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J W Barrett

Publications and source records attributed to J W Barrett.

13 recordsLinked to original sources
PubMed2000

Modulating chemokines: more lessons from viruses.

Chemokines are crucial effector molecules involved in orchestrating the host inflammatory response against invading pathogens. Viruses have devised several strategies for exploiting or neutralizing chemokines or their receptors to further their own propagation or elude host defenses. Insight into strategies used by viruses to modulate chemokines might help generate novel approaches for treating viral diseases and chemokine-mediated inflammatory disorders.

Animals↗
PubMed1998

Concomitant primary infection of the midgut epithelial cells and the hemocytes of Trichoplusia ni by Autographa californica nucleopolyhedrovirus.

We have constructed a modified Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) to express the green fluorescent protein (GFP) under the polyhedrin promoter and used it to study the infection process of AcMNPV in Trichoplusia ni larvae. T. ni larvae that ingested the virus showed localized expression of GFP in the midgut epithelial cells and the hemocytes at 12 h post infection (hpi). The presence of GFP-related fluorescence in the midgut columnar cells indicated that the virus was not only replicating, but also synthesizing the late viral proteins. Studies using the transmission electron microscope showed that the virus infected the midgut columnar cells. At the same time a proportion of the parental virus travelled through the midgut epithelial layer, possibly utilizing the plasma membrane reticular system, entered the hemocoel and infected the hemocytes. This resulted in the simultaneous infection of the midgut epithelial cells and the hemocytes. Subsequently, the budded virus (BV) released from the infected hemocytes into the hemolymph caused secondary infection within the tracheal epithelial cells. The virus then rapidly spread through the tracheal system allowing the infection of a variety of other tissues such as the epidermis and the fat body.

Animals↗
PubMed1998

Characterization of the nucleoside triphosphate phosphohydrolase I gene from the Choristoneura fumiferana entomopoxvirus.

Poxviruses carry the enzyme, nucleoside triphosphate phosphohydrolase I (NPH I), required for early viral transcription in the cytoplasm of infected cells. The gene (nph I) encoding this enzyme from Choristoneura fumiferana entomopoxvirus (CfEPV) has been located in the viral genome, cloned and characterized. It has an open reading frame of 1941 nucleotides, potentially encoding a protein with a predicted molecular mass of 76.04 kDa and a pI of 8.83. It has a TAAATG motif where the trinucleotide ATG represents the translational start signal an AT-rich (88%) sequence and an early transcription termination signal (TTTTTAT) upstream of the ATG codon. Northern blot analysis of mRNA from infected larvae showed that a single 4.0 kb transcript which appeared late at day 20 post infection (p.i.) and its transcription continued till day 37 p.i.. Primer extension experiments suggested that the main transcripts started at 15 bases upstream of AUG codon. NPH I homologues have been found in the genomes of other entomopoxviruses and vertebrate poxviruses. Alignment of their amino acid sequences suggested three conserved domains, two of which are considered as ATP binding domains. The most similar homologue is from the closely related entomopoxvirus. Choristoneura biennis EPV (CbEPV) where 98.2% of nucleotide and 97.2% of amino acid identities are observed, respectively. A single nucleotide difference in CfEPV nph I was sufficient to distinguish it from CbEPV by PCR amplification and digestion with a restriction enzyme.

Acid Anhydride Hydrolases↗
PubMed1998

Studies of the nucleopolyhedrovirus infection process in insects by using the green fluorescence protein as a reporter.

A recombinant Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) expressing the green fluorescence protein (GFP) under the control of the AcMNPV polyhedrin promoter was constructed to study the spatial and temporal regulation of baculovirus infection in a permissive host. Larvae that ingested AcMNPV-GFP showed localized expression of GFP in the midgut epithelial cells, as well as hemocytes, at 24 h postinfection. The presence of fluorescence in these tissues indicated not only that the virus was replicating but also that the very late viral proteins were being synthesized. Secondary infection occurred within the tracheal cells throughout the body cavity, confirming earlier reports, and these foci of infection allowed entry of the virus into other tissues, such as the epidermis and the fat body.

