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The SARS-CoV-2 genome encodes for approximately 30 proteins. Within the international project COVID19-NMR, we distribute the spectroscopic analysis of the viral proteins and RNA. Here, we report NMR chemical shift assignments for the protein Nsp3b, a domain of Nsp3. The 217-kDa large Nsp3 protein contains multiple structurally independent, yet functionally related domains including the viral papain-like protease and Nsp3b, a macrodomain (MD). In general, the MDs of SARS-CoV and MERS-CoV were suggested to play a key role in viral replication by modulating the immune response of the host. The MDs are structurally conserved. They most likely remove ADP-ribose, a common posttranslational modification, from protein side chains. This de-ADP ribosylating function has potentially evolved to protect the virus from the anti-viral ADP-ribosylation catalyzed by poly-ADP-ribose polymerases (PARPs), which in turn are triggered by pathogen-associated sensing of the host immune system. This renders the SARS-CoV-2 Nsp3b a highly relevant drug target in the viral replication process. We here report the near-complete NMR backbone resonance assignment (1H, 13C, 15N) of the putative Nsp3b MD in its apo form and in complex with ADP-ribose. Furthermore, we derive the secondary structure of Nsp3b in solution. In addition, 15N-relaxation data suggest an ordered, rigid core of the MD structure. These data will provide a basis for NMR investigations targeted at obtaining small-molecule inhibitors interfering with the catalytic activity of Nsp3b. [ABSTRACT FROM AUTHOR]

The mid-Atlantic region of the United States has a wide diversity ofnatural resources. Human pressures on these natural resources are intense. These factors have resulted in the collection of substantial amounts of environmental information about the region by EPA (both Regional and Research Offices), other governmental agencies, industry, and environmental groups. EPA Regional Offices comprehend first hand the importance of environmental data and are extremely supportive of investments in these data. Environmental data are used prominently in a variety of strategic planning and resource management initiatives. In EPA Region 3, the use of scientifically-sound environmental data is, in fact, one of our strategic programmatic goals. Environmental information is captured and assessed continuously by Regional staff, sometimes working in partnership with other Federal and State agencies,to derive relevant resource management conclusions The restoration goals for the Chesapeake Bay are based on environmental indicators andresulting data. Attainment of the water quality objectives for streams and coastal estuaries are predicated on monitoring data. Our initiative in the Mid-Atlantic Highlands area uses environmental indicators to measure the condition of forests and streams. Landscape-level indicators will provide unique opportunities for the use of data in planning and management activities in support of the principles of community-based activism and sustainable development. Significant value isadded to these data during their use by Regional managers. Regional programs, such as the Chesapeake Bay Program and several National Estuary Programs, are founded in environmental data. Environmental information is used by the Regional program managers to ascertain whether programs are accomplishing their intended objectives. Finally, Regional programs provide a crucial means for disseminating this information to broad segments of the public, so that a better informed and educated [ABSTRACT FROM AUTHOR]

SARS-CoV-2 (SCoV2) and its variants of concern pose serious challenges to the public health. The variants increased challenges to vaccines, thus necessitating for development of new intervention strategies including anti-virals. Within the international Covid19-NMR consortium, we have identified binders targeting the RNA genome of SCoV2. We established protocols for the production and NMR characterization of more than 80 % of all SCoV2 proteins. Here, we performed an NMR screening using a fragment library for binding to 25 SCoV2 proteins and identified hits also against previously unexplored SCoV2 proteins. Computational mapping was used to predict binding sites and identify functional moieties (chemotypes) of the ligands occupying these pockets. Striking consensus was observed between NMR-detected binding sites of the main protease and the computational procedure. Our investigation provides novel structural and chemical space for structure-based drug design against the SCoV2 proteome., (© 2022 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com , we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form., Competing Interests: CH was employed by Signals GmbH & Co. KG. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Altincekic, Korn, Qureshi, Dujardin, Ninot-Pedrosa, Abele, Abi Saad, Alfano, Almeida, Alshamleh, de Amorim, Anderson, Anobom, Anorma, Bains, Bax, Blackledge, Blechar, Böckmann, Brigandat, Bula, Bütikofer, Camacho-Zarco, Carlomagno, Caruso, Ceylan, Chaikuad, Chu, Cole, Crosby, de Jesus, Dhamotharan, Felli, Ferner, Fleischmann, Fogeron, Fourkiotis, Fuks, Fürtig, Gallo, Gande, Gerez, Ghosh, Gomes-Neto, Gorbatyuk, Guseva, Hacker, Häfner, Hao, Hargittay, Henzler-Wildman, Hoch, Hohmann, Hutchison, Jaudzems, Jović, Kaderli, Kalniņš, Kaņepe, Kirchdoerfer, Kirkpatrick, Knapp, Krishnathas, Kutz, zur Lage, Lambertz, Lang, Laurents, Lecoq, Linhard, Löhr, Malki, Bessa, Martin, Matzel, Maurin, McNutt, Mebus-Antunes, Meier, Meiser, Mompeán, Monaca, Montserret, Mariño Perez, Moser, Muhle-Goll, Neves-Martins, Ni, Norton-Baker, Pierattelli, Pontoriero, Pustovalova, Ohlenschläger, Orts, Da Poian, Pyper, Richter, Riek, Rienstra, Robertson, Pinheiro, Sabbatella, Salvi, Saxena, Schulte, Schiavina, Schwalbe, Silber, Almeida, Sprague-Piercy, Spyroulias, Sreeramulu, Tants, Tārs, Torres, Töws, Treviño, Trucks, Tsika, Varga, Wang, Weber, Weigand, Wiedemann, Wirmer-Bartoschek, Wirtz Martin, Zehnder, Hengesbach and Schlundt.)

