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Biomedical subjects

C Upton

Publications and source records attributed to C Upton.

At least 19 recordsLinked to original sources

Emergency asthma inhalers in school.

Despite there being a lack of direct evidence of the effectiveness of providing emergency inhalers to schools, the balance of evidence at present suggests the benefits outweigh any possible harm. However, unless UK prescribing law or its interpretation is changed, this will remain an action which opens teachers, nurses, and doctors to possible legal and professional sanctions, and may nullify their institutional or professional indemnity. As a consequence, provision will remain patchy and research into the value of emergency inhalers will be inhibited. A position statement from one or more responsible organisations such as the Royal College of Paediatrics and Child Health, the British Thoracic Society, or the British Paediatric Respiratory Society could persuade a reassessment from the Medicines Control Agency. This is also an issue which could be addressed in the forthcoming National Service Framework for children.

Acute Disease↗

Nucleotide sequence analysis of RNA-2 of a flat apple isolate of Cherry rasp leaf virus with regions showing greater identity to animal picornaviruses than to related plant viruses.

RNA-2 of a flat apple isolate of Cherry rasp leaf virus (CRLV-FA) appears to consist of 3274 nucleotides, excluding a 3' poly (A) tail. The data supports re-classification of CRLV in a new genus in the family Comoviridae. A single open reading frame (ORF) encoding a putative 108 kDa polyprotein was identified. Potential protease cleavage sites were identified which would result in the production of a putative movement protein (41 kDa), and 3 capsid protein subunits (24, 20, and 22 kDa, respectively). A 5'-UTR and 3'-UTR were identified, 248 nt and 146 nt long, respectively. The genome organisation of CRLV-FA RNA-2 is similar to that of Apple latent spherical virus (ALSV) RNA-2, a new member of the family Comoviridae. The Vp25 amino acid sequences were unique to CRLV-FA and ALSV (54% identity), with no relationship identified to any other virus. CRLV-FA Vp20 and Vp24 amino acid sequences were closely related to ALSV (59 and 65%, respectively) but the only other relationships identified were with a range of animal ssRNA positive-strand viruses.

Amino Acid Sequence↗

Avoiding drug errors.

Although no statistics are available, medication errors occur relatively frequently and should be a target for Clinical Governance activities. Organisations need to create a culture where risk management regarding medication is incorporated.

Humans↗

Conformationally-restricted ligands for the histamine H1 receptor.

Potent H1-antagonistic activity in a series of novel indeno[2,1-c]pyridines and their 4-arylpiperidinol precursors is reported; one compound shows an in vitro activity four times that of the standard mepyramine that it was screened against. Their failure to translate this protection to in vivo tests is discussed.

Animals↗

Nucleotide sequence and genome organisation of cherry mottle leaf virus and its relationship to members of the Trichovirus genus.

The nucleotide sequence of cherry mottle leaf virus (CMLV) was determined and compared to sequences of a number of plant viruses including the type member of the Trichovirus genus (apple chlorotic leafspot virus, ACLSV), and members of the Vitivirus genus including grapevine virus B, (GVB). The CMLV genome was determined to consist of 8003 nt excluding the poly(A) tail at the 3' end of the genome. The overall A + U content of CMLV genomic RNA was 59.1%, which is similar to ACLSV, but significantly different from GVB. Four putative open reading frames were identified (ORFs 1, 2, 3, and 4) encoding proteins of M(r) 215.8 kDa, 47 kDa, 21.6 kDa, and 15.3 kDa, respectively. This differs from ACLSV which has 3 ORFS, and GVB which has 5 ORFs. Protein database searches showed no matches of CMLV ORF4 with ACLSV sequences, but found similarities between ORF4 of CMLV and ORF5 of GVB, suggesting that this may be a nucleic acid-binding protein. CMLV and ACLSV formed a common virus clade in phylogenetic analysis of the coat protein amino acid sequence and except for CMLV's ORF4, these viruses show high levels of similarity throughout the genome. CMLV appears to be a member of the Trichovirus genus.

Amino Acid Sequence↗

Viral genome organizer: a system for analyzing complete viral genomes.

