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  • 1
    Publication Date: 2016-07-19
    Description: Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 82 (2016): 1496-1503, doi:10.1128/AEM.02456-15.
    Description: The coalescence of next generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial communities. Delineating host-microbial associations has applied benefits ranging from clinical treatments to protecting our natural waters. Microbial communities follow some broad-scale patterns observed for macro-organisms, but it remains unclear how specialization of intestinal vertebrate-associated communities to a particular host environment influences broad-scale patterns in microbial abundance and distribution. We analyzed the V6 region of 16S rRNA gene amplified from 106 fecal samples spanning Aves, Mammalia, and Actinopterygii (ray-finned fish). The interspecific abundance-occupancy relationship—where widespread taxa tend to be more abundant than narrowly distributed taxa—among operational taxonomic units (OTUs) was investigated within and among host species. In a separate analysis, specialists OTUs that were highly abundant in a single host and rare in all other hosts were identified using a multinomial model without excluding under-sampled OTUs a priori. We also show that intestinal microbes in humans and other vertebrates studied follow a similar interspecific abundance-occupancy relationship compared to plants and animals, as well as microbes in ocean and soil environments; but because intestinal host-associated communities have undergone intense specialization, this trend is violated by a disproportionately large number of specialist taxa. Although it is difficult to distinguish the effects of dispersal limitations, host selection, historical contingency, and stochastic processes on community assembly, results suggest bacterial taxa can be shared among diverse vertebrate hosts in ways similar to those of ‘free-living’ bacteria.
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 2
    Publication Date: 2016-09-22
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 9 (2015): 90–100, doi:10.1038/ismej.2014.97.
    Description: Delineating differences in gut microbiomes of human and animal hosts contributes towards understanding human health and enables new strategies for detecting reservoirs of waterborne human pathogens. We focused upon Blautia, a single microbial genus that is important for nutrient assimilation as preliminary work suggested host-related patterns within members of this genus. In our dataset of 57 M sequence reads of the V6 region of the 16S ribosomal RNA gene in samples collected from seven host species, we identified 200 high-resolution taxonomic units within Blautia using oligotyping. Our analysis revealed 13 host-specific oligotypes that occurred exclusively in fecal samples of humans (three oligotypes), swine (six oligotypes), cows (one oligotype), deer (one oligotype), or chickens (two oligotypes). We identified an additional 171 oligotypes that exhibited differential abundance patterns among all the host species. Blautia oligotypes in the human population obtained from sewage and fecal samples displayed remarkable continuity. Oligotypes from only 10 Brazilian human fecal samples collected from individuals in a rural village encompassed 97% of all Blautia oligotypes found in a Brazilian sewage sample from a city of three million people. Further, 75% of the oligotypes in Brazilian human fecal samples matched those in US sewage samples, implying that a universal set of Blautia strains may be shared among culturally and geographically distinct human populations. Such strains can serve as universal markers to assess human fecal contamination in environmental samples. Our results indicate that host-specificity and host-preference patterns of organisms within this genus are driven by host physiology more than dietary habits.
    Description: This study was funded by the NIH grant R01AI091829-01A1 to SLM.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
    Publication Date: 2019-07-13
    Description: Glyoxal (CHOCHO) is produced in the atmosphere by the oxidation of volatile organic compounds(VOCs). Like formaldehyde (HCHO), another VOC oxidation product, it is measurable from space by solar backscatter. Isoprene emitted by vegetation is the dominant source of CHOCHO and HCHO in most of the world. We use aircraft observations of CHOCHO and HCHO from the Southeast Nexus (SENEX) campaign over the southeast US in summer 2013 to better understand the CHOCHO time-dependent yield from isoprene oxidation, its dependence on nitrogen oxides (NO (sub x) triple bonded to NO plus NO2), the behavior of the CHOCHO-HCHO relationship, the quality of Ozone Monitoring Instrument (OMI) CHOCHO satellite observations, and the implications for using CHOCHO observations from space as constraints on isoprene emissions. We simulate the SENEX and OMI observations with the Goddard Earth Observing System chemical transport model (GEOSChem) featuring a new chemical mechanism for CHOCHO formation from isoprene. The mechanism includes prompt CHOCHO formation under low-NO (sub x) conditions following the isomerization of the isoprene peroxy radical (ISOPO2).The SENEX observations provide support for this prompt CHOCHO formation pathway, and are generally consistent with the GEOS-Chem mechanism. Boundary layer CHOCHO and HCHO are strongly correlated in the observations and the model, with some departure under low-NO (sub x) conditions due to prompt CHOCHO formation. SENEX vertical profiles indicate a free-tropospheric CHOCHO background that is absent from the model. The OMI CHOCHO data provide some support for this free-tropospheric background and show southeast US enhancements consistent with the isoprene source but a factor of 2 too low. Part of this OMI bias is due to excessive surface reflectivities assumed in the retrieval. The OMI CHOCHO and HCHO seasonal data over the southeast US are tightly correlated and provide redundant proxies of isoprene emissions. Higher temporal resolution in future geostationary satellite observations may enable detection of the prompt CHOCHO production under low-NO (sub x) conditions apparent in the SENEX data.
