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  • 1
    Electronic Resource
    Electronic Resource
    Protein I of Neisseria gonorrhoeae outer membrane is a porin (1981)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 12 (1981), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1981.tb07663.x
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    In Situ Measurement and Numerical Simulation of Oxygen Limited Biotransformation (1989)
    Oxford, UK : Blackwell Publishing Ltd
    Ground water monitoring & remediation 9 (1989), S. 0 
    Details
    ISSN: 1745-6592
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Geosciences
    Notes: Enhanced subsurface biorestoration is rapidly becoming recognized as a valuable tool for the restoration of hydrocarbon-contaminated aquifers and sediments. Previous field and laboratory studies at a former wood creosoting facility near Conroe, Texas, have indicated that insufficient oxygen is the primary factor limiting the biotransformation of polynuclear aromatics (PNAs) in sediments and ground water at this site. A series of laboratory experiments and field push-pull injection tests were performed as part of this project to: (1) study the effect of low oxygen concentrations on the biotransformation of PNAs; (2) identify the minimum concentration of PNAs that could be achieved through the addition of oxygen alone; (3) confirm that enhanced subsurface biorestoration is feasible at this site; and (4) test an existing numerical model of the biotransformation process (BIOPLUME). The laboratory studies demonstrated that biotransformation of the PNAs was not inhibited at dissolved oxygen concentrations as low as 0.7 mg/L although this work did suggest that there may be a minimum PNA concentration of 30 to 70 μg/L total PNAs below which biotransformation was inhibited. The field push-pull tests confirmed that addition of oxygen was effective in enhancing the subsurface biodegradation of the PNAs. The minimum concentration achieved using oxygen alone was approximately 60 μg/L total PNAs. Minimal biotransformation of these compounds was observed without oxygen addition. The numerical model BIOPLUME was tested against monitoring data from the field experiments and appears to provide a good approximation of the biodegradation process.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1745-6592.1989.tb01123.x
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  • 3
    Electronic Resource
    Electronic Resource
    Investigation and Remediation of a 1,2–Dichloroethane Spill Part I: Short and Long-Term Remediation Strategies (1999)
    Oxford, UK : Blackwell Publishing Ltd
    Ground water monitoring & remediation 19 (1999), S. 0 
    Details
    ISSN: 1745-6592
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Geosciences
    Notes: Release of an estimated 150,000 gallons (568,000 L).of 1.2–dichloroethane (EDC) from a buried pipeline into a ditch and surrounding soil resulted in shallow subsurface contamination of a Gulf Coast site. Short-term remediation included removal of EDC DNAPI. (dense nonaqueous phase liquid) by dredging and vacuuming the ditch, and by dredging the river where the ditch discharged. EDC saturation in shallow impacted sediments located beneath the ditch was at or below residual saturation and these sediments were therefore left in place. The ditch was lined, backfilled, and capped. Long-term remediation includes EDC DNAPL recovery and hydraulic containment from the shallow zone with long-term monitoring of the shallow, intermediate, and deep (200 foot) aquifers. Ground water, DNAPL., and dissolved phase models were used to guide field investigations and the selection of an effective remedial action strategy. The DNAPL. modeling was conducted for a two-dimensional vertical cross section of the site, and included the three aquifers separated by two aquitards with microfractures. These aquitards were modeled using a dual porosity approach. Matrix and fracture properties of the aquitards used for DNAPL modeling were determined from small-scale laboratory properties. These properties were consistent with effective hydraulic conductivity determined from ground water flow modeling. A sensitivity analysis demonstrated that the vertical migration of EDC was attenuated by dissolution of EDC into the matrix of the upper aquitard. When the organic/water entry pressure of the aquitard matrix, or the solubility of EDC were decreased to unrealislically low values. EDC DNAPL. accumulated in the aquifer below the upper aquitard.EDC DNALM, did not reach the regional (deepest) aquifer in any of the cases modeled. The limited extent of vertical EDC migration predicted is supported by ground water monitoring conducted over the four years since the spill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1745-6592.1999.tb00226.x
