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The soils and sediments beneath our feet can contain an astonishing amount of carbon -- more than in all of the world's plants and the atmosphere combined -- and represents a significant potential source of the greenhouse gas carbon dioxide. In a new study, Stanford scientists have uncovered a previously unknown mechanism that explains why microbes sometimes fail to break down all the plant and animal matter, leaving carbon underfoot. Understanding where, and how long, this buried organic matter lingers is crucial for scientists and policymakers to better predict and respond to climate change. "Our picture of how organic matter is broken down in soils and sediments is incomplete," said study lead author Kristin Boye, an associate staff scientist at the Stanford Synchrotron Radiation Lightsource at the SLAC National Accelerator Laboratory and former postdoctoral scholar at Stanford's School of Earth, Energy & Environmental Sciences. "With this study, we are gaining new insights into the mechanisms of carbon preservation in low- or no-oxygen subterranean environments." In oxygen-starved places such as marshes and in floodplains, microorganisms do not equally break down all of the available organic matter, the study shows. Instead, carbon compounds that do not provide enough energy to be worthwhile for microorganisms to degrade end up accumulating. This passed-over carbon, however, does not necessarily stay locked away below ground in the long run. Being water soluble, the carbon can seep into nearby oxygen-rich waterways, where microbes readily consume it. To date, models of local ecosystems and broader climate change have failed to take into account this newfound carbon preservation mechanism, having focused chiefly on microbial enzymes and the availability of other elements for organic matter breakdown. "Soils and sediments are a huge and dynamic reservoir of carbon," said study senior author Scott Fendorf, a professor of soil biogeochemistry at Stanford Earth. "That's why we worry about turnover times here with regard to how fast organic carbon is degraded and released as carbon dioxide into the atmosphere." Tracking the fate of the carbon For the new study, published today in Nature Geoscience, the research team collected core samples of buried sediments from four floodplains in the upper Colorado River Basin in the states of Colorado and New Mexico. The approximately 3-foot-long, column-shaped samples went deep enough to reach oxygen-starved layers where microbes must switch from doing the microbial equivalent of breathing oxygen to breathing sulfur. In either case, the microbes combine oxygen or sulfur with carbon-based food to produce energy and release either carbon dioxide or sulfur dioxide into the atmosphere. (That sulfur dioxide is responsible for the distinctive smell of oxygen-poor wetlands.) To identify where in the sediment samples microbes had made the switch, the researchers turned to the Stanford Synchrotron Radiation Lightsource facility. The synchrotron machine generates extremely bright X-ray light that, when shone upon the samples, generates a signal revealing the chemistry of the sulfur. The presence of sulfide minerals indicates where the microbes began making use of sulfur alongside carbon to power their biochemical machinery. The question was whether the switch to sulfur influenced the carbon sources the microbes ate or left behind. To find out, the researchers relied on unique instrumentation and collaborations within the Environmental Molecular Sciences Laboratory at the Pacific Northwest National Laboratory in Richmond, Washington. With the aid of a very strong magnet, an instrument called a mass spectrometer at the lab characterized the water-soluble organic material. The tests found that, in contrast to the layers where oxygen was available, leftover carbon compounds in the sediment samples where sulfur had been used for respiration were mostly of the sort that requires more energy to degrade than would be liberated through the degradation itself. Of no use, then, to growing microbes, these carbon compounds had remained within the deeper sediment layers. Floodplains, like those sampled in the study, rank among the most common areas globally for the internment of plant and animal matter by water-borne sediments. The oxygen-poor conditions created underground there are known to sequester carbon, but as the study suggests, partly for reasons previously unrecognized and with unforeseen consequences. For such flood-prone, low-lying areas are by definition close to waterways. Soluble, unused organic material can migrate quite easily into an aerated waterway for subsequent breakdown, triggering algae blooms and other water quality issues while also leading to carbon dioxide production. Models of how living organisms, the ground, bodies of water and the atmosphere recycle carbon will increasingly need to incorporate key nuances, like the preservation mechanism described in the new Stanford study, in order to inform scientists' understanding as well as policymakers' decisions. "Getting the constraints right on what really controls the processes of carbon breakdown is essential," said Fendorf. "That's what our study helps illuminate." Other co-authors on the study, titled "Thermodynamically controlled preservation of organic carbon in floodplains," include Vincent Noel, Sharon Bone and John Bargar of the SLAC National Accelerator Laboratory; Malak Tfaily of the Pacific Northwest National Laboratory; and Kenneth Williams of the Lawrence Berkeley National Laboratory. Funding was provided by the U.S. Department of Energy, the Office of Biological and Environmental Research, the SLAC National Accelerator Laboratory and the Lawrence Berkeley National Laboratory.


