Bacteria recruit other species with long-range electrical signals

Biologists at UC San Diego who recently found that bacteria resolve social conflicts within their communities and communicate with one another like neurons in the brain have discovered another human-like trait in these apparently not-so-simple, single-celled creatures. Bacteria living in diverse communities called "biofilms" create what are essentially electronic advertisements, the scientists report in a paper published in this week's issue of the journal Cell, by sending long-range electrical signals to other bacterial species that can lead to the recruitment of new members to their biofilm community. "We've discovered that bacterial biofilm communities can actively modulate the motile behavior of diverse bacterial species through electrical signals," said Gürol Süel, a professor of molecular biology, Associate Director of the San Diego Center for Systems Biology and Howard Hughes Medical Institute -- Simons Faculty Scholar at UC San Diego, who headed the research effort. "In this way, bacteria within biofilms can exert long-range and dynamic control over the behavior of distant cells that are not part of their communities." Biofilms are communities of bacteria and other microorganisms that form thin structures on surfaces -- such as the tartar that develops on teeth -- that are highly resistant to chemicals and antibiotics. Because not much is known about how they form, recruit other microorganisms and resist attack, such information about their behavior has practical applications -- from preventing tartar formation on teeth to avoiding Staph infections in hospitals. But the idea that bacteria ensconced in their protective biofilm villages behave like sophisticated marketing agents -- advertising the presence of their communities by sending out electronic messages -- overturns fundamental beliefs that both scientists and the general public have about these supposedly lowly creatures. "Our study shows that bacteria living in biofilm communities do something similar to sending electronic messages to friends," said Jacqueline Humphries, a doctoral student working in Süel's laboratory and the first author of the paper. "In fact, the mechanism we discovered is general. We found that bacteria from one species can send long-range electrical signals that will lead to the recruitment of new members from another species. As a result, we've identified a new mechanism and paradigm for inter-species signaling." The UC San Diego biologists discovered in their laboratory work, which integrated experiments with mathematical modeling, that a biofilm composed of a single species of Bacillus subtilis bacteria was able to recruit bacteria of a different species -- in this case, Pseudomonas aeruginosa -- through electrical signaling. Using microfluidic growth chambers, the biologists documented the process by which potassium ion electrical signaling generated by B. subtilis biofilms attracted distant cells within the chambers to the edge of electrically oscillating biofilms. Süel and his team of graduate students and postdoctoral fellows discovered in the summer of 2015 that oscillations within biofilm communities resolved a social conflict between individual cells that were cooperating, but also had to compete for food. Bacteria at the outer edge of the biofilm are closest to nutrients necessary for growth and could starve the sheltered interior cells. But the scientists discovered that oscillating biofilms develop what they call "metabolic codependence" by putting the brakes periodically on the outer cells' growth to give the interior cells access to nutrients. Not long after, Süel and his team discovered that bacteria living in biofilm communities communicate with one another electronically through proteins called "ion channels," an electrical signaling method similar to that used by neurons in the human brain. Their most recent discovery -- that bacteria in biofilms can recruit other species with long-range electrical signals -- could turn out to be not only the most surprising of the team's findings, but perhaps the most significant for our understanding of how bacteria impact human health. "Our latest discovery suggests that the composition of mixed species bacterial communities, such as our gut microbiome, could be regulated through electrical signaling," said Süel. "It may even be possible that bacterial and human gut cells can interact electrically within the human gut. Our work may in the future even lead to new electrical-based biomedical approaches to control bacterial behavior and communities." Other co-authors of the paper were biologists Jintao Liu and Arthur Prindle, postdoctoral researchers in Süel's laboratory; biologist Fang Yuan, a doctoral student in the lab; UC San Diego physicist Liyang Xiong; Heidi Arjes of Stanford University and Lev Tsimring, a research scientist and associate director of UC San Diego's Biocircuits Institute.     Source:University of California - San Diego

Was a researcher just served a world first CRISPR meal?