    Keywords: Environment Pollution; Geophysics
    Type: GSFC-E-DAA-TN47279 , Atmospheric Chemistry and Physics (e-ISSN 1680-7324); 17; 14; 8725-8738
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  • 4
    Publication Date: 2019-07-13
    Description: Formaldehyde (HCHO) column data from satellites are widely used as a proxy for emissions of volatile organic compounds (VOCs), but validation of the data has been extremely limited. Here we use highly accurate HCHO aircraft observations from the NASA SEAC4RS (Studies of Emissions, Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys) campaign over the southeast US in August-September 2013 to validate and intercompare six retrievals of HCHO columns from four different satellite instruments (OMI (Ozone Monitoring Instrument), GOME (Global Ozone Monitoring Experiment) 2A, GOME (Global Ozone Monitoring Experiment) 2B and OMPS (Ozone Mapping and Profiler Suite)) and three different research groups. The GEOS (Goddard Earth Observing System)-Chem chemical transport model is used as a common intercomparison platform. All retrievals feature a HCHO maximum over Arkansas and Louisiana, consistent with the aircraft observations and reflecting high emissions of biogenic isoprene. The retrievals are also interconsistent in their spatial variability over the southeast US (r equals 0.4 to 0.8 on a 0.5 degree by 0.5 degree grid) and in their day-to-day variability (r equals 0.5 to 0.8). However, all retrievals are biased low in the mean by 20 to 51 percent, which would lead to corresponding bias in estimates of isoprene emissions from the satellite data. The smallest bias is for OMI-BIRA (Ozone Monitoring Instrument - Belgian Institute for Space Aeronomy), which has high corrected slant columns relative to the other retrievals and low scattering weights in its air mass factor (AMF) calculation. OMI-BIRA has systematic error in its assumed vertical HCHO shape profiles for the AMF calculation, and correcting this would eliminate its bias relative to the SEAC (sup 4) RS data. Our results support the use of satellite HCHO data as a quantitative proxy for isoprene emission after correction of the low mean bias. There is no evident pattern in the bias, suggesting that a uniform correction factor may be applied to the data until better understanding is achieved.