Animals↗
PubMed1997

Cloning, sequencing and transcriptional analysis of the Choristoneura fumiferana entomopoxvirus spheroidin gene.

The Choristoneura fumiferana entomopoxvirus (CfEPV) spheroidin gene was identified and localized on three XbaI restriction fragments (total size 4.73 kb). The fragments were cloned and sequenced. The spheroidin gene had an open reading frame of 2997 nucleotides encoding a putative protein with a predicted size of 115 kDa. Sequence analysis indicated that the putative protein contained 14 potential N-glycosylation sites (Asn-X-Thr; Asn-X-Ser), that are probably not used since the protein migrates on SDS-PAGE as a 115 kDa band. The protein is rich in cysteine residues (34), which explains the need for reducing agents when dissolving the occlusion bodies with alkali. The spheroidin gene sequence contains motifs characteristic of the late genes of poxviruses. These include the typical TAAATG sequence at the beginning of the coding region and two early gene termination signals (TTTTTNT) in the untranslated region of the gene. The promoter region has three TAA termination signals immediately upstream of the ATG start site. Spheroidin (SPH) appears to be conserved among different EPVs. There was 82.2% identity and 97.2% similarity at the amino acid level between the SPHs of CfEPV and Amsacta moorei EPV. Less conservation was seen with the SPH from Melolontha melolontha EPV (39.8% identity and 73.4% similarity). Transcriptional analyses of the spheroidin gene by Northern blots showed that the transcript had a size of approximately 3 kb, which is in agreement with the length of the ORF. Primer extension results, anchor PCR and sequencing confirmed that there was a poly (A)17 tract at the 5' end of the spheroidin gene transcript, a structure typical of late gene transcripts of poxviruses.

Amino Acid Sequence↗
PubMed1997

Semantic quality through semantic definition: refining the Read Codes through internal consistency.

Checks of internal consistency in controlled medical vocabularies facilitate their development and assist refinement of the underlying terminological model. Two simple checks of consistency between knowledge in the subtype hierarchy and that in semantic definitions of concepts are described. It is proposed that these checks are a helpful adjunct to, but not a replacement for, large-scale involvement of domain experts in construction of controlled vocabularies.

Classification↗
PubMed1996

The putative LEF-1 proteins from two distinct Choristoneura fumiferana multiple nucleopolyhedroviruses share domain homology to eukaryotic primases.

We have identified the lef-1 genes from two multiple nucleopolyhedroviruses that infect natural populations of Choristoneura fumiferana. The lef-1 genes in both viruses are directly upstream and in the opposite orientation of their respective ecdysteroid UDP-glucosyltransferase (egt) genes. This gene organization pattern is similar to that found in the genomes of AcMNPV and of OpMNPV. As well, the coding regions and putative protein sequences share a high degree of similarity. Alignment of the predicted amino acid sequences of all known baculovirus lef-1 genes suggests that the LEF-1 proteins have a relatively high degree of conservation, particularly at four identified and distinct domains. Moreover, LEF-1 proteins bear clear similarity to some eukaryotic primases, predominately at three of the four domains where certain amino acids are absolutely conserved.

Amino Acid Sequence↗
PubMed1995

Characterization, sequencing and phylogeny of the ecdysteroid UDP-glucosyltransferase gene from two distinct nuclear polyhedrosis viruses isolated from Choristoneura fumiferana.

