James W. Brown

Works (24)

Updated: July 5th, 2023 16:04

2012 journal article

Modeling the Thermoproteaceae RNase P RNA

RNA BIOLOGY, 9(9), 1155–1160.

By: P. Chan *, J. Brown n & T. Lowe *

author keywords: RNase P; Archaea; tRNA processing; RNA catalysis; RNA secondary structure
MeSH headings : Archaeal Proteins / chemistry; Archaeal Proteins / genetics; Archaeal Proteins / metabolism; Models, Molecular; RNA Processing, Post-Transcriptional / physiology; RNA, Archaeal / chemistry; RNA, Archaeal / genetics; RNA, Archaeal / metabolism; RNA, Transfer / genetics; RNA, Transfer / metabolism; Ribonuclease P / chemistry; Ribonuclease P / genetics; Ribonuclease P / metabolism; Thermoproteaceae / chemistry; Thermoproteaceae / genetics; Thermoproteaceae / metabolism
TL;DR: A new Rfam search model is described to enable efficient detection of the diminutive archaeal Type T RNase P RNAs, which are missed by existing Rfam models and establish effective score detection thresholds. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2010 journal article

Discovery of a minimal form of RNase P in Pyrobaculum

Proceedings of the National Academy of Sciences, 107(52), 22493–22498.

By: L. Lai *, P. Chan *, A. Cozen *, D. Bernick *, J. Brown n, V. Gopalan *, T. Lowe *

author keywords: catalytic RNA; gene finding; RNA processing
MeSH headings : Archaeal Proteins / genetics; Archaeal Proteins / isolation & purification; Archaeal Proteins / metabolism; Base Sequence; Biocatalysis; Computational Biology / methods; Electrophoresis, Polyacrylamide Gel; Genome, Archaeal / genetics; Molecular Sequence Data; Nucleic Acid Conformation; Pyrobaculum / classification; Pyrobaculum / enzymology; Pyrobaculum / genetics; RNA Precursors / chemistry; RNA Precursors / genetics; RNA Precursors / metabolism; RNA, Archaeal / genetics; RNA, Archaeal / metabolism; RNA, Catalytic / genetics; RNA, Catalytic / metabolism; RNA, Transfer / chemistry; RNA, Transfer / genetics; RNA, Transfer / metabolism; Ribonuclease P / genetics; Ribonuclease P / isolation & purification; Ribonuclease P / metabolism; Sequence Homology, Nucleic Acid; Species Specificity; Substrate Specificity
TL;DR: An effective combination of next-generation RNA sequencing, computational genomics, and biochemistry is illustrated to identify a divergent, formerly undetectable variant of an essential noncoding RNA gene. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, Crossref
Added: August 6, 2018

2010 journal article

The small nucleolar ribonucleoprotein (snoRNP) database

RNA, 16(4), 664–666.

By: J. Ellis *, D. Brown * & J. Brown n

author keywords: sRNA; sRNP; small nucleolar RNA; small nucleolar RNP
MeSH headings : Databases, Genetic; Internet; Metagenomics; RNA, Small Nucleolar / chemistry; Ribonucleoproteins, Small Nucleolar / chemistry; Ribonucleoproteins, Small Nucleolar / genetics; Ribonucleoproteins, Small Nucleolar / metabolism
TL;DR: The snoRNP database is a web-based collection of snoRNAs and snoRNA-associated protein sequences from a wide range of species and currently contains 8994 sno RNA sequences from Bacteria, Archaea, and Eukaryotes and 589 sno RNAs- associated protein sequences. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2009 journal article

The RNA structure alignment ontology

RNA, 15(9), 1623–1631.

By: J. Brown*, A. Birmingham, P. Griffiths, F. Jossinet*, R. Kachouri-Lafond*, R. Knight, B. Lang, N. Leontis ...

author keywords: databases; ontology; sequences; structural bioinformatics
MeSH headings : Animals; Base Sequence; Humans; Models, Biological; Molecular Sequence Data; Nucleic Acid Conformation; Phylogeny; RNA / analysis; RNA / chemistry; Sequence Alignment / methods; Sequence Alignment / trends; Sequence Analysis, RNA / methods; Sequence Homology, Nucleic Acid; Software
TL;DR: The notion of "correspondence" is introduced, which is an equivalence relation between RNA elements in sets of sequences as the basis of an RNA alignment ontology, to enable the development of new representations of RNA data and of software tools that resolve the expansion problems with current RNA sequence alignments. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2008 journal article

Characterization of diazotrophs containing Mo-independent nitrogenases, isolated from diverse natural environments

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 74(11), 3471–3480.

