Biomedical subjects

S Butcher

Publications and source records attributed to S Butcher.

At least 19 recordsLinked to original sources

PubMed2005

WebACT--an online companion for the Artemis Comparison Tool.

UNLABELLED: WebACT is an online resource which enables the rapid provision of simultaneous BLAST comparisons between up to five genomic sequences in a format amenable for visualization with the well-known Artemis Comparison Tool (ACT). Comparisons can be generated on-the-fly using sequences directly retrieved via EMBL database queries, or by entering or uploading user sequences. Furthermore, pre-computed comparisons are available between all publicly available, completed prokaryotic genomes and plasmids currently contained within the Genome Reviews database (372 sequences, representing 175 different species). The system is designed to minimize the volume of downloaded data and maximize performance. Genome sequences, annotation and pre-computed comparisons are stored in a relational database allowing flexible querying based on user-defined sequence regions, from whole genome to a defined region flanking a specified gene. Comparison and sequence files, whether computed online or retrieved from the database of pre-computed genome comparisons, can be viewed online using ACT and are available for download. AVAILABILITY: Freely accessible at http://www.webact.org. SUPPLEMENTARY INFORMATION: User guide and worked examples are available at http://www.webact.org/WebACT/docs.

Computational Biology↗

PubMed2001

Neutrophil ageing and immunesenescence.

As humans age, their morbidity and mortality from infection increases, their response to vaccination declines and they have an increased incidence of inflammatory diseases and cancer. The reasons for these effects are clearly complex, but reduced efficiency of the innate and adaptive immune system is likely to be important in the pathology of old age. Age-related changes in the adaptive immune system are well-documented and include alterations in T cell phenotype and effector functions and a reduced ability of B cells to produce high affinity antibody. In contrast, the innate immune system has been less well researched and the perception amongst many immunogerontologists is that this branch of the immune system is only moderately affected by age. However, it is becoming increasingly clear that the adaptive and innate immune systems co-operate at several levels to ensure the optimal immune response and any decline in adaptive immunity will impact upon the function of the innate immune system and vice-versa. Here, we review the literature concerning intrinsic age-related changes in neutrophil responses and consider how changes in lymphocyte function with age might further compromise efficiency of neutrophil function.

Aging↗

PubMed2000

Bile acids reduce the apoptosis-inducing effects of sodium butyrate on human colon adenoma (AA/C1) cells: implications for colon carcinogenesis.

Butyrate is produced in the colon by fermentation of dietary fibre and induces apoptosis in colon adenoma and cancer cell lines, which may contribute to the protective effect of a high fibre diet against colorectal cancer (CRC). However, butyrate is present in the colon together with unconjugated bile acids, which are tumour promoters in the colon. We show here that bile acids deoxycholate (DCA) and chenodeoxycholate (CDCA), at levels present in the colon, gave a modest increase in cell proliferation and decreased spontaneous apoptosis in AA/C1 adenoma cells. Bile acids significantly inhibited the induction of apoptosis by butyrate in AA/C1 cells. However, the survival-inducing effects of bile acids on AA/C1 cells could be overcome by increasing the concentration of sodium butyrate. These results suggest that dysregulation of apoptosis in colonic epithelial cells by dietary factors is a key factor in the pathophysiology of CRC.

Adenoma↗

PubMed2000

Review article: ageing and the neutrophil: no appetite for killing?

In the armoury of the immune system developed to combat the various micro-organisms that could invade the host, the neutrophil forms the first line of defence against rapidly dividing bacteria and fungi. However, as humans age they become more susceptible to infection with these microbes and this has been ascribed to a decline in immune status, termed immune senescence. Here we summarize the literature specifically concerning the attenuation of neutrophil function with age and the possible mechanisms underlying their reduced response to infectious agents.

Aging↗

PubMed1999

Refinement of the chromosome 5p locus for familial calcium pyrophosphate dihydrate deposition disease.

Familial calcium pyrophosphate dihydrate deposition disease (CPPDD) is a disease of articular cartilage that is radiographically characterized by chondrocalcinosis due to the deposition of calcium-containing crystals in affected joints. We have documented the disease in an Argentinean kindred of northern Italian ancestry and in a French kindred from the Alsace region. Both families presented with a common phenotype including early age at onset and deposition of crystals of calcium pyrophosphate dihydrate in a similar pattern of affected joints. Affected family members were karyotypically normal. Linkage to the short arm of chromosome 5 was observed, consistent with a previous report of linkage of the CPPDD phenotype in a large British kindred to the 5p15 region. However, recombinants in the Argentinean kindred have enabled us to designate a region<1 cM in length between the markers D5S416 and D5S2114 as the CPPDD locus.