For (probably) the first time ever, plants modified with the "genetic scissors" CRISPR-Cas9 has been cultivated, harvested and cooked. Stefan Jansson, professor in Plant Cell and Molecular Biology at Umeå University, served pasta with "CRISPRy" vegetable fry to a radio reporter. Although the meal only fed two people, it was still the first step towards a future where science can better provide farmers and consumers across the world with healthy, beautiful and hardy plants. CRISPR (Clustered regularly interspaced short palindromic repeats)-Cas9 is a complicated name for an easy, but targeted, way of changing the genes of an organism. The decisive discovery was published in 2012 by researchers at Umeå University, and the "Swiss army knife of genetic engineering" has been predicted to change the world. With CRISPR-Cas9, researchers can either replace one of the billions of "letters" present in an organism's genome (i.e. the entire gene pool consisting of DNA) or remove short segments, similar to when you edit a written text in a word processor. The technology is called "gene editing" or "genome editing." The first clinical applications are underway; maybe we can soon cure hereditary disease using this technology. However, the situation differs somewhat in the agricultural field. There, the issue is not IF researchers can create plants leading to a more sustainable land management, but rather if these will be allowed in farming. Will plants whose genome has been edited using CRISPR-Cas9 fall under GMO legislation or not? If they do, it makes them illegal to plant in great parts of the world. If not, they will -- just like other plants -- be allowed to be grown at the farmers own discretion. The EU has avoided answering the question, but in November 2015 the Swedish Board of Agriculture interpreted the law as if only a segment of DNA has been removed and no "foreign DNA" has been inserted, it is not to be regarded as a genetically modified organism -- a GMO. That also means that the plant can be cultivated without prior permission. In spring 2016, American authorities stated that they agreed. The organism in question there was a mushroom who had lost the part of its DNA that made it go brown. This opens up for using the technology to develop plants of the future. This summer has been the first time that plants that have been gene-edited using CRISPR-Cas9 -- in a way that does not classify the plant as GMO -- have been allowed to be cultivated outside of the lab. This is definitely the first time in Europe, and even if it been done before in other parts of the world, it has been kept secret. This time, it was a cabbage plant and the Radio Sweden gardening show "Odla med P1" took part in the harvest leading to the probably first-ever meal of CRISPR-Cas9 genome-edited plants. The first CRISPR meal to have been enjoyed was "Tagliatelle with CRISPRy fried vegetables." "The CRISPR-plants in question grew in a pallet collar in a garden outside of Umeå in the north of Sweden and were neither particularly different nor nicer looking than anything else," says plant scientist Stefan Jansson. But they represent both a new phase of agriculture where scientific advances will be implemented in new plant species and that to a small or large extent will be made available to farmers across the world. In other words: a meal for the future.     Source:Umeå universitet