By: D. Betancourt, T. Loveless n, J. Brown* & P. Bishop n

MeSH headings : Aerobiosis; Anaerobiosis; Bacteria / classification; Bacteria / enzymology; Bacteria / genetics; Bacteria / isolation & purification; Bacterial Proteins / genetics; Blotting, Southern; Coenzymes / pharmacology; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; DNA, Ribosomal / chemistry; DNA, Ribosomal / genetics; Environmental Microbiology; Gram-Positive Bacteria / classification; Gram-Positive Bacteria / enzymology; Gram-Positive Bacteria / genetics; Gram-Positive Bacteria / isolation & purification; Molecular Sequence Data; Molybdenum / pharmacology; Nitrogenase / genetics; Nitrogenase / metabolism; Phylogeny; Polymerase Chain Reaction; Proteobacteria / classification; Proteobacteria / enzymology; Proteobacteria / genetics; Proteobacteria / isolation & purification; RNA, Ribosomal, 16S / genetics; Sequence Analysis, DNA; Sequence Homology
TL;DR: It is shown that diazotrophs with Mo-independent nitrogenases can be readily isolated from diverse natural environments and are specifically related to fluorescent pseudomonads and azotobacteria. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2007 journal article

Is Alba an RNase P subunit?

RNA BIOLOGY, 4(3), 169–172.

By: J. Ellis*, J. Barnes & J. Brown n

author keywords: ribonuclease P; archaea; rihozyme; Methanothermobacter thermoautotrophicus; Mth1483; Rpp25
MeSH headings : Archaeal Proteins / chemistry; Archaeal Proteins / isolation & purification; Archaeal Proteins / physiology; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / isolation & purification; DNA-Binding Proteins / physiology; Endoribonucleases; Humans; Methanobacteriaceae / enzymology; Protein Subunits / chemistry; Protein Subunits / physiology; RNA, Catalytic; Ribonuclease P / chemistry; Ribonuclease P / isolation & purification; Ribonuclease P / physiology
TL;DR: Using the same biochemical methods used to show that four other proteins homologous to eukaryotic RNase P proteins are bona fideRNase P subunits in Archaea, it is found that there is no evidence that Alba is an RN enzyme P subunit. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2006 journal article

The RNA Ontology Consortium: An open invitation to the RNA community

RNA, 12(4), 533–541.

By: N. Leontis *, R. Altman *, H. Berman *, S. Brenner *, J. Brown n, D. Engelke, S. Harvey *, . Holbrook* ...

author keywords: biological ontology; RNA; sequence alignments; 3D structure; RNA motifs
MeSH headings : Databases, Genetic; Information Dissemination; Internet; RNA; Sequence Alignment; Societies
TL;DR: The ROC will work closely with the PDB/NDB structural databases and the Gene, Sequence, and Open Biomedical Ontology Consortia to integrate the RO with existing biological ontologies to extend existing content while maintaining interoperability. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2005 journal article

Bartonella quintana in Cynomolgus Monkey (Macaca fascicularis)

Emerging Infectious Diseases, 11(12), 1931–1934.

By: L. O'Rourke*, C. Pitulle n, B. Hegarty n, S. Kraycirik*, K. Killary*, P. Grosenstein*, J. Brown n, E. Breitschwerdt n 

MeSH headings : Animals; Bartonella quintana / classification; Bartonella quintana / genetics; Bartonella quintana / isolation & purification; Female; Macaca fascicularis / blood; Macaca fascicularis / microbiology; Phylogeny; Trench Fever / blood; Trench Fever / microbiology; Trench Fever / veterinary
TL;DR: This report describes naturally acquired B. quintana infection in a nonhuman primate. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018

2005 journal article

Structural implications of novel diversity in eucaryal RNase P RNA

RNA, 11(5), 739–751.