Calcium Pyrophosphate↗

PubMed1998

MAFA-L, an ITIM-containing receptor encoded by the human NK cell gene complex and expressed by basophils and NK cells.

The natural killer cell gene complex on human chromosome 12p12-13 encodes several C-type lectin receptor genes expressed by NK cells and other hematopoietic cells. We have identified a novel receptor gene in this region encoding a putative type II transmembrane glycoprotein. The product is 54% identical to the rat mast cell function-associated antigen (MAFA), which inhibits mast cell activation by IgE. The human MAFA-like receptor (MAFA-L) and the rat MAFA protein are expressed by basophils and both have an immunoreceptor tyrosine-based inhibitory motif in the cytoplasmic tail, consistent with an inhibitory role in basophil activation. Unlike rat MAFA, expression of the MAFA-L gene is not limited to mast cells and basophils. In common with other genes in the NK cell gene complex MAFA-L is also expressed by natural killer cells as well as the monocyte-like cell-line U937. Expression in NK cells is restricted to peripheral blood NK cells, decidual NK cells do not express MAFA-L. While MAFA-L and rat MAFA might have a similar role in basophils, the expression of MAFA-L in other cell types implies additional functions for this molecule. The presence of the MAFA-L gene in the human NK cell complex indicates that this locus encodes C-type lectin receptors expressed by a variety of cells important in host defense.

Amino Acid Sequence↗

PubMed1997

A linkage study across the T cell receptor A and T cell receptor B loci in families with rheumatoid arthritis.

OBJECTIVE: To examine whether the T cell receptor (TCR) A or TCRB loci exhibit linkage with disease in multiplex rheumatoid arthritis (RA) families. METHODS: A linkage study was performed in 184 RA families from the UK Arthritis and Rheumatism Council Repository, each containing at least 1 affected sibpair. The microsatellites D14S50, TCRA, and D14S64 spanning the TCRA locus and D7S509, Vbeta6.7, and D7S688 spanning the TCRB locus were used as DNA markers. The subjects were genotyped using a semiautomated polymerase chain reaction-based method. Two-point and multipoint linkage analyses were performed. RESULTS: Nonparametric single-marker likelihood odds (LOD) scores were 0.49 (P = 0.07) for D14S50, 0.65 (P = 0.04) for TCRA, 0.07 (P = 0.29) for D14S64, 0.01 (P = 0.43) for D7S509, 0.0 (P = 0.50) for Vbeta6.7, and 0.0 (P = 0.50) for D7S688. By multipoint analysis, there was no evidence of linkage at TCRB (LOD score 0), and the maximum LOD score at the TCRA locus was 0.37 (at D14S50). The presence of a susceptibility locus (LOD score < -2.0) was excluded, with lambda > or = 1.8 at TCRA and > or = 1.4 at TCRB. CONCLUSION: These linkage studies provide no significant evidence of a major germline-encoded TCRA or TCRB component of susceptibility to RA.

Alleles↗

PubMed1997

Genetic mapping of susceptibility loci in the genes involved in rheumatoid arthritis.

Eighty-nine multicase rheumatoid arthritis families, each containing at least one affected sib pair, have been studied for evidence of genetic linkage to a panel of 315 microsatellite DNA markers. The families were located through the UK national data repository of the Arthritis and Rheumatism Council. Microsatellites were genotyped by semiautomated technology using Applied Biosystems sequencers (ABI 373). Using the SIBPAIR statistical package, linkage to HLA was confirmed (p < 0.0003). Several possible linkages outside HLA were noted, including at least one (p < 0.004) that merits further investigation.

Arthritis, Rheumatoid↗

PubMed1996

Constitutive expression of prostaglandin endoperoxide G/H synthetase (PGHS)-2 but not PGHS-1 in hum an tracheal epithelial cells in vitro.