Quantum knots are real

The very first experimental observations of knots in quantum matter have just been reported in Nature Physics by scientists at Aalto University (Finland) and Amherst College (USA). The scientists created knotted solitary waves, or knot solitons, in the quantum-mechanical field describing a gas of superfluid atoms, also known as a Bose-Einstein condensate. In contrast to knotted ropes, the created quantum knots exist in a field that assumes a certain direction at every point of space. The field segregates into an infinite number of linked rings, each with its own field direction. The resulting structure is topologically stable as it cannot be separated without breaking the rings. In other words, one cannot untie the knot within the superfluid unless one destroys the state of the quantum matter. - To make this discovery we exposed a Rubidium condensate to rapid changes of a specifically tailored magnetic field, tying the knot in less than a thousandth of a second. After we learned how to tie the first quantum knot, we have become rather good at it. Thus far, we have tied several hundred such knots, says Professor David Hall, Amherst College. The scientists tied the knot by squeezing the structure into the condensate from its outskirts. This required them to initialize the quantum field to point in a particular direction, after which they suddenly changed the applied magnetic field to bring an isolated null point, at which the magnetic field vanishes, into the center of the cloud. Then they just waited for less than a millisecond for the magnetic field to do its trick and tie the knot. -For decades, physicists have been theoretically predicting that it should be possible to have knots in quantum fields, but nobody else has been able to make one. Now that we have seen these exotic beasts, we are really excited to study their peculiar properties. Importantly, our discovery connects to a diverse set of research fields including cosmology, fusion power, and quantum computers, says research group leader Mikko Möttönen, Aalto University. Knots have been used and appreciated by human civilizations for thousands of years. For example, they have enabled great seafaring expeditions and inspired intricate designs and patterns. The ancient Inca civilization used a system of knots known as quipu to store information. In modern times, knots have been thought to play important roles in the quantum-mechanical foundations of nature, although they have thus far remained unseen in quantum dynamics. In everyday life, knots are typically tied on ropes or strings with two ends. However, these kinds of knots are not what mathematicians call topologically stable since they can be untied without cutting the rope. In stable knots, the ends of the ropes are glued together. Such knots can be relocated within the rope but cannot be untied without scissors. Mathematically speaking, the created quantum knot realizes a mapping referred to as Hopf fibration that was discovered by Heinz Hopf in 1931. The Hopf fibration is still widely studied in physics and mathematics. Now it has been experimentally demonstrated for the first time in a quantum field. -This is the beginning of the story of quantum knots. It would be great to see even more sophisticated quantum knots to appear such as those with knotted cores. Also it would be important to create these knots in conditions where the state of the quantum matter would be inherently stable. Such system would allow for detailed studies of the stability of the knot itself, says Mikko Möttönen.     Source:Aalto University

Scientists tie the tightest knot ever achieved

Scientists at The University of Manchester have produced the most tightly knotted physical structure ever known -- a scientific achievement which has the potential to create a new generation of advanced materials. The University of Manchester researchers, led by Professor David Leigh in Manchester's School of Chemistry, have developed a way of braiding multiple molecular strands enabling tighter and more complex knots to be made than has previously been possible. The breakthrough knot has eight crossings in a 192-atom closed loop -- which is about 20 nanometres long (ie 20 millionths of a millimeter). Being able to make different types of molecular knots means that scientists should be able to probe how knotting affects strength and elasticity of materials which will enable them to weave polymer strands to generate new types of materials. Professor David Leigh said: "Tying knots is a similar process to weaving so the techniques being developed to tie knots in molecules should also be applicable to the weaving of molecular strands. "For example, bullet-proof vests and body armour are made of kevlar, a plastic that consists of rigid molecular rods aligned in a parallel structure -- however, interweaving polymer strands have the potential to create much tougher, lighter and more flexible materials in the same way that weaving threads does in our everyday world. "Some polymers, such as spider silk, can be twice as strong as steel so braiding polymer strands may lead to new generations of light, super-strong and flexible materials for fabrication and construction." Professor David Leigh said he and his team were delighted to have achieved this scientific landmark. He explained the process behind their success: "We 'tied' the molecular knot using a technique called 'self-assembly', in which molecular strands are woven around metal ions, forming crossing points in the right places just like in knitting -- and the ends of the strands were then fused together by a chemical catalyst to close the loop and form the complete knot. "The eight-crossings molecular knot is the most complex regular woven molecule yet made by scientists." The research breakthrough will be published in the journal Science on 13 January 2017 in a paper entitled: 'Braiding a molecular knot with eight crossings'     Source:University of Manchester

