he says. "Previous research has shown that microRNA miR-22 is linked to breast cancer and other blood disorders which sometimes turn into AML, but we found in this study that it could be an essential anti-tumor gate keeper in AML when it is down-regulated, meaning its function is minimized.
 
"When we forced miR-22 expression, we saw difficulty in leukemia cells developing, growing and thriving. miR-22 targets multiple cancer causing genes (CRTC1, FLT3 and MYCBP) and blocks certain pathways (CREB and MYC). The down-regulation, or decreased output, of miR-22 in AML is caused by the loss of the number of DNA being copied and/or stopping their expression through a pathway called TET1/GFI1/EZH2/SIN3A. Also, nanoparticles carrying miR-22 DNA oligonucleotides (short nucleic acid molecules) prevented leukemia advancement.”
 
Chen, who conducted the study using bone marrow transplant samples and animal models, says that the ten-eleven translocation proteins (TET1/2/3) in mammals help to control genetic expression in normal developmental processes in contrast to mutations that cause function loss and tumor-slowing with TET2, which is observed in blood and stem cell cancers. 
 
"We recently reported that TET1 plays an essential cancer generating role in certain AML where it activates expression of homeobox genes, which are a large family of similar genes that direct the formation of many body structures during early embryonic development,” he says. "However, it is unknown whether TET1 can also function as a repressor for cellular function in cancer, and its role in microRNA expression has rarely been studied.”
 
Chen says these findings are important in targeting a cancer that is both common and fatal. "The majority of patients with ALM usually don’t survive longer than five years, even with chemotherapy, which is why the development of new effective therapies based on the underlying mechanisms of the disease is so important,” he says, adding that this pathogenesis as well as drug response to AML is unclear. "Our study uncovers a previously unappreciated signaling pathway (TET1/GFI1/EZH2/SIN3A⊣miR-22⊣CREB-MYC) and provides new insights into genetic mechanisms causing and progressing AML and also highlights the clinical potential of miR-22-based AML therapy. More research on this pathway and ways to target it are necessary.”
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Secret Flexibility Found in Protein-Protein Interactions

Secret Flexibility Found in Protein-Protein Interactions | Amazing Science | Scoop.it
Proteins transact much of a cell’s daily business. Messages are sent from one part of the cell to another, for instance, by a protein bucket brigade — one attaches to another, which then switches on another, which then modifies another, and so on, culminating in a string of alterations that delivers the message. A protein’s particular shape helps determine what it can attach to and therefore what it can do. Finding out which proteins another protein will stick to is often the first step in understanding its role in the cell.

Marc Vidal, a biologist at Dana-Farber, has a long history of tracing such protein partnerships on a grand scale. His lab looks to see how large numbers of proteins interact with one another and how those interactions might change in someone with a disease. But it can be frustrating to do this when you aren’t sure whether you should assume that proteins from the same gene do the same thing. Even if we perfectly understand a particular genome sequence, “we still don’t have a perfect knowledge of the components that are encoded by the genome,” Vidal said. “And the reason is that the good old rules don’t hold.”

To see just how often the old rules might be broken, the Vidal lab and their collaborators gathered a set of proteins made from about 1,500 genes — about 8 percent of our total complement. They sorted out which proteins came from the same genes, finding that about 500 of the genes made at least two. Then they ran multiple tests in which each of the proteins was given the chance to attach to more than 15,000 other proteins often found in the cell. Finally, they compared each protein’s results to those of its sibling proteins — all those proteins made by the same gene. How often did sibling proteins attach to the same partners? How often did they not?

The answer was rather unexpected. “It was so striking,” said David Hill, a scientist at Dana-Farber, that he thought, “This can’t be right; we’ve got to figure out what we did wrong.” But the results held up to prodding. They found that 61 percent of sibling protein pairs share some but not all of their interactions. Moreover, nearly one in five of all sibling protein pairs had nothing in common. Comparing the proteins in their data set with proteins made by separate genes, the team found that in many cases the sibling proteins’ interactions were as different as if they’d had totally unrelated origins.
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Researchers create a first frequency comb of time-bin entangled qubits

Researchers create a first frequency comb of time-bin entangled qubits | Amazing Science | Scoop.it
An international team of researchers has built a chip that generates multiple frequencies from a robust quantum system that produces time-bin entangled photons. In contrast to other quantum state realizations, entangled photons don't need bulky equipment to keep them in their quantum state, and they can transmit quantum information across long distances. The new device creates entangled photons that span the traditional telecommunications spectrum, making it appealing for multi-channel quantum communication and more powerful quantum computers.

