Works Published in 2004

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Displaying works 1 - 20 of 57 in total

Sorted by most recent date added to the index first, which may not be the same as publication date order.

2004 journal article

Conformational changes in Sindbis virions resulting from exposure to low pH and interactions with cells suggest that cell penetration may occur at the cell surface in the absence of membrane fusion

Virology, 324(2), 373–386.

By: A. Paredes*, D. Ferreira n, M. Horton n, A. Saad*, H. Tsuruta*, R. Johnston*, W. Klimstra*, K. Ryman* ...

author keywords: Sindbis virus; electron cryo-microscopy; pH conditions; structure; infection; membrane fusion
MeSH headings : Animals; Cell Fusion; Cell Line; Cricetinae; Cryoelectron Microscopy; Hydrogen-Ion Concentration; Membrane Fusion; Microscopy, Electron; Protein Conformation; Sindbis Virus / chemistry; Sindbis Virus / physiology; Sindbis Virus / ultrastructure; Viral Envelope Proteins / chemistry; Viral Envelope Proteins / ultrastructure; Virion / chemistry; Virion / physiology; Virus Replication
TL;DR: Investigation of the requirements for the induction of virus-mediated, low pH-induced cell-cell fusion and cell-virus fusion found that exposure to acid pH was required to establish conditions for membrane fusion but that membrane fusion did not occur until return to neutral pH. (via Semantic Scholar)
Source: Crossref
Added: October 9, 2021

2004 journal article

Rapid preparative purification of West Nile and Sindbis virus PCR products utilizing a microbore anion-exchange column

Journal of Virological Methods, 120(2), 141–149.

By: R. Hernandez n, S. Nelson n, J. Salm n, D. Brown n & A. Alpert

author keywords: Sindbis virus; West Nile virus; PCR products; preparative anion-exchange HPLC purification
MeSH headings : Anions / analysis; Anions / isolation & purification; Chromatography, High Pressure Liquid; DNA, Viral / analysis; DNA, Viral / isolation & purification; Polymerase Chain Reaction / methods; Sindbis Virus / genetics; Sindbis Virus / isolation & purification; Time Factors; Virology / methods; West Nile virus / genetics; West Nile virus / isolation & purification
TL;DR: This paper describes a simple and relatively inexpensive micro-preparative HPLC method to purify and analyze nM quantities of DNA that differs from existing methodologies because separation is based on size and charge as well as the overall G + C content of the PCR product. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Crossref
Added: October 9, 2021

2004 journal article

Global Analysis of the Membrane Subproteome of Pseudomonas aeruginosaUsing Liquid Chromatography-Tandem Mass Spectrometry

Journal of Proteome Research, 3(3), 434–444.

By: J. Blonder*, M. Goshe*, W. Xiao*, D. Camp*, M. Wingerd*, R. Davis*, R. Smith*

author keywords: proteome; membrane proteins; low abundance; LC-MS/MS; affinity labeling
MeSH headings : Affinity Labels / chemistry; Amino Acid Sequence; Chromatography, Liquid; Databases, Protein; Mass Spectrometry; Membranes / metabolism; Molecular Sequence Data; Multiprotein Complexes / metabolism; Proteome; Pseudomonas aeruginosa / metabolism
TL;DR: Key integral inner and outer membrane proteins involved in adaptation and antibiotic resistance were conclusively identified, including the detection of 53% of all predicted opr-type porins (outer integral membrane proteins) and all the components of the mexA-mexB-oprM transmembrane protein complex. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Source: Crossref
Added: November 22, 2020

2004 journal article

Digital Imaging Workflow in Modern Microscopy

Microscopy and Microanalysis, 10(S02), 1256–1257.

By: J. Mackenzie n

TL;DR: Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004. (via Semantic Scholar)
Source: Crossref
Added: November 22, 2020

2004 journal article

Characterization of Human UDP-glucose Dehydrogenase

Journal of Biological Chemistry, 279(22), 23590–23596.

