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Article ; Online: Expression of divergent methyl/alkyl coenzyme M reductases from uncultured archaea.

Shao, Nana / Fan, Yu / Chou, Chau-Wen / Yavari, Shadi / Williams, Robert V / Amster, I Jonathan / Brown, Stuart M / Drake, Ian J / Duin, Evert C / Whitman, William B / Liu, Yuchen

Communications biology

2022 Volume 5, Issue 1, Page(s) 1113

Abstract: ... carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step ... with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed ...

Abstract	Methanogens and anaerobic methane-oxidizing archaea (ANME) are important players in the global carbon cycle. Methyl-coenzyme M reductase (MCR) is a key enzyme in methane metabolism, catalyzing the last step in methanogenesis and the first step in anaerobic methane oxidation. Divergent mcr and mcr-like genes have recently been identified in uncultured archaeal lineages. However, the assembly and biochemistry of MCRs from uncultured archaea remain largely unknown. Here we present an approach to study MCRs from uncultured archaea by heterologous expression in a methanogen, Methanococcus maripaludis. Promoter, operon structure, and temperature were important determinants for MCR production. Both recombinant methanococcal and ANME-2 MCR assembled with the host MCR forming hybrid complexes, whereas tested ANME-1 MCR and ethyl-coenzyme M reductase only formed homogenous complexes. Together with structural modeling, this suggests that ANME-2 and methanogen MCRs are structurally similar and their reaction directions are likely regulated by thermodynamics rather than intrinsic structural differences.
MeSH term(s)	Archaea/genetics ; Archaea/metabolism ; Mesna/metabolism ; Oxidoreductases/metabolism ; Methane/metabolism
Chemical Substances	methyl coenzyme M reductase (EC 2.8.4.1) ; Mesna (NR7O1405Q9) ; Oxidoreductases (EC 1.-) ; Methane (OP0UW79H66)
Language	English
Publishing date	2022-10-20
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-022-04057-6
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Article ; Online: Posttranslational Methylation of Arginine in Methyl Coenzyme M Reductase Has a Profound Impact on both Methanogenesis and Growth of Methanococcus maripaludis.

Lyu, Zhe / Shao, Nana / Chou, Chau-Wen / Shi, Hao / Patel, Ricky / Duin, Evert C / Whitman, William B

Journal of bacteriology

2020 Volume 202, Issue 3

Abstract: ... chain alkanes, methyl coenzyme M reductase (Mcr) and its homologs play a key role in the global ...

Abstract	Catalyzing the key step for anaerobic production and/or oxidation of methane and likely other short-chain alkanes, methyl coenzyme M reductase (Mcr) and its homologs play a key role in the global carbon cycle. The McrA subunit possesses up to five conserved posttranslational modifications (PTMs) at its active site. It was previously suggested that methanogenesis marker protein 10 (Mmp10) could play an important role in methanogenesis. To systematically examine its physiological role,
MeSH term(s)	Arginine/metabolism ; Binding Sites ; Blotting, Western ; Catalytic Domain ; Computational Biology ; Mass Spectrometry ; Methanococcus/pathogenicity ; Methylation ; Oxidoreductases/chemistry ; Oxidoreductases/genetics ; Oxidoreductases/metabolism ; Protein Processing, Post-Translational ; Substrate Specificity
Chemical Substances	Arginine (94ZLA3W45F) ; Oxidoreductases (EC 1.-) ; methyl coenzyme M reductase (EC 2.8.4.1)
Language	English
Publishing date	2020-01-15
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00654-19
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Article ; Online: Assembly of Methyl Coenzyme M Reductase in the Methanogenic Archaeon Methanococcus maripaludis.

Lyu, Zhe / Chou, Chau-Wen / Shi, Hao / Wang, Liangliang / Ghebreab, Robel / Phillips, Dennis / Yan, Yajun / Duin, Evert C / Whitman, William B

Journal of bacteriology

2018 Volume 200, Issue 7

Abstract: Methyl coenzyme M reductase (MCR) is a complex enzyme that catalyzes the final step in biological ...