The viral genome organizer (VGO) is designed to simplify the characterization and annotation of complete viral genomes (particularly those of large poxviruses) and to help researchers discover new genes and detect gene fragmentation. VGO is based on Genotator [Harris, N.L., 1997. Genome Res. 7, 754-762], an annotation workbench designed for the analysis of eukaryotic genomic sequences. VGO automates a number of database search routines (FASTA, BLASTP, PSI-BLAST and TBLASTN), processes the results through a multiple-alignment viewer (MView; [Brown, N.P., Leroy, C., Sander, C. , 1998. Bioinformatics 14, 380-381]) and serves to manage the hundreds of DNA, protein and database search results files that must be organized when dealing with large complete poxviral genomes. It also directs the generation a self-dotplot of the genome by Dotter [Sonnhammer, E.L.L., Durbin, R., 1995. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167: GC1-10. http://www.sanger.ac. uk/Software/Dotter/] to uncover repeated genes and sequences and provides Internet links to programs for generation of restriction maps and analysis of potential PCR primers. The user-friendly graphical interface displays DNA and protein sequences, links to search results, ORFs, stop-start codons, restriction sites and flags of database searches. Currently, VGO and associated programs run in an X-windows environment on commonly available UNIX machines.

Databases, Factual↗

Analysis of host response modifier ORFs of ectromelia virus, the causative agent of mousepox.

From the right-hand end of the ectromelia virus (strain Moscow) genome, 32318 bps have been sequenced, and characterized to include a total of 18 open reading frames (ORFs) and six regions which apparently no longer code for functional proteins. At least six of the ORFs appear to be involved in blocking the inflammatory/immune host response to infection, and therefore probably contribute significantly to the virulence of this virus in its natural host, the mouse. One of these genes encoded an isolog of the poxvirus chemokine binding protein, and was shown to be the most abundant protein secreted from ectromelia virus infected cells. Two regions were found to have significant similarity to poxvirus genes encoding tumor necrosis factor (TNF) binding proteins. Both are distinct from cytokine response modifier (crm)B and crmC but only one is predicted to encode a functional TNF binding protein. A novel similarity between the C-terminal domain of poxvirus TNF binding proteins and several other poxvirus proteins is also presented. The results are discussed in the context of ectromelia virus pathogenesis of mice.

Amino Acid Sequence↗

Screening predicted coding regions in poxvirus genomes.

The amino acid composition and pI values were calculated for the predicted proteins of a series of complete poxvirus genomes. Many of the vaccinia virus (strain Copenhagen) minor ORFs, thought not to be functional genes, were found to have significantly more or less of several amino acids than a set of the largest 150 vaccinia virus proteins. Very high isoelectric point (pI) values were also correlated with a group of the minor ORFs. Analysis of molluscum contagiosum virus ORFs by amino acid composition and pI identified a number of ORFs previously denoted as doubtful and highlighted several others that could be similarly classified. The use of amino acid composition and pI appears to be a generally applicable tool to aid identification of viral ORFs that are unlikely to be functional genes.

Amino Acids↗

BLAST Search Updater: a notification system for new database matches.

UNLABELLED: BLAST Search Updater (BSU) can help molecular biologists perform large numbers of BLAST searches routinely and screen the results for novel matches. The search result files (HTML format) and delta files (novel matches) are WWW viewable and BSU also emails users alignments of new matches. AVAILABILITY: BSU runs on UNIX machines and is freely available to academic users at http://athena.bioc.uvic.ca/genomes/. Additional figures and description are also available. CONTACT: cupton@uvic.ca

Computational Biology↗

Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes.

SUMMARY: The Viral Genome DataBase (VGDB) contains detailed information of the genes and predicted protein sequences from 15 completely sequenced genomes of large (&100 kb) viruses (2847 genes). The data that is stored includes DNA sequence, protein sequence, GenBank and user-entered notes, molecular weight (MW), isoelectric point (pI), amino acid content, A + T%, nucleotide frequency, dinucleotide frequency and codon use. The VGDB is a mySQL database with a user-friendly JAVA GUI. Results of queries can be easily sorted by any of the individual parameters. AVAILABILITY: The software and additional figures and information are available at http://athena.bioc.uvic.ca/genomes/index.html .

Databases, Factual↗

Ectromelia virus virulence factor p28 acts upstream of caspase-3 in response to UV light-induced apoptosis.