In all genomes, most amino acids are encoded by more than one codon. Synonymous codons can modulate protein production and folding, but the mechanism connecting codon usage to protein homeostasis is not known. Here we show that synonymous codon variants in the gene encoding gamma-B crystallin, a mammalian eye-lens protein, modulate the rates of translation and cotranslational folding of protein domains monitored in real time by Förster resonance energy transfer and fluorescence-intensity changes. Gamma-B crystallins produced from mRNAs with changed codon bias have the same amino acid sequence but attain different conformations, as indicated by altered in vivo stability and in vitro protease resistance. 2D NMR spectroscopic data suggest that structural differences are associated with different cysteine oxidation states of the purified proteins, providing a link between translation, folding, and the structures of isolated proteins. Thus, synonymous codons provide a secondary code for protein folding in the cell., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Residues of toxic chemicals in human tissues and fluids can be important indicators of exposure. Urine collected from a subsample of the second National Health and Nutrition Examination Survey was analyzed for organochlorine, organophosphorus, and chlorophenoxy pesticides or their metabolites. Urine concentration was also measured. The most frequently occurring residue in urine was pentachlorophenol (PCP), found in quantifiable concentrations in 71.6% of the general population with an estimated geometric mean level of 6.3 ng/ml. Percent quantifiable levels of PCP were found to be highest among males. Quantifiable concentrations of 3,5,6-trichloro-2-pyridinol (5.8%), 2,4,5-trichlorophenol (3.4%), para-nitrophenol (2.4%), dicamba (1.4%), malathion dicarboxylic acid (0.5%), malathion alpha-monocarboxylic acid (1.1%), and 2,4-D (0.3%) were found, but at much lower frequencies. No quantifiable levels of 2,4,5-T or silvex were found. Preliminary analyses showed an apparent relationship between residue concentration and two measures of urine concentration (osmolality and creatinine). A large segment of the general population of the United States experienced exposure to certain pesticides, including some considered biodegradable, during the years 1976-1980.

In December 1990 the U.S. Environmental Protection Agency sponsored a workshop to discuss the applicability of an interim "toxicity equivalency factor" (TEF) approach to assessing risks posed by exposures to complex mixtures of polychlorinated biphenyls (PCBs). The group concluded that application of the TEF approach to PCBs would be less straightforward than it was in the case of chlorinated dibenzo-p-dioxins and dibenzofurans (CDDs/CDFs). It appears that "dioxin"-like properties of some PCB congeners are amenable to a TEF treatment that is compatible with that used for CDDs/CDFs. Such a scheme also seems to have utility in assessing risks to wildlife. Other non-"dioxin"-like toxic endpoints (e.g., neurotoxicity) appear to have a different structure-activity-related mechanism-of-action that requires a separate TEF scheme. The workshop identified data gaps in toxicology and analytical chemistry that hinder adoption of proposed TEF schemes for PCBs at this time.

Halogenated organic compounds are highly lipophilic chemicals that are persistent in the environment as a result of their use and chemical stability. Some of these compounds are also present in the environment as metabolites or oxidation products of a parent compound or as by-products formed in the production of chlorinated compounds. Chronic exposure to the general population results mainly through the food chain. Because they are lipophilic, and because many are metabolized slowly, these chemicals tend to concentrate in body fat tissue. This contribution has described these halogenated organic compounds, discussed their use, regulation and prohibition throughout the world, and reviewed published studies on the levels of these chemicals found in the adipose tissue of humans and animals. For many years, residues of halogenated organic compounds have been detected in the human adipose tissue of individuals in a number of countries, including those in Europe, Asia, and Africa, as well as in the U.S. The levels detected have been used as an index of the level of general population exposure of these compounds over time. Over the past two decades, most countries have observed a steady decline of this level of exposure, reflecting a reduction in the use of these compounds, restrictions on or banning of their use, and a corresponding decrease in their environmental levels. The levels of concentrations vary from chemical to chemical as well as from isomer to isomer. Since the use of aldrin and dieldrin has now been banned or restricted in the U.S. and a number of other countries, residue levels have slowly decreased. Mean values in human adipose tissue in the U.S. and some foreign countries ranged from 0.04 to 0.40 ppm for dieldrin. Aldrin was detected only in Argentina and Poland in the 1970s and endrin was not detected anywhere at anytime. By 1978, all products containing BHC registered in the U.S. has been either discontinued or reformulated to incorporate lindane rather than BHC. The potential for exposure to BHC is virtually nonexistent in the U.S.; however, exposure to lindane is possible since products containing this chemical are still marketed, and used particularly in the manufacture of human medicine. DDT was banned for agricultural purposes in the U.S. in 1972, although it is still used elsewhere for public health vector control. Since the decline in use of DDT, however, the average levels of concentration have also declined. Heptachlor, chlordane, and trans-nonachlor (a component of both heptachlor and chlordane) are chlorinated cyclodienes.(ABSTRACT TRUNCATED AT 400 WORDS)