Primary cultures of human tracheal epithelial (HTE) cells cultured in vitro, in defined serum-free media, express prostaglandin endoperoxide G/H synthase (PGHS) activity and produce prostaglandin E2 (PGE2). In contrast to every other cell type studied to date, HTE cells appear to constitutively express PGHS-2, the 'inducible' form of the enzyme, while expressing little or no PGHS-1, the 'housekeeping' isoenzyme in vitro. Prostaglandin synthesis in HTE cells was reduced by a selective PGHS-2 inhibitor, N-[2-cyclohexyloyl-4-nitrophenyl] methane-sulfonamide (NS398), with an IC50 of approximately 1 microM. Immunoblotting and immunoprecipitation of enzymatic activity with isozyme-specific antisera revealed only the PGHS-2 isoform. Full length human cDNA probes detected only PGHS-2 message in Northern blots. Neither PGHS-2 activity nor mRNA levels were dependent on, nor stimulated by peptide growth factors present in the defined serum-free growth medium, or by serum. Prolonged maintenance in the absence of retinoic acid, however, lead to a decline in PGHS activity. Phorbol-myristate acetate (PMA) induced PGHS-2 activity and mRNA and neither PMA-induced, nor constitutive PGHS-2 expression was suppressed by corticosteroids. Actinomycin D-treatment for six hours reduced the PGHS-2 activity and mRNA to only 50% that of untreated cells, suggesting that PGHS-2 mRNA is extremely stable in these cells. HTE cells, at least in vitro, appear unique among prostaglandin-producing cells in that they express PGHS-2, constitutively, independent of regulation by growth factors, serum, or corticosteroids and fail to express PGHS-1 under any culture condition studied.

Adrenal Cortex Hormones↗

PubMed1995

Repeated sequences isolated from Bordetella pertussis induce DNA rearrangements and deletions at high frequency.

Two repeated sequences (RS) from Bordetella pertussis were cloned in Escherichia coli and sequenced. The RS, called RSBP1 and RSBP3, are highly homologous to other B. pertussis RS. The recombinant plasmids containing RSBP1 and RSBP3 or transposon-like structures of these elements were not stable but segregated plasmids with deletions or rearranged DNA. RS of B. pertussis seem to be able to stimulate both intra- and inter-genomic RecA-independent recombination events. In at least one case, the observed deletion had occurred precisely between the RS terminus and a site with sequence homology to the terminus. The high frequency rearrangements associated with the RS imply that the RS are transposable elements.

Base Sequence↗

PubMed1995

Specific DNA binding by different classes of human p53 mutants.

The p53 protein is a multifunctional transcription factor which orchestrates cellular responses to DNA damage, so helping to conserve genomic stability. It may also regulate genes involved in intercellular signalling, such as thrombospondin, a negative regulator of angiogenesis and metastatic spread. Activation of p53 target genes requires sequence-specific DNA binding, a function which maps to the central core of the protein. Missense point mutations within this domain inactivate p53 tumour suppressor function and involve either (i) DNA contact residues, or (ii) residues important for conformational structure. Using in vitro techniques we have analysed seven DNA contact mutants and 17 structural mutants known to occur in cancer. We show that DNA contact mutants can be carried into specific DNA interaction when co-expressed with wild type protein. For structural mutants, 9/17 retained DNA binding capacity and, with one exception, DNA binding correlated with conformational flexibility of the mutant protein. The exception was Asp281, which appeared essential for DNA interaction, probably due to its ability to form salt bridges with DNA contact residues Arg273 and Arg280. We suggest that different classes of p53 mutant may prove amenable to different strategies for restoration of wild type tumour suppressor function as means of anti-cancer therapy.

Amino Acid Sequence↗

PubMed1995

Temperature sensitivity for conformation is an intrinsic property of wild-type p53.

The tumour-suppressor protein p53 is a metal-binding transcription factor with sequence-specific DNA-binding capacity. In cancer, mutation of p53 disrupts protein conformation with consequent loss of DNA binding and associated tumour-suppressor function. In vitro, the conformation and DNA-binding activity of wild-type p53 are subject to redox modulation and are abrogated by exposure to metal chelators. In the present study, we have used the chelator 1, 10-phenanthroline (OP) to probe the effect of temperature on the conformational stability of p53 translated in vitro. Whereas low temperature (30 degrees C) stabilised wild-type p53 conformation and protected against chelation, high temperature (41 degrees C) promoted destabilisation and enhanced chelation, indicating that temperature influences the folding of wild-type p53. Destabilisation of p53 tertiary structure induced protein aggregation through hydrophobic interactions, consistent with the notion that wild-type p53 contains a hydrophobic core which may become exposed by metal chelation. These results indicate that temperature sensitivity for conformation is an intrinsic property of wild-type p53 and suggests that small changes in temperature may directly affect p53 function.

3T3 Cells↗

PubMed1995

Linkage of the gene that encodes the alpha 1 chain of type V collagen (COL5A1) to type II Ehlers-Danlos syndrome (EDS II).