First look inside nanoscale catalysts shows 'defects' are useful

Using one of the world's brightest light sources to peer inside some of the world's smallest particles, scientists have confirmed a longstanding hypothesis: that atomic disorder or "defects" at the edges of nanoparticles is what makes them effective as chemical change agents. The process by which a change agent, or catalyst, accelerates a chemical reaction is key to the creation of many materials essential to daily life, such as plastics, fuels and fertilizers. Known as catalysis, this process is a basic pillar of the chemical industry, making chemical reactions more efficient and less energy-demanding, and reducing or even eliminating the use and generation of hazardous substances. Although catalysts have been used in industry for more than a century, scientists have yet to observe how their structure impacts their effectiveness as change agents. That's because catalysts are typically tiny metallic nanoparticles made of precious metals such as Platinum, Palladium or Rhenium. The extreme smallness that makes nanoparticles such effective catalysts also makes it hard to see how they work. If scientists could peer inside individual nanoparticles' chemical reactions at a nanoscopic level, they would gather a treasure of useful knowledge for the design of improved catalysts to address the pressing energy needs of the 21st century. That type of knowledge may now be close at hand, thanks to new research published January 11 in the journal Nature. In the new study -- led by Dr. Elad Gross from the Institute of Chemistry and the Center for Nanoscience and Nanotechnology at the Hebrew University of Jerusalem, and Prof. F. Dean Toste from the College of Chemistry at University of California, Berkeley, and Chemical Science Division at Lawrence Berkeley National Laboratory -- researchers directly observed for the first time how metallic nanoparticles, used as catalysts in numerous industrial processes, activate catalytic processes. Using a light source one million times brighter than the sun, the researchers were able to observe chemical reactivity on single Platinum particles similar to those used as industrial catalysts. What they found is that chemical reactivity primarily occurs on the particles' periphery or edges, while lower reactivity occurs at the particles' center. The different reactivity observed at the center and edges of Platinum particles corresponds to the different properties of the Platinum atoms in the two locations. The atoms are mostly flat at the center, while they're corrugated and less-ordered at the edges. This disorderly or "defective" structure means that Platinum atoms at the edges are not totally surrounded by other Platinum atoms, and will therefore form stronger interactions with reactant molecules. Stronger interactions can activate the reactant molecules and initiate a chemical reaction that will transform the reactant molecule into a desired product. The research findings validate a well-known hypothesis in the world of catalysis, which correlates high catalytic reactivity with high density of atomic defects. It also shows, for the first time, that the enhanced reactivity of defected sites can be identified at the single-particle level. "Our findings provide insights about the ways by which the atomic structure of catalysts controls their reactivity. This knowledge can direct the design of improved catalysts that will make chemical process greener, by decreasing the amount of energy that is consumed in the process and preventing the formation of unwanted, potentially hazardous, products," said Dr. Elad Gross, from the Institute of Chemistry and the Center for Nanoscience and Nanotechnology at the Hebrew University of Jerusalem. To peer into individual nanoparticles, researchers focused a bright infrared beam generated in a synchrotron source (Advanced Light Source, Lawrence Berkeley National Laboratory) into a thin probe with an apex diameter of 20 nanometers. The probe acts as an antenna, localizes the infra-red light in a specific range, and by that provides the capabilities to identify molecules which reside on the surface of the catalytic nanoparticles. By scanning the particles with the nanometric probe while it is being radiated by the infrared light, the researchers were able to identify the locations and conditions in which chemical reaction occurs on the surface of single particle. The Hebrew University of Jerusalem is Israel's leading academic and research institution, producing one-third of all civilian research in Israel. For more information, visit     Source:The Hebrew University of Jerusalem