Abstract	Methyl coenzyme M reductase (MCR) is a complex enzyme that catalyzes the final step in biological methanogenesis. To better understand its assembly, the recombinant MCR from the thermophile
MeSH term(s)	Binding Sites ; Catalysis ; Metalloporphyrins/chemistry ; Methane/metabolism ; Methanococcus/enzymology ; Methanococcus/metabolism ; Oxidation-Reduction ; Oxidoreductases/chemistry ; Oxidoreductases/genetics ; Oxidoreductases/metabolism ; Protein Processing, Post-Translational/genetics
Chemical Substances	Metalloporphyrins ; factor F430 (73145-13-8) ; Oxidoreductases (EC 1.-) ; methyl coenzyme M reductase (EC 2.8.4.1) ; Methane (OP0UW79H66)
Language	English
Publishing date	2018-03-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00746-17
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Article ; Online: Escherichia coli Harboring mcr-1 and blaCTX-M on a Novel IncF Plasmid: First Report of mcr-1 in the United States.

McGann, Patrick / Snesrud, Erik / Maybank, Rosslyn / Corey, Brendan / Ong, Ana C / Clifford, Robert / Hinkle, Mary / Whitman, Timothy / Lesho, Emil / Schaecher, Kurt E

Antimicrobial agents and chemotherapy

2016 Volume 60, Issue 7, Page(s) 4420–4421

Language	English
Publishing date	2016-07
Publishing country	United States
Document type	Letter
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/AAC.01103-16
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Article ; Online: Genetic confirmation of the role of sulfopyruvate decarboxylase in coenzyme M biosynthesis in Methanococcus maripaludis.

Sarmiento, Felipe / Ellison, Courtney K / Whitman, William B

Archaea (Vancouver, B.C.)

2013 Volume 2013, Page(s) 185250

Abstract: Coenzyme M is an essential coenzyme for methanogenesis. The proposed biosynthetic pathway consists ... of the gene comE by transposon mutagenesis resulted in a partial coenzyme M auxotroph, which grew poorly ... in the absence of coenzyme M and retained less than 3% of the wild type level of coenzyme M biosynthesis ...

Abstract	Coenzyme M is an essential coenzyme for methanogenesis. The proposed biosynthetic pathway consists of five steps, of which the fourth step is catalyzed by sulfopyruvate decarboxylase (ComDE). Disruption of the gene comE by transposon mutagenesis resulted in a partial coenzyme M auxotroph, which grew poorly in the absence of coenzyme M and retained less than 3% of the wild type level of coenzyme M biosynthesis. Upon coenzyme M addition, normal growth of the mutant was restored. Moreover, complementation of the mutation with the wild type comE gene in trans restored full growth in the absence of coenzyme M. These results confirm that ComE plays an important role in coenzyme M biosynthesis. The inability to yield a complete CoM auxotroph suggests that either the transposon insertion failed to completely inactivate the gene or M. maripaludis possesses a promiscuous activity that partially complemented the mutation.
MeSH term(s)	Amino Acid Sequence ; Archaeal Proteins/genetics ; Archaeal Proteins/metabolism ; Carboxy-Lyases/genetics ; Carboxy-Lyases/metabolism ; DNA Transposable Elements/genetics ; Genes, Archaeal ; Mesna/metabolism ; Methane/biosynthesis ; Methanococcus/enzymology ; Methanococcus/genetics ; Methanococcus/metabolism ; Molecular Sequence Data ; Mutation/genetics ; Sequence Alignment
Chemical Substances	Archaeal Proteins ; DNA Transposable Elements ; Carboxy-Lyases (EC 4.1.1.-) ; Mesna (NR7O1405Q9) ; Methane (OP0UW79H66)
Language	English
Publishing date	2013-09-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2133011-6
ISSN	1472-3654 ; 1472-3646
ISSN (online)	1472-3654
ISSN	1472-3646
DOI	10.1155/2013/185250
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Article ; Online: Erratum for McGann et al., Escherichia coli Harboring mcr-1 and blaCTX-M on a Novel IncF Plasmid: First Report of mcr-1 in the United States.

McGann, Patrick / Snesrud, Erik / Maybank, Rosslyn / Corey, Brendan / Ong, Ana C / Clifford, Robert / Hinkle, Mary / Whitman, Timothy / Lesho, Emil / Schaecher, Kurt E

Antimicrobial agents and chemotherapy

2016 Volume 60, Issue 8, Page(s) 5107

Language	English
Publishing date	2016-08
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	217602-6
ISSN	1098-6596 ; 0066-4804
ISSN (online)	1098-6596
ISSN	0066-4804
DOI	10.1128/AAC.01353-16
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Article: Thermoanaerobacter sulfurigignens sp. nov., an anaerobic thermophilic bacterium that reduces 1 M thiosulfate to elemental sulfur and tolerates 90 mM sulfite.

