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Wednesday, January 24th, 2018

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    1:00p
    New type of virus found in the ocean

    A type of virus that dominates water samples taken from the world’s oceans has long escaped analysis because it has characteristics that standard tests can’t detect. However, researchers at MIT and the Albert Einstein College of Medicine have now managed to isolate and study representatives of these elusive viruses, which provide a key missing link in virus evolution and play an important role in regulating bacterial populations, as a new study reports.

    Viruses are the main predators of bacteria, and the findings suggest that the current view of bacterial virus diversity has a major blind spot. These conclusions have emerged through detailed analysis of marine samples led by MIT postdoc Kathryn Kauffman, professor of civil and environmental engineering Martin Polz, professor Libusha Kelly of Albert Einstein College of Medicine, and nine others. The results are being reported this week in the journal Nature.

    The newly identified viruses lack the “tail” found on most catalogued and sequenced bacterial viruses, and have several other unusual properties that have led to their being missed by previous studies. To honor that fact, the researchers named this new group the Autolykiviridae — after a character from Greek mythology who was storied for being difficult to catch. And, unlike typical viruses that prey on just one or two types of bacteria, these tailless varieties can infect dozens of different types, often of different species, underscoring their ecological relevance.

    This research “opens new avenues for furthering our understanding of the roles of viruses in the ocean,” says Jed Fuhrman, the McCulloch-Crosby Chair of Marine Biology at the University of Southern California, who was not involved in this work. “In a practical sense, it also shows how we need to alter some commonly used methods in order to capture these kinds of viruses for various studies,” he says. “I’d say it is an important advance in the field.”

    Current environmental models of virus-bacteria interactions are based on the well-studied tailed viruses, Kauffman explains, so they may be missing important aspects of the interactions taking place in nature.

    “We already knew that viruses are very important there,” Kauffman says, referring to the surface ocean, where the researchers’ samples were drawn, and where about 10 million viruses are found in every milliliter of water. Polz says that while “most of the viruses studied in labs have tails, most of those in the ocean don’t.” So the team decided to study one subset of tailless viruses, which infects a group of bacteria called Vibrio. After extensive tests, they found “that some of these were infecting unusually large numbers of hosts,” he says.

    After sequencing representatives of the Autolykiviridae, the researchers found “their genomes were quite different from other viruses,” Polz says. For one thing, their genomes are very short: about 10,000 bases, compared to the typical 40,000-50,000 for tailed viruses. “When we found that, we were surprised,” he says.

    With the new sequence information, the researchers were able to comb through databases and found that such viruses exist in many places. The research also showed that these viruses tend to be underrepresented in databases because of the ways samples are typically handled in labs. The methods the team developed to obtain these viruses from environmental samples could help researchers avoid such losses of information in the future. In addition, Kauffman says, typically the way researchers test for viral activity is by infecting bacteria with the viral sample and then checking the samples a day later to look for signs that patches of the bacteria have been killed off. But these particular nontailed viruses often act more slowly, and the killed-off regions don’t show up until several days have passed — so their presence was never noticed in most studies.

    The new group of viruses may especially be widespread. “We don’t think it’s ocean-specific at all,” Polz says. For example, the viruses may even be prevalent in the human biome, and they may play roles in major biogeochemical cycles, he says, such as the cycling of carbon.

    Another important aspect of theses findings is that the Autolykiviridae were shown to be  members of an ancient viral lineage that is defined by specific types of capsids, the protein shell encasing the viral DNA. Though this lineage is known to be very diverse in animals and protists — and includes viruses such as the adenoviruses that infect humans, and the giant viruses that infect algae — very few viruses of this kind have been found to infect bacteria.

    “This work substantially changes the existing ideas on the composition of the ocean virome by showing that the content of small, tailless viruses … is comparable to that of the tailed viruses … that are currently thought to dominate the virosphere,” says Eugene V. Koonin, a senior investigator at the National Institutes of Health, who was not involved in this research. “This work is important also for understanding the evolution of the virus world because it shows that viruses related to the most common viruses of eukaryotes (such as adenoviruses, poxviruses, and others), at least in terms of the capsid structure, are much wider-spread in prokaryotes than previously suspected.”

