Aurelia Butler

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    in Heart

    Electrical bacteria may help clean oil spills and curb methane emissions

    The small motorboat anchors in the middle of the Chesapeake Bay. Shrieks of wintering birds assault the vessel’s five crew members, all clad in bright orange flotation suits. One of the crew slowly pulls a rope out of the water to retrieve a plastic tube, about the length of a person’s arm and filled with mud from the bottom of the bay. As the tube is hauled on board, the stench of rotten eggs fills the air.

    “Chesapeake Bay mud is stinky,” says Sairah Malkin, a biogeochemist at the University of Maryland Center for Environmental Science in Cambridge who is aboard the boat. The smell comes from sulfuric chemicals called sulfides within the mud. They’re quite toxic, Malkin explains.

    Malkin and her team venture out onto the bay every couple of months to sample the foul muck and track the abundance of squiggling mud dwellers called cable bacteria. The microbes are living wires: Their threadlike bodies — thinner than a human hair — can channel electricity.

    Sairah Malkin, of the University of Maryland Center for Environmental Science, cuts holes in a large sediment coring tube to sample mud collected from the bottom of the Chesapeake Bay.Clara Fuchsman

    Cable bacteria use that power to chemically rewire their surroundings. While some microbes in the area produce sulfides, the cable bacteria remove those chemicals and help prevent them from moving up into the water column. By managing sulfides, cable bacteria may protect fish, crustaceans and other aquatic organisms from a “toxic nightmare,” says Filip Meysman, a biogeochemist at the University of Antwerp in Belgium. “They’re kind of like guardian angels in these coastal ecosystems.”

    Now, scientists are studying how these living electrical filaments might do good in other ways. Laboratory experiments show that cable bacteria can support other microbes that consume crude oil, so researchers are investigating how to encourage the bacteria’s growth to help clean up oil spills. What’s more, researchers have shown that cable bacteria could help slash emissions of a potent greenhouse gas — methane — into the atmosphere.

    There’s plenty of evidence that cable bacteria exert a strong influence over their microbial neighbors, Meysman says. The next step, he says, is to figure out how to channel that influence for the greater good.

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    Electric life

    Under the microscope, cable bacteria resemble long sausage links. Their multicellular bodies can grow up to 5 centimeters long. Embedded in the envelope of each cell are parallel “wires” of conductive proteins, which the bacteria use to channel electrons. According to Meysman, the wires are more conductive than the semi­conductors found in electronics.

    About a decade ago, a team of scientists first discovered cable bacteria, in sediment collected from the bottom of Denmark’s Aarhus Bay. Since then, cable bacteria have been found on at least four continents, in streams, lakes, estuaries and coastal environments. “Name me a country, and I’ll show you where the cable bacteria are,” Meysman says.

    Most often, cable bacteria nestle shallow in the sediment, with one end positioned near the surface where there is oxygen and the other end plugged into deeper, sulfide-rich zones. Using their filamentous bodies as electrical conduits, cable bacteria snatch electrons from sulfides on one end and off-load them to oxygen — an eager electron acceptor — at the other, says Nicole Geerlings, a biogeochemist at Utrecht University in the Netherlands. Similar to how batteries charge and release energy by transferring electrons between an anode and cathode, cable bacteria power themselves by channeling electrons, she says. “The electron transport gives [cable bacteria] energy.”

    This unique lifestyle allows cable bacteria to survive in an environment that many organisms could not endure.

    A cable bacterium (right) has a multicellular, segmented body that can grow up to 5 centimeters. Electrically conductive, parallel fibers (visible in the close-up at left) encase the body.From left: N. Geerlings/Utrecht Univ.; Silvia Hidalgo Martinez/Univ. of Antwerp

    Toxic fire wall

    In 2015, Malkin, Meysman and colleagues reported that cable bacteria may help to counteract the onset of euxinia — a fatal buildup of sulfides in oxygen-starved bodies of water. Euxinia can trigger mass die-offs of fish, crustaceans and other aquatic life.

    The lethal phenomenon can occur after fertilizers or sewage are washed into the sea or lakes. That flow of nutrients can trigger algal blooms. When those nutrients are depleted, the blooms die, and large quantities of organic matter sink and accumulate on the sediment. Microbes then decompose the dead material, devouring much of the oxygen in the surrounding water in the process. When oxygen levels become critically low, sulfides may begin to leak from the sediment into the water, giving rise to euxinia.