By: S. Marquez, J. Harris, S. Kelley, J. Brown, S. Dawson, E. Roberts, N. Pace

Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

Evolutionary origins of the RNA-guided nucleotide-modification complexes: from the primitive translation apparatus?

Trends in Biochemical Sciences, 29(7), 343–350.

By: E. Tran n, J. Brown n & E. Maxwell n

MeSH headings : Amino Acid Sequence; Conserved Sequence; DNA Methylation; Evolution, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Protein Biosynthesis; Protein Conformation; RNA / genetics; RNA / physiology; Ribonucleoproteins / chemistry; Ribonucleoproteins / genetics; Ribonucleotides / metabolism; Ribosomes / chemistry; Ribosomes / genetics
TL;DR: The trans -acting, RNA-guided nucleotide-modification complexes of the modern RNP world seem to have evolved from cis -acting RNA or RNP elements contained in the primitive translation apparatus during the transition from the ancient RNA world to the modernRNP world. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, Crossref
Added: August 6, 2018

2003 journal article

Genes within genes within bacteria

TRENDS IN BIOCHEMICAL SCIENCES, 28(10), 521–523.

By: J. Ellis n & J. Brown n

MeSH headings : Bacteria / metabolism; Base Sequence; Escherichia coli / genetics; Gene Expression Regulation, Bacterial; Genome, Bacterial; Models, Genetic; Molecular Sequence Data; Ribonuclease P / genetics; Ribosomal Proteins / genetics; Thermus thermophilus / genetics
TL;DR: Recently, an unusual gene structure has been described in species of the genus Thermus, in which the rpmH coding sequence was found to be entirely overlapped by the unusually large rnpA (RNase P protein subunit) sequence. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2002 journal article

Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins

RNA, 8(3), 296–306.

By: T. Hall n & J. Brown n

author keywords: archaebacteria; Methanobacterium thermoautotrophicum strain Delta H; Methanothermobacter thermoautotrophicus; ribonuclease P
MeSH headings : Amino Acid Sequence; Animals; Antibody Formation; Blotting, Western; Cell Nucleus / enzymology; Centrifugation, Density Gradient; Cesium / chemistry; Chlorides / chemistry; Chromatography, Affinity; Endoribonucleases / genetics; Endoribonucleases / isolation & purification; Endoribonucleases / metabolism; Eukaryotic Cells / enzymology; Humans; Methanobacterium / enzymology; Molecular Sequence Data; Precipitin Tests; Protein Subunits; RNA, Archaeal / chemistry; RNA, Archaeal / genetics; RNA, Archaeal / metabolism; RNA, Bacterial / metabolism; RNA, Catalytic / genetics; RNA, Catalytic / isolation & purification; RNA, Catalytic / metabolism; RNA, Fungal / genetics; RNA, Fungal / metabolism; Rabbits; Recombinant Proteins / immunology; Recombinant Proteins / isolation & purification; Recombinant Proteins / metabolism; Ribonuclease P; Saccharomyces cerevisiae / enzymology; Sequence Homology, Amino Acid
TL;DR: RNase P in Archaea is therefore composed of an RNA subunit similar to bacterial RNase P RNA and multiple protein subunits similar to those in the eukaryotic nucleus. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2002 journal article

Investigation of the phylogenetic relationships within the genus Bartonella based on comparative sequence analysis of the rnpB gene, 16S rDNA and 23S rDNA

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 52(2002 Nov), 2075–2080.

By: C. Pitulle*, C. Strehse, J. Brown & E. Breitschwerdt 

author keywords: 16S rDNA; 23S rDNA; RNase P RNA; phylogeny; genus Bartonella
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2002 journal article

RNAML: A standard syntax for exchanging RNA information

RNA, 8(6), 707–717.

By: A. Waugh*, P. Gendron *, R. Altman *, J. Brown n, D. Case *, D. Gautheret *, S. Harvey *, N. Leontis * ...

author keywords: data storage; file format; knowledge representation; XML
MeSH headings : Databases, Nucleic Acid; Nucleic Acid Conformation; Programming Languages; RNA / chemistry
TL;DR: This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures and permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2001 journal article

Characterization of RNAse P holoenzymes from methanococcusjannaschii and methanothermobacter thermoautotrophicus

Biological Chemistry Hoppe-Seyler, 382(8), 1171–1177.