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  • 4
    Electronic Resource
    Electronic Resource
    Investigation and Remediation of a 1,2-Dichloroethane Spill Part II: Documentation of Natural Attenuation (1999)
    Oxford, UK : Blackwell Publishing Ltd
    Ground water monitoring & remediation 19 (1999), S. 0 
    Details
    ISSN: 1745-6592
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Geosciences
    Notes: A release of 1,2-dichloroethane. also known as ethylene dichloride (EDC), resulted in shallow subsurface freephase contamination of a Gulf Coast site in the southern United States. The site stratigraphy consists primarily of a low permeability, surficial peat. silt, and clay zone underlain by fractured clay; a confined 12 in deep sand ground water flow zone; a confined 21 m deep fine sand zone of limited ground water flow, followed by a deep aquitard. The Gumbo clay and sandy clay aquitard below the release area overlies and protects the 61 m deep Upper Chicot Aquifer, which is a confined regional aquifer. An ongoing recovery and hydraulic containment program from the primary impacted and laterally and vertically restricted shallow 40-foot sand zone has effectively recovered dense nonaqueous phase liquid (DNAPL) and contained dissolved phase EDC.Natural attenuation of EDC was demonstrated through (1) a laboratory microcosm study substantiating the ability of the native microbial population in the deeper aquifer lo degrade EDC under anaerobic environmental conditions found at the site. (2) field investigations showing reductions in EDC concentrations over time in many of the wells on site, and (3) an evaluation of the ground water for EDC and its degradation products and oilier geo-chemical parameters such as dissolved oxygen, redox potential, and pH. Degradation products of EDC found in the field investigations included 2-chloroeihanol, ethanol. ethene, and ethane. Dissolved EDC concentrations in selected wells between the first recorded samples and the fourth quarter of 1997 ranged from greater than 4% to 99% reductions. First-order exponential decay half-lives ranged from 0.21 to 4.2 years for wells showing decreases in FDC concentrations over time. Elevated methane concentrations indicated carbon dioxide to be the major terminal electron acceptor.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1745-6592.1999.tb00227.x
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  • 5
    Electronic Resource
    Electronic Resource
    An Extraction and Regularization Approach to Additive Clustering (1999)
    Springer
    Journal of classification 16 (1999), S. 255-281 
    Details
    ISSN: 1432-1343
    Keywords: Key words: Overlapping clustering; Additive clustering; ADCLUS.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003579900056
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  • 6
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    Functional genomics and phylogenetic evidence suggest genus-wide cobalamin production by the globally distributed marine nitrogen fixer Trichodesmium (2018)
    Frontiers Media
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 9 (2018): 189, doi:10.3389/fmicb.2018.00189.
    Description: Only select prokaryotes can biosynthesize vitamin B12 (i.e., cobalamins), but these organic co-enzymes are required by all microbial life and can be vanishingly scarce across extensive ocean biomes. Although global ocean genome data suggest cyanobacteria to be a major euphotic source of cobalamins, recent studies have highlighted that 〉95% of cyanobacteria can only produce a cobalamin analog, pseudo-B12, due to the absence of the BluB protein that synthesizes the α ligand 5,6-dimethylbenzimidizole (DMB) required to biosynthesize cobalamins. Pseudo-B12 is substantially less bioavailable to eukaryotic algae, as only certain taxa can intracellularly remodel it to one of the cobalamins. Here we present phylogenetic, metagenomic, transcriptomic, proteomic, and chemical analyses providing multiple lines of evidence that the nitrogen-fixing cyanobacterium Trichodesmium transcribes and translates the biosynthetic, cobalamin-requiring BluB enzyme. Phylogenetic evidence suggests that the Trichodesmium DMB biosynthesis gene, bluB, is of ancient origin, which could have aided in its ecological differentiation from other nitrogen-fixing cyanobacteria. Additionally, orthologue analyses reveal two genes encoding iron-dependent B12 biosynthetic enzymes (cbiX and isiB), suggesting that iron availability may be linked not only to new nitrogen supplies from nitrogen fixation, but also to B12 inputs by Trichodesmium. These analyses suggest that Trichodesmium contains the genus-wide genomic potential for a previously unrecognized role as a source of cobalamins, which may prove to considerably impact marine biogeochemical cycles.
