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J Spencer

Publications and source records attributed to J Spencer.

At least 91 records · Page 5Linked to original sources
PubMed1998

The crystal structure of the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia at 1.7 A resolution.

The structure of the L1 metallo-beta-lactamase from the opportunistic pathogen Stenotrophomonas maltophilia has been determined at 1.7 A resolution by the multiwavelength anomalous dispersion (MAD) approach exploiting both the intrinsic binuclear zinc centre and incorporated selenomethionine residues. L1 is unique amongst all known beta-lactamases in that it exists as a tetramer. The protein exhibits the alphabeta/betaalpha fold found only in the metallo-beta-lactamases and displays several unique features not previously observed in these enzymes. These include a disulphide bridge and two substantially elongated loops connected to the active site of the enzyme. Two closely spaced zinc ions are bound at the active site with tetrahedral (Zn1) and trigonal bipyramidal (Zn2) co-ordination, respectively; these are bridged by a water molecule which we propose acts as the nucleophile in the hydrolytic reaction. Ligation of the second zinc ion involves both residues and geometry which have not been previously observed in the metallo-beta-lactamases. Simulated binding of the substrates ampicillin, ceftazidime and imipenem suggests that the substrate is able to bind to the enzyme in a variety of different conformations whose common features are direct interactions of the beta-lactam carbonyl oxygen and nitrogen with the zinc ions and of the beta-lactam carboxylate with Ser187. We describe a catalytic mechanism whose principal features are a nucleophilic attack of the bridging water on the beta-lactam carbonyl carbon, electrostatic stabilisation of a negatively charged tetrahedral transition state and protonation of the beta-lactam nitrogen by a second water molecule co-ordinated by Zn2. Further, we propose that direct metal:substrate interactions provide a substantial contribution to substrate binding and that this may explain the lack of specificity which is a feature of this class of enzyme.

Bacillus↗
PubMed1998

Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome.

Single-nucleotide polymorphisms (SNPs) are the most frequent type of variation in the human genome, and they provide powerful tools for a variety of medical genetic studies. In a large-scale survey for SNPs, 2.3 megabases of human genomic DNA was examined by a combination of gel-based sequencing and high-density variation-detection DNA chips. A total of 3241 candidate SNPs were identified. A genetic map was constructed showing the location of 2227 of these SNPs. Prototype genotyping chips were developed that allow simultaneous genotyping of 500 SNPs. The results provide a characterization of human diversity at the nucleotide level and demonstrate the feasibility of large-scale identification of human SNPs.

Algorithms↗
PubMed1998

Expression of membrane-associated proteins by strains of enteroaggregative Escherichia coli.

Certain strains of enteroaggregative Escherichia coli express an outer membrane-associated protein, involved with the adhesion of these bacteria to HEp-2 cells. Strains of enteroaggregative E. coli hybridising with DNA probes for aggregative adhesion, diffuse adhesion and aggregative adhesion fimbriac II expressed an outer membrane-associated protein of 18 kDa regulated by magnesium ions. Strains hybridising with the aggregative adhesion probe only expressed a 20-kDa outer membrane-associated protein regulated by calcium and magnesium. The present study describes two populations of enteroaggregative E. coli which appear to adhere to HEp-2 cells by expressing antigenically distinct, negatively charged membrane-associated proteins.

Animals↗
PubMed1998

Base-specific sequences that bias somatic hypermutation deduced by analysis of out-of-frame human IgVH genes.

Somatic hypermutation introduces mutations into IgV genes during affinity maturation of the B cell response. Mutations are introduced nonrandomly, and are generally targeted to the complementarity determining regions (CDRs). Subsequent selection against mutations that result in lower affinity or nonfunctional Ig increases the relative number of mutations in the CDRs. Investigation of somatic hypermutation is hampered by the effects of selection. We have avoided this by studying out-of-frame human IgVH4.21 and 251 genes, which, being unused alleles, are unselected. By comparison of the frequency of A, C, G, and T nucleotides at positions -3 to +3 around mutated or unmutated A, C, and G nucleotides, we have identified flanking sequences that most commonly surround mutated bases. Distinct trends in flanking sequences that were unique for each base were observed. Statistically significant trends that were common to both IgVH4.21 and 251 were used to deduce motifs that bias somatic hypermutation. The motifs deduced from this data, with targeted bases in regular type, are AANB, WDCH, and DGHD (where W = A/T, B = C/G/T, D = A/G/T, H = A/C/T, and N = any base). Mutations from C and G in two further groups of out-of-frame human IgVH genes, not used in the deduction of the motifs, occurred significantly within the motifs for C and G. The proposed target sequence for G is within the reverse complement of the target sequence for C, suggesting that the hypermutation mechanism may target only G or C. The mutation in the complementary base would appear on the other strand following replication.

