Works (18)

Updated: July 5th, 2023 15:59

2008 journal article

Functional-genomics-based identification and characterization of open reading frames encoding alpha-glucoside-processing enzymes in the hyperthermophilic archaeon Pyrococcus furiosus

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 74(4), 1281–1283.

By: D. Comfort n, C. Chou n, S. Conners n, A. VanFossen n & R. Kelly n

MeSH headings : Computational Biology; Gene Expression Regulation, Bacterial / genetics; Genomics / methods; Open Reading Frames / genetics; Pyrococcus furiosus / enzymology; Pyrococcus furiosus / genetics; alpha-Glucosidases / genetics; beta-Amylase / genetics
TL;DR: Bioinformatics analysis and transcriptional response information for Pyrococcus furiosus led to the identification of a novel isomaltase representing a new glycoside hydrolase family, a novel GH57 β-amylase, and an extracellular starch-binding protein. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2007 journal article

Impact of substrate glycoside linkage. and elemental sulfur on bioenergetics, of and hydrogen production by the hyperthermophilic Archaeon Pyrococcus furiosus

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 73(21), 6842–6853.

By: C. Chou n, K. Shockley n, S. Conners n, D. Lewis n, D. Comfort n, M. Adams*, R. Kelly n

MeSH headings : Archaea; Chemical Phenomena; Chemistry; Gene Expression Regulation, Archaeal; Genome, Archaeal; Glycosides / metabolism; Hot Temperature; Hydrogen / metabolism; Oligonucleotide Array Sequence Analysis; Open Reading Frames; Pyrococcus furiosus / enzymology; Pyrococcus furiosus / genetics; Pyrococcus furiosus / physiology; Sulfur / metabolism
Sources: Web Of Science, ORCID
Added: August 6, 2018

2007 journal article

Responses of wild-type and resistant strains of the hyperthermophilic bacterium Thermotoga maritima to chloramphenicol challenge

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 73(15), 5058–5065.

By: C. Montero n, M. Johnson n, C. Chou n, S. Conners n, S. Geouge n, S. Tachdjian n, J. Nichols n, R. Kelly n

MeSH headings : Anti-Bacterial Agents / pharmacology; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Base Sequence; Chloramphenicol / pharmacology; Drug Resistance, Bacterial / genetics; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Hot Temperature; Microbial Sensitivity Tests; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis; Point Mutation; Proteome; RNA, Ribosomal, 23S / genetics; Thermotoga maritima / drug effects; Thermotoga maritima / genetics; Thermotoga maritima / growth & development; Transcription, Genetic
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2007 journal article

Role of the beta 1 subunit in the function and stability of the 20S proteasome in the hyperthermophilic archaeon Pyrococcus furiosus

JOURNAL OF BACTERIOLOGY, 189(2), 583–590.

By: L. Madding n, J. Michel n, K. Shockley n, S. Conners n, K. Epting n, M. Johnson n, R. Kelly n

MeSH headings : Archaeal Proteins / genetics; Archaeal Proteins / metabolism; Archaeal Proteins / physiology; Calorimetry, Differential Scanning; Genome, Archaeal; Hot Temperature; Molecular Chaperones / genetics; Molecular Chaperones / metabolism; Proteasome Endopeptidase Complex / genetics; Proteasome Endopeptidase Complex / metabolism; Proteasome Endopeptidase Complex / physiology; Protein Subunits / genetics; Protein Subunits / metabolism; Protein Subunits / physiology; Pyrococcus furiosus / genetics; Pyrococcus furiosus / metabolism; Temperature; Transcription, Genetic
TL;DR: Results indicate that the β1 subunit in the P. furiosus 20S proteasome plays a thermostabilizing role and influences biocatalytic properties, suggesting that β subunit composition is a factor in archaeal proteasom function during thermal stress, when polypeptide turnover is essential to cell survival. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2006 journal article

Colocation of genes encoding a tRNA-mRNA hybrid and a putative signaling peptide on complementary strands in the genome of the hyperthermophilic bacterium Thermotoga maritima

JOURNAL OF BACTERIOLOGY, 188(19), 6802–6807.

By: C. Montero n, D. Lewis n, M. Johnson n, S. Conners n, E. Nance n, J. Nichols n, R. Kelly n

MeSH headings : Amino Acid Sequence; Anti-Bacterial Agents / pharmacology; Chloramphenicol / pharmacology; Coculture Techniques; DNA, Bacterial / genetics; Gene Expression; Gene Expression Regulation, Bacterial; Genes, Bacterial; Genome, Bacterial; Intracellular Signaling Peptides and Proteins / genetics; Methanococcus; RNA, Bacterial / analysis; RNA, Bacterial / genetics; RNA, Messenger / analysis; RNA, Messenger / genetics; Reverse Transcriptase Polymerase Chain Reaction; Sequence Alignment; Synteny; Thermotoga maritima / genetics; Transcription, Genetic
TL;DR: Specific DNA probes were designed and used in real-time PCR assays to follow the separate transcriptional responses of the colocated open reading frames (ORFs) during transition from exponential to stationary phase, chloramphenicol challenge, and syntrophic coculture with Methanococcus jannaschii. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2006 journal article

Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103(10), 3816–3821.