By: B. Sommer*, J. Barycki* & M. Simpson*

MeSH headings : Binding Sites; Catalytic Domain / genetics; Cysteine; Humans; Lysine; Oxidation-Reduction; Protein Conformation; Streptococcus pyogenes; Structure-Activity Relationship; Uridine Diphosphate Glucose Dehydrogenase / chemistry; Uridine Diphosphate Glucose Dehydrogenase / genetics; Uridine Diphosphate Glucose Dehydrogenase / metabolism
TL;DR: Cloned, expressed, and affinity-purified the human UGDH and determined its steady state kinetic parameters, which are consistent with the postulated role of Cys-276 as a catalytic residue and supports its position in the reaction mechanism for the human enzyme. (via Semantic Scholar)
Source: Crossref
Added: August 28, 2020

2004 journal article

Mutagenicity in Salmonella of halonitromethanes: a recently recognized class of disinfection by-products in drinking water

Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 562(1-2), 39–65.

By: B. Kundu*, S. Richardson*, P. Swartz*, P. Matthews*, A. Richard* & D. DeMarini*

MeSH headings : Biotransformation; Disinfectants / chemistry; Disinfectants / pharmacology; Methane / analogs & derivatives; Methane / chemistry; Methane / pharmacology; Mutagenicity Tests; Nitroparaffins / chemistry; Nitroparaffins / pharmacology; Salmonella / genetics; Water Supply / analysis
TL;DR: Nine HNMs were evaluated in the Salmonella plate-incorporation assay +/- S9 using strains TA98, TA100, TA104, TPT100, and the glutathione transferase theta (GSTT1-1)-expressing strain RSJ100 and were mutagenic, most with and without S9. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Source: Crossref
Added: August 28, 2020

2004 journal article

Comparative mutagenicity of halomethanes and halonitromethanes in Salmonella TA100: structure–activity analysis and mutation spectra

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 554(1-2), 335–350.

By: B. Kundu*, S. Richardson*, C. Granville*, D. Shaughnessy*, N. Hanley*, P. Swartz*, A. Richard*, D. DeMarini*

author keywords: halonitromethanes; halomethanes; mutagenicity; Salmonella; drinking water; mutation spectra
MeSH headings : Biotransformation; Methane / analogs & derivatives; Methane / pharmacokinetics; Methane / toxicity; Mutagens / pharmacokinetics; Mutagens / toxicity; Mutation; Salmonella / drug effects; Salmonella / genetics; Structure-Activity Relationship
TL;DR: The HNMs were generally more potent mutagens than their HM homologues, and the brominated forms of both classes of DBPs were more mutagenic and cytotoxic than their chlorinated homologue. (via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation (OpenAlex)
Source: Crossref
Added: August 28, 2020

2004 journal article

Status of systems biology - does it have a future?

Drug Discovery Today: BIOSILICO, 2(5), 171–174.

By: S. Naylor* & J. Cavanagh n

Source: Crossref
Added: August 28, 2020

2004 journal article

Structural Stability and Dynamics of Hydrogenated and Perdeuterated Cytochrome P450cam (CYP101)†

Biochemistry, 43(27), 8744–8753.

By: F. Meilleur*, J. Contzen*, D. Myles* & C. Jung*

MeSH headings : Binding Sites; Camphor 5-Monooxygenase / chemistry; Camphor 5-Monooxygenase / genetics; Camphor 5-Monooxygenase / metabolism; Carbon Monoxide / metabolism; Deuterium / chemistry; Enzyme Stability; Hydrogen / chemistry; Kinetics; Phase Transition; Photolysis; Point Mutation / genetics; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Pseudomonas putida / enzymology; Pseudomonas putida / genetics; Spectroscopy, Fourier Transform Infrared; Temperature
TL;DR: The analyses presented here show that perdeuterated P450cam is structurally similar to its hydrogenated counterpart, despite its reduced thermal stability, suggesting that information obtained from the neutron structure will be representative of the normal hydrogenated P 450cam. (via Semantic Scholar)
Source: ORCID
Added: January 6, 2020

2004 patent

Geminivirus resistant transgenic plants

Washington, DC: U.S. Patent and Trademark Office.