Ectromelia virus (EV) virulence factor p28 (EVp28) is a member of a family of poxvirus proteins that are defined largely by the presence of a C-terminal RING finger motif and localization to virus factories within the cytoplasm of infected cells. Previously, overexpression of the Shope fibroma virus (SFV) homologue, N1R, in vaccinia virus (VV)-infected BGMK cells was found to inhibit virus-induced apoptosis. Here, we report that both EVp28 and overexpression of SFV N1R in poxvirus-infected HeLa cells protect specifically from UV light-induced apoptosis, but not from apoptosis induced by Fas or TNF. Further, we report that both VV and EV protect from apoptosis induced by UV, Fas and TNF. Immunoblot analysis indicates that EVp28 acts upstream of caspase-3, blocking activation of the protease in response to UV irradiation. Although no difference was found in replication of an EVp28(-) mutant virus, which expresses a truncated p28 protein lacking the RING motif, compared to EV wild-type in HeLa cells, UV irradiation of infected HeLa cells reduced the replication of the EV mutant compared with wild-type EV.

Apoptosis↗

Single primer pair designs that facilitate simultaneous detection and differentiation of peach mosaic virus and cherry mottle leaf virus.

Peach mosaic virus (PMV) and cherry mottle leaf virus (CMLV) are viruses which are related serologically and share common Prunus hosts, but cause distinct diseases. An RT-PCR procedure using a single oligonucleotide primer pair that allows simultaneous detection and differentiation of the two viruses was developed. A sense primer with 100% complementarity to PMV and 83% complementarity to the corresponding site of the CMLV genome was combined with either of two antisense primers (one of PMV origin and the other of CMLV origin) with 3' end complementarity at variable sites. This allowed the differential amplification of PMV and CMLV specific fragments, 419 and 705 bp, respectively. When oligo (dT) was used to generate the cDNA template, differential amplification was not observed, only amplification of the homologous virus associated with the antisense primer. This indicates polyadenylation of both viruses. Incorporation of the antisense primer into cDNA at the reverse transcription step was shown to be essential for this approach. The PMV primer pair reliably detected all isolates of PMV tested by RT-PCR analysis, both in peach leaf and budwood tissue.

Base Sequence↗

Cytotoxic response of ovarian cancer cell lines to IFN-gamma is associated with sustained induction of IRF-1 and p21 mRNA.

Interferon-gamma (IFN-gamma) has some anti-tumour activity in human ovarian cancer. This cytokine inhibited proliferation in three of four ovarian cancer cell lines in vitro. We then compared the action of IFN-gamma in two cell lines, one sensitive and one resistant to its growth inhibitory effects. IFN-gamma signalling appeared normal in both cell lines, with stat1 DNA binding activity detectable at 30 min. Continuous exposure to IFN-gamma for 2-3 days was necessary for an irreversible effect on cell growth and apoptosis in cells sensitive to growth inhibition. During this time there was an increase in mRNA for the CKI p21, but no alterations in mRNA levels for other members of the CKI family. Maintenance of p21 mRNA required continuous mRNA synthesis. mRNA for the transcription factor IRF-1 was also induced in growth inhibited cells with similar kinetics to those observed for p21. Maximal induction of both p21 and IRF-1 mRNA was observed after 2-3 days IFN-gamma exposure as the cells became committed to cell death. There was also a rapid increase in p21 and IRF-1 mRNA in cells resistant to the growth inhibitory effects of IFN-gamma, but this increase was not maintained. Thus, continuous interaction with the IFN-gamma receptor, together with a sustained induction of p21 and IRF-1, is associated with growth inhibitory and apoptotic effects of IFN-gamma in ovarian cancer cells.

Adenocarcinoma↗

Novel nitrated derivatives of 5,8-diazabenzo[c]phenanthrene and 9,14-diazadibenz[a,e]acephenanthrylene: new classes of potent mutagenic compounds.

We report the synthesis of 4-nitro-5,8-diazabenzo[c]phenanthrene (4-NDBP) and 11-nitro-9,14-diazadibenz[a,e]acephenanthrylene (11-NDDA) and the remarkable mutagenic activity of the latter. These two compounds and their non-nitrated parents, 5, 8-diazabenzo[c]phenanthrene (DBP) and 9,14-diazadibenz[a, e]acephenanthrylene (DDA), were screened in Ames plate incorporation assays against Escherichia coli WP2uvrA and Salmonella typhimurium TA98 both in the presence and absence of S9 liver fraction from Aroclor 1254-induced rats. None of the four compounds were cytotoxic up to the limits of their solubility and none showed mutagenic activity in E.coli WP2uvrA, which suggested that any such activity they may have had was not mediated via a base substitution mechanism. DBP and DDA also displayed a lack of activity in TA98 up to their precipitating doses (560 and 33.5 microg/plate, respectively). The two nitrated compounds, however, were genotoxic. 4-NDBP was active at a dose of 500 ng/plate, in the absence of S9, producing 80.0 +/- 28.0 prototrophic organisms (equivalent to 44 revertants/nmol) and at 0.5 ng/plate, in the presence of S9, giving 147 +/- 6.6 revertants (equivalent to 81 000/nmol) and allowed the description of this tetracycle as a potent mutagen. Much more striking was the activity of 11-NDDA: in the absence of S9 a dose of 8.0 ng produced 2000 revertants/nmol and, remarkably, in the presence of S9 80 pg produced the equivalent of 643 000 revertants/nmol. This makes the hexacyclic 11-NDDA the most potent mutagen to date, in the Ames procedures described here.