    Sediments near the bottom of this core sample, taken from the Chesapeake Bay, are probably dark due to the presence of sulfides, while sediments near the top are lighter because cable bacteria have removed the sulfides.S. Malkin

    While studying cable bacteria in a brackish body of water in the Netherlands, Malkin and colleagues discovered a thin layer of rust coating the lake’s bottom. As the cable bacteria pulled electrons from sulfides, converting the noxious chemicals into less-harmful sulfates, the water within the sediment became more acidic, which dissolved some minerals containing iron. The now-mobile iron percolated upward in the sediment, until it interacted with oxygen to form rust.

    This layer of rust could capture sulfides that would otherwise flow into the water, acting as a “fire wall” that could delay euxinia for over a month, or even prevent it altogether, the researchers reported. Even when the cable bacteria’s population dropped, the rust layer persisted, protecting other aquatic creatures from sulfide exposure. The rust may explain why even though instances of nutrient pollution, algal blooms and oxygen depletion are relatively common, reports of euxinia are rare.

    Oil cleanup

    Some researchers are trying to harness the bacteria’s electrical abilities to tackle another devastating threat to coastal ecosystems — oil spills.

    When an oil spill happens in a body of water, booms, skimmers or sorbents are often deployed to limit the spread of hydrocarbons on the surface. But oil may also wash onto beaches, mix with sediments in shallow waters and aggregate onto sinking particles of organic debris, hitching a ride to the seafloor.

    Cleaning up oil at the bottom of the sea is a difficult job, says Ugo Marzocchi, a biogeochemist at Aarhus University in Denmark. “I am not aware of a very effective way to remove hydrocarbons from the seafloor,” he says. “In inland freshwater systems, what is generally done is to dig out the sediments,” he says, an expensive strategy that would be even more costly at sea.

    [embedded content]
    Electrical cable bacteria (white filaments) emerge from the seafloor sediment (at bottom) stretching their bodies to reach a zone of oxygen in the water. The stringy organisms use the oxygen to offload electrons they’ve harvested from harmful sulfides found in the sediment. As sulfide concentrations go down, the water becomes more habitable to microbes that can clean up oil spills.

    Some soil-dwelling microorganisms can use hydrocarbons to fuel their metabolism, and researchers have been studying how some of these oil burners might assist in the cleanup of contaminated sediments. But as they break down hydrocarbons, the microbes generate those concerning sulfides, which are detrimental to the microbes’ own survival, Marzocchi says. In other words, the microbes can help clean up the oil for only so long before they’re overwhelmed by their own toxic waste.

    Cable bacteria might be just the solution, Marzocchi thought. In 2016, researchers reported finding evidence of the electrical microbes in a tar oil-contaminated groundwater aquifer in Germany. Knowing that cable bacteria could occupy sediments contaminated with hydrocarbons, Marzocchi and colleagues reasoned that these bacteria might be able to assist oil-burning microbes and accelerate oil cleanup.

    The researchers filled several containers with oil-contaminated sediment from Aarhus Bay — which contained naturally occurring oil-eating bacteria. The group then injected a few containers with cable bacteria and monitored the degree of hydrocarbon degradation in all of the containers over seven weeks. By the end of the test, the concentration of alkanes — a type of hydrocarbon — in the sediment with cable bacteria had dropped from 0.125 milligrams per gram of sediment to 0.086 milligrams per gram — a 31 percent drop. That’s 23 percentage points more than the 9 percent decrease in the control samples. Cable bacteria helped accelerate the metabolic activity of their oil-eating neighbors by converting the toxic sulfides into sulfates. The sulfates didn’t harm the oil-eating microbes — in fact, they used the chemicals as fuel.

    The researchers are now trying to develop methods to promote cable bacteria growth in the field and see if it’s possible to enhance their effect on oil degradation. One catch is that in oil-contaminated sediment, oxygen is quickly used up by the microbes that break down hydrocarbons. That’s a problem since cable bacteria need access to oxygen. Salts that slowly release oxygen or nitrate — which cable bacteria can use in place of oxygen — might help spur the electrical organisms’ growth at oil spills. But more work is needed to identify the right chemical components and dosage, Marzocchi says.