Lee, Yong-Jin / Dashti, Mona / Prange, Alexander / Rainey, Fred A / Rohde, Manfred / Whitman, William B / Wiegel, Juergen

International journal of systematic and evolutionary microbiology

2007 Volume 57, Issue Pt 7, Page(s) 1429–1434

Abstract: ... conditions was 2.4 h. The DNA G+C content was 34-35 mol% (HPLC). The two strains reduced up to 1 M ...

Abstract	Two anaerobic thermophilic bacteria, designated strains JW/SL824 and JW/SL-NZ826(T), were isolated from an acidic volcanic steam outlet on White Island, New Zealand. Cells were rod-shaped, spore-forming, motile and Gram-stain negative, but contained Gram-type positive cell wall. Strain JW/SL-NZ826(T) utilized various carbohydrates including xylose and glucose. The fermentation end products produced from glucose in the absence of thiosulfate were lactate, ethanol, acetate, CO(2) and H(2). The temperature range for growth was 34-72 degrees C, with an optimum at 63-67 degrees C. The pH(60 degrees C) range for growth was 4.0-8.0, with an optimum at 5.0-6.5. The doubling time of strain JW/SL-NZ826(T) under optimal growth conditions was 2.4 h. The DNA G+C content was 34-35 mol% (HPLC). The two strains reduced up to 1 M thiosulfate to elemental sulfur without sulfide formation, which is a trend typically observed among species belonging to the genus Thermoanaerobacterium. Sulfur globules containing short and long sulfur chains but no S(8)-ring sulfur were produced inside and outside the cells. Up to 90 mM sulfite was tolerated. This tolerance is assumed to be an adaptation to the geochemistry of the environment of White Island. The 16S rRNA gene sequence analysis, however, indicated that the two strains belonged to the genus Thermoanaerobacter, with similarities in the range 95.6-92.7 %. Therefore, strains JW/SL-NZ824 and JW/SL-NZ826(T) represent a novel taxon, for which the name Thermoanaerobacter sulfurigignens sp. nov. is proposed, with strain JW/SL-NZ826(T) (=ATCC 700320(T)=DSM 17917(T)) as the type strain. Based on this and previous studies, an emended description of the genus Thermoanaerobacter is given.
MeSH term(s)	Carbohydrate Metabolism ; DNA, Bacterial/chemistry ; DNA, Bacterial/genetics ; DNA, Ribosomal/chemistry ; DNA, Ribosomal/genetics ; Fermentation ; Genes, rRNA ; Glucose/metabolism ; Hydrogen-Ion Concentration ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; New Zealand ; Oxidation-Reduction ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Soil Microbiology ; Sulfites/metabolism ; Sulfur/metabolism ; Temperature ; Thermoanaerobacter/classification ; Thermoanaerobacter/genetics ; Thermoanaerobacter/isolation & purification ; Thermoanaerobacter/metabolism ; Thiosulfates/metabolism
Chemical Substances	DNA, Bacterial ; DNA, Ribosomal ; RNA, Bacterial ; RNA, Ribosomal, 16S ; Sulfites ; Thiosulfates ; Sulfur (70FD1KFU70) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2007-06-20
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2002336-4
ISSN	1466-5034 ; 1466-5026
ISSN (online)	1466-5034
ISSN	1466-5026
DOI	10.1099/ijs.0.64748-0
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Article ; Online: Modeling Ethics: Approaches to Data Creep in Higher Education.

Whitman, Madisson

Science and engineering ethics

2021 Volume 27, Issue 6, Page(s) 71

Abstract: Though rapid collection of big data is ubiquitous across domains, from industry settings to academic contexts, the ethics of big data collection and research are contested. A nexus of data ethics issues is the concept of creep, or repurposing of data for ...

Abstract	Though rapid collection of big data is ubiquitous across domains, from industry settings to academic contexts, the ethics of big data collection and research are contested. A nexus of data ethics issues is the concept of creep, or repurposing of data for other applications or research beyond the conditions of original collection. Data creep has proven controversial and has prompted concerns about the scope of ethical oversight. Institutional review boards offer little guidance regarding big data, and problematic research can still meet ethical standards. While ethics seem concrete through institutional deployment, I frame ethics as produced. Informed by my ethnographic research at a large public university in the U.S., I explore ethics through two models: ethics as institutional procedures and ethics as acts and intentions. The university where I conducted fieldwork is the development grounds for a predictive model that uses student data to anticipate academic success. While students consent to data collection, the circumstances of consent and the degree to which they are informed are not so apparent, as many data are a product of creep. Drawing from interviews and participant observation with administrators, data scientists, developers, and students, I examine data ethics, from a larger institutional model to everyday enactments related to data creep. After demonstrating the limits of such models, I propose a remodeling of ethics that draws on recent works on data, justice, and refusal to pose generative questions for rethinking ethics in institutional contexts.
MeSH term(s)	Big Data ; Data Collection ; Ethics Committees, Research ; Humans ; Informed Consent ; Organizations ; Social Justice
Language	English
Publishing date	2021-11-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2136491-6
ISSN	1471-5546 ; 1353-3452
ISSN (online)	1471-5546
ISSN	1353-3452
DOI	10.1007/s11948-021-00346-1
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Article ; Online: The Potential of a Digital Weight Management Program to Support Specialist Weight Management Services in the UK National Health Service: Retrospective Analysis.