    Koonin adds, “I further wonder whether the viruses reported here might only represent the tip of the proverbial iceberg, because capsid proteins can be highly diverged in sequence so that many are missed even in sensitive database searches. The findings are also of practical importance because the tailless viruses appear to play a major ecological role in the ocean, being responsible for a substantial fraction of bacteria-killing.”

    The work was supported by the National Science Foundation and the Woods Hole Oceanographic Institution’s Ocean Ventures Fund.

    1:00p
    How some facial malformations arise

    About 1 in 750 babies born in the United States has some kind of craniofacial malformation, accounting for about one-third of all birth defects.

    Many of these craniofacial disorders arise from mutations of “housekeeping” genes, so called because they are required for basic functions such as building proteins or copying DNA. All cells in the body require these housekeeping genes, so scientists have long wondered why these mutations would produce defects specifically in facial tissues.

    Researchers at MIT and Stanford University have now discovered how one such mutation leads to the facial malformations seen in Treacher-Collins Syndrome, a disorder that affects between 1 in 25,000 and 1 in 50,000 babies and produces underdeveloped facial bones, especially in the jaw and cheek.

    The team found that embryonic cells that form the face are more sensitive to the mutation because they more readily activate a pathway that induces cell death in response to stress. This pathway is mediated by a protein called p53. The new findings mark the first time that scientists have determined how mutations in housekeeping genes can have tissue-specific effects during embryonic development.

    “We were able to narrow down, at the molecular level, how issues with general regulators that are used to make ribosomes in all cells lead to defects in specific cell types,” says Eliezer Calo, an MIT assistant professor of biology and the lead author of the study.

    Joanna Wysocka, a professor of chemical and systems biology at Stanford University, is the senior author of the study, which appears in the Jan. 24 online edition of Nature.

    From mutation to disease

    Treacher-Collins Syndrome is caused by mutations in genes that code for proteins required for the assembly and function of polymerases. These proteins, known as TCOF1, POLR1C, and POLR1D, are responsible for transcribing genes that make up cell organelles called ribosomes. Ribosomes are critical to all cells.

    “The question we were trying to understand is, how is it that when all cells in the body need ribosomes to function, mutations in components that are required for making the ribosomes lead to craniofacial disorders? In these conditions, you would expect that all the cell types of the body would be equally affected, but that’s not the case,” Calo says.

    During embryonic development, these mutations specifically affect a type of embryonic cells known as cranial neural crest cells, which form the face. The researchers already knew that the mutations disrupt the formation of ribosomes, but they didn’t know exactly how this happens. To investigate that process, the researchers engineered larvae of zebrafish and of an aquatic frog known as Xenopus to express proteins harboring those mutations.

    Their experiments revealed that the mutations lead to impairment in the function of an enzyme called DDX21. When DDX21 dissociates from DNA, the genes that encode ribosomal proteins do not get transcribed, so ribosomes are missing key components and can’t function normally. However, this DDX21 loss only appears to happen in cells that are highly sensitive to p53 activation, including cranial neural crest cells. These cells then undergo programmed cell death, which leads to the facial malformations seen in Treacher-Collins Syndrome, Calo says.

    Other embryonic cells, including other types of neural crest cells, which form nerves and other parts of the body such as connective tissue, are not affected by the loss of DDX21.

    Role of DNA damage

    The researchers also found that mutations of POLR1C and POLR1D also cause damage to stretches of DNA that encode some of the RNA molecules that make up ribosomes. The amount of DNA damage correlated closely with the severity of malformations seen in individual larvae, and mutations in POLR1C led to far more DNA damage than mutations in POLR1D. The researchers believe these differences in DNA damage may explain why the severity of Treacher-Collins Syndrome can vary widely among individuals.