    Meanwhile, scientists are investigating how cable bacteria might help reduce emission of another hydrocarbon — one that accumulates in the sky.

    Methane at the root

    Colorless, odorless methane is the simplest hydrocarbon (SN: 8/15/20, p. 8). It consists of a single carbon atom attached to a quartet of hydrogen atoms. And it’s a potent greenhouse gas — more than 25 times as effective at trapping heat in the atmosphere as carbon dioxide.

    One major source of methane is rice paddies (SN: 9/25/21, p. 16). During the growing season, rice farmers typically flood their fields to help stave off weeds and pests. Methane-producing microbes — aptly named methanogens — thrive in these waterlogged soils. Paddy-dwelling methanogens are so prolific that rice fields are estimated to generate about 11 percent of all human-induced methane emissions.

    But cable bacteria like paddies too. In 2019, Vincent Scholz, a microbiologist at Aarhus University, and colleagues reported that cable bacteria could flourish among the roots of rice plants and several other aquatic plant species.

    In an experiment, pots of rice plants grown in soils with cable bacteria (right) developed orange layers of rust and emitted less methane than pots without cable bacteria (left).V.V. Scholz/Aarhus Univ.

    That discovery inspired the researchers to investigate how the bacteria interact with methanogens in soils that grow rice. The team grew its own rice plants — some potted in soils with cable bacteria, and some without — and monitored methane emissions.

    To the researchers’ surprise, adding cable bacteria reduced rice soil methane emissions by 93 percent. In the process of removing electrons from sulfides, the bacteria generate sulfates, which other microbes can use as fuel. These sulfate-consuming microbes outcompeted methanogens for nutrients such as hydrogen and acetate in the rice soils, the researchers found. The results were “quite amazing,” Scholz says, though the effectiveness of the electrical microbes in real rice fields has yet to be tested.

    There are signs that cable bacteria are already plugged into real rice paddy soils. After analyzing genetic data collected from rice paddies in the United States, India, Vietnam and China, Scholz and colleagues reported in 2021 the presence of cable bacteria at sites in all four countries. Scholz is in Northern California this summer studying how cable bacteria live in rice fields and whether they’re already impacting methane emissions. He is also exploring ways to introduce cable bacteria to rice fields where they don’t yet exist or enhance the microbes’ numbers in fields where they do.

    There is still much to discover about how the wispy electrical conductors influence our world, Malkin says. Back in the Chesapeake Bay, she and colleagues have found that cable bacteria tend to flourish in the spring, a surge that has also been observed in the Netherlands. The findings add to a growing body of work that suggests cable bacteria are opportunistic organisms that interact with their environments in similar ways all around the world.

    If cable bacteria are already hard at work across the planet, then a bit of coaxing from researchers may be all it takes to turn the mud-dwelling creatures into the most helpful neighbors that a living thing could ask for. More

  • 150 Shares119 Views

    in Computers Math

    How to help assembly-line robots shift gears and pick up almost anything

    At the beginning of the COVID-19 pandemic, car manufacturing companies such as Ford quickly shifted their production focus from automobiles to masks and ventilators.
    To make this switch possible, these companies relied on people working on an assembly line. It would have been too challenging for a robot to make this transition because robots are tied to their usual tasks.
    Theoretically, a robot could pick up almost anything if its grippers could be swapped out for each task. To keep costs down, these grippers could be passive, meaning grippers pick up objects without changing shape, similar to how the tongs on a forklift work.
    A University of Washington team created a new tool that can design a 3D-printable passive gripper and calculate the best path to pick up an object. The team tested this system on a suite of 22 objects — including a 3D-printed bunny, a doorstop-shaped wedge, a tennis ball and a drill. The designed grippers and paths were successful for 20 of the objects. Two of these were the wedge and a pyramid shape with a curved keyhole. Both shapes are challenging for multiple types of grippers to pick up.
    The team will present these findings Aug. 11 at SIGGRAPH 2022.
    “We still produce most of our items with assembly lines, which are really great but also very rigid. The pandemic showed us that we need to have a way to easily repurpose these production lines,” said senior author Adriana Schulz, a UW assistant professor in the Paul G. Allen School of Computer Science & Engineering. “Our idea is to create custom tooling for these manufacturing lines. That gives us a very simple robot that can do one task with a specific gripper. And then when I change the task, I just replace the gripper.”
    Passive grippers can’t adjust to fit the object they’re picking up, so traditionally, objects have been designed to match a specific gripper. More