The ecdysteroid UDP-glucosyltransferase (egt) gene isolated from a plaque-purified isolate of Choristoneura fumiferana multinucleocapsid nuclear polyhedrosis virus (CfMNPV) was compared to its homologue from a defective MNPV virus (CfDEF) present in wild type virus populations infecting the eastern spruce budworm, C. fumiferana. The egt genes were located in the same relative position within the virus genomes and their genomic location and arrangement were similar to that found in Autographa californica MNPV (AcMNPV) and Orgyia pseudotsugata MNPV (OpMNPV). The genes encoded 491 and 494 amino acid open reading frames respectively, and were 67% identical at the amino acid level and 74% identical at the nucleotide level. Transcripts of the egt of CfMNPV peaked around 12 h post-infection (p.i.) and disappeared after 36 h p.i. Transcripts of the egt of CfDEF peaked between 6 and 9 h p.i. and were not detected 24 h p.i. The egt from CfMNPV was more similar to the partially sequenced egt identified from OpMNPV, at the nucleotide and amino acid levels, than it was to the egt from the CfDEF, AcMNPV, Bombyx mori NPV, Lymantria dispar MNPV or Spodoptera exigua MNPV. Phylogenetic analysis of egt supported the baculovirus evolution scheme suggested by polyhedrin sequence analysis.

Amino Acid Sequence↗
PubMed1994

A genomic clone of a type I cab gene encoding a light harvesting chlorophyll a/b binding protein of photosystem II identified from lodgepole pine.

A type I cab gene encoding chlorophyll a and b binding protein from lodgepole pine (Pinus contorta Dougl., var. latifolia (Engelm.)) has been isolated and sequenced. The gene encodes a proposed 40 amino acid transit peptide and a 234 amino acid mature CAB polypeptide. There is no evidence of an intron and examination of the type-specific amino acids confirm this to be a photosystem II type I cab gene. The coding region is highly conserved with a similar gene from Scots pine, the homology extending into the 5' and 3' untranslated regions. Sequence comparison of the 1-kb region upstream of the translation start codon from the lodgepole pine cab gene exhibited little similarity to identified regulatory regions in pea, tobacco, wheat, and Arabidopsis cab genes. The cab gene, which is 62% G + C rich, is surrounded by 70-75% A + T rich regions, which may confer some regulatory feature on its expression.

Amino Acid Sequence↗
PubMed1992

Maternal transmission of mitochondrial DNA in interspecific hybrids of Populus.

Restriction fragment analysis was conducted to investigate the mode of inheritance of mitochondrial (mt) DNA in F1 progeny of two P. deltoides x P. deltoides, three P. deltoides x P. nigra, and two P. deltoides x P. maximowiczii controlled crosses, and in Populus x canadensis by using 16 restriction endonucleases and two heterologous probes of cloned mtDNA fragments of maize. Five restriction fragment length polymorphisms (RFLPs) of mtDNA differentiated P. deltoides from P. nigra, whereas three RFLPs of mtDNA separated P. deltoides from P. maximowiczii. In all cases, F1 progeny of P. deltoides x P. nigra, and P. deltoides x P. maximowiczii, crosses had mtDNA restriction fragments of only their maternal P. deltoides parents. P. x canadensis had mtDNA restriction fragments of only P. deltoides. F1 progeny of intraspecific P. deltoides crosses also had the same mtDNA fragments as their maternal parent. The results clearly demonstrate uniparental-maternal inheritance of the mitochondrial genome in F1 interspecific hybrids of P. deltoides with P. nigra and P. maximowiczii.

Crosses, Genetic↗
PubMedDate not supplied

Read Code quality assurance: from simple syntax to semantic stability.

As controlled clinical vocabularies assume an increasing role in modern clinical information systems, so the issue of their quality demands greater attention. In order to meet the resulting stringent criteria for completeness and correctness, a quality assurance system comprising a database of more than 500 rules is being developed and applied to the Read Thesaurus. The authors discuss the requirement to apply quality assurance processes to their dynamic editing database in order to ensure the quality of exported products. Sources of errors include human, hardware, and software factors as well as new rules and transactions. The overall quality strategy includes prevention, detection, and correction of errors. The quality assurance process encompasses simple data specification, internal consistency, inspection procedures and, eventually, field testing. The quality assurance system is driven by a small number of tables and UNIX scripts, with "business rules" declared explicitly as Structured Query Language (SQL) statements. Concurrent authorship, client-server technology, and an initial failure to implement robust transaction control have all provided valuable lessons. The feedback loop for error management needs to be short.

Clinical Medicine↗