 

"The advantages of our chip are that it's compact and cheap. It's also unique that it operates on multiple channels," said Michael Kues, Institut National de la Recherche Scientifique (INRS), University of Quebec, Canada. The researchers will present their results at the Conference on Lasers and Electro-Optics (CLEO), which is held June 5 -10 in San Jose, California.

 

The basis of quantum communications and computing lies in qubits, the quantum equivalent of classical bits. Instead of representing a one or a zero, qubits can exhibit an unusual property called superposition to represent both numbers simultaneously.

 

In order to take full advantage of superposition to perform difficult calculations or send information securely, another weird quantum mechanical property called entanglement enters the picture. Entanglement was famously called "spooky action at a distance" by Albert Einstein. It links particles so that measurements on one instantaneously affect the other.

 

Kues and his colleagues used photons to realize their qubits and entangled them by sending two short laser pulses through an interferometer, a device that directs light beams along different paths and then recombines them, to generate double pulses.

 

To generate multiple frequencies, Kres and his colleagues sent the pulses through a tiny ring, called a microring resonator. The resonator generates photon pairs on a series of discrete frequencies, using spontaneous form-wave mixing, thus creating a frequency comb.

 

The interferometer the team used has one long arm and one short arm, and when a single photon comes out of the system, it is in a superposition of time states, as if it traveled through both the long arm and the short arm simultaneously. Time-bin entanglement is a particularly robust form of photon entanglement. Photons can also have their polarization entangled, but waveguides and other types of optical equipment may alter polarization states.

 

Other research groups have generated time-bin entangled photons, but Kues and his colleagues are the first to create photons with multiple frequencies using the same chip. This feature can enable multiplexed and multi-channel quantum communications and increased quantum computation information capacity. Kues notes that the chip could improve quantum key distribution, a process that lets two parties share a secret key to encrypt messages with theoretically unbreakable security. It could also serve as a component of a future quantum computer.

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Researchers create artificial protein to control assembly of buckyballs

Researchers create artificial protein to control assembly of buckyballs | Amazing Science | Scoop.it

"This is a proof-of-principle study demonstrating that proteins can be used as effective vehicles for organizing nano-materials by design," says senior author Gevorg Grigoryan, an assistant professor of computer science at Dartmouth. "If we learn to do this more generally - the programmable self-assembly of precisely organized molecular building blocks—this will lead to a range of new materials towards a host of applications, from medicine to energy."

 

The study appears in the journal in Nature Communications.

According to the U.S. National Nanotechnology Initiative, scientists and engineers are finding a wide variety of ways to deliberately make materials at the nanoscale - or the atomic and molecular level—to take advantage of their enhanced properties such as higher strength, lighter weight, increased control of light spectrum and greater chemical reactivity than their larger-scale counterparts.

 

Proteins are "smart" molecules, encoded by our genes, which organize and orchestrate essentially all molecular processes in our cells. The goal of the new study was to create an artificial protein that would self-organize into a new material—an atomically periodic lattice of buckminster fullerene molecules.

 

Buckminster fullerene (buckyball for short) is a sphere-like molecule composed of 60 carbon atoms shaped like a soccer ball. Buckyballs have an array of unusual properties, which have excited scientists for several decades because of their potential applications. Buckyballs are currently used in nanotechology due to their high heat resistance and electrical superconductivity, but the molecule is difficult to organize in desired ways, which hampers its use in the development of novel materials.

 

In their new research, Grigoryan and his colleagues show that their artificial protein does interact with buckyball and indeed does organize it into a lattice. Further, they determined the 3-dimensional structure of this lattice, which represents the first ever atomistic view of a protein/buckyball complex."Learning to engineer self-assembly would enable the precise organization of molecules by design to create matter with tailored properties," Grigoryan says.

 

"In this research, we demonstrate that proteins can direct the self-assembly of buckminsterfullerene into ordered superstructures. Further, excitingly, we have observed this protein/buckyball lattice conducts electricity, something that the protein-alone lattice does not do. Thus, we are beginning to see emergent material behaviors that can arise from combing the fascinating properties of buckyball and the abilities of proteins to organize matter at the atomic scale. Taken together, our findings suggest a new means of organizing fullerene molecules into a rich variety of lattices to generate new properties by design."

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New CRISPR System Targets Both DNA and RNA

New CRISPR System Targets Both DNA and RNA | Amazing Science | Scoop.it

With a staggering number of papers published in the past several years involving the characterization and use of the CRISPR/Cas9 gene editing system, it is surprising that researchers are still finding new features of the versatile molecular scissor enzyme. Now, a collaborative team of scientists led by researchers at the Max Planck Institute and a co-discoverer of CRISPR’s genome editing capabilities has uncovered a feature of the CRISPR-associated protein Cpf1 that has previously not been observed in this family of enzymes—dual RNA and DNA cleavage activity.