    Keywords: Environment Pollution
    Type: GSFC-E-DAA-TN41610 , Atmospheric Chemistry and Physics (ISSN 1680-7316) (e-ISSN 1680-7324); 16; 21; 13477-13490
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  • 5
    Publication Date: 2019-07-13
    Description: Formation of organic nitrates (RONO2) during oxidation of biogenic volatile organic compounds (BVOCs: isoprene, monoterpenes) is a significant loss pathway for atmospheric nitrogen oxide radicals (NOx), but the chemistry of RONO2 formation and degradation remains uncertain. Here we implement a new BVOC oxidation mechanism (including updated isoprene chemistry, new monoterpene chemistry, and particle uptake of RONO2) in the GEOS-Chem global chemical transport model with approximately 25 times 25 km(exp 2) resolution over North America. We evaluate the model using aircraft (SEAC4RS) and ground-based (SOAS) observations of NOx, BVOCs, and RONO2 from the Southeast US in summer 2013. The updated simulation successfully reproduces the concentrations of individual gas- and particle-phase RONO2 species measured during the campaigns. Gas-phase isoprene nitrates account for 2550 of observed RONO2 in surface air, and we find that another 10 is contributed by gas-phase monoterpene nitrates. Observations in the free troposphere show an important contribution from long-lived nitrates derived from anthropogenic VOCs. During both campaigns, at least 10 of observed boundary layer RONO2 were in the particle phase. We find that aerosol uptake followed by hydrolysis to HNO3 accounts for 60 of simulated gas-phase RONO2 loss in the boundary layer. Other losses are 20 by photolysis to recycle NOx and 15 by dry deposition. RONO2 production accounts for 20 of the net regional NOx sink in the Southeast US in summer, limited by the spatial segregation between BVOC and NOx emissions. This segregation implies that RONO2 production will remain a minor sink for NOx in the Southeast US in the future even as NOx emissions continue to decline. XXXX We have used airborne and ground-based observations from two summer 2013 campaigns in the Southeast US (SEAC4RS, SOAS) to better understand the chemistry and impacts of alkyl and multi-functional organic nitrates (RONO2). We used the observations, along with findings from recent laboratory, field, and modeling studies, to update and evaluate biogenic volatile organic compound (BVOC) oxidation schemes in the GEOS-Chem chemical transport model (CTM). From there, we used the updated CTM with 0:25 0:3125 ( 2525 km2) horizontal resolution to examine RONO2 speciation, chemical production/loss processes, and importance as a sink for NOx. Our improved mechanism provides a state-of-the-science description of isoprene oxidation in the presence of NOx, with
    Keywords: Geosciences (General)
    Type: GSFC-E-DAA-TN41615 , Atmospheric Chemistry and Physics (ISSN 1680-7316) (e-ISSN 1680-7324); 16; 9; 5969-5991
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  • 6
    Publication Date: 2019-07-13
    Description: Ozone pollution in the Southeast US involves complex chemistry driven by emissions of anthropogenic nitrogen oxide radicals (NOx = NO + NO2) and biogenic isoprene. Model estimates of surface ozone concentrations tend to be biased high in the region and this is of concern for designing effective emission control strategies to meet air quality standards. We use detailed chemical observations from the SEAC4RS aircraft campaign in August and September 2013, interpreted with the GEOS-Chem chemical transport model at 0.25 deg. x 0.3125 deg. horizontal resolution, to better understand the factors controlling surface ozone in the Southeast US. We find that the National Emission Inventory (NEI) for NOx from the US Environmental Protection Agency (EPA) is too high. This finding is based on SEAC4RS observations of NOx and its oxidation products, surface network observations of nitrate wet deposition fluxes, and OMI satellite observations of tropospheric NO2 columns. Our results indicate that NEI NOx emissions from mobile and industrial sources must be reduced by 30-60%, dependent on the assumption of the contribution by soil NOx emissions. Upper tropospheric NO2 from lightning makes a large contribution to satellite observations of tropospheric NO2 that must be accounted for when using these data to estimate surface NOx emissions. We find that only half of isoprene oxidation proceeds by the high-NOx pathway to produce ozone; this fraction is only moderately sensitive to changes in NOx emissions because isoprene and NOx emissions are spatially segregated. GEOS-Chem with reduced NOx emissions provides an unbiased simulation of ozone observations from the aircraft, and reproduces the observed ozone production efficiency in the boundary layer as derived from a 15 regression of ozone and NOx oxidation products. However, the model is still biased high by 8 +/- 13 ppb relative to observed surface ozone in the Southeast US. Ozonesondes launched during midday hours show a 7 ppb ozone decrease from 1.5 km to the surface that GEOS-Chem does not capture. This bias may reflect a combination of excessive vertical mixing and net ozone production in the model boundary layer.