  • 75 Shares159 Views

    in Computers Math

    Teaching computers to predict efficient catalysis

    Researchers from Aarhus and Berlin have developed a new algorithm that can teach computers to predict how complex molecules will bind to the surface of catalysts. This is important when you have to produce synthetic fuels, for example. And it’s almost like playing extreme Tetris.
    Imagine a game of Tetris where you not only have to stack the pieces in three dimensions, but the pieces are also much more complicated than the seven geometric shapes you normally use in the game.
    In this case, the pieces are large and complex molecules that are to bind to another material in a chemical reaction.
    To make things even harder, both the molecules and the other material have several places on the surface where they can bind to each other — and it is crucial that the binding is neither too weak nor too strong.
    The binding has to be exactly right, otherwise the other material cannot function as a catalyst (see fact box at the end of the text).
    Such an extreme game of Tetris perfectly illustrates the challenges that researchers all over the world encounter when working on developing new and better catalysts for a wide range of technical-chemical processes. More

  • 113 Shares109 Views

    in Computers Math

    Engineers develop stickers that can see inside the body

    Ultrasound imaging is a safe and noninvasive window into the body’s workings, providing clinicians with live images of a patient’s internal organs. To capture these images, trained technicians manipulate ultrasound wands and probes to direct sound waves into the body. These waves reflect back out to produce high-resolution images of a patient’s heart, lungs, and other deep organs.
    Currently, ultrasound imaging requires bulky and specialized equipment available only in hospitals and doctor’s offices. But a new design by MIT engineers might make the technology as wearable and accessible as buying Band-Aids at the pharmacy.
    In a paper appearing today in Science, the engineers present the design for a new ultrasound sticker — a stamp-sized device that sticks to skin and can provide continuous ultrasound imaging of internal organs for 48 hours.
    The researchers applied the stickers to volunteers and showed the devices produced live, high-resolution images of major blood vessels and deeper organs such as the heart, lungs, and stomach. The stickers maintained a strong adhesion and captured changes in underlying organs as volunteers performed various activities, including sitting, standing, jogging, and biking.
    The current design requires connecting the stickers to instruments that translate the reflected sound waves into images. The researchers point out that even in their current form, the stickers could have immediate applications: For instance, the devices could be applied to patients in the hospital, similar to heart-monitoring EKG stickers, and could continuously image internal organs without requiring a technician to hold a probe in place for long periods of time.
    If the devices can be made to operate wirelessly — a goal the team is currently working toward — the ultrasound stickers could be made into wearable imaging products that patients could take home from a doctor’s office or even buy at a pharmacy. More

  • 150 Shares179 Views

    in Computers Math

    New hardware offers faster computation for artificial intelligence, with much less energy

    As scientists push the boundaries of machine learning, the amount of time, energy, and money required to train increasingly complex neural network models is skyrocketing. A new area of artificial intelligence called analog deep learning promises faster computation with a fraction of the energy usage.
    Programmable resistors are the key building blocks in analog deep learning, just like transistors are the core elements for digital processors. By repeating arrays of programmable resistors in complex layers, researchers can create a network of analog artificial “neurons” and “synapses” that execute computations just like a digital neural network. This network can then be trained to achieve complex AI tasks like image recognition and natural language processing.
    A multidisciplinary team of MIT researchers set out to push the speed limits of a type of human-made analog synapse that they had previously developed. They utilized a practical inorganic material in the fabrication process that enables their devices to run 1 million times faster than previous versions, which is also about 1 million times faster than the synapses in the human brain.
    Moreover, this inorganic material also makes the resistor extremely energy-efficient. Unlike materials used in the earlier version of their device, the new material is compatible with silicon fabrication techniques. This change has enabled fabricating devices at the nanometer scale and could pave the way for integration into commercial computing hardware for deep-learning applications.
    “With that key insight, and the very powerful nanofabrication techniques we have at MIT.nano, we have been able to put these pieces together and demonstrate that these devices are intrinsically very fast and operate with reasonable voltages,” says senior author Jesús A. del Alamo, the Donner Professor in MIT’s Department of Electrical Engineering and Computer Science (EECS). “This work has really put these devices at a point where they now look really promising for future applications.”
    “The working mechanism of the device is electrochemical insertion of the smallest ion, the proton, into an insulating oxide to modulate its electronic conductivity. Because we are working with very thin devices, we could accelerate the motion of this ion by using a strong electric field, and push these ionic devices to the nanosecond operation regime,” explains senior author Bilge Yildiz, the Breene M. Kerr Professor in the departments of Nuclear Science and Engineering and Materials Science and Engineering. More