 

In the CRISPR/Cas9 system, the enzyme Cas9 cuts viral DNA at a location specified by an RNA molecule—the CRISPR RNA (crRNA)—in complex with another RNA, the so-called tracrRNA. This is the bacterial version of an immune system and helps put pathogens out of action. In sharp contrast to CRISPR/Cas9, Cpf1 can process the pre-crRNA on its own, and then using the processed RNA to target and cut DNAspecifically. Not requiring a host-derived RNase and the tracrRNA makes this the most minimalistic CRISPR immune system yet. The mechanism of combining two separate catalytic modalities in one allows for possible new avenues for sequence specific genome engineering, most importantly facilitation of targeting multiple sites at once or multiplexing.

 

Previous work from the Max Planck team described a system that consists of two RNAs forming a duplex (tracrRNA and pre-crRNA), with tracrRNA maturing pre-crRNA to crRNA, in the presence of the protein Cas9. Moreover, the research group demonstrated that tracrRNA and crRNA together, either in the form of the duplex of two guide RNAs or a fused single guide RNA, are required to guide the Cas9 enzyme accurately to the matching target DNA sequence—outlining the molecular mechanisms of the primary CRISPR/Cas9 system.

 

"Although the workings of CRISPR/Cas9 sound simple, the details of the mechanisms involved are rather subtle," explained senior study author Emmanuelle Charpentier, Ph.D., director at the Max Planck Institute for Infection Biology and co-discoverer of CRISPR/Cas9’s role in genome editing.

 

In this new study, the investigators showed that the immune defense mechanism of some bacteria a simpler in structure than CRISPR/Cas9. In addition to Cas9, these bacteria use the enzyme Cpf1 for cleaving foreign DNA. This resulted in identifying a dual nuclease role for Cpf1.

 

“We demonstrate a novel mechanism in CRISPR–Cas immunity. We show that type V-A Cpf1 fromFrancisella novicida is a dual-nuclease that is unique to crRNA biogenesis and target DNA interference,” the authors wrote. “Cpf1 cleaves pre-crRNA upstream of a hairpin structure formed within the CRISPR repeats and thereby generates intermediate crRNAs that are processed further, leading to mature crRNAs. After recognition of a 5′-YTN-3′ protospacer adjacent motif on the non-target DNA strand and subsequent probing for an eight-nucleotide seed sequence, Cpf1, guided by the single mature repeat-spacer crRNA, introduces double-stranded breaks in the target DNA to generate a 5′ overhang.”

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You can now be identified by your ‘brainprint’ with 100% accuracy

You can now be identified by your ‘brainprint’ with 100% accuracy | Amazing Science | Scoop.it

Binghamton University researchers have developed a biometric identification method called Cognitive Event-RElated Biometric REcognition (CEREBRE) for identifying an individual’s unique “brainprint.” They recorded the brain activity of 50 subjects wearing an electroencephalograph (EEG) headset while looking at selected images from a set of 500 images.

 

The researchers found that participants’ brains reacted uniquely to each image — enough so that a computer system that analyzed the different reactions was able to identify each volunteer’s “brainprint” with 100 percent accuracy.

In their original brainprint study in 2015, published in Neurocomputing (see ‘Brainprints’ could replace passwords), the research team was able to identify one person out of a group of 32 by that person’s responses, with 97 percent accuracy. That study only used words. Switching to images made a huge difference.

 

It’s only a three-point difference, but going from 97 to 100 percent makes possible a reliable system for high-security situations, such as “ensuring the person going into the Pentagon or the nuclear launch bay is the right person,” said Assistant Professor of Psychology Sarah Laszlo. “You don’t want to be 97 percent accurate for that, you want to be 100 percent accurate.”

Laszlo says brain biometrics are appealing because they can be cancelled (meaning the person can simple do another EEG session) and cannot be imitated or stolen by malicious means, the way a finger or retina can (as in the movieMinority Report).

“If someone’s fingerprint is stolen, that person can’t just grow a new finger to replace the compromised fingerprint — the fingerprint for that person is compromised forever.

 

Fingerprints are ‘non-cancellable.’ Brainprints, on the other hand, are potentially cancellable. So, in the unlikely event that attackers were actually able to steal a brainprint from an authorized user, the authorized user could then ‘reset’ their brainprint,” Laszlo explained.

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Scientists take next step towards observing quantum physics in real life

Scientists take next step towards observing quantum physics in real life | Amazing Science | Scoop.it

Small objects like electrons and atoms behave according to quantum mechanics, with quantum effects like superposition, entanglement and teleportation. One of the most intriguing questions in modern science is if large objects – like a coffee cup - could also show this behavior. Scientists at the TU Delft have taken the next step towards observing quantum effects at everyday temperatures in large objects. They created a highly reflective membrane, visible to the naked eye, that can vibrate with hardly any energy loss at room temperature. The membrane is a promising candidate to research quantum mechanics in large objects.