    Keywords: Meteorology and Climatology
    Type: GSFC-E-DAA-TN41263 , Atmospheric Chemistry and Physics (ISSN 1680-7316) (e-ISSN 1680-7324); 16; 21; 13561-13577
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  • 7
    Publication Date: 2019-11-30
    Description: Ozone pollution in the Southeast US involves complex chemistry driven by emissions of anthropogenic nitrogen oxide radicals (NO(x) triple bond NO + NO2) and biogenic isoprene. Model estimates of surface ozone concentrations tend to be biased high in the region and this is of concern for designing effective emission control strategies to meet air quality standards. We use detailed chemical observations from the SEAC(exp 4)RS aircraft campaign in August and September 2013, interpreted with the GEOS-Chem chemical transport model at 0.25 deg x 0.3125 deg horizontal resolution, to better understand the factors controlling surface ozone in the Southeast US. We find that the National Emission Inventory (NEI) for NO(x) from the US Environmental Protection Agency (EPA) is too high. This finding is based on SEAC(exp 4)RS observations of NO(x) and its oxidation products, surface network observations of nitrate wet deposition fluxes, and OMI satellite observations of tropospheric NO2 columns. Our results indicate that NEI NO(x) emissions from mobile and industrial sources must be reduced by 30-60%, dependent on the assumption of the contribution by soil NO(x) emissions. Upper-tropospheric NO2 from lightning makes a large contribution to satellite observations of tropospheric NO2 that must be accounted for when using these data to estimate surface NO(x) emissions. We find that only half of isoprene oxidation proceeds by the high-NO(x) pathway to produce ozone; this fraction is only moderately sensitive to changes in NO(x) emissions because isoprene and NO(x) emissions are spatially segregated. GEOS-Chem with reduced NO(x) emissions provides an unbiased simulation of ozone observations from the aircraft and reproduces the observed ozone production efficiency in the boundary layer as derived from a regression of ozone and NO(x) oxidation products. However, the model is still biased high by 6 plus or minus 14 ppb relative to observed surface ozone in the Southeast US. Ozonesondes launched during midday hours show a 7 ppb ozone decrease from 1.5 km to the surface that GEOS-Chem does not capture. This bias may reflect a combination of excessive vertical mixing and net ozone production in the model boundary layer.
    Keywords: Environment Pollution
    Type: GSFC-E-DAA-TN51584 , Atmospheric Chemistry and Physics (ISSN 1680-7316) (e-ISSN 1680-7324); 16; 21; 13561-13577
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  • 8
    Publication Date: 2019
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 9
    Publication Date: 2013-02-27
    Description: Background: Genetic susceptibility to colonic inflammation is poorly defined at the gene level. Although Genome Wide Association studies (GWAS) have identified loci in the human genome which confer susceptibility to Inflammatory Bowel Disease (Crohn's and Ulcerative Colitis), it is not clear if precise loci exist which confer susceptibility to inflammation at specific locations within the gut e.g. small versus large intestine. Susceptibility loci for colitis in particular have been defined in the mouse, although specific candidate genes have not been identified to date. We have previously shown that infection with Trichuris muris (T. muris) induces chronic colitis in susceptible mouse strains with clinical, histological, and immunological homology to human colonic Crohn's disease. We performed an integrative analysis of colitis susceptibility, using an F2 inter-cross of resistant (BALB/c) and susceptible (AKR) mice following T. muris infection. Quantitative Trait Loci (QTL), polymorphic and expression data were analysed alongside in silico workflow analyses to discover novel candidate genes central to the development and biology of chronic colitis. Results: 7 autosomal QTL regions were associated with the establishment of chronic colitis following infection. 144 QTL genes had parental strain SNPs and significant gene expression changes in chronic colitis (expression fold-change 〉= +/-1.4). The T. muris QTL on chromosome 3 (Tm3) mapped to published QTL in 3 unrelated experimental models of colitis and contained 33 significantly transcribed polymorphic genes. Phenotypic pathway analysis, text mining and time-course qPCR replication highlighted several potential cis-QTL candidate genes in colitis susceptibility, including FcgR1, Ptpn22, RORc, and Vav3. Conclusion: Genetic susceptibility to induced colonic mucosal inflammation in the mouse is conserved at Tm3 and overlays Cdcs1.1. Genes central to the maintenance of intestinal homeostasis reside within this locus, implicating several candidates in susceptibility to colonic inflammation. Combined methodology incorporating genetic, transcriptional and pathway data allowed identification of biologically relevant candidate genes, with Vav3 newly implicated as a colitis susceptibility gene of functional relevance.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 10
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