Uses of pesticides and related agrochemicals have been regulated in the United States since 1948. The United States government has supported human and environmental monitoring for pesticides and selected toxic chemicals for the past 15 yr. The initial ambient monitoring systems were designed to determine average concentrations of pesticides and related chemicals in human and environmental media on a nationwide basis and determine changes in these concentrations over time. The results of these surveys showed that almost all of the general human population and various environmental components contained low concentrations of chlorinated pesticides. As the Environmental Protection Agency (EPA) restricted many uses of the chlorinated pesticides, the organophosphorous and carbamate pesticides which replaced them were not as easily monitored by ambient surveys. Special monitoring studies had to be done more frequently to produce data on these compounds which were not as persistent or accumulative in the environment. Currently, a re-evalution has begun to determine pesticide monitoring data needs for the next 5 to 10 yr, modify existing ambient surveys, and plan needed short-term studies to efficiently meet regulatory data needs. Ambient monitoring for trends in chemical levels in humans and the environment will continue in the United States at a reduced level, and many exposure data needs will be met with use-specific monitoring studies.

Chlordane was, prior to regulatory action by EPA in 1976, an extensively used insecticide for both household and agricultural pest control purposes. It was readily available to the general public for many years; thus, human exposure, including poisonings, has been documented. A case reporting fatal chlordane ingestion with residue levels in various body tissues is presented. Analyses were performed by gas-liquid chromatography. The highest residue levels were reported in stomach contents, liver, brain, and adipose tissue.

Hexachlorobenzene (HCB) is a chemical of concern to the US Environmental Protection Agency. Although the use of HCB as a fungicide has virtually been eliminated, detectable levels of HCB are still found in nearly all people in the USA. This paper describes an examination of HCB-residue levels from the US National Human Adipose Tissue Survey, which is an annual programme to collect a nationwide sample of adipose-tissue specimens and analyse them for the presence of toxic compounds. The specimens are collected from surgical patients and autopsied cadavers according to a multistage statistical survey design that allows identification of geographic and demographic subpopulations with elevated HCB levels, and thus may help to indicate sources of human exposure to this chemical. Data on HCB body-burden levels are available for the years 1974-1983, excluding 1980 and 1982. The estimated average residue level of 6115 specimens is 0.053 ppm, the ninetieth percentile value is 0.09 ppm and the range is 'not detected' to 4.33 ppm. The analysis reveals that while the percentage of individuals with detectable levels is increasing, the annual average level is decreasing. A large percentage of specimens with elevated HCB levels comes from the Pacific census division and the oldest age group. In comparison, world-wide detectable levels are approaching 100% and average residue levels tend to increase with age. World-wide HCB levels are higher in females, which contrasts with findings from the National Human Adipose Tissue Survey.

Between September 1973 and February 1974, 57 samples of human milk were collected from women residing in selected areas of Arkansas and Mississippi. Residues of p.p'-DDT, p.p'-DDE, p.p'-TDE, beta-BHC, dieldrin, heptachlor epoxide, oxychlordane, and trans-nonachlor were measured by electroncapture gas chromatography; trace amounts of o,p'-DDT and polychlorinated biphenyls were also detected. Additional analytical procedures were employed to confirm the presence of specific residues.

Agricultural uses of the insecticide DDT were cancelled by the U.S. Environmental Protection Agency December 31, 1972. However, the domestic use of DDT had begun to decline before this action. Beginning July 1969, residues of DDT and its metabolites were measured in human adipose tissue collected through an annual national survey. Levels of total DDT equivalent residues in human adipose have decreased slightly, but the frequencies of finding DDT or its metabolites have remained high. The most marked decline in residue concentration has been found in the youngest age group (0-14 years). Approximately 80 percent of the total DDT equivalent found in this survey was DDE. These data show that the reduction of the agricultural uses of DDT has decreased human exposure to and storage of this chemical.

A case of fatal suicidal ingestion of diazinon insecticide is presented. Diazinon concentrations in post-mortem body fluids and tissues were determined using electron capture and flame ionization gas-liquid chromatography. The highest concentrations of diazinon were found in blood, stomach contents, bile and adipose tissue.