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Demonstration of DNA switch could lead to new bioelectronics

Demonstration of DNA switch could lead to new bioelectronics | Amazing Science | Scoop.it

A team of researchers from the University of California, Davis and the University of Washington have demonstrated that the conductance of DNA can be modulated by controlling its structure, thus opening up the possibility of DNA’s future use as an electromechanical switch for nanoscale computing. Although DNA is commonly known for its biological role as the molecule of life, it has recently garnered significant interest for use as a nanoscale material for a wide-variety of applications.

 

In their paper published in Nature Communications, the team demonstrated that changing the structure of the DNA double helix by modifying its environment allows the conductance (the ease with which an electric current passes) to be reversibly controlled. This ability to structurally modulate the charge transport properties may enable the design of unique nanodevices based on DNA. These devices would operate using a completely different paradigm than today’s conventional electronics.

 

“As electronics get smaller they are becoming more difficult and expensive to manufacture, but DNA-based devices could be designed from the bottom-up using directed self-assembly techniques such as ‘DNA origami’,” said Josh Hihath, assistant professor of electrical and computer engineering at UC Davis and senior author on the paper. DNA origami is the folding of DNA to create two- and three-dimensional shapes at the nanoscale level.

 

“Considerable progress has been made in understanding DNA’s mechanical, structural, and self-assembly properties and the use of these properties to design structures at the nanoscale. The electrical properties, however, have generally been difficult to control,” said Hihath.

 

In addition to potential advantages in fabrication at the nanoscale level, such DNA-based devices may also improve the energy efficiency of electronic circuits.  The size of devices has been significantly reduced over the last 40 years, but as the size has decreased, the power density on-chip has increased. Scientists and engineers have been exploring novel solutions to improve the efficiency.

 

“There’s no reason that computation must be done with traditional transistors. Early computers were fully mechanical and later worked on relays and vacuum tubes,” said Hihath. “Moving to an electromechanical platform may eventually allow us to improve the energy efficiency of electronic devices at the nanoscale.”

 

This work demonstrates that DNA is capable of operating as an electromechanical switch and could lead to new paradigms for computing. To develop DNA into a reversible switch, the scientists focused on switching between two stable conformations of DNA, known as the A-form and the B-form. In DNA, the B-form is the conventional DNA duplex that is commonly associated with these molecules. The A-form is a more compact version with different spacing and tilting between the base pairs. Exposure to ethanol forces the DNA into the A-form conformation resulting in an increased conductance.

 

Similarly, by removing the ethanol, the DNA can switch back to the B-form and return to its original reduced conductance value.

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Virus trading cards

Virus trading cards | Amazing Science | Scoop.it

Viruses are surprisingly symmetrical, and each trading card shows the structure of the viral capsid - the protein shell protecting the genetic material inside a virus. To make the 3D animations I used UCSF Chimera, a free molecular modeling program. When scientists discover a new protein structure they upload it to the worldwide Protein Data Bank. Each entry is assigned a unique ID number, which you can use to call up the structure in programs like Chimera or PyMol.

Use Tom Goddard’s tutorial to learn how to display viral capsids, and it’s actually a fairly simple process. You can even 3D print structures straight from Chimera.

 

Molecular Modeling: Molecular graphics and analyses were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).

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Tracking Zika Virus' Evolution

Tracking Zika Virus' Evolution | Amazing Science | Scoop.it

Sequence analysis of 41 viral strains reveals more than a half-century of change.

 

Comparing the sequences of 30 strains of Zika virus isolated from humans, 10 from mosquitoes, and one from monkeys has revealed significant evolutionary change over the past 70 years, according to a study published today (April 15) in Cell Host & Microbe. Specifically, the sequences of the viral strains showed notable divergence between the Asian and African lineages and suggest that modern Zika virus strains derived from the Asian lineage, as they are more similar to the Malaysian/1966 strain than the Nigerian/1968 strain. Additionally, the gene for the pre-membrane precursor protein has very high variability among the Zika strains examined, which modeling work suggests may affect the protein’s structure.

 

“We believe these changes may, at least partially, explain why the virus has demonstrated the capacity to spread exponentially in the human population in the Americas,” study coauthor Genhong Cheng of the University of California, Los Angeles, said in a press release. “These changes could enable the virus to replicate more efficiently, invade new tissues that provide protective niches for viral propagation, or evade the immune system, leading to viral persistence.”