Coumarins↗

Shope fibroma virus RING finger protein N1R binds DNA and inhibits apoptosis.

Shope fibroma virus (SFV) N1R gene encodes a RING finger protein that localizes to virus factories within the cytoplasm of infected cells. Altered proteins, with deletions and site-specific mutations, were transiently expressed in vaccinia virus-infected cells to discern regions of the protein that are required for localization. We have determined that at least part of the RING finger region is necessary for localization but that the RING motif alone is not sufficient. A chimeric protein, however, in which the RING finger region of the herpes simplex virus-1 ICP0 protein replaces the SFV N1R RING motif does localize to virus factories. A region of five highly conserved amino acids at the amino terminus of SFV N1R is also critical for localization. We report that the SFV N1R protein binds double- and single-stranded DNA, suggesting a mechanism for localization, and that overexpression of this protein in vaccinia virus-infected cells reduces apoptosis-associated fragmentation of nuclear DNA.

Amino Acid Sequence↗

Stereochemical studies of the isomerization of novel 2-alkyl-9-phenyl-2,3,4,4a- and 2,3,4,9-tetrahydro-1H-indeno[2,1-c]pyridines.

The published synthetic route to the antihistaminic tetrahydroindeno[2,1-c]pyridines (phenindamines) relies on catalytic reduction of the precursor dihydroindenopyridines. This reduction gives mixtures of 9,9a- and 4a,9a-enes and the clinically active 4a,9a isomer has to be isolated by recrystallization of an appropriate salt. The structure of the product recovered depends on the anion used to isolate the proton salt and appears to be arbitrary. To rationalize this outcome a series of novel N-2 alkylated tetrahydroindeno[2,1-c]pyridines and their diene precursors has been synthesized from accessible piperidines. The structures and geometry of the piperidines and the dihydro- and tetrahydroindenopyridines have been determined by 1H and 13C NMR. An unusual feature of the proton spectra of the piperidines is the resonance of the axial protons at lower field than their equatorial counterparts. By controlling the reaction conditions for the reduction of the dihydroindenopyridines to their tetrahydro derivatives the kinetic or thermodynamic product can be selected as required. A predictable outcome for the reductions investigated was achieved and is generally applicable.

Histamine H1 Antagonists↗

Novel 5,8-diazabenzo[c]phenanthrenes: synthesis and mutagenicity.

The polycyclic aromatic hydrocarbons have been recognized as carcinogens and mutagens since the early part of this century. More recently their aza and polyaza derivatives have been shown to have the same biological activity. A major source of these compounds is the combustion of fresh or metamorphosed plant materials; this contributes to the environmental burden of, and exposure to, these carcinogens. We report the synthesis and characterization of a series of novel 5,8-diazabenzo[c]phenanthrenes which are isosteric with the known epidermal carcinogen benzo[c]phenanthrene but have not yet been reported as components of soot or diesel particulate matter. The synthesis of the compounds exploits a versatile, double Friedlander reaction between the appropriately substituted 2,2'-diaminobenzophenone and beta-diketones, with yields of purified product ranging from 30-90%. The nucleophilic substitution of these diazabenzophenanthrenes with ethanolamine is also described. This strategy will enable further elaboration of these heterocyclic nuclei at a later date. Mutagenicity testing of these agents was performed using spot tests and in Ames plate-incorporation assays using Escherichia coli WP2 and WP2uvrA as test organisms. The plate-incorporation assays were performed in the presence or absence of metabolic enzymes contained in the S9 liver fraction from Aroclor 1254-induced rats, to investigate whether bioactivation of the diazabenzophenanthrenes contributed to their toxicity. No differences between these two protocols were observed, with neither test showing reversion to prototrophic behaviour. Furthermore, the compounds were not toxic to the test organism. These initial results suggest that these compounds are not mutagenic in the Ames tests employed.

Animals↗