    Calo’s lab is now studying why affected cells experience greater levels of DNA damage in those particular sequences. The researchers are also looking for compounds that could potentially prevent craniofacial defects by making the cranial neural crest cells more resistant to p53-induced cell death. Such interventions could have a big impact but would have to be targeted very early in embryonic development, as the cranial neural crest cells begin forming the tissue layers that will become the face at about three weeks of development in human embryos.

    The research was funded by the National Institutes of Health, Howard Hughes Medical Institute, and March of Dimes Foundation.

    1:59p
    Ultrathin needle can deliver drugs directly to the brain

    MIT researchers have devised a miniaturized system that can deliver tiny quantities of medicine to brain regions as small as 1 cubic millimeter. This type of targeted dosing could make it possible to treat diseases that affect very specific brain circuits, without interfering with the normal function of the rest of the brain, the researchers say.

    Using this device, which consists of several tubes contained within a needle about as thin as a human hair, the researchers can deliver one or more drugs deep within the brain, with very precise control over how much drug is given and where it goes. In a study of rats, they found that they could deliver targeted doses of a drug that affects the animals’ motor function.

    “We can infuse very small amounts of multiple drugs compared to what we can do intravenously or orally, and also manipulate behavioral changes through drug infusion,” says Canan Dagdeviren, the LG Electronics Career Development Assistant Professor of Media Arts and Sciences and the lead author of the paper, which appears in the Jan. 24 issue of Science Translational Medicine.

    “We believe this tiny microfabricated device could have tremendous impact in understanding brain diseases, as well as providing new ways of delivering biopharmaceuticals and performing biosensing in the brain,” says Robert Langer, the David H. Koch Institute Professor at MIT and one of the paper’s senior authors.

    Michael Cima, the David H. Koch Professor of Engineering in the Department of Materials Science and Engineering and a member of MIT’s Koch Institute for Integrative Cancer Research, is also a senior author of the paper.

    Targeted action

    Drugs used to treat brain disorders often interact with brain chemicals called neurotransmitters or the cell receptors that interact with neurotransmitters. Examples include l-dopa, a dopamine precursor used to treat Parkinson’s disease, and Prozac, used to boost serotonin levels in patients with depression. However, these drugs can have side effects because they act throughout the brain.

    “One of the problems with central nervous system drugs is that they’re not specific, and if you’re taking them orally they go everywhere. The only way we can limit the exposure is to just deliver to a cubic millimeter of the brain, and in order to do that, you have to have extremely small cannulas,” Cima says.

    The MIT team set out to develop a miniaturized cannula (a thin tube used to deliver medicine) that could target very small areas. Using microfabrication techniques, the researchers constructed tubes with diameters of about 30 micrometers and lengths up to 10 centimeters. These tubes are contained within a stainless steel needle with a diameter of about 150 microns. “The device is very stable and robust, and you can place it anywhere that you are interested,” Dagdeviren says.

    The researchers connected the cannulas to small pumps that can be implanted under the skin. Using these pumps, the researchers showed that they could deliver tiny doses (hundreds of nanoliters) into the brains of rats. In one experiment, they delivered a drug called muscimol to a brain region called the substantia nigra, which is located deep within the brain and helps to control movement.

    Previous studies have shown that muscimol induces symptoms similar to those seen in Parkinson’s disease. The researchers were able to generate those effects, which include stimulating the rats to continually turn in a clockwise direction, using their miniaturized delivery needle. They also showed that they could halt the Parkinsonian behavior by delivering a dose of saline through a different channel, to wash the drug away.

    “Since the device can be customizable, in the future we can have different channels for different chemicals, or for light, to target tumors or neurological disorders such as Parkinson’s disease or Alzheimer’s,” Dagdeviren says.

    This device could also make it easier to deliver potential new treatments for behavioral neurological disorders such as addiction or obsessive compulsive disorder, which may be caused by specific disruptions in how different parts of the brain communicate with each other.