 

But it is not possible to directly test whether these mutations affect the virus’s spread in humans, virologist Vincent Racaniello noted on his blog. “It’s easy to blame mutations in the viral genome for novel patterns of transmission or pathogenesis,” he wrote. “There is no reason to assume that such changes influence virulence, disease patterns, or transmission in humans.”

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Winds a quarter the speed of light spotted leaving mysterious binary systems

Winds a quarter the speed of light spotted leaving mysterious binary systems | Amazing Science | Scoop.it

Two black holes in nearby galaxies have been observed devouring their companion stars at a rate exceeding classically understood limits, and in the process, kicking out matter into surrounding space at astonishing speeds of around a quarter the speed of light.

 

The researchers, from the University of Cambridge, used data from the European Space Agency's (ESA) XMM-Newton space observatory to reveal for the first time strong winds gusting at very high speeds from two mysterious sources of x-ray radiation. The discovery, published in the journal Nature, confirms that these sources conceal a compact object pulling in matter at extraordinarily high rates.

 

When observing the Universe at x-ray wavelengths, the celestial sky is dominated by two types of astronomical objects: supermassive black holes, sitting at the centres of large galaxies and ferociously devouring the material around them, and binary systems, consisting of a stellar remnant - a white dwarf, neutron star or black hole - feeding on gas from a companion star.

 

In both cases, the gas forms a swirling disc around the compact and very dense central object. Friction in the disc causes the gas to heat up and emit light at different wavelengths, with a peak in x-rays. But an intermediate class of objects was discovered in the 1980s and is still not well understood. Ten to a hundred times brighter than ordinary x-ray binaries, these sources are nevertheless too faint to be linked to supermassive black holes, and in any case, are usually found far from the centre of their host galaxy.

 

"We think these so-called 'ultra-luminous x-ray sources' are special binary systems, sucking up gas at a much higher rate than an ordinary x-ray binary," said Dr Ciro Pinto from Cambridge's Institute of Astronomy, the paper's lead author. "Some of these sources host highly magnetised neutron stars, while others might conceal the long-sought-after intermediate-mass black holes, which have masses around one thousand times the mass of the Sun. But in the majority of cases, the reason for their extreme behaviour is still unclear."

 

Pinto and his colleagues collected several days' worth of observations of three ultra-luminous x-ray sources, all located in nearby galaxies located less than 22 million light-years from the Milky Way. The data was obtained over several years with the Reflection Grating Spectrometer on XMM-Newton, which allowed the researchers to identify subtle features in the spectrum of the x-rays from the sources. In all three sources, the scientists were able to identify x-ray emission from gas in the outer portions of the disc surrounding the central compact object, slowly flowing towards it.

 

But two of the three sources - known as NGC 1313 X-1 and NGC 5408 X-1 - also show clear signs of x-rays being absorbed by gas that is streaming away from the central source at 70,000 kilometres per second - almost a quarter of the speed of light. "This is the first time we've seen winds streaming away from ultra-luminous x-ray sources," said Pinto. "And the very high speed of these outflows is telling us something about the nature of the compact objects in these sources, which are frantically devouring matter."

 

While the hot gas is pulled inwards by the central object's gravity, it also shines brightly, and the pressure exerted by the radiation pushes it outwards. This is a balancing act: the greater the mass, the faster it draws the surrounding gas; but this also causes the gas to heat up faster, emitting more light and increasing the pressure that blows the gas away. There is a theoretical limit to how much matter can be pulled in by an object of a given mass, known as the Eddington limit. The limit was first calculated for stars by astronomer Arthur Eddington, but it can also be applied to compact objects like black holes and neutron stars.

 

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Hubble discovers moon orbiting the dwarf planet Makemake

Hubble discovers moon orbiting the dwarf planet Makemake | Amazing Science | Scoop.it
Peering to the outskirts of our solar system, NASA's Hubble Space Telescope has spotted a small, dark moon orbiting Makemake, the second brightest icy dwarf planet—after Pluto—in the Kuiper Belt.

 

The moon—provisionally designated S/2015 (136472) 1 and nicknamed MK 2—is more than 1,300 times fainter than Makemake. MK 2 was seen approximately 13,000 miles from the dwarf planet, and its diameter is estimated to be 100 miles across. Makemake is 870 miles wide. The dwarf planet, discovered in 2005, is named for a creation deity of the Rapa Nui people of Easter Island.

 

The Kuiper Belt is a vast reservoir of leftover frozen material from the construction of our solar system 4.5 billion years ago and home to several dwarf planets. Some of these worlds have known satellites, but this is the first discovery of a companion object to Makemake. Makemake is one of five dwarf planets recognized by the International Astronomical Union.

 

The observations were made in April 2015 with Hubble's Wide Field Camera 3. Hubble's unique ability to see faint objects near bright ones, together with its sharp resolution, allowed astronomers to pluck out the moon from Makemake's glare. The discovery was announced today in a Minor Planet Electronic Circular.