VW pleads guilty to emissions cheating

 Volkswagen has pleaded guilty to three criminal charges in the US and will pay fines totalling $4.3bn (£3.5bn) to settle charges over the emissions-rigging scandal. The firm will pay $2.8bn in criminal fines and $1.5bn in civil penalties. US Attorney-General Loretta Lynch said VW denied and then lied in a bid to cover up its actions. The fines amounted to one of the biggest clean air penalties ever achieved, she added. Six VW executives and managers have also been charged over their role in the emissions cheating. Matthias Müller, Volkswagen Group chief executive, said the German car maker "deeply regrets" its actions. Hans Dieter Pötsch, chairman of VW's supervisory board, said: "We are no longer the same company we were 16 months ago." The Department of Justice said VW had a long-running scheme to sell about 590,000 diesel vehicles in the US fitted with a defeat device to cheat on emissions tests. VW will be on probation for three years and be overseen by an independent monitor during that period. It has agreed to co-operate with the DofJ's investigation and prosecution of six executives involved in the crimes. The firm is pleading guilty to "participating in a conspiracy to defraud" the US and its American customers, as well as breaking the Clean Air Act by using cheating software in its cars. VW is also charged with obstruction of justice for destroying documents related to the scheme, and with importing the cars into the US "by means of false statements about the vehicles' compliance with emissions limits". There are still investor and consumer lawsuits pending in Europe. The $4.3bn fines means that the total costs associated with the emissions cheating scandal are set to exceed the $19.2bn the company has set aside to deal with the issue. VW has already agreed to a $15bn civil settlement with environmental authorities and car owners in the US. Analysis: Theo Leggett, business correspondent Volkswagen has been humiliated by the US authorities - punished for using illegal software to disguise the level of emissions produced by its diesel powered cars. Not only has it been hit with heavy fines, but it has also had to plead guilty to criminal charges and sign up to a 'Statement of Facts' - an agreed version of events that sets out exactly what it did wrong. Taken alongside the $15bn deal to compensate consumers, buy back cars and pay for environmental measures agreed last year, the new fines mean VW will have to pay out $19.3bn in the US alone. That's more than $32,000 for each of the 600,000 cars sold with defeat device software in the region. Yet the settlement is actually good news for Volkswagen. It was always going to face a hefty bill for trying to deceive US regulators. Now, at least, it knows how much it will have to pay. It is still facing potentially damaging lawsuits from investors and car buyers in Europe, but a large chunk of the legal uncertainty has now been removed. However, it looks as though US regulators are far from finished. Six executives are now facing charges over their alleged role in the affair - and prosecutors have already made it clear they believe senior figures were involved in attempts to cover up what was going on. So the pressure on the company itself may now ease, but it's likely some individuals will be holding long meetings with their lawyers. The scandal erupted in September 2015 when the US Environmental Protection Agency (EPA) found that many VW cars sold in America had a "defeat device" - or software - in diesel engines that could detect when they were being tested and adjust the performance accordingly to improve results. The German car giant subsequently admitted cheating emissions tests in the US and many countries throughout the world, including the UK. On Monday it emerged that VW executives knew about emissions cheating two months before the scandal broke, but chose not to tell US regulators, according to court papers. '10-year conspiracy' The executives involved include Oliver Schmidt, who headed VW's US environmental regulatory compliance office from 2012 until March 2015. He was arrested while on holiday in Florida at the weekend. On Monday he was charged with conspiracy to defraud and has been remanded ahead of a court appearance on Thursday. He is one of the six executives the DoJ said were being charged for their roles in the "nearly 10-year conspiracy". The others include VW brand head of development Hainz-Jakob Neusser and former VW head of engine development Jens Hadler. "This wasn't simply the action of some faceless, multinational corporation," said deputy Attorney-General Sally Yates. "This conspiracy involved flesh-and-blood individuals who used their positions within Volkswagen to deceive both regulators and consumers."   Source:BBC    