Jiao C.,University of Michigan | Flanner M.G.,University of Michigan | Balkanski Y.,CEA Saclay Nuclear Research Center | Bauer S.E.,Columbia University | And 30 more authors.
Atmospheric Chemistry and Physics | Year: 2014

Though many global aerosols models prognose surface deposition, only a few models have been used to directly simulate the radiative effect from black carbon (BC) deposition to snow and sea ice. Here, we apply aerosol deposition fields from 25 models contributing to two phases of the Aerosol Comparisons between Observations and Models (AeroCom) project to simulate and evaluate within-snow BC concentrations and radiative effect in the Arctic. We accomplish this by driving the offline land and sea ice components of the Community Earth System Model with different deposition fields and meteorological conditions from 2004 to 2009, during which an extensive field campaign of BC measurements in Arctic snow occurred. We find that models generally underestimate BC concentrations in snow in northern Russia and Norway, while overestimating BC amounts elsewhere in the Arctic. Although simulated BC distributions in snow are poorly correlated with measurements, mean values are reasonable. The multi-model mean (range) bias in BC concentrations, sampled over the same grid cells, snow depths, and months of measurements, are-4.4 (-13.2 to +10.7) ng g−1 for an earlier phase of AeroCom models (phase I), and +4.1 (-13.0 to +21.4) ng g−1 for a more recent phase of AeroCom models (phase II), compared to the observational mean of 19.2 ng g−1. Factors determining model BC concentrations in Arctic snow include Arctic BC emissions, transport of extra-Arctic aerosols, precipitation, deposition efficiency of aerosols within the Arctic, and meltwater removal of particles in snow. Sensitivity studies show that the model-measurement evaluation is only weakly affected by meltwater scavenging efficiency because most measurements were conducted in non-melting snow. The Arctic (60-90° N) atmospheric residence time for BC in phase II models ranges from 3.7 to 23.2 days, implying large inter-model variation in local BC deposition efficiency. Combined with the fact that most Arctic BC deposition originates from extra-Arctic emissions, these results suggest that aerosol removal processes are a leading source of variation in model performance. The multi-model mean (full range) of Arctic radiative effect from BC in snow is 0.15 (0.07-0.25) W m−2 and 0.18 (0.06-0.28) W m−2 in phase I and phase II models, respectively. After correcting for model biases relative to observed BC concentrations in different regions of the Arctic, we obtain a multi-model mean Arctic radiative effect of 0.17 W m−2 for the combined AeroCom ensembles. Finally, there is a high correlation between modeled BC concentrations sampled over the observational sites and the Arctic as a whole, indicating that the field campaign provided a reasonable sample of the Arctic. © 2014 Author (s).


Scientists at the U.S. Department of Energy's National Renewable Energy Laboratory (NREL) made the surprise discovery that a metabolic pathway to take up CO exists and functions in a microorganism capable of breaking down and fermenting cellulosic biomass to produce biofuels including hydrogen and hydrocarbons. Clostridium thermocellum is among the most efficient bacteria in directly converting cellulosic materials into hydrogen and hydrocarbons biofuels. Most bacteria feeding upon organic carbon compounds, such as glucose or xylose, release CO as a waste byproduct, decreasing the maximum amount of products the microorganism can produce per carbon atom measured as carbon efficiency. Other scientists have found the addition of a form of CO , known as bicarbonate, into the medium containing the bacterium actually promotes the growth of C. thermocellum, yet its mechanistic details remained a puzzle. This enhanced growth implied the bacterium had the ability to use CO and prompted NREL researchers to investigate the phenomena enhancing the bacterium's growth. "It took us by surprise that this microbe can recapture some of the CO released during growth while they consume sugars derived from cellulosic biomass," said Katherine J. Chou, a staff scientist with NREL's Photobiology group and co-author of the new paper "CO -fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum." The research is in the new issue of the journal Proceedings of the National Academy of Sciences of the United States of America. Using carbon isotopes coupled with mass spectrometry analysis, the researchers were able to track how CO enters the cell, identify the enzymes critical to CO uptake, and how CO incorporates into products thereby discovering a new metabolic route unknown to the scientific community. Many species of bacteria have the pathway in place for CO uptake, but before the new research, the pathway was not associated with the role of carbon dioxide assimilation (otherwise known as CO fixation). The pathway enables the bacterium to use both CO and organic carbons during its growth, which is counter-intuitive because it's much more common for this type of organism to use one and not the other, especially in heterotrophic microbes. NREL researchers and their collaborators determined adding bicarbonate increased the apparent carbon efficiency of C. thermocellum from 65.7 percent to 75.5 percent. The finding underscores the metabolic plasticity of the microbe and raises various possibilities on how the bacterium is able to use both organic carbons and CO without breaking the rules of thermodynamics in energy conservation. The discovery also provides a paradigm shift in the fundamental understandings of carbon metabolism in a cellulose degrading bacterium. "Our findings pave the way for future engineering of the bacterium as a way to improve carbon efficiency and to reduce the amount of CO released into the environment," Chou said. With the observed improved carbon efficiency, this work inspires future research to redirect more cellular electrons in support of increased hydrogen production, a key goal for the funded research. In addition to Chou, the co-authors from NREL are Wei Xiong, Lauren Magnusson, Lisa Warner, and Pin-Ching Maness. Two BioEnergy Science Center (BESC) co-authors are Paul Lin and James Liao from the University of California, Los Angeles, where Chou earned her Ph.D. in chemical and biomolecular engineering. The latest research into the bacterium was financed by the NREL Director's Fellowship Program, Energy Department's Fuel Cell Technologies Office, as well as Office of Biological and Environmental Research in the DOE Office of Science. NREL is the U.S. Department of Energy's primary national laboratory for renewable energy and energy efficiency research and development. NREL is operated for the Energy Department by The Alliance for Sustainable Energy, LLC.