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Exosomes - History and Promise

Exosomes - History and Promise | Amazing Science | Scoop.it
It was discovered some time ago that eukaryotic cells regularly secrete such structures as microvesicles, macromolecular complexes, and small molecules into their ambient environment. Exosomes are one of the types of natural nanoparticles (or nanovesicles) that have shown promise in many areas of research, diagnostics and therapy. They are small lipid membrane vesicles (30-120 nm) generated by fusion of cytoplasmic endosomal multivesicular bodies within the cell surface. Exosomes are found throughout the body in such fluids as blood, saliva, urine, and breast milk. Furthermore, all types of cells secrete them in in vitro culture. It is believed that they have many natural functions, including acting as transporters of nucleic acids (mostly RNA), cytosolic proteins and metabolites to many cells, tissues or organs throughout the body. Much remains to be understood regarding how they are formed, as well as of their targeting and ultimate physiological activity. But many don’t realize that some activities have been rather thoroughly demonstrated─ such as their function in some sort of either local or more systemic intercellular communication.
Exosomes as ToolsGeneral interest in exosomes is now growing for many reasons. One is because of the observation of their natural activity with antigen-presenting cells and in immune responses in the body. Their potential as very powerful biomedical tools of both diagnostic and therapeutic value is now being more widely reported. Applications described include using them as immunotherapeutic reagents, vectors of engineered genetic constructs, and vaccine particles. They’ve also been described as tools in the diagnosis or prognosis of a wide variety of disorders, such as cancer and neurodegenerative diseases. Also, their potential in tissue-level microcommunication is driving interest in such therapeutic activities as cardiac repair following heart attacks. Their potential as biomarkers is being explored because their content has been described as a “fingerprint” of differentiation or signaling or regulation status of the cell generating them. For example, by monitoring the exosomes secreted by transplanted cells, one may be able to predict the status or potentially even the outcome of cell therapy procedures. Clinical trials are in progress for exosomes in many therapeutic functions, for many indications. One example is using dendritic cell-derived exosomes to initiate immune response to cancers.Exosome Manufacturing
Exosome product manufacturing involves many distinct areas of study. First of all, we are interested in their efficient and robust generation at a sufficient scale. Also, because they are found in such raw materials as animal serum, avoiding process-related contaminants is a concern. Finally, a variety of means of separating them from other types of extracellular vesicles and cell debris is under study. As exosomes are being examined in so many applications, their production involves many distinct platforms and concerns. First of all, an appropriate and effective culture mode is required for any cell line that is specifically required by the application. Also, one must consider the quality systems and regulatory status of the materials and manufacturing environment for the particular product addressed. Finally, a robust process must be described for the scale and duration of production demanded. As things exist now, their production can be described as 1) the at-scale expansion and culture of the parent cell-line, 2) the collection or harvest of the culture media containing the secreted exosomes, and 3) the isolation or purification of the desired exosomes from not only other macrovesicles, macromolecular complexes, and small molecules, but from such other process contaminants as cellular debris and culture media components.
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Dynamic models of the complex microbial metapopulation of lake mendota

Dynamic models of the complex microbial metapopulation of lake mendota | Amazing Science | Scoop.it
Population modelling: Understanding lake microbes A lake microbe population model developed by US researchers reveals how environmental factors affect community dyamics.

 

Like many other environments, Lake Mendota, WI, USA, is populated by many thousand microbial species. Only about 1,000 of these constitute between 80 and 99% of the total microbial community, depending on the season, whereas the remaining species are rare. The functioning and resilience of the lake ecosystem depend on these microorganisms, and it is therefore important to understand their dynamics throughout the year.

 


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Could Earth's light blue color be a signature of life?

Could Earth's light blue color be a signature of life? | Amazing Science | Scoop.it

In 1990, Voyager 1 captured the most distant portrait of our planet ever taken, revealing that from beyond Pluto's orbit, Earth appears as nothing more than a "pale blue dot." In a new study, researchers have tested whether Earth's color is a unique feature of life-friendly planets. If so, searching for exoplanets displaying this hue could help in singling out worlds potentially brimming with alien life.

 

As it turns out, Earth's delicate color can be closely mimicked by hypothetical exoplanet types that are completely uninhabitable. A broader portion of Earth's overall spectrum, however, does display a subtle signature only attributable, insofar as we know, to life. Seeking this signature from pale blue worlds in stars' habitable zones with future telescopes could be a powerful tool for identifying worlds deserving of intense further scrutiny.