    Description: This work was funded by NSF research grants OCE-1260233, OCE-1260490, OCE-1657757, and OCE-143566.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
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    Comment on “The complex effects of ocean acidification on the prominent N2-fixing cyanobacterium Trichodesmium” (2017)
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Science 357 (2017): eaao0067, doi:10.1126/science.aao0067.
    Description: Hong et al. (Reports, 5 May 2017, p. 527) suggested that previous studies of the biogeochemically significant marine cyanobacterium Trichodesmium showing increased growth and nitrogen fixation at projected future high CO2 levels suffered from ammonia or copper toxicity. They reported that these rates instead decrease at high CO2 when contamination is alleviated. We present and discuss results of multiple published studies refuting this toxicity hypothesis.
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 8
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    Mechanisms of increased Trichodesmium fitness under iron and phosphorus co-limitation in the present and future ocean (2016)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 7 (2016): 12081, doi:10.1038/ncomms12081.
    Description: Nitrogen fixation by cyanobacteria supplies critical bioavailable nitrogen to marine ecosystems worldwide; however, field and lab data have demonstrated it to be limited by iron, phosphorus and/or CO2. To address unknown future interactions among these factors, we grew the nitrogen-fixing cyanobacterium Trichodesmium for 1 year under Fe/P co-limitation following 7 years of both low and high CO2 selection. Fe/P co-limited cell lines demonstrated a complex cellular response including increased growth rates, broad proteome restructuring and cell size reductions relative to steady-state growth limited by either Fe or P alone. Fe/P co-limitation increased abundance of a protein containing a conserved domain previously implicated in cell size regulation, suggesting a similar role in Trichodesmium. Increased CO2 further induced nutrient-limited proteome shifts in widespread core metabolisms. Our results thus suggest that N2-fixing microbes may be significantly impacted by interactions between elevated CO2 and nutrient limitation, with broad implications for global biogeochemical cycles in the future ocean.
    Description: Grant support was provided by U.S. National Science Foundation OCE 1260490 to D.A.H., E.A.W. and F.-X.F., and OCE OA 1220484 and G.B. Moore Foundation 3782 and 3934 to M.A.S.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 9
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    Metabolomics as an emerging tool in the search for astrobiologically relevant biomarkers (2020)
    Mary Ann Liebert
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L., Kujawinski, E. B., Azua-Bustos, A., Lee, M. D., Marlow, J., Perl, S. M., & Cleaves, H. J. Metabolomics as an emerging tool in the search for astrobiologically relevant biomarkers. Astrobiology, (2020), doi:10.1089/ast.2019.2135.
    Description: It is now routinely possible to sequence and recover microbial genomes from environmental samples. To the degree it is feasible to assign transcriptional and translational functions to these genomes, it should be possible, in principle, to largely understand the complete molecular inputs and outputs of a microbial community. However, gene-based tools alone are presently insufficient to describe the full suite of chemical reactions and small molecules that compose a living cell. Metabolomic tools have developed quickly and now enable rapid detection and identification of small molecules within biological and environmental samples. The convergence of these technologies will soon facilitate the detection of novel enzymatic activities, novel organisms, and potentially extraterrestrial life-forms on solar system bodies. This review explores the methodological problems and scientific opportunities facing researchers who hope to apply metabolomic methods in astrobiology-related fields, and how present challenges might be overcome.
    Description: This study was partially supported by the ELSI Origins Network (EON), which is supported by a grant from the John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the John Templeton Foundation. This work was partially supported by a JSPS KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas “Hadean Bioscience,” grant number JP26106003, and also partially supported by Project “icyMARS,” funded by the European Research Council, ERC Starting Grant No. 307496. A.A-B thanks the contribution from the Project “MarsFirstWater,” funded by the European Research Council, ERC Consolidator Grant No. 818602 and the HFSP Project UVEnergy RGY0066/2018.
    Keywords: Biomarkers ; Biosignatures ; Metabolism ; Molecular fossils ; Biogeochemistry
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Growth Mode Transition in Complex Oxide Heteroepitaxy: Atomically Resolved Studies (2016)
    American Chemical Society (ACS)
    Details
    Publication Date: 2016-04-12
    Description: Crystal Growth & Design DOI: 10.1021/acs.cgd.5b01826
    Print ISSN: 1528-7483
    Electronic ISSN: 1528-7505
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Chemical Society (ACS)
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