News Article | December 22, 2016
Site: www.eurekalert.org

LA JOLLA, CA - December 21, 2016 - A new study led by scientists at The Scripps Research Institute (TSRI) is the first to show exactly how the drug Arbidol stops influenza infections. The research reveals that Arbidol stops the virus from entering host cells by binding within a recessed pocket on the virus. The researchers believe this new structural insight could guide the development of future broad-spectrum therapeutics that would be even more potent against influenza virus. "This is a very interesting molecule, and now we know where it binds and precisely how it works," said study senior author Ian Wilson, Hanson Professor of Structural Biology, chair of the Department of Integrative Structural and Computational Biology and member of the Skaggs Institute for Chemical Biology at TSRI. The study was published today in the journal Proceedings of the National Academy of Sciences. Arbidol (also called umifenovir) is an anti-flu treatment sold in Russia and China by the Russian pharmaceutical company Pharmstandard. The drug is currently in stage-four clinical trials in the United States. The drug targets many strains of influenza, giving it an advantage over seasonal vaccines that target only a handful of strains. The new study sheds light on exactly how it accomplishes this feat. Scientists had long been curious whether Arbidol bound to the viral proteins used to recognize host cells--or with the viral "fusion machinery" that enters and infects host cells. To answer this question, the researchers used a high-resolution imaging technique called X-ray crystallography to create 3D structures showing how Arbidol binds to two different strains of influenza virus. The structures revealed that Arbidol binds to the virus's fusion machinery, as some had suspected. The small molecule binds to a viral protein called hemagglutinin, stopping the virus from rearranging its conformation in a way that enables the virus to fuse its membrane with a host cell. "We found that the small molecule binds to a hidden pocket in hemagglutinin," said study first author Rameshwar U. Kadam, senior research associate at TSRI. He added that the drug acts as a sort of "glue" to hold the subunits of hemagglutinin together. "Arbidol is the first influenza treatment shown to use a hemagglutinin-binding approach," he said. This vulnerable pocket is "conserved," meaning it is likely important for viral function--and more difficult to mutate as the virus spreads--suggesting why Arbidol has relatively broad use in fighting many strains of the virus, including emerging strains. The new findings also help scientists understand how Arbidol compares to influenza treatments such as Tamiflu. Wilson explained that Tamiflu prevents the virus from getting out of cells, while Arbidol prevents it from getting in. This means Arbidol, or future drugs that take a similar approach, could be given as a preventative treatment before an outbreak hits. "When we had the 2009 H1N1 pandemic, the vaccine came too late," said Wilson. "If we had a front-line therapeutic, that could have worked much better until a vaccine was ready." Wilson said the next step for researchers is to discover and/or design other small molecule therapeutics that can bind even more tightly with the hemagglutinin. This study, "Structural basis of influenza virus fusion inhibition by the antiviral drug Arbidol," was supported by the National Institutes of Health (grant R56 AI117675) and an Early Mobility Postdoctoral Fellowship from the Swiss National Science Foundation. This study used resources funded in whole or in part by the National Cancer Institute (grant Y1-CO-1020); the National Institute of General Medical Science (grant Y1-GM-1104); the U.S. Department of Energy, Basic Energy Sciences, Office of Science (contracts DE-AC02-06CH11357 and DE-AC02-76SF00515); the U.S. Department of Energy, Office of Biological and Environmental Research and by the National Institute of General Medical Science (grant P41GM103393). The Scripps Research Institute (TSRI) is one of the world's largest independent, not-for-profit organizations focusing on research in the biomedical sciences. TSRI is internationally recognized for its contributions to science and health, including its role in laying the foundation for new treatments for cancer, rheumatoid arthritis, hemophilia, and other diseases. An institution that evolved from the Scripps Metabolic Clinic founded by philanthropist Ellen Browning Scripps in 1924, the institute now employs more than 2,500 people on its campuses in La Jolla, CA, and Jupiter, FL, where its renowned scientists--including two Nobel laureates and 20 members of the National Academy of Science, Engineering or Medicine--work toward their next discoveries. The institute's graduate program, which awards PhD degrees in biology and chemistry, ranks among the top ten of its kind in the nation. For more information, see http://www. .