By: L. Hanley-Bowdoin, B. Orozco, L. Kong & W. Gruissem

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

2004 journal article

The effect of the ethylene action inhibitor 1-cyclopropenylmethyl butyl ether on early plant growth

JOURNAL OF PLANT GROWTH REGULATION, 23(4), 307–312.

By: S. Saleh-Lakha*, V. Grichko n, E. Sisler n & B. Glick*

author keywords: ethylene; 1-MCP; inhibitor; mung bean; rooting; canola; cuttings; ACC
TL;DR: In rooting studies, mung bean seedlings treated with 1-cyclopropenylmethyl butyl ether prior to root excision had fewer numbers of roots than control plants that were not treated with the ethylene action inhibitor, but the inhibitor was still effective in decreasing the number of roots, compared to its non-treated counterpart. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Rapid, efficient isolation of murine gonadotropes and their use in revealing control of follicle-stimulating hormone by paracrine pituitary factors

ENDOCRINOLOGY, 145(12), 5832–5839.

MeSH headings : Activins / pharmacology; Animals; Cell Separation / methods; Follicle Stimulating Hormone / metabolism; Follistatin / pharmacology; Luteinizing Hormone / metabolism; Mice; Mice, Inbred Strains; Mice, Transgenic; Paracrine Communication / drug effects; Paracrine Communication / physiology; Pituitary Gland / cytology; Pituitary Gland / metabolism
TL;DR: Data show that paracrine factors from pituitary nongonadotropes can play a major role in controlling FSHbeta at the pituitaries level, including all cells that produce endocrine hormones. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Crystal structures of Ral-GppNHp and Ral-GDP reveal two binding sites that are also present in Ras and Rap

STRUCTURE, 12(11), 2025–2036.

By: N. Nicely n, J. Kosak n, V. Serrano n & C. Mattos n

MeSH headings : Amino Acid Sequence; Binding Sites; Catalytic Domain; Crystallography, X-Ray; Guanosine Diphosphate / chemistry; Guanosine Diphosphate / metabolism; Guanosine Triphosphate / analogs & derivatives; Guanosine Triphosphate / chemistry; Guanosine Triphosphate / metabolism; Models, Molecular; Molecular Sequence Data; Protein Conformation; Sequence Homology, Amino Acid; rap GTP-Binding Proteins / chemistry; rap GTP-Binding Proteins / metabolism; ras Proteins / chemistry; ras Proteins / metabolism
TL;DR: Clustering of conserved residues on the surface of Ral-GppNHp identifies two putative sites for protein-protein interaction, one of which is adjacent to switch I and the other is modulated by switch II and is obstructed in RAl-GDP. (via Semantic Scholar)
UN Sustainable Development Goal Categories
8. Decent Work and Economic Growth (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Role of catalase and oxyR in the viable but nonculturable state of Vibrio vulnificus

FEMS MICROBIOLOGY ECOLOGY, 50(3), 133–142.

By: I. Kong*, T. Bates*, A. Hulsmann*, H. Hassan n, B. Smith* & J. Oliver*

author keywords: VBNC; oxidative stress; catalase; H2O2; nonculturability
MeSH headings : Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Catalase / metabolism; Cold Temperature; Colony Count, Microbial; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; Gene Deletion; Hydrogen Peroxide / toxicity; Microbial Viability; Molecular Sequence Data; Sequence Analysis, DNA; Trans-Activators / genetics; Trans-Activators / metabolism; Vibrio vulnificus / drug effects; Vibrio vulnificus / genetics; Vibrio vulnificus / growth & development; Vibrio vulnificus / physiology
TL;DR: This is the first study providing direct evidence for the metabolic basis of nonculturability and the viable but nonculturable state and an oxyR mutant which lacks catalase activity is generated. (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

Pattern of 4-thiouridine-induced cross-linking in 16S ribosomal RNA in the Escherichia coli 30S subunit

BIOCHEMISTRY, 43(28), 8923–8934.