    “Even if scientists and clinicians can identify a therapeutic molecule to treat neural disorders, there remains the formidable problem of how to delivery the therapy to the right cells — those most affected in the disorder. Because the brain is so structurally complex, new accurate ways to deliver drugs or related therapeutic agents locally are urgently needed,” says Ann Graybiel, an MIT Institute Professor and a member of MIT’s McGovern Institute for Brain Research, who is also an author of the paper.

    Measuring drug response

    The researchers also showed that they could incorporate an electrode into the tip of the cannula, which can be used to monitor how neurons’ electrical activity changes after drug treatment. They are now working on adapting the device so it can also be used to measure chemical or mechanical changes that occur in the brain following drug treatment.

    The cannulas can be fabricated in nearly any length or thickness, making it possible to adapt them for use in brains of different sizes, including the human brain, the researchers say.

    “This study provides proof-of-concept experiments, in large animal models, that a small, miniaturized device can be safely implanted in the brain and provide miniaturized control of the electrical activity and function of single neurons or small groups of neurons. The impact of this could be significant in focal diseases of the brain, such as Parkinson’s disease,” says Antonio Chiocca, neurosurgeon-in-chief and chairman of the Department of Neurosurgery at Brigham and Women’s Hospital, who was not involved in the research.

    The research was funded by the National Institutes of Health and the National Institute of Biomedical Imaging and Bioengineering.

    5:00p
    Novel methods of synthesizing quantum dot materials

    For quantum dot (QD) materials to perform well in devices such as solar cells, the nanoscale crystals in them need to pack together tightly so that electrons can hop easily from one dot to the next and flow out as current. MIT researchers have now made QD films in which the dots vary by just one atom in diameter and are organized into solid lattices with unprecedented order. Subsequent processing pulls the QDs in the film closer together, further easing the electrons’ pathway. Tests using an ultrafast laser confirm that the energy levels of vacancies in adjacent QDs are so similar that hopping electrons don’t get stuck in low-energy dots along the way.

    Taken together, the results suggest a new direction for ongoing efforts to develop these promising materials for high performance in electronic and optical devices.

    In recent decades, much research attention has focused on electronic materials made of quantum dots, which are tiny crystals of semiconducting materials a few nanometers in diameter. After three decades of research, QDs are now being used in TV displays, where they emit bright light in vivid colors that can be fine-tuned by changing the sizes of the nanoparticles. But many opportunities remain for taking advantage of these remarkable materials.

    “QDs are a really promising underlying materials technology for energy applications,” says William Tisdale, the ARCO Career Development Professor in Energy Studies and an associate professor of chemical engineering.

    QD materials pique his interest for several reasons. QDs are easily synthesized in a solvent at low temperatures using standard procedures. The QD-bearing solvent can then be deposited on a surface — small or large, rigid or flexible — and as it dries, the QDs are left behind as a solid. Best of all, the electronic and optical properties of that solid can be controlled by tuning the QDs.

    “With QDs, you have all these degrees of freedom,” says Tisdale. “You can change their composition, size, shape, and surface chemistry to fabricate a material that’s tailored for your application.”

    The ability to adjust electron behavior to suit specific devices is of particular interest. For example, in solar photovoltaics (PVs), electrons should pick up energy from sunlight and then move rapidly through the material and out as current before they lose their excess energy. In light-emitting diodes (LEDs), high-energy “excited” electrons should relax on cue, emitting their extra energy as light.

    With thermoelectric (TE) devices, QD materials could be a game-changer. When TE materials are hotter on one side than the other, they generate electricity. So TE devices could turn waste heat in car engines, industrial equipment, and other sources into power — without combustion or moving parts. The TE effect has been known for a century, but devices using TE materials have remained inefficient. The problem: While those materials conduct electricity well, they also conduct heat well, so the temperatures of the two ends of a device quickly equalize. In most materials, measures to decrease heat flow also decrease electron flow.

    “With QDs, we can control those two properties separately,” says Tisdale. “So we can simultaneously engineer our material so it’s good at transferring electrical charge but bad at transporting heat.”