Adenine↗
PubMed1998

Malignant melanoma metastatic to the ovary: presentation and radiological characteristics.

Cutaneous melanomas rarely metastasize to the ovary; however, we have recently encountered three cases which have proved a diagnostic dilemma. All presented with a pelvic mass and a past history of cutaneous melanoma but both ultrasound examination and CT scanning proved inconclusive and neither was able to accurately characterize the lesions. Magnetic resonance imaging (MRI) was able to demonstrate the presence of melanin in one of the ovarian lesions as peripheral high signal change on T1-weighted images. The two lesions without melanin failed to show this feature. MRI may therefore be useful in the diagnosis of ovarian melanoma but only if melanin is present.

Adult↗
PubMed1998

Histamine, xanthine oxidase generated oxygen-derived free radicals and Helicobacter pylori in gastroduodenal inflammation and ulceration.

OBJECTIVE: The relationship between Helicobacter pylori (H. pylori), xanthine oxidase (XO)-induced oxygen derived free radicals (ODFR) and histamine in the induction of human gastroduodenal disorders was investigated. PATIENTS AND METHODS: Histamine concentration, XO and xanthine dehydrogenase (XD) activities were measured in endoscopically obtained biopsies from 66 symptomatic patients. RESULTS: H. pylori infection was associated with lower oxyntic and duodenal histamine in 'normal' controls (group N) (p < 0.002 and p < 0.05, respectively). Patients with gastroduodenal disease tended to have reduced mucosal concentration of histamine, but comparing H. pylori positive and negative patients, infection did not lead to a further fall in histamine concentration. H. pylori positive duodenal ulcer (DU) patients tended to have higher XO activity than group N (p = 0.051) and had a significantly lowered activity of XD, the precursor of XO (p' < 0.05). Histamine concentration at the ulcer-edge was lower while XO activity was higher than in the distant normal mucosa (p < 0.05, respectively). Gastritis (group GL) with H. pylori also had lower XD than H. pylori positive group N (p' < 0.025) but no corresponding rise in XO activity. In group N, duodenal mucosal histamine and XD activity were inversely related (Rs = -0.51, p < 0.025). CONCLUSIONS: These findings support the hypothesis that histamine, xanthine oxidase related ODFR, and H. pylori may be closely associated in the manifestations of chronic duodenal ulcer.

Adult↗
PubMed1998

Analysis of immunoglobulin genes in splenic marginal zone lymphoma suggests ongoing mutation.

Splenic marginal zone lymphoma (SMZL) is a low-grade primary splenic B cell lymphoma, originally thought to be related to splenic marginal zone B cells. Later studies showed that SMZL sometimes may be accompanied by villous lymphocytes in the peripheral blood, a condition previously characterized as splenic lymphoma with villous lymphocytes (SLVL). The relationship between SMZL and splenic marginal zone B cells has recently been called into question. We report four further cases of SMZL, two of which were associated with villous lymphocytes in the peripheral blood. In addition to immunophenotypical analysis, we have studied the IgV(H) genes in each case, because the extent and patterns of their mutation can indicate the normal B cell counterpart of lymphomas. The IgV(H) genes in the four cases of SMZL studied are mutated, which is consistent with their origin from postfollicular marginal zone B cells. Evidence of ongoing mutation was also observed. This contrasts with a study showing that blood-borne tumor cells in SLVL show no sign of ongoing mutation. It is possible that the ongoing mutations in the cases studied here are acquired in a splenic microenvironment, such as that found in the follicle center.

Aged↗
PubMed1998

Noninvasive identification of materials inside USP vials with Raman spectroscopy and a Raman spectral library.

A commercial dispersive Raman spectrometer operating at 785 nm with a CCD detector was used to acquire spectra of USP reference materials inside amber USP vials. The laser and collection beams were directed through the bottom of the vials, resulting in a 60% loss of signal. The Raman shift was calibrated with a 4-acetamidophenol standard, and spectral response was corrected with a luminescent standard. After these corrections, the Raman spectra obtained inside the USP vial and on open powders differed by less than 5%. A spectral library of 309 reference materials was constructed, with spectral acquisition times ranging from 1 to 60 s. Of these, 8% had significant fluorescent background but observable Raman features, while 3% showed only fluorescence. A blind test of 26 unknowns revealed the accuracy of the library search to be 88-96%, depending on search algorithm, and 100% if operator discretion was permitted. The tolerance of the library search to degraded signal-to-noise ratio, resolution, and Raman shift accuracy were tested, and the search was very robust. The results demonstrate that Raman spectroscopy provides a rapid, noninvasive technique for compound identification.