News Article | December 20, 2016
Site: www.eurekalert.org

Scientists at Washington University School of Medicine in St. Louis have detailed the structure of a molecule that has been implicated in Alzheimer's disease. Knowing the shape of the molecule -- and how that shape may be disrupted by certain genetic mutations -- can help in understanding how Alzheimer's and other neurodegenerative diseases develop and how to prevent and treat them. The study is published Dec. 20 in the journal eLife. The idea that the molecule TREM2 is involved in cognitive decline -- the hallmark of neurodegenerative diseases, including Alzheimer's -- has gained considerable support in recent years. Past studies have demonstrated that certain mutations that alter the structure of TREM2 are associated with an increased risk of developing late-onset Alzheimer's, frontal temporal dementia, Parkinson's disease and sporadic amyotrophic lateral sclerosis (ALS). Other TREM2 mutations are linked to Nasu-Hakola disease, a rare inherited condition that causes progressive dementia and death in most patients by age 50. "We don't know exactly what dysfunctional TREM2 does to contribute to neurodegeneration, but we know inflammation is the common thread in all these conditions," said senior author Thomas J. Brett, PhD, an assistant professor of medicine. "Our study looked at these mutations in TREM2 and asked what they do to the structure of the protein itself, and how that might impact its function. If we can understand that, we can begin to look for ways to correct it." The analysis of TREM2 structure, completed by first author, Daniel L. Kober, a doctoral student in Brett's lab, revealed that the mutations associated with Alzheimer's alter the surface of the protein, while those linked to Nasu-Hakola influence the "guts" of the protein. The difference in location could explain the severity of Nasu-Hakula, in which signs of dementia begin in young adulthood. The internal mutations totally disrupt the structure of TREM2, resulting in fewer TREM2 molecules. The surface mutations, in contrast, leave TREM2 intact but likely make it harder for the molecule to connect to proteins or send signals as normal TREM2 molecules would. TREM2 lies on the surface of immune cells called microglia, which are thought to be important "housekeeping" cells. Via a process called phagocytosis, such cells are responsible for engulfing and cleaning up cellular waste, including the amyloid beta that is known to accumulate in Alzheimer's disease. If the microglia lack TREM2, or the TREM2 that is present doesn't function properly, the cellular housekeepers can't perform their cleanup tasks. "Exactly what TREM2 does is still an open question," Brett said. "We know mice without TREM2 have defects in microglia, which are important in maintaining healthy brain biology. Now that we have these structures, we can study how TREM2 works, or doesn't work, in these neurodegenerative diseases." TREM2 also has been implicated in other inflammatory conditions, including chronic obstructive pulmonary disease and stroke, making the structure of TREM2 important for understanding chronic and degenerative diseases throughout the body, he added. This work was supported by the National Institutes of Health (NIH), grant numbers R01-HL119813, R01-AG044546, R01-AG051485, R01-HL120153, R01-HL121791, K01-AG046374, T32-GM007067, K08-HL121168, and P50-AG005681-30.1; the Burroughs-Wellcome Fund; the Alzheimer's Association, grant number AARG-16-441560; and the American Heart Association, grant number PRE22110004. Results were derived from work performed at Argonne National Laboratory (ANL) Structural Biology Center. ANL is operated by U. Chicago Argonne, LLC, for the U.S. DOE, Office of Biological and Environmental Research, supported by grant number DE-AC02-06CH11357. Kober DL, Alexander-Brett JM, Karch CM, Cruchaga C, Colonna M, Holtzman MJ, Brett TJ. Neurodegenerative disease mutations in TREM2 reveal a functional surface and distinct loss-of-function mechanisms. eLife. Dec. 20, 2016. Washington University School of Medicine's 2,100 employed and volunteer faculty physicians also are the medical staff of Barnes-Jewish and St. Louis Children's hospitals. The School of Medicine is one of the leading medical research, teaching and patient-care institutions in the nation, currently ranked sixth in the nation by U.S. News & World Report. Through its affiliations with Barnes-Jewish and St. Louis Children's hospitals, the School of Medicine is linked to BJC HealthCare.