  • 150 Shares99 Views

    in Physics

    This stick-on ultrasound patch could let you watch your own heart beat

    Picture a smartwatch that doesn’t just show your heart rate, but a real-time image of your heart as it beats in your chest. Researchers may have taken the first step down that road by creating a wearable ultrasound patch — think of a Band-Aid with sonar — that provides a flexible way to see deep inside the body. 

    Ultrasound, which maps tissues and fluids by recording how sound waves bounce off them, can help doctors examine organs for damage, diagnose cancer or even track bacteria (SN: 1/3/18). But most ultrasound machines aren’t portable, and the wearable ones either struggle to spot details or can be used for only short periods. 

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    The new patch can work for up to 48 hours straight — even while the user is doing something active, like exercising. And the miniature device sees just as well as a more unwieldy hospital machine, researchers report in the July 29 Science. 

    “This is just the beginning,” says Xuanhe Zhao, a mechanical engineer at MIT. His team plans to make the patch wireless and able to interface with a user’s phone, which could then show the ultrasound signals as 3-D images. 

    The medical possibilities range wide. Stick a patch over a person’s heart, and the frequent images it takes could help predict heart attacks and blood clots potentially months before disaster hits, explains Aparna Singh, a biomedical engineer at Columbia University. Placed on a COVID-19 patient, the patch — which is only about the size of a quarter — could be an easy way to catch lung problems as they develop.

    “This also has a huge potential to be available for developing countries,” where limited access to hospitals can make monitoring patients difficult, Singh says. The patch costs about $100 to make. One of the researchers’ next steps will be to try to make the device cheaper. More

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    in Computers Math

    Friendly skies? Study charts COVID-19 odds for plane flights

    What are the chances you will contract Covid-19 on a plane flight? A study led by MIT scholars offers a calculation of that for the period from June 2020 through February 2021. While the conditions that applied at that stage of the Covid-19 pandemic differ from those of today, the study offers a method that could be adapted as the pandemic evolves.
    The study estimates that from mid-2020 through early 2021, the probability of getting Covid-19 on an airplane surpassed 1 in 1,000 on a totally full flight lasting two hours at the height of the early pandemic, roughly December 2020 and January 2021. It dropped to about 1 in 6,000 on a half-full two-hour flight when the pandemic was at its least severe, in the summer of 2020. The overall risk of transmission from June 2020 through February 2021 was about 1 in 2,000, with a mean of 1 in 1,400 and a median of 1 in 2,250.
    To be clear, current conditions differ from the study’s setting. Masks are no longer required for U.S. domestic passengers; in the study’s time period, airlines were commonly leaving middle seats open, which they are no longer doing; and newer Covid-19 variants are more contagious than the virus was during the study period. While those factors may increase the current risk, most people have received Covid-19 vaccinations since February 2021, which could serve to lower today’s risk — though the precise impact of those vaccines against new variants is uncertain.
    Still, the study does provide a general estimate about air travel safety with regard to Covid-19 transmission, and a methodology that can be applied to future studies. Some U.S. carriers at the time stated that onboard transmission was “virtually nonexistent” and “nearly nonexistent,” but as the research shows, there was a discernible risk. On the other hand, passengers were not exactly facing coin-flip odds of catching the virus in flight, either.
    “The aim is to set out the facts,” says Arnold Barnett, a management professor at MIT and aviation risk expert, who is co-author of a recent paper detailing the study’s results. “Some people might say, ‘Oh, that doesn’t sound like very much.’ But if we at least tell people what the risk is, they can make judgments.”
    As Barnett also observes, a round-trip flight with a change of planes and two two-hour segments in each direction counts as four flights in this accounting, so a 1 in 1,000 probability, per flight, would lead to approximately a 1 in 250 chance for such a trip as a whole. More