 

"One important takeaway is that color should be used with caution because we found it's relatively easy to make lifeless planets that are pale blue in color," said lead author Joshua Krissansen-Totton, a doctoral student at the University of Washington. "With that said, I was very excited to find that Earth's spectrum has an intriguing signature that is biogenic, unique and potentially quite useful."

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Scientists use DNA to build the world's tiniest thermometer

Scientists use DNA to build the world's tiniest thermometer | Amazing Science | Scoop.it

Researchers at University of Montreal have created a programmable DNA thermometer that is 20,000x smaller than a human hair. This scientific advance reported this week in the journalNano Letters may significantly aid our understanding of natural and human designed nanotechnologies by enabling to measure temperature at the nanoscale.

 

Over 60 years ago, researchers discovered that the DNA molecules that encode our genetic information can unfold when heated. "In recent years, biochemists also discovered that biomolecules such as proteins or RNA (a molecule similar to DNA) are employed as nanothermometers in living organisms and report temperature variation by folding or unfolding," says senior author Prof. Alexis Vallée-Bélisle. "Inspired by those natural nanothermometers, which are typically 20,000x smaller than a human hair, we have created various DNA structures that can fold and unfold at specifically defined temperatures."

 

One of the main advantages of using DNA to engineer molecular thermometers is that DNA chemistry is relatively simple and programmable. "DNA is made from four different monomer molecules called nucleotides: nucleotide A binds weakly to nucleotide T, whereas nucleotide C binds strongly to nucleotide G," explains David Gareau, first author of the study. "Using these simple design rules we are able to create DNA structures that fold and unfold at a specifically desired temperature." "By adding optical reporters to these DNA structures, we can therefore create 5 nm-wide thermometers that produce an easily detectable signal as a function of temperature," adds Arnaud Desrosiers, co-author of this study.

 

These nanoscale thermometers open many exciting avenues in the emerging field of nanotechnology, and may even help us to better understand molecular biology. "There are still many unanswered questions in biology," adds Prof. Vallée-Bélisle, "For example, we know that the temperature inside the human body is maintained at 37° C, but we have no idea whether there is a large temperature variation at the nanoscale inside each individual cell." One question currently under investigation by the research team is to determine whether nanomachines and nanomotors developed by nature over millions years of evolution also overheat when functioning at high rate. "In the near future, we also envision that these DNA-based nanothermometers may be implement in electronic-based devices in order to monitor local temperature variation at the nanoscale," concludes Prof. Vallée-Bélisle.

 

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Intelligent? Brainless slime can 'learn' without a nervous system

Intelligent? Brainless slime can 'learn' without a nervous system | Amazing Science | Scoop.it
What is intelligence? The definitions vary, but all infer the use of grey matter, whether in a cat or a human, to learn from experience.

 

A slime made up of independent, single cells, they found, can "learn" to avoid irritants despite having no central nervous system. "Tantalizing results suggest that the hallmarks for learning can occur at the level of single cells," the team wrote in a paper published in the journal Proceedings of the Royal Society B.

 

For the study, researchers from Belgium and France sought to demonstrate "habituation learning" in a brainless organism. Habituation learning is when original behaviour changes in response to repeated stimulus—think of a human losing their fear of needles after being repeatedly exposed to them in phobia therapy.

 

The team wanted to see whether an organism without a nervous system could similarly "learn" from experience and change its behavior accordingly.

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Machine learning rivals human skills in cancer detection

Machine learning rivals human skills in cancer detection | Amazing Science | Scoop.it

Two announcements yesterday (April 21) suggest that deep learning algorithms rival human skills in detecting cancer from ultrasound images and other sources.

 

Samsung Medison, a global medical equipment company and an affiliate of Samsung Electronics, has just updated its RS80A ultrasound imaging system with a deep learning algorithm for breast-lesion analysis. The “S-Detect for Breast” feature uses big data collected from breast-exam cases and recommends whether the selected lesion is benign or malignant. It’s used in in lesion segmentation, characteristic analysis, and assessment processes, providing “more accurate results.”

 

“We saw a high level of conformity from analyzing and detecting lesion in various cases by using the S-Detect,” said professor Han Boo Kyung, a radiologist at Samsung Medical Center. “Users can reduce taking unnecessary biopsies and doctors-in-training will likely have more reliable support in accurately detecting malignant and suspicious lesions.”

 

Meanwhile, researchers from the Regenstrief Institute and Indiana University School of Informatics and Computing at Indiana University-Purdue University Indianapolis say they’ve found that open-source machine learning tools are as good as — or better than — humans in extracting crucial meaning from free-text (unstructured) pathology reports and detecting cancer cases. The computer tools are also faster and less resource-intensive. U.S. states require cancer cases to be reported to statewide cancer registries for disease tracking, identification of at-risk populations, and recognition of unusual trends or clusters. This free-text information can be difficult for health officials to interpret, which can further delay health department action, when action is needed.