News Article | November 10, 2016
Site: www.eurekalert.org

Researchers at Johns Hopkins report they have laid the foundation to develop novel antibiotics that work against incurable, antibiotic-resistant bacteria like tuberculosis by targeting an enzyme essential to the production and integrity of bacterial cell walls. The findings, they say, suggest that antibiotic drugs specifically targeting the recently discovered LD-transpeptidase enzyme, which is needed to build bacterial cell walls in some bacteria, could potentially cure many antibiotic-resistant infections. An additional implication of the research, the Johns Hopkins team says, is that drugs targeting the enzyme could offer quicker, cheaper and more easily accessible treatment against tuberculosis, a disease that still kills more people worldwide than any other infection, according to the Centers for Disease Control and Prevention. A summary of the findings is published on Nov. 7 in Nature Chemical Biology. "The complexity of TB treatment and growing prevalence of antibiotic resistance is a serious threat to public health," says Gyanu Lamichhane, Ph.D. associate professor of medicine at the Johns Hopkins University School of Medicine. His team joined with the research team of Craig Townsend, Ph.D., the Alsoph H. Corwin Professor of Chemistry at The Johns Hopkins University's Krieger School of Arts and Sciences, to tackle this complex issue. "Our research offers steps toward the design of new antibiotics that attack a previously untargeted bacterial enzyme," says Townsend. At the root of their investigation, Lamichhane says, is the fact than more than half of antibiotics prescribed today are of a class called beta-lactams, which work by interrupting the function of the DD-transpeptidase enzyme that creates bacterial cell walls. Without it, bacteria quickly die. However, in 2005, a team of researchers found a second wall-building enzyme, LD-transpeptidase, that allows bacteria like the ones that cause TB to survive antibiotic treatments. "We looked at the structure of LD-transpeptidase, thought about how it works and started making new compounds that could be used against it," says Townsend. Pankaj Kumar, Ph.D., postdoctoral fellow in infectious diseases at the Johns Hopkins University School of Medicine, began the research in the new study by extracting LD-transpeptidase from many species of bacteria and examining its detailed molecular structure with a sophisticated imaging system known as protein X-ray crystallography using the Advanced Photon Source at the Argonne National Laboratory in Chicago. By analyzing the enzyme's structure, Johns Hopkins researchers were able to design new compounds in the carbapenem group, a subclass of the beta-lactam antibiotics that bind to the LD-transpeptidase wall-building enzyme and stop its function. In live bacterial cultures, the carbapenems were shown by Lamichhane's and Townsend's groups to stop the enzyme's wall-building activity. The new compounds were even effective against the ESKAPE pathogens, a group of six bacterial species that the Centers for Disease Control and Prevention has identified as a threat because of their propensity for developing antibiotic resistance. Following these successes, Amit Kaushik, Ph.D., a postdoctoral fellow in infectious diseases at the Johns Hopkins University School of Medicine, tested two carbapenems in vivo against TB in mice infected with TB. Researchers infected mice with tuberculosis bacteria and separated them into different treatment groups. The rodents' lungs were sampled periodically over a period of three weeks, and the results showed that even without use of classic TB antibiotic treatments, the new carbapenems, specifically biapenem, cured TB infection in mice. "Our data show that the carbapenems successfully treated TB infections alone by attacking the right enzyme," says Lamichhane. Townsend and Lamichhane say the focus of their research is now on creating variations of their original compound that are designed to target specific bacteria. Many commonly prescribed antibiotics today work on a broad spectrum of bacterial species, meaning that in addition to killing off bad bacteria, they also destroy the friendly bacteria our bodies need to function normally and whose destruction can cause dangerous side effects. Lamichhane believes that the future of antibiotic treatments relies on our ability to be good antimicrobial stewards and treat specific bacteria without affecting our bodies' natural microbiome. Not only will this cut down on antibiotic side effects, but it will also slow the development of antibiotic resistance in the bacterial species not being targeted. The researchers are now in the process of initiating clinical trials to test the safety and efficacy of some of these new compounds. Antibiotic resistance has been an ever-present threat since the discovery of penicillin in 1928. Scientists and physicians have historically kept up with resistant bacteria through the frequent introduction of new antibiotic treatments. However, the research and development of antibiotics plummeted in the 1980s as other drugs became more profitable to produce. Because of the decreased incentive to invest in new antibiotics and the liberal use of antibiotics we already have, many bacterial species have quickly outpaced our ability to treat them. The Centers for Disease Control and Prevention estimates that annually, 2 million illnesses and 23,000 deaths are caused by antibiotic-resistant bacteria in the United States alone, and that 70 percent of hospital-acquired infections are now antibiotic-resistant. Other authors on this study include Evan P. Lloyd, Trevor A. Zandi, Rohini Mattoo, Nicole C. Ammerman and Drew T. Bell of The Johns Hopkins University; Shao-Gang Li, Joel S. Freundlich and Alexander L. Perryman of Rutgers University Medical School; Sean Ekins of Collaborations in Chemistry; and Stephan L. Ginell of the Argonne National Laboratory. This study was funded by the National Institutes of Health (R21AI111739 and DP2OD008459) and the U.S. Department of Energy Office of Biological and Environmental Research (contract number DE-AC02-06CH11357).