By: R. Barrangou*, M. Azcarate-Peril*, T. Duong*, S. Conners n, R. Kelly n & T. Klaenhammer*

author keywords: ATP-binding cassette; carbon catabolite repression; fructooligosaccharide; galactoside-pentose hexuronide
MeSH headings : ATP-Binding Cassette Transporters / genetics; ATP-Binding Cassette Transporters / metabolism; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Carbohydrate Metabolism / genetics; Gastrointestinal Tract / microbiology; Gene Expression Profiling; Genes, Bacterial; Humans; Lactobacillus acidophilus / genetics; Lactobacillus acidophilus / metabolism; Models, Biological; Oligonucleotide Array Sequence Analysis; Phosphoenolpyruvate Sugar Phosphotransferase System / genetics; Reverse Transcriptase Polymerase Chain Reaction
TL;DR: The transport and catabolic machinery involved in carbohydrate utilization by Lactobacillus acidophilus was characterized genetically by using whole-genome cDNA microarrays, and genes central to glycolysis were among the most highly expressed in the genome. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2006 review

Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species

[Review of ]. FEMS MICROBIOLOGY REVIEWS, 30(6), 872–905.

By: S. Conners n, E. Mongodin, M. Johnson n, C. Montero n, K. Nelson & R. Kelly n

author keywords: Thermotoga; hyperthermophiles; functional genomics
MeSH headings : Bacterial Proteins / chemistry; Bacterial Proteins / metabolism; Bacterial Proteins / physiology; Biotechnology; Carbohydrate Metabolism; Genetic Variation; Genome, Bacterial; Genomics; Gram-Negative Anaerobic Straight, Curved, and Helical Rods / genetics; Gram-Negative Anaerobic Straight, Curved, and Helical Rods / physiology; Hot Temperature; Iron / metabolism; Monosaccharides / biosynthesis; Phylogeny; Polysaccharides / biosynthesis; Signal Transduction; Sulfur / metabolism; Thermotoga maritima / genetics; Thermotoga maritima / isolation & purification; Thermotoga maritima / physiology
TL;DR: Structural genomics efforts aimed at the model hyperthermophile Thermotoga maritima proteome have yielded hundreds of high-resolution datasets and predicted functions for uncharacterized proteins, particularly for carbohydrate utilization and iron-sulfur cluster synthesis and repair. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2006 journal article

The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 72(1), 811–818.

By: M. Johnson n, S. Conners n, C. Montero n, C. Chou n, K. Shockley n & R. Kelly n

MeSH headings : Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Coculture Techniques; DNA, Complementary; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Hot Temperature; Methanococcus / growth & development; Oligonucleotide Array Sequence Analysis; Phenotype; Proteome; Thermotoga maritima / classification; Thermotoga maritima / genetics; Thermotoga maritima / growth & development; Thermotoga maritima / metabolism; Transcription, Genetic
TL;DR: The results demonstrate that syntrophic interactions can impact the transcriptome of heterotrophs in methanogenic coculture, and this factor should be considered in examining the microbial ecology in anaerobic environments. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
15. Life on Land (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2006 journal article

Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus

JOURNAL OF BACTERIOLOGY, 188(6), 2115–2125.

By: H. Lee*, K. Shockley n, G. Schut*, S. Conners n, C. Montero n, M. Johnson n, C. Chou n, S. Bridger n ...

MeSH headings : Archaeal Proteins / genetics; Bacterial Proteins / genetics; DNA, Archaeal / chemistry; DNA, Archaeal / genetics; Gene Expression Profiling; Gene Expression Regulation, Archaeal; Glucose / metabolism; Glucosephosphates / metabolism; Glucosyltransferases / genetics; Glycogen Debranching Enzyme System / genetics; Glycoside Hydrolases / genetics; Monosaccharide Transport Proteins / genetics; Oligonucleotide Array Sequence Analysis; Pyrococcus furiosus / genetics; Pyrococcus furiosus / metabolism; Sequence Analysis, DNA; Starch / metabolism; Substrate Specificity
TL;DR: Starch metabolism in P. furiosus was examined by biochemical analyses in conjunction with global transcriptional response data for cells grown on a variety of glucans, and several hypothetical proteins encoded by three gene clusters are also involved in the transport and processing of alpha-glucan substrates by this organism. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

Aflatoxin conducive and non-conducive growth conditions reveal new gene associations with aflatoxin production

FUNGAL GENETICS AND BIOLOGY, 42(6), 506–518.