    Making good arrays

    One challenge in working with QDs has been to make particles that are all the same size and shape. During QD synthesis, quadrillions of nanocrystals are deposited onto a surface, where they self-assemble in an orderly fashion as they dry. If the individual QDs aren’t all exactly the same, they can’t pack together tightly, and electrons won’t move easily from one nanocrystal to the next.

    Three years ago, a team in Tisdale’s lab led by Mark Weidman PhD ’16 demonstrated a way to reduce that structural disorder. In a series of experiments with lead-sulfide QDs, team members found that carefully selecting the ratio between the lead and sulfur in the starting materials would produce QDs of uniform size.

    “As those nanocrystals dry, they self-assemble into a beautifully ordered arrangement we call a superlattice,” Tisdale says.

    Scattering electron microscope images of those superlattices taken from several angles show lined-up, 5-nanometer-diameter nanocrystals throughout the samples and confirm the long-range ordering of the QDs.

    For a closer examination of their materials, Weidman performed a series of X-ray scattering experiments at the National Synchrotron Light Source at Brookhaven National Laboratory. Data from those experiments showed both how the QDs are positioned relative to one another and how they’re oriented, that is, whether they’re all facing the same way. The results confirmed that QDs in the superlattices are well ordered and essentially all the same.

    “On average, the difference in diameter between one nanocrystal and another was less than the size of one more atom added to the surface,” says Tisdale. “So these QDs have unprecedented monodispersity, and they exhibit structural behavior that we hadn’t seen previously because no one could make QDs this monodisperse.”

    Controlling electron hopping

    The researchers next focused on how to tailor their monodisperse QD materials for efficient transfer of electrical current. “In a PV or TE device made of QDs, the electrons need to be able to hop effortlessly from one dot to the next and then do that many thousands of times as they make their way to the metal electrode,” Tisdale explains.

    One way to influence hopping is by controlling the spacing from one QD to the next. A single QD consists of a core of semiconducting material — in this work, lead sulfide — with chemically bound arms, or ligands, made of organic (carbon-containing) molecules radiating outward. The ligands play a critical role — without them, as the QDs form in solution, they’d stick together and drop out as a solid clump. Once the QD layer is dry, the ligands end up as solid spacers that determine how far apart the nanocrystals are.

    A standard ligand material used in QD synthesis is oleic acid. Given the length of an oleic acid ligand, the QDs in the dry superlattice end up about 2.6 nanometers apart — and that’s a problem.

    “That may sound like a small distance, but it’s not,” says Tisdale. “It’s way too big for a hopping electron to get across.”

    Using shorter ligands in the starting solution would reduce that distance, but they wouldn’t keep the QDs from sticking together when they’re in solution. “So we needed to swap out the long oleic acid ligands in our solid materials for something shorter” after the film formed, Tisdale says.

    To achieve that replacement, the researchers use a process called ligand exchange. First, they prepare a mixture of a shorter ligand and an organic solvent that will dissolve oleic acid but not the lead sulfide QDs. They then submerge the QD film in that mixture for 24 hours. During that time, the oleic acid ligands dissolve, and the new, shorter ligands take their place, pulling the QDs closer together. The solvent and oleic acid are then rinsed off.

    Tests with various ligands confirmed their impact on interparticle spacing. Depending on the length of the selected ligand, the researchers could reduce that spacing from the original 2.6 nanometers with oleic acid all the way down to 0.4 nanometers. However, while the resulting films have beautifully ordered regions — perfect for fundamental studies — inserting the shorter ligands tends to generate cracks as the overall volume of the QD sample shrinks.

    Energetic alignment of nanocrystals

    One result of that work came as a surprise: Ligands known to yield high performance in lead-sulfide-based solar cells didn’t produce the shortest interparticle spacing in their tests.

    “Reducing that spacing to get good conductivity is necessary,” says Tisdale. “But there may be other aspects of our QD material that we need to optimize to facilitate electron transfer.”

    One possibility is a mismatch between the energy levels of the electrons in adjacent QDs. In any material, electrons exist at only two energy levels — a low ground state and a high excited state. If an electron in a QD film receives extra energy — say, from incoming sunlight — it can jump up to its excited state and move through the material until it finds a low-energy opening left behind by another traveling electron. It then drops down to its ground state, releasing its excess energy as heat or light.