In order to uncover the structure of these proteins, researchers used a technique called protein crystallography. Like a mosquito trapped in amber, compounds that are crystallized are placed in array in identical positions and ordered so that scientists can target them with X-ray beams and work backwards from the scattering patterns produced to recreate their three-dimensional structures atom by atom. In the first study, a group of researchers from the Structural Biology Center, which is funded by DOE's Office of Science, mapped out a protein responsible for breaking down organic compounds in soil bacteria, an important process for recycling carbon in the ecosystem. The bacteria used, called Acinetobacter, is located mostly in soil and water habitats, where it helps to change aromatic compounds (named for their ring shape) into forms that can be used as food. One of the sources of aromatic compounds found in soil is lignin, a tough polymer that is an essential part of all plants and that's hard for many organisms to digest. "But Acinetobacter can utilize these aromatic compounds as their sole source of carbon," said Andrzej Joachimiak, who co-authored both studies and is the director of the Structural Biology Center and the Midwest Center for Structural Genomics at Argonne. In order for Acinetobacter to break down the aromatic compounds, it needs to produce catabolic enzymes, molecular machines built from an organism's DNA that break down molecules into smaller parts that can be digested. Whether or not membrane transporters and catabolic enzymes are produced falls to the HcaR regulator, a sort of molecular policeman that controls when the genes that code for these enzymes can be activated. Joachimiak and his colleagues found that the regulator works in a cycle, activating genes when aromatic compounds are present and shutting genes down when the compounds are used up. "By nature it is very efficient," Joachimiak said. "If you don't have aromatic compounds inside a cell, the operon is shut down." The research team didn't stop at mapping out the regulator itself; to discover how the cycle worked, they crystalized the HcaR regulator during interactions with its two major inputs: the aromatic compounds and DNA. The group found that when aromatic compounds are not present in the cell, two wings found on either side of the HcaR regulator wrap around the DNA. This action is mirrored on both sides of the regulator, covering the DNA regulatory site and preventing genes from being activated. "This is something that has never been seen before," Joachimiak said. When the aromatic compounds are present, however, they attach themselves to the HcaR regulator, making it so stiff that it can no longer grapple with the DNA. Joachimiak said that this knowledge could help outside of the lab, with applications such as a sensor for harmful pesticides and as a template for converting more carbon in soil. "If we can train bacteria to better degrade lignin and other polymers produced by plants during photosynthesis, more natural carbon sources can be utilized for example for production of biofuels and bioproducts," Joachimiak said. The paper was published earlier this year by the Journal of Biological Chemistry under the title "How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator." It was supported by the National Institutes of Health and the U.S. Department of Energy (Office of Biological and Environmental Research). A second paper focuses on a family of proteins identified as DUF89, which stands for "domain unknown function." This family is conserved across all three branches of the phylogenetic tree, which means that it is likely essential to many life forms. DUF89 has been identified as a type of enzyme called a phosphatase, which strips molecules of their phosphate groups. The paper's authors hypothesized that DUF89 proteins use this ability to save useful proteins in a cell from rogue molecules which could alter their structure, making them useless or destructive. The study found that DUF89 proteins use a metal ion, probably manganese, to lure in potentially harmful molecules and a water molecule to break off their phosphate group. DUF89 proteins could have an important role in breaking down a specific type of disruptive molecule: sugar. When the concentration of sugar in blood reaches high levels, simple sugars can have unwanted side reactions with proteins and DNA through a process called glycation. "We always have to deal with these side reactions that happen in our cells, and when we get older, we have an accumulation of these errors in our cells," Joachimiak said. Joachimiak said that this research could help scientists develop DUF89 treatments from non-human sources as a way to combat glycation in the bloodstream. The paper was published on the Nature Chemical Biology website on June 20 under the title "A family of metal-dependent phosphatases implicated in metabolite damage-control." Other authors on the paper were from the University of Florida, the University of Toronto, the University of California-Davis and Brookhaven National Laboratory. It was supported by the National Science Foundation, Genome Canada, the Ontario Genomics Institution, the Ontario Research Fund, the Natural Sciences and Engineering Research Council of Canada, the National Institutes of Health, the C.V. Griffin Sr. Foundation and the U.S. Department of Energy (Office of Basic Energy Sciences and Office of Biological and Environmental Research). Both studies used X-rays from the Advanced Photon Source, a DOE Office of Science User Facility, using beamlines 19-ID and 19-BM. Both also stem from the goal of the Midwest Center for Structural Genomics, which is to discover the structure and function of proteins potentially important to biomedicine. Joachimiak said that despite the new findings from these studies, when it comes to understanding what proteins do, we still have a long way to go. "When we sequence genomes, we can predict proteins, but when we predict those sequences we can only say something about function for about half of them," Joachimiak said. Explore further: New crystallization method to ease study of protein structures More information: Youngchang Kim et al. How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator, Journal of Biological Chemistry (2016). DOI: 10.1074/jbc.M115.712067 Lili Huang et al. A family of metal-dependent phosphatases implicated in metabolite damage-control, Nature Chemical Biology (2016). DOI: 10.1038/nchembio.2108