  • 125 Shares199 Views

    in Computers Math

    A 'nano-robot' built entirely from DNA to explore cell processes

    Constructing a tiny robot from DNA and using it to study cell processes invisible to the naked eye… You would be forgiven for thinking it is science fiction, but it is in fact the subject of serious research by scientists from Inserm, CNRS and Université de Montpellier at the Structural Biology Center in Montpellier[1]. This highly innovative “nano-robot” should enable closer study of the mechanical forces applied at microscopic levels, which are crucial for many biological and pathological processes. It is described in a new study published in Nature Communications.
    Our cells are subject to mechanical forces exerted on a microscopic scale, triggering biological signals essential to many cell processes involved in the normal functioning of our body or in the development of diseases.
    For example, the feeling of touch is partly conditional on the application of mechanical forces on specific cell receptors (the discovery of which was this year rewarded by the Nobel Prize in Physiology or Medicine). In addition to touch, these receptors that are sensitive to mechanical forces (known as mechanoreceptors) enable the regulation of other key biological processes such as blood vessel constriction, pain perception, breathing or even the detection of sound waves in the ear, etc.
    The dysfunction of this cellular mechanosensitivity is involved in many diseases — for example, cancer: cancer cells migrate within the body by sounding and constantly adapting to the mechanical properties of their microenvironment. Such adaptation is only possible because specific forces are detected by mechanoreceptors that transmit the information to the cell cytoskeleton.
    At present, our knowledge of these molecular mechanisms involved in cell mechanosensitivity is still very limited. Several technologies are already available to apply controlled forces and study these mechanisms, but they have a number of limitations. In particular, they are very costly and do not allow us to study several cell receptors at a time, which makes their use very time-consuming if we want to collect a lot of data.
    DNA origami structures
    In order to propose an alternative, the research team led by Inserm researcher Gaëtan Bellot at the Structural Biology Center (Inserm/CNRS/Université de Montpellier) decided to use the DNA origami method. This enables the self-assembly of 3D nanostructures in a pre-defined form using the DNA molecule as construction material. Over the last ten years, the technique has allowed major advances in the field of nanotechnology.
    This enabled the researchers to design a “nano-robot” composed of three DNA origami structures. Of nanometric size, it is therefore compatible with the size of a human cell. It makes it possible for the first time to apply and control a force with a resolution of 1 piconewton, namely one trillionth of a Newton — with 1 Newton corresponding to the force of a finger clicking on a pen. This is the first time that a human-made, self-assembled DNA-based object can apply force with this accuracy.
    The team began by coupling the robot with a molecule that recognizes a mechanoreceptor. This made it possible to direct the robot to some of our cells and specifically apply forces to targeted mechanoreceptors localized on the surface of the cells in order to activate them.
    Such a tool is very valuable for basic research, as it could be used to better understand the molecular mechanisms involved in cell mechanosensitivity and discover new cell receptors sensitive to mechanical forces. Thanks to the robot, the scientists will also be able to study more precisely at what moment, when applying force, key signaling pathways for many biological and pathological processes are activated at cell level.
    “The design of a robot enabling the in vitro and in vivo application of piconewton forces meets a growing demand in the scientific community and represents a major technological advance. However, the biocompatibility of the robot can be considered both an advantage for in vivo applications but may also represent a weakness with sensitivity to enzymes that can degrade DNA. So our next step will be to study how we can modify the surface of the robot so that it is less sensitive to the action of enzymes. We will also try to find other modes of activation of our robot using, for example, a magnetic field,” emphasizes Bellot.
    [1] Also contributed to this research: the Institute of Functional Genomics (CNRS/Inserm/Université de Montpellier), the Max Mousseron Biomolecules Institute (CNRS/Université de Montpellier/ENSCM), the Paul Pascal Research Center (CNRS/Université de Bordeaux) and the Physiology and Experimental Medicine: Heart-Muscles laboratory (CNRS/Inserm/Université de Montpellier). More