Crystallization method offers new option for carbon capture from ambient air

Scientists at the Department of Energy's Oak Ridge National Laboratory have found a simple, reliable process to capture carbon dioxide directly from ambient air, offering a new option for carbon capture and storage strategies to combat global warming. Initially, the ORNL team was studying methods to remove environmental contaminants such as sulfate, chromate or phosphate from water. To remove those negatively charged ions, the researchers synthesized a simple compound known as guanidine designed to bind strongly to the contaminants and form insoluble crystals that are easily separated from water. In the process, they discovered a method to capture and release carbon dioxide that requires minimal energy and chemical input. Their results are published in the journal Angewandte Chemie International Edition. "When we left an aqueous solution of the guanidine open to air, beautiful prism-like crystals started to form," ORNL's Radu Custelcean said. "After analyzing their structure by X-ray diffraction, we were surprised to find the crystals contained carbonate, which forms when carbon dioxide from air reacts with water." Decades of research has led to the development of carbon capture and long-term storage strategies to lessen the output or remove power plants' emissions of carbon dioxide, a heat-trapping greenhouse gas contributing to a global rise in temperatures. Carbon capture and storage strategies comprise an integrated system of technologies that collects carbon dioxide from the point of release or directly from the air, then transports and stores it at designated locations. A less traditional method that absorbs carbon dioxide already present in the atmosphere, called direct air capture, is the focus of ORNL's research described in this paper, although it could also be used at the point where carbon dioxide is emitted. Once carbon dioxide is captured, it needs to be released from the compound so the gas can be transported, usually through a pipeline, and injected deep underground for storage. Traditional direct air capture materials must be heated up to 900 degrees Celsius to release the gas -- a process that often emits more carbon dioxide than initially removed. The ORNL-developed guanidine material offers a less energy-intensive alternative. "Through our process, we were able to release the bound carbon dioxide by heating the crystals at 80-120 degrees Celsius, which is relatively mild when compared with current methods," Custelcean said. After heating, the crystals reverted to the original guanidine material. The recovered compound was recycled through three consecutive carbon capture and release cycles. While the direct air capture method is gaining traction, according to Custelcean, the process needs to be further developed and aggressively implemented to be effective in combatting global warming. Also, they need to gain a better understanding of the guanidine material and how it could benefit existing and future carbon capture and storage applications. The research team is now studying the material's crystalline structure and properties with the unique neutron scattering capabilities at ORNL's Spallation Neutron Source (SNS), a DOE Office of Science User Facility. By analyzing carbonate binding in the crystals, they hope to better understand the molecular mechanism of carbon dioxide capture and release and help design the next generation of sorbents. The scientists also plan to evaluate the use of solar energy as a sustainable heat source to release the bound carbon dioxide from the crystals.     Source:Oak Ridge National Laboratory

The future of biomaterial manufacturing: Spider silk production from bacteria

A new video article in JoVE, the Journal of Visualized Experiments, demonstrates procedures to harvest and process synthetic spider silk from bacteria. The procedure presented in the video article revolutionizes the spider silk purification process by standardizing a key step known as "post-spin." In this step, silk molecules are stretched by a mechanical actuator to increase fiber strength. These mechanical improvements produce uniform spider silk and remove human error from the spinning process. As a result, the synthetic silk is much closer to the natural fibers produced by the female black widow spider than what was previously possible, and the procedure provides a scalable ground work to utilize spider silk in material manufacturing. Due to their mechanical properties, synthetic spider silks have numerous manufacturing and industrial applications. Of particular interest is the high tensile strength of black widow silk, which is comparable to Kevlar in strength, but is lighter and of a lower density. If scientists could reproduce the mechanical properties of spider spun silk in the laboratory, the material could be used to replace Kevlar, carbon fiber and steel. Increased production of this new biomaterial will have an impact on a wide variety of products where spider silk's properties are valuable, ranging from bulletproof vests and aircraft bodies to bridge cables and medical sutures. While scientists have been able to produce spider silk with the same biochemical integrity of the natural fibers for some time, it has remained difficult to mimic a spider's "post-spin" techniques. The natural post-spin process stretches the fiber in order to align the fiber molecules, and increases the fiber's tensile strength. To solve this problem, Dr. Craig Vierra from the University of the Pacific developed a technique that removes human variability by using a mechanical actuator. Built by Dr. Vierra and his laboratory group, the mechanical actuator can reliably stretch fibers to a specified length, mimicking the spider's natural post-spin. Dr. Vierra tells us, "The procedure decreases the variance in the mechanical properties that are seen. Before this procedure, there was a tremendous amount of variation in synthetic fibers." Dr. Vierra continues his work with black widow spiders and synthetic silk production. "We're working on fusing what we've learned here and expanding the procedure en masse." Eventually, the lab aims to make spider silk a renewable resource for material production that may change how we engineer the future. Concerning publication in JoVE, Dr. Vierra notes the decision was made because, "The visual representation is significant because most research articles don't go into the step by step procedure (to collect spider silk). Also, many of the processes need a visual representation to fully grasp."     Source:The Journal of Visualized Experiments
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