By adding a few water molecules to the GFP chromophore—the part of the molecule responsible for its color—the scientists simulated crystallographic water molecules in GFPs. When water is added, the excited state that generates fluorescence is more stable. Water apparently shuts the channel to electron emissions, effectively shutting off electron autodetachment competition and allowing fluorescence. The scientists' findings provide a more accurate understanding of this extremely useful protein. The two water molecules shown on the December 14 cover of The Journal of Chemical Physics make a huge difference in the behavior of the GFP. In turn, this can lead to eventual control and manipulation of processes where GFP is used. GFPs (see sidebar) are invaluable as markers for monitoring processes in living cells, such as in cancer research, where GFP-labeled cells model how cancer spreads to organs. Their versatility and value has led to the synthesis of new types of GFPs with different colors and new classes of photoactivatable fluorescent proteins for use in ultra-resolution imaging and optical data storage of raw data images from living cells and tissues. The photophysics of GFP and its chromophore depends on its local structure and environment. Despite extensive experimental and computational studies, many open questions remain about the key fundamental variables governing this process. One question is what controls the efficiency of light emission. When GFP absorbs light, only some of the energy is converted into a fluorescent signal, with the rest being lost by a process known as relaxation or deactivation. The fraction of energy emitted as fluorescence versus that lost by relaxation dictates GFP's efficiency. What the PNNL and LSU scientists wanted to know was how the protein's internal environment—in this case, water—affects specific types of relaxation. "We know the relaxation that competes against the fluorescence is critically dependent on the GFP chromophore's local environments, but we don't fully understand the details of why it happens," said PNNL chemical physicist Dr. Xue-Bin Wang, senior author of the article. "If we get rid of surrounding molecules by using the gas phase, the fluorescence goes away. And in solution, no fluorescence occurs at room temperature. But fluorescence returns at low temperatures. Is it caused by the intrinsic electronic structure properties of the chromophore in the protein? Or is it caused by other molecules in its environment? Our results showed it was the latter." GFP is centrally important to modern cell biology. Its discovery and development garnered the 2008 Nobel Prize in Chemistry for scientists Osamu Shimomura, Martin Chalfie, and Roger Tsien. Gaining a fundamental molecular understanding of how GFP works can lead to the ability to control, engineer, or manipulate systems for new applications, such as biosensors, or for advanced imaging. In the cartoons shown here, the GFP molecules are shown in full, and with the side of the surrounding barrel cut away (right) to reveal the chromophore, which is highlighted as a ball-and-stick model. Fluorescence arises when a molecule absorbs certain colors of visible light and then reemits a different, lower energy color. The interactions of the chromophore with its surroundings will dramatically affect the fluorescent properties of GFP, such as the color or intensity of the fluorescence. Researchers are currently trying to understand the underlying physics of these processes. By adding water and comparing the computation with experimental results, the scientists could determine that their theory of the molecules' structure was accurate. The team combined negative ion photoelectron spectroscopy (NIPES) with theoretical calculations to create a probe to identify the exact conformers of clusters of the p-hydroxybenzylidene-2,3-dimethylimidazolinone anion (HBDI-), a model of the GFP chromophore. They used NWChem, an open-source computational chemistry software package supported by the Department of Energy (DOE) Office of Biological and Environmental Research (BER) and developed at PNNL with unique capabilities regarding excited states and structure characterization, and the supercomputer Cascade, at EMSL. In a previous study by Wang and collaborators at the Chinese Academy of Sciences, the GFP chromophore itself was studied in the gas phase. In the current study, the scientists took another step farther by adding the water molecules. The notable addition was the use of advanced computer simulation techniques developed in collaboration with LSU. "In the current paper, the important component was coming up with an accurate theory. In an experiment, when we obtain a signal, we don't 'see' what is happening. Computer simulations using NWChem and EMSL supercomputing resources, give us the necessary details," said co-author Dr. Karol Kowalski. "It's a puzzle," said computational scientist Dr. Marat Valiev, one of the co-authors. "You can't interrogate the protein system as a whole to obtain key molecular-level parameters governing photoresponses of GFP. We have to disassemble it piece by piece, examine each piece, and then put it back together, which is best approached through combining experiment and simulation." The scientists showed that the first few water molecules progressively stabilize the excited state of the chromophore. "This could be an important role of water molecules in GFPs that has not yet been fully explored," said Wang. Explore further: Researchers transform fluorescent proteins into a scaffold for manipulating genes More information: S. H. M. Deng et al. Vibrationally Resolved Photoelectron Spectroscopy of the Model GFP Chromophore Anion Revealing the Photoexcited S State Being Both Vertically and Adiabatically Bound against the Photodetached D Continuum , The Journal of Physical Chemistry Letters (2014). DOI: 10.1021/jz500869b Kiran Bhaskaran-Nair et al. Probing microhydration effect on the electronic structure of the GFP chromophore anion: Photoelectron spectroscopy and theoretical investigations, The Journal of Chemical Physics (2015). DOI: 10.1063/1.4936252