Ehlers-Danlos syndrome (EDS) is a group of heritable disorders of connective tissue with skin, ligaments and blood vessels being the main sites affected. The commonest variant (EDS II) exhibits an autosomal dominant mode of inheritance and is characterized by joint hypermobility, cigarette paper scars, lax skin and excessive bruising. As yet no gene has been linked to EDS II, nor has linkage been established to a specific region of the genome. However, several candidate genes encoding proteins of the extracellular matrix have been excluded. Using an intragenic simple sequence repeat polymorphism, we report linkage of the COL5A1 gene, which encodes the alpha 1(V) chain of type V collagen, to EDS II. A maximum LOD score (Zmax) for linkage of 8.3 at theta = 0.00 was generated for a single large pedigree.

Chromosome Mapping↗

PubMed1994

Increased salt concentration reversibly destabilizes p53 quaternary structure and sequence-specific DNA binding.

Growth suppression by p53 correlates with sequence-specific DNA binding and is determined by tertiary and quaternary protein structures. Exposure to 300 mM NaCl did not affect p53 tertiary structure, but dissociated high-molecular-mass complexes with concomitant loss of specific DNA binding. Both effects were reversible. We conclude that high salt can reversibly destabilize the quaternary structure of p53 that is most efficient for sequence-specific DNA binding.

Animals↗

PubMed1993

Isolation of a phospholipid-free protein shell of bacteriophage PRD1, an Escherichia coli virus with an internal membrane.

PRD1 is a double-stranded DNA virus infecting Escherichia coli and Salmonella typhimurium. It has an icosahedral outer protein capsid which encloses the viral membrane, inside of which resides the phage genome. In this investigation we demonstrate the detergent resistance of the intact virus particles. The membrane of empty DNA-free particles, however, is very sensitive to detergent action. We assume that their sensitivity is due to the access of detergents through a portal structure to the virus interior. Using the anionic detergent sodium dodecyl sulfate, it is possible to obtain a shell structure composed of the major coat protein P3 alone. The treatment of empty particles with the milder nonionic detergents n-octyl beta-D-glucopyranoside and Triton X-100 yielded P3 particles which retained the membrane-associated proteins P7 and P11. Deoxycholic acid treatment yielded shells of intermediate composition between those obtained with the nonionic detergents and sodium dodecyl sulfate.

Capsid↗

PubMed1993

[Nucleotide sequence and properties of a transposon-like structure cloned from a Bordetella pertussis chromosome].

The 2.3 kb BamHI-EcoRI subclone has been isolated and sequenced from the 15 kb BamHI chromosomal fragment of Bordetella pertussis comprising also the vir gene. The sequence contained one copy of a transposon-like structure, very similar to the RSs of B. pertussis recently characterized, the unique sequence of B. pertussis chromosomal DNA and an inverted sequence complementary to 402 bp of 3' end of the B. pertussis RS element. The fragment of plasmid pUC4K containing the gene for kanamycin resistance (Km) was integrated in the XhoI site of the unique portion of the transposon-like structure of plasmid DNA (Ap(r), Km(r)). The clones in amount of 2% tested had the Ap-S phenotype. The recombinant plasmid from the Ap(s) phenotype clones lost one of the repeats and a portion of the gene bla as a result of deletion. The conclusion is drawn that RSs of B. pertussis stimulate the formation of deletions.

Ampicillin Resistance↗

PubMed1992

The class 1 outer membrane protein of Neisseria meningitidis produced in Bacillus subtilis can give rise to protective immunity.

The class 1 outer membrane protein of Neisseria meningitidis B:15:P1.7,16 was expressed in Bacillus subtilis in high yield as intracellular aggregates. These were easy to isolate and the protein (called BacP1) could be solubilized under denaturing conditions. Sera of mice immunized with thus-solubilized BacP1 contained high titres of antibodies that reacted with the class 1 protein of the meningococcal envelope in immunoblots but did not react with native meningococcal envelope in enzyme immunoassays (EIA) or with intact meningococci in bactericidal assays. However, when the BacP1 protein was complexed with heterologous (Salmonella) lipopolysaccharide, the ensuing sera reacted with meningococcal envelope preparations in both EIA and immunoblots, showed subtype-specific bactericidal activity, and were protective in an infant rat meningitis model.

Amino Acid Sequence↗

PubMed1991

High level production of Escherichia coli outer membrane proteins OmpA and OmpF intracellularly in Bacillus subtilis.

A high yield of Escherichia coli outer membrane proteins OmpA (about 200 mg/l) and OmpF (about 100 mg/l) was obtained in Bacillus subtilis when produced intracellularly. The yield was more than 100-fold higher than the yield of these proteins by a similar vector containing the complete signal sequence of alpha-amylase of B. amyloliquefaciens. Both proteins isolated after breakage of the B. subtilis cells by low-speed centrifugation were about 70% pure and could be solubilized by Sarkosyl, SDS and guanidine hydrochloride.

Amino Acid Sequence↗