By: M. Price n, B. Shannon n, T. Sabrina n, A. Robert n & G. Payne n

author keywords: aflatoxin; gene expression; regulation; Aspergillus flavus; Aspergillus parasiticus
MeSH headings : Aflatoxins / biosynthesis; Aspergillus / genetics; Aspergillus / metabolism; Gene Expression; Gene Expression Profiling; Gene Expression Regulation, Fungal; Genes, Fungal; Hydrogen-Ion Concentration; Nitrogen / metabolism; Oligonucleotide Array Sequence Analysis; RNA, Fungal / analysis; RNA, Messenger / analysis; Regulon; Temperature
TL;DR: To understand the effect of nitrogen source, carbon source, temperature, and pH on the regulation of AF biosynthesis, a targeted cDNA microarray consisting of genes associated with AF production over time was employed. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

An expression-driven approach to the prediction of carbohydrate transport and utilization regulons in the hyperthermophilic bacterium Thermotoga maritima

JOURNAL OF BACTERIOLOGY, 187(21), 7267–7282.

By: S. Conners n, C. Montero n, D. Comfort n, K. Shockley n, M. Johnson n, . Chhabra n, R. Kelly n

MeSH headings : 5' Flanking Region / genetics; ATP-Binding Cassette Transporters / chemistry; ATP-Binding Cassette Transporters / genetics; Biological Evolution; Biological Transport / genetics; Carbohydrate Metabolism; Computational Biology; Gene Duplication; Gene Expression Profiling; Genes, Bacterial; Genes, Regulator; Genomics; Monosaccharide Transport Proteins / genetics; Nucleic Acid Conformation; Oligosaccharides / metabolism; Pentose Phosphate Pathway / genetics; Regulon / physiology; Rhamnose / metabolism; Thermotoga maritima / genetics; Thermotoga maritima / metabolism; Xylose / metabolism
TL;DR: The results indicate that T. maritima relies extensively on ABC transporters for carbohydrate uptake, many of which are likely controlled by local regulators responsive to either the transport substrate or a key metabolic degradation product. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

Genorne-wide transcriptional variation within and between steady states for continuous growth of the hyperthermophile Thermotoga maritima

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 71(9), 5572–5576.

By: K. Shockley n, K. Scott*, M. Pysz n, S. Conners n, M. Johnson n, C. Montero n, R. Wolfinger*, R. Kelly n

TL;DR: Maltose-limited, continuous growth of the hyperthermophile Thermotoga maritima at different temperatures and dilution rates showed that transcriptome-wide variation in gene expression within mechanical steady states was minimal compared to that between steady states, supporting the efficacy of chemostat-based approaches for functional genomics studies. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
15. Life on Land (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

Population density-dependent regulation of exopolysaccharide formation in the hyperthermophilic bacterium Thermotoga maritima

MOLECULAR MICROBIOLOGY, 55(3), 664–674.

By: M. Johnson n, C. Montero n, S. Conners n, K. Shockley n, S. Bridger n & R. Kelly n

MeSH headings : Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Culture Media; Ecosystem; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genome, Archaeal; Genome, Bacterial; Methanococcus / genetics; Methanococcus / growth & development; Methanococcus / metabolism; Oligonucleotide Array Sequence Analysis; Polysaccharides, Bacterial / metabolism; Signal Transduction; Temperature; Thermotoga maritima / growth & development; Thermotoga maritima / metabolism; Transcription, Genetic
TL;DR: Results point to the existence of peptide‐based quorum sensing in hyperthermophilic bacteria and indicate that cellular communication should be considered as a component of the microbial ecology within hydrothermal habitats. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 article

Functional genomics-based studies of the microbial ecology of hyperthermophilic micro-organisms

Johnson, M. R., Montero, C. I., Conners, S. B., Shockley, K. R., Pysz, M. A., & Kelly, R. M. (2004, April). BIOCHEMICAL SOCIETY TRANSACTIONS, Vol. 32, pp. 188–192.