Richards, Rebecca / Wren, Gina / Whitman, Michael

JMIR diabetes

2024 Volume 9, Page(s) e52987

Abstract: ... Eligible participants were adults with a BMI ≥35 kg/m: Results: A total of 1130 participants with a mean ... baseline BMI of 46.3 (SD 31.6) kg/m: Conclusions: The findings suggested that Second Nature's DWMI has ...

Abstract	Background: Digital weight management interventions (DWMIs) have the potential to support existing specialist weight management services (SWMS) in the National Health Service (NHS) to increase access to treatment for people living with obesity and type 2 diabetes. At present, there is limited real-world evidence and long-term outcomes on the potential effectiveness of DWMIs to support such services. Objective: This study aimed to examine real-world data to evaluate the impact of Second Nature's 12-month DWMI for patients living with obesity with or without type 2 diabetes, referred from NHS primary care services, on sustained weight loss over a 2-year period. Methods: Retrospective data were extracted in August 2023 for participants who participated in the program between January 1, 2017, and January 8, 2021. Eligible participants were adults with a BMI ≥35 kg/m Results: A total of 1130 participants with a mean baseline BMI of 46.3 (SD 31.6) kg/m Conclusions: The findings suggested that Second Nature's DWMI has the potential to support people living with obesity and type 2 diabetes remotely to achieve clinically significant and sustained weight loss at 2 years from baseline. Further research is needed to compare the intervention to standard care and assess integration with multidisciplinary clinical teams and pharmacotherapy in order to support this study's findings.
Language	English
Publishing date	2024-01-24
Publishing country	Canada
Document type	Journal Article
ISSN	2371-4379
ISSN (online)	2371-4379
DOI	10.2196/52987
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Article ; Online: Construct validation of Minnesota Multiphasic Personality Inventory-3 (MMPI-3) scales relevant to the assessment of bipolar spectrum disorders.

Whitman, Megan R / Sellbom, Martin

Journal of clinical psychology

2023 Volume 79, Issue 11, Page(s) 2583–2601

Abstract: Background: The Minnesota Multiphasic Personality Inventory-3 (MMPI-3) is a commonly used psychological test that includes several scales relevant to measuring manic and depressive symptoms of bipolar spectrum disorders.: Aims: The goal of the ... ...

Abstract	Background: The Minnesota Multiphasic Personality Inventory-3 (MMPI-3) is a commonly used psychological test that includes several scales relevant to measuring manic and depressive symptoms of bipolar spectrum disorders. Aims: The goal of the present study was to evaluate the construct validity of MMPI-3 scale scores with respect to self-report measures of bipolar psychopathology. Materials & methods: Using a sample of 644 university students in New Zealand, we calculated correlations between scores on the MMPI-3 and the Hypomanic Personality Scale-Short Form (HPS-SF) total and factor scores and the Altman Self-Report Mania Scale (ASRM) total and item scores. Results: For associations against the HPS-SF, almost all of the hypotheses were supported, whereas for the ASRM scale, several were not. We also estimated a series of regression models predicting HPS-SF and ASRM scores from meaningfully associated MMPI-3 scores. Hypomanic Activation (RC9), Activation (ACT), and Self-Importance (SFI) scores emerged as the most consistent and substantial predictors of criteria, with SFI scores being more specifically associated with total scores and criteria related to Social Vitality. Several internalizing and thought dysfunction MMPI-3 scales were also meaningfully associated with scores on the HPS-SF and ASRM. Discussion & conclusion: Implications and limitations, such as the use of a university student convenience sample, are discussed.
Language	English
Publishing date	2023-07-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	219160-x
ISSN	1097-4679 ; 0021-9762
ISSN (online)	1097-4679
ISSN	0021-9762
DOI	10.1002/jclp.23568
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