Koch D.,Columbia University | Koch D.,Office of Biological and Environmental Research | Bauer S.E.,Columbia University | Del Genio A.,NASA | And 8 more authors.
Journal of Climate | Year: 2011

The authors simulate transient twentieth-century climate in the Goddard Institute for Space Studies (GISS) GCM, with aerosol and ozone chemistry fully coupled to one another and to climate including a full dynamic ocean. Aerosols include sulfate, black carbon (BC), organic carbon, nitrate, sea salt, and dust. Direct and BCsnow-albedo radiative effects are included. Model BC and sulfur trends agree fairly well with records from Greenland and European ice cores and with sulfur deposition in North America; however, the model underestimates the sulfur decline at the end of the century in Greenland. Global BC effects peak early in the century (1940s); afterward the BC effects decrease at high latitudes of the Northern Hemisphere but continue to increase at lower latitudes. The largest increase in aerosol optical depth occurs in the middle of the century (1940s-80s) when sulfate forcing peaks and causes global dimming. After this, aerosols decrease in eastern North America and northern Eurasia leading to regional positive forcing changes and brightening. These surface forcing changes have the correct trend but are too weak. Over the century, the net aerosol direct effect is 20.41 W m-2, the BC-albedo effect is 20.02 W m-2, and the net ozone forcing is 10.24 W m-2. Themodel polar stratospheric ozone depletion develops, beginning in the 1970s. Concurrently, the sea salt load and negative radiative flux increase over the oceans around Antarctica. Net warming over the century is modeled fairlywell; however, the model fails to capture the dynamics of the observedmidcentury cooling followed by the late century warming.Over the century, 20%ofArcticwarming and snow-ice cover loss is attributed to the BCalbedo effect. However, the decrease in this effect at the end of the century contributes to Arctic cooling. To test the climate responses to sulfate and BC pollution, two experiments were branched from 1970 that removed all pollution sulfate or BC. Averaged over 1970-2000, the respective radiative forcings relative to the full experiment were 10.3 and 20.3 W m-2; the average surface air temperature changes were +0.2° and -0.03°C. The small impact of BC reduction on surface temperature resulted from reduced stability and loss of low-level clouds. © 2011 American Meteorological Society.


Schmidt G.A.,NASA | Kelley M.,NASA | Kelley M.,Trinnovim LLC | Nazarenko L.,NASA | And 68 more authors.
Journal of Advances in Modeling Earth Systems | Year: 2014

We present a description of the ModelE2 version of the Goddard Institute for Space Studies (GISS) General Circulation Model (GCM) and the configurations used in the simulations performed for the Coupled Model Intercomparison Project Phase 5 (CMIP5). We use six variations related to the treatment of the atmospheric composition, the calculation of aerosol indirect effects, and ocean model component. Specifically, we test the difference between atmospheric models that have noninteractive composition, where radiatively important aerosols and ozone are prescribed from precomputed decadal averages, and interactive versions where atmospheric chemistry and aerosols are calculated given decadally varying emissions. The impact of the first aerosol indirect effect on clouds is either specified using a simple tuning, or parameterized using a cloud microphysics scheme. We also use two dynamic ocean components: the Russell and HYbrid Coordinate Ocean Model (HYCOM) which differ significantly in their basic formulations and grid. Results are presented for the climatological means over the satellite era (1980-2004) taken from transient simulations starting from the preindustrial (1850) driven by estimates of appropriate forcings over the 20th Century. Differences in base climate and variability related to the choice of ocean model are large, indicating an important structural uncertainty. The impact of interactive atmospheric composition on the climatology is relatively small except in regions such as the lower stratosphere, where ozone plays an important role, and the tropics, where aerosol changes affect the hydrological cycle and cloud cover. While key improvements over previous versions of the model are evident, these are not uniform across all metrics. Key Points Description of the GISS ModelE2 contribution to CMIP5 Impact on evaluation of structural changes in composition and ocean treatment Ocean model choice is an important structural uncertainty © 2014. American Geophysical Union. All Rights Reserved.

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