 

“We think that its no longer necessary for humans to spend time reviewing text reports to determine if cancer is present or not,” said study senior author Shaun Grannis*, M.D., M.S., interim director of the Regenstrief Center of Biomedical Informatics.

 

“We have come to the point in time that technology can handle this. A human’s time is better spent helping other humans by providing them with better clinical care. Everything — physician practices, health care systems, health information exchanges, insurers, as well as public health departments — are awash in oceans of data. How can we hope to make sense of this deluge of data? Humans can’t do it — but computers can.”

This is especially relevant for underserved nations, where a majority of clinical data is collected in the form of unstructured free text, he said.

 

The researchers sampled 7,000 free-text pathology reports from over 30 hospitals that participate in the Indiana Health Information Exchange and used open source tools, classification algorithms, and varying feature selection approaches to predict if a report was positive or negative for cancer. The results indicated that a fully automated review yielded results similar or better than those of trained human reviewers, saving both time and money.

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Water molecules confined in nanochannels exhibit quantum tunneling behavior

Water molecules confined in nanochannels exhibit quantum tunneling behavior | Amazing Science | Scoop.it
Water molecules confined in nanochannels exhibit tunneling behavior that smears out the positions of the hydrogen atoms into a pair of corrugated rings.

 

Tunneling is a quantum effect that lets particles go through microscopic barriers in a single bound. A study of water trapped in an emerald-like crystal reveals tunneling of water molecules among multiple orientations, so that each molecule is essentially in six configurations at once. The researchers showed with neutron scattering experiments that the tunneling causes the water’s hydrogen atoms to spread out into ring-like distributions. This new form of water is a more symmetric structure that is predicted to have zero electric dipole moment—the property that normally allows water to form hydrogen bonds and perform well as a solvent.

 

Tunneling occurs when an object traverses a barrier without having enough energy to do so classically. Certain molecules can tunnel among rotational orientations. A representative example is the methyl group (CH3)(CH3), which is a carbon atom bound to three hydrogens in a symmetric pyramid configuration. Electric forces from nearby atoms generate repulsion that resists any rotation around the pyramid axis. However, the hydrogens can tunnel through these barriers from one pyramid corner to the next. This discrete hopping couples together rotational orientations, causing an observable splitting of the ground state into multiple levels with slightly different energies.

 

 Recently, optical spectroscopy revealed energy splitting in the terahertz spectrum of water molecules in the gemstone beryl, suggesting that the molecule is hopping among multiple states [1]. The crystal structure of beryl(Be3Al2Si6O18)(Be3Al2Si6O18) contains channels with hexagonal cross-sections that can trap water molecules. The channels periodically narrow into “cages” roughly 0.5 nanometers wide by 0.9 nanometers long and only big enough for one water molecule. The previously observed splitting suggested that the confined water was rotationally tunneling inside the channels, but a more direct test was necessary. Now Alexander Kolesnikov from Oak Ridge National Laboratory (ORNL) in Tennessee and his colleagues have performed a series of neutron scattering measurements on a beryl sample containing water.

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The role of big data in medicine

The role of big data in medicine | Amazing Science | Scoop.it

Technology is revolutionizing our understanding and treatment of disease, says the founding director of the Icahn Institute for Genomics and Multiscale Biology at New York’s Mount Sinai Health System.

 

The role of big data in medicine is one where we can build better health profiles and better predictive models around individual patients so that we can better diagnose and treat disease.

 

One of the main limitations with medicine today and in the pharmaceutical industry is our understanding of the biology of disease. Big data comes into play around aggregating more and more information around multiple scales for what constitutes a disease—from the DNA, proteins, and metabolites to cells, tissues, organs, organisms, and ecosystems. Those are the scales of the biology that we need to be modeling by integrating big data. If we do that, the models will evolve, the models will build, and they will be more predictive for given individuals.

 

It’s not going to be a discrete event—that all of a sudden we go from not using big data in medicine to using big data in medicine. I view it as more of a continuum, more of an evolution. As we begin building these models, aggregating big data, we’re going to be testing and applying the models on individuals, assessing the outcomes, refining the models, and so on. Questions will become easier to answer. The modeling becomes more informed as we start pulling in all of this information. We are at the very beginning stages of this revolution, but I think it’s going to go very fast, because there’s great maturity in the information sciences beyond medicine.

 

The life sciences are not the first to encounter big data. We have information-power companies like Google and Amazon and Facebook, and a lot of the algorithms that are applied there—to predict what kind of movie you like to watch or what kind of foods you like to buy—use the same machine-learning techniques. Those same types of methods, the infrastructure for managing the data, can all be applied in medicine.


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