MeSH headings : Base Sequence; Escherichia coli / genetics; Molecular Sequence Data; Molecular Structure; Photochemistry; RNA, Ribosomal, 16S / chemistry; Ribosomes / chemistry; Sequence Analysis, RNA; Thiouridine / chemistry; Ultraviolet Rays
TL;DR: The locations of RNA-RNA cross-links in 16S rRNA were determined after in vivo incorporation of 4-thiouridine (s(4)U) into RNA in a strain of Escherichia coli deficient in pyrimidine synthesis and irradiation at >320 nm to find RNA cross- links different from UVB-induced cross- Links that would be valuable for monitoring the 30S subunit in functional complexes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Microarray analyses of gene expression during adventitious root development in Pinus contorta (1[w])

PLANT PHYSIOLOGY, 135(3), 1526–1539.

By: M. Brinker n, L. Zyl n, W. Liu n, D. Craig n, R. Sederoff n, D. Clapham n, S. Arnold n

MeSH headings : Cell Division; Gene Expression Regulation, Developmental / genetics; Gene Expression Regulation, Plant / genetics; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis / methods; Pinus / genetics; Pinus / growth & development; Plant Proteins / genetics; Plant Roots / genetics; Plant Roots / growth & development; Polymerase Chain Reaction
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
6. Clean Water and Sanitation (OpenAlex)
13. Climate Action (Web of Science)
Source: Web Of Science
Added: August 6, 2018

2004 journal article

H-1, N-15, and C-13 chemical shift assignments of the Vibrio harveyi histidine phosphotransferase protein LuxU

JOURNAL OF BIOMOLECULAR NMR, 29(4), 551–552.

MeSH headings : Bacterial Proteins / chemistry; Carbon Isotopes; Hydrogen; Magnetic Resonance Spectroscopy; Nitrogen Isotopes; Phosphoproteins / chemistry; Vibrio / chemistry; Vibrio / enzymology
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Gene expression during formation of earlywood and latewood in loblolly pine: Expression profiles of 350 genes

PLANT BIOLOGY, 6(6), 654–663.

By: U. Egertsdotter*, L. Zyl n, J. MacKay*, G. Peter*, M. Kirst n, C. Clark n, R. Whetten n, R. Sederoff n

author keywords: microarray analysis; Pinus taeda; earlywood; latewood; transcript abundance
MeSH headings : Expressed Sequence Tags; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; Microarray Analysis; Pinus taeda / genetics; Pinus taeda / metabolism; Reverse Transcriptase Polymerase Chain Reaction; Seasons; Transcription, Genetic
Source: Web Of Science
Added: August 6, 2018

2004 journal article

Evaluation of the DNA Binding Tendencies of the Transition State Regulator AbrB†

Biochemistry, 43(51), 16106–16118.

By: B. Bobay n, L. Benson n, S. Naylor n, B. Feeney n, A. Clark n, M. Goshe n, M. Strauch n, R. Thompson n, J. Cavanagh n

MeSH headings : Bacillus subtilis / metabolism; Circular Dichroism; DNA / chemistry; DNA / metabolism; Kinetics; Protein Binding / physiology; Spectrometry, Mass, Electrospray Ionization; Transcription Factors / chemistry; Transcription Factors / metabolism
TL;DR: This comprehensive and corroborative spectroscopic study endorses the use of microESI-MS for rapidly ascertaining qualitative binding trends in noncovalent systems in a high-throughput manner. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, Crossref
Added: August 6, 2018

2004 journal article

X-ray structural and simulation analysis of a protein mutant: The value of a combined approach

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 55(3), 733–742.

By: C. Mattos n, J. Cohen*, D. Green*, B. Tidor* & M. Karplus n

MeSH headings : Bacteriophage T4 / enzymology; Computer Simulation; Crystallography, X-Ray; Enzyme Stability; Histidine / chemistry; Hydrogen Bonding; Models, Molecular; Muramidase / chemistry; Muramidase / genetics; Mutation; Proteins / chemistry; Proteins / genetics; Static Electricity
TL;DR: Comparisons between the experimental and calculated values for the difference between the free energy of denaturation of the mutant and the wild type show the importance of the combined use of simulations and crystallography for interpreting the effects of mutations on the energetics of the system. (via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: Web Of Science
Added: August 6, 2018

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