By: M. Johnson n, C. Montero n, S. Conners n, K. Shockley n, M. Pysz n & R. Kelly n

author keywords: ecology; functional qenomics; hyperthermophile; microarray; mixed culture
MeSH headings : Biofilms; DNA, Complementary / metabolism; Ecology; Gene Transfer Techniques; Genes, Archaeal; Genome; Genome, Archaeal; Microscopy, Fluorescence; Oligonucleotide Array Sequence Analysis; Phylogeny; RNA, Ribosomal, 16S / genetics; Temperature
TL;DR: Functional genomics-based approaches are described, using cDNA microarrays, to gain insight into how ecological features such as biofilm formation, species interaction, and possibly even gene transfer may occur in native environments, as well as to determine what genes or sets of genes may be tied to environmental functionality. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 review

Transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium Thermotoga maritima

[Review of ]. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 70(10), 6098–6112.

By: M. Pysz n, S. Conners n, C. Montero n, K. Shockley n, M. Johnson n, D. Ward n, R. Kelly n

MeSH headings : ATP-Binding Cassette Transporters / genetics; ATP-Binding Cassette Transporters / metabolism; Base Sequence; Biofilms / growth & development; Bioreactors; DNA, Bacterial / genetics; Gene Expression Profiling; Genes, Bacterial; Iron / metabolism; Models, Biological; Oligonucleotide Array Sequence Analysis; Oxidative Stress; Polysaccharides, Bacterial / genetics; Polysaccharides, Bacterial / metabolism; Sulfur / metabolism; Temperature; Thermotoga maritima / genetics; Thermotoga maritima / physiology; Thermotoga maritima / ultrastructure; Transcription, Genetic
TL;DR: In addition to revealing insights into the phenotype of sessile T. maritima communities, the methodology developed here can be extended to study other anaerobic biofilm formation processes as well as to examine aspects of microbial ecology in hydrothermal environments. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2004 journal article

Transcriptional analysis of dynamic heat-shock response by the hyperthermophilic bacterium Thermotoga maritima

EXTREMOPHILES, 8(3), 209–217.

By: M. Pysz n, D. Ward n, K. Shockley n, C. Montero n, S. Conners n, M. Johnson n, R. Kelly n

author keywords: cDNA microarray; groESL; heat shock; hrcA; hyperthermophile; Thermotoga
MeSH headings : Base Sequence; DNA, Bacterial / genetics; Endopeptidases / genetics; Gene Expression; Genome, Bacterial; Heat-Shock Response / genetics; Hot Temperature; Oligonucleotide Array Sequence Analysis; SOS Response, Genetics; Sigma Factor / genetics; Thermotoga maritima / genetics; Thermotoga maritima / metabolism; Transcription, Genetic
TL;DR: The results reported here indicate that, while T. maritima shares core elements of the bacterial heat-shock response with mesophiles, the thermal stress regulatory strategies of this organism differ significantly, and it remains to be elucidated whether these differences are related to thermophilicity or phylogenetic placement. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
15. Life on Land (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2003 journal article

Carbohydrate-induced differential gene expression patterns in the hyperthermophilic bacterium Thermotoga maritima

JOURNAL OF BIOLOGICAL CHEMISTRY, 278(9), 7540–7552.

By: . Chhabra, K. Shockley*, S. Conners*, K. Scott*, R. Wolfinger* & R. Kelly*

MeSH headings : Carbohydrate Metabolism; Carbohydrate Sequence; Carbohydrates / chemistry; Carbon / metabolism; DNA, Complementary / metabolism; Down-Regulation; Gene Expression Regulation, Bacterial; Hydrolases / chemistry; Hydrolases / metabolism; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis; Open Reading Frames; Thermotoga maritima / metabolism; Up-Regulation
TL;DR: The transcriptional response of T. maritima to specific carbohydrate growth substrates indicated that sugar backbone- and linkage-specific regulatory networks are operational in this organism during the uptake and utilization of carbohydrate substrates, and suggests that this organism is capable of adapting to a variety of growth environments containing carbohydrate growth substrate. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2003 journal article

Heat shock response by the hyperthermophilic archaeon Pyrococcus furiosus

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 69(4), 2365–2371.

By: K. Shockley n, D. Ward n, . Chhabra n, S. Conners n, C. Montero n & R. Kelly n

MeSH headings : Archaeal Proteins / genetics; Archaeal Proteins / metabolism; Blotting, Northern; Gene Expression Profiling; Gene Expression Regulation, Archaeal; Heat-Shock Response; Oligonucleotide Array Sequence Analysis; Protein Folding; Pyrococcus furiosus / genetics; Pyrococcus furiosus / metabolism; Transcription, Genetic
TL;DR: Collective transcriptional analysis of heat shock response in the hyperthermophilic archaeon Pyrococcus furiosus was examined by using a targeted cDNA microarray in conjunction with Northern analyses and differential gene expression suggests that P.furiosus relies on a cooperative strategy of rescue, proteolysis, and stabilization to cope with polypeptide processing during thermal stress. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018

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