By: A. Andrews, T. Hall & J. Brown

Source: NC State University Libraries
Added: August 6, 2018

2001 journal article

New insight into RNase P RNA structure from comparative analysis of the archaeal RNA

RNA, 7(2), 220–232.

By: J. Harris n, E. Haas n, D. Williams  n, D. Frank * & J. Brown n

author keywords: Archaea; archaebacteria; ribonuclease P; ribozyme; rnpB
MeSH headings : Base Sequence; Cells, Cultured; DNA Primers / chemistry; Endoribonucleases / chemistry; Escherichia coli / enzymology; Escherichia coli / genetics; Escherichia coli Proteins; Genes, Bacterial / genetics; Molecular Sequence Data; Nucleic Acid Conformation; Phylogeny; Plasmids; Polymerase Chain Reaction; RNA, Archaeal / classification; RNA, Archaeal / genetics; RNA, Bacterial / chemistry; RNA, Bacterial / isolation & purification; RNA, Catalytic / chemistry; RNA, Catalytic / isolation & purification; Ribonuclease P; Sequence Alignment; Sequence Analysis, DNA
TL;DR: A detailed comparative analysis of archaeal RNase P RNA structure and a comparison of the resulting structural information with that of the bacterial RNA reveals that the ArchaealRNase P RNAs are strikingly similar to those of Bacteria. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2001 chapter

The ribonuclease P family

In Ribonucleases: Pt. A (Vol. 341, pp. 56–77). San Diego, CA: Academic Press.

By: T. Hall & J. Brown

Source: NC State University Libraries
Added: August 6, 2018

1999 journal article

RNase P RNAs from some Archaea are catalytically active

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 96(14), 7803–7808.

By: J. Pannucci n, E. Haas n, T. Hall n, J. Harris n & J. Brown n

MeSH headings : Archaea / enzymology; Archaea / genetics; Bacillus / enzymology; Bacillus / genetics; Base Sequence; Conserved Sequence; Endoribonucleases / chemistry; Endoribonucleases / genetics; Endoribonucleases / metabolism; Kinetics; Methanobacterium / enzymology; Methanobacterium / genetics; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Phylogeny; RNA, Archaeal / chemistry; RNA, Archaeal / genetics; RNA, Archaeal / metabolism; RNA, Bacterial / metabolism; RNA, Catalytic / chemistry; RNA, Catalytic / genetics; RNA, Catalytic / metabolism; Ribonuclease P
TL;DR: The properties of the archaeal RNase P RNAs (high ionic-strength requirement, low affinity for substrate, and catalytic reconstitution by bacterialRNase P protein) are similar to synthetic RNases that contain all of the catalytic core of the bacterial RNA but lack phylogenetically variable, stabilizing elements. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

1999 journal article

The Ribonuclease P Database

NUCLEIC ACIDS RESEARCH, 27(1), 314–314.

By: J. Brown n

MeSH headings : Databases, Factual; Endoribonucleases / chemistry; Endoribonucleases / genetics; Endoribonucleases / metabolism; Eukaryotic Cells / chemistry; Eukaryotic Cells / metabolism; Information Storage and Retrieval; Internet; Models, Molecular; Nucleic Acid Conformation; Organelles / chemistry; Organelles / genetics; Organelles / metabolism; Phylogeny; Protein Structure, Secondary; RNA, Archaeal / chemistry; RNA, Archaeal / genetics; RNA, Archaeal / metabolism; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Bacterial / metabolism; RNA, Catalytic / chemistry; RNA, Catalytic / genetics; RNA, Catalytic / metabolism; Ribonuclease P; Ribonucleoproteins / chemistry; Ribonucleoproteins / genetics; Ribonucleoproteins / metabolism; Sequence Alignment; Software
TL;DR: Ribonuclease P is responsible for the 5'-maturation of tRNA precursors, and in bacteria the RNA subunit alone is catalytically active in vitro, i.e., it is a ribozyme. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

1998 journal article

Evolutionary variation in bacterial RNase P RNAs

NUCLEIC ACIDS RESEARCH, 26(18), 4093–4099.