    In solid crystals, those two energy levels are a fixed characteristic of the material itself. But in QDs, they vary with particle size. Make a QD smaller and the energy level of its excited electrons increases. Again, variability in QD size can create problems. Once excited, a high-energy electron in a small QD will hop from dot to dot — until it comes to a large, low-energy QD.

    “Excited electrons like going downhill more than they like going uphill, so they tend to hang out on the low-energy dots,” says Tisdale. “If there’s then a high-energy dot in the way, it takes them a long time to get past that bottleneck.”

    So the greater mismatch between energy levels — called energetic disorder — the worse the electron mobility. To measure the impact of energetic disorder on electron flow in their samples, Rachel Gilmore PhD ’17 and her collaborators used a technique called pump-probe spectroscopy — as far as they know, the first time this method has been used to study electron hopping in QDs.

    QDs in an excited state absorb light differently than do those in the ground state, so shining light through a material and taking an absorption spectrum provides a measure of the electronic states in it. But in QD materials, electron hopping events can occur within picoseconds — 10-12 of a second — which is faster than any electrical detector can measure.

    The researchers therefore set up a special experiment using an ultrafast laser, whose beam is made up of quick pulses occurring at 100,000 per second. Their setup subdivides the laser beam such that a single pulse is split into a pump pulse that excites a sample and — after a delay measured in femtoseconds (10-15 seconds) — a corresponding probe pulse that measures the sample’s energy state after the delay. By gradually increasing the delay between the pump and probe pulses, they gather absorption spectra that show how much electron transfer has occurred and how quickly the excited electrons drop back to their ground state.

    Using this technique, they measured electron energy in a QD sample with standard dot-to-dot variability and in one of the monodisperse samples. In the sample with standard variability, the excited electrons lose much of their excess energy within 3 nanoseconds. In the monodisperse sample, little energy is lost in the same time period — an indication that the energy levels of the QDs are all about the same.

    By combining their spectroscopy results with computer simulations of the electron transport process, the researchers extracted electron hopping times ranging from 80 picoseconds for their smallest quantum dots to over 1 nanosecond for the largest ones. And they concluded that their QD materials are at the theoretical limit of how little energetic disorder is possible. Indeed, any difference in energy between neighboring QDs isn’t a problem. At room temperature, energy levels are always vibrating a bit, and those fluctuations are larger than the small differences from one QD to the next.

    “So at some instant, random kicks in energy from the environment will cause the energy levels of the QDs to line up, and the electron will do a quick hop,” says Tisdale.

    The way forward

    With energetic disorder no longer a concern, Tisdale concludes that further progress in making commercially viable QD materials will require better ways of dealing with structural disorder. He and his team tested several methods of performing ligand exchange in solid samples, and none produced films with consistent QD size and spacing over large areas without cracks. As a result, he now believes that efforts to optimize that process “may not take us where we need to go.”

    What’s needed instead is a way to put short ligands on the QDs when they’re in solution and then let them self-assemble into the desired structure.

    “There are some emerging strategies for solution-phase ligand exchange,” he says. “If they’re successfully developed and combined with monodisperse QDs, we should be able to produce beautifully ordered, large-area structures well suited for devices such as solar cells, LEDs, and thermoelectric systems.”

    QD synthesis and spectroscopy were supported by the US Department of Energy, Office of Basic Energy Sciences. Structural studies of QD solids were supported by the MIT Energy Initiative Seed Fund Program. Mark Weidman and Rachel Gilmore were partially supported by a National Science Foundation Graduate Research Fellowship. Measurements were performed at the Center for Functional Nanomaterials at Brookhaven National Laboratory, the Cornell High Energy Synchrotron Source, and the MRSEC Shared Experimental Facilities at MIT. 

    This article appeared in the Autumn 2017 issue of Energy Futures, the magazine of the MIT Energy Initiative.

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