By: E. Haas n & J. Brown

MeSH headings : Bacteria / enzymology; Bacteria / genetics; Base Sequence; Conserved Sequence; Endoribonucleases / chemistry; Endoribonucleases / genetics; Evolution, Molecular; Genetic Variation; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Phylogeny; RNA, Bacterial / chemistry; RNA, Bacterial / genetics; RNA, Catalytic / chemistry; RNA, Catalytic / genetics; Ribonuclease P
TL;DR: In a remarkable case of convergent molecular evolution, most of the unusual structural elements of type B RNase P RNAs of the low G+C Gram-positive Bacteria have evolved independently in Thermomicrobium roseum, a member of the green non-sulfur Bacteria. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

1998 journal article

Stem-loop structure in the 5 ' region of potato virus X genome required for plus-strand RNA accumulation

JOURNAL OF MOLECULAR BIOLOGY, 284(3), 591–608.

By: E. Miller  n, C. Plante n, K. Kim n, J. Brown n & C. Hemenway n

author keywords: RNA structure; RNA virus; RNA replication; potato virus X; stem-loop
MeSH headings : Base Sequence; Genome, Viral; Molecular Sequence Data; Mutagenesis, Site-Directed; Nucleic Acid Conformation; Plants, Toxic; Potexvirus / genetics; Protoplasts / virology; RNA, Viral / chemistry; RNA, Viral / metabolism; Thermodynamics; Tobacco / metabolism; Tobacco / virology
TL;DR: Data indicate that multiple features of SL1 are critical for accumulation of PVX plus-strand RNA, including a UUCG tetraloop, indicating that the sequence of this element was important beyond just providing stabilization of the structure. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
3. Good Health and Well-being (OpenAlex)
13. Climate Action (Web of Science)
Source: Web Of Science
Added: August 6, 2018

1998 journal article

The Ribonuclease P Database

NUCLEIC ACIDS RESEARCH, 26(1), 351–352.

By: J. Brown n

MeSH headings : Computer Communication Networks; Databases, Factual; Endoribonucleases / chemistry; Endoribonucleases / genetics; Endoribonucleases / metabolism; Information Storage and Retrieval; RNA, Catalytic / chemistry; RNA, Catalytic / genetics; RNA, Catalytic / metabolism; Ribonuclease P
TL;DR: The Ribonuclease P Sequence database is a compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional models, and accessory information. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

1997 journal article

Intracellular localization and unique conserved sequences of three small nucleolar RNAs

NUCLEIC ACIDS RESEARCH, 25(8), 1591–1596.

By: N. Selvamurugan *, O. Joost*, E. Haas n, J. Brown n, N. Galvin* & G. Eliceiri*

MeSH headings : Animals; Base Sequence; Cell Nucleolus / metabolism; Chickens; Conserved Sequence; DNA Primers; Female; Humans; Mice; Molecular Sequence Data; Nucleic Acid Conformation; Oocytes / physiology; Polymerase Chain Reaction; RNA Precursors / metabolism; RNA, Small Nuclear / biosynthesis; RNA, Small Nuclear / chemistry; Rats; Sequence Homology, Nucleic Acid; Xenopus laevis; Zebrafish
TL;DR: Human and frog E1, E2 and E3 RNAs injected into the cytoplasm of frog oocytes migrated to the nucleus and specifically to the nucleolus, indicating that the nucleolar and nuclear localization signals of these snoRNAs reside within their evolutionarily conserved segments. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

1997 journal article

The ribonuclease P database

NUCLEIC ACIDS RESEARCH, 25(1), 263–264.

By: J. Brown n

MeSH headings : Databases, Factual; Endoribonucleases / chemistry; Endoribonucleases / genetics; Protein Structure, Secondary; RNA, Catalytic / chemistry; RNA, Catalytic / genetics; Ribonuclease P; Sequence Alignment
TL;DR: Ribonuclease P is responsible for the 5'-maturation of tRNA precursors, and in bacteria (and some Archaea) the RNA subunit alone is catalytically active in vitro, i.e. it is a ribozyme. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

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