Drug Packaging↗
PubMed1998

Histamine and tissue fibrinolytic activity in duodenal ulcer disease.

Patients with duodenal ulcer have lower gastroduodenal mucosal histamine and a reduced tissue fibrinolysis at the ulcer edge. In the duodenal mucosa fibrinolysis is regulated by the tissue-type and urokinase-type plasminogen activators; and inhibitors type 1 and type 2. Trends across ordered groups leading from mucosa of nonulcer control subjects, "normal" mucosa of ulcer patients, to ulcer edge were found in tissue-type plasminogen activator concentration, histamine concentration, and histamine methyltransferase activity. Concentrations of tissue-type activator, inhibitor type 1, and histamine were significantly lower at ulcer edge than at normal. An inverse correlation was found between histamine methyltransferase and plasminogen activator activities, methyltransferase and tissue-type activator, and methyltransferase and histamine. These results support the hypothesis that in active ulceration, reduction in tissue fibrinolytic activity is closely associated with enhanced release and metabolism of histamine.

Duodenal Ulcer↗
PubMed1998

Sri Lanka. Political violence and ethnic conflict.

In recent years, Sri Lanka has experienced 2 violent rebellions in which youths have played a prominent role, 1 in the majority Sinhala community and 1 in the minority Tamil community. The former was crushed, but the latter remains ongoing, with the Liberation Tigers of Tamil Eelam, who claim to represent the Tamil minority, battling the Sinhala-dominated government. Prospects for peace in the short- and medium term appear poor. These events have generated an impressive body of interdisciplinary interpretation, but several important topics have received relatively little attention. Most ongoing research is being carried out by anthropologists, historians, and political scientists, but psychological insights would offer important complementary perspectives.

Civil Disorders↗
PubMed1998

Changes to mucins in uninvolved mucosa and at the tumour site in gastric adenocarcinoma of intestinal type.

1. Mucin histochemistry is markedly altered in the stomach in intestinal-type adenocarcinoma. To increase understanding of these changes we have examined the content and distribution of carbohydrate in mucus glycopolypeptides isolated from non-malignant antrum, and from the uninvolved gastric mucosa and tumour site of patients with this disease. 2. The content of carbohydrate declined by 12.6% (P = 0.02) in mucus glycopolypeptides from uninvolved gastric mucosa when compared with those from non-malignant antrum, and by a further 25.4% (P < 0.001) in mucus glycopolypeptides from the tumour site. The first of these changes was accompanied by a significant decrease in the number of carbohydrate chains/1000 amino acid residues, and a significant increase in the number of monosaccharide units in each carbohydrate chain. The second of these changes was accompanied by significant decreases in both the number of carbohydrate chains/1000 amino acid residues, and in the number of monosaccharide units in each carbohydrate chain. 3. The number of sulphated monosaccharide units/100 carbohydrate chains increased from a mean of 7.2 in mucus glycopolypeptides from non-malignant antrum to a mean of 27.2 (P < 0.001) in preparations from uninvolved gastric mucosa and 22.7 (P < 0.001) in preparations from the tumour site. 4. Evidence is presented that these structural changes to mucus glycopolypeptides from the malignant stomach are due to an abnormal mucin biosynthesis by metaplastic goblet cells and/or immature gastric-type mucous cells within the uninvolved mucosa, and immature mucous cells at the tumour site.

ABO Blood-Group System↗
PubMed1998

Strong intrinsic biases towards mutation and conservation of bases in human IgVH genes during somatic hypermutation prevent statistical analysis of antigen selection.

Immunoglobulin V region genes acquire point mutations during affinity maturation of the T-cell-dependent B-cell response. It has been proposed that both selection by antigen and characteristics of the DNA sequence are involved in determining the distribution of mutations along the genes. There is a tendency for replacement mutations to occur in the complementarity-determining regions and for silent mutations to accumulate in the framework regions of used genes. By analysing a group of highly mutated human IgVH4-34 (VH4. 21) and family 5 genes derived from human gut-associated lymphoid tissues, which were out-of-frame between VH and JH (and therefore not used) we have investigated the distribution of mutations acquired in the absence of selection. We observed that these genes may show the statistical hallmarks of selected genes, suggesting that intrinsic biases alone may be enough to give the appearance of selection. These data suggest that analysis of the distribution of mutations in IgVH genes cannot be used reliably to state whether antigenic selection of the B-cell carrying the genes occurred. In-frame genes had more silent mutations than the out-of-frame genes and lacked stop codons. These characteristics were considered to be indicative of selection in the in-frame genes derived from human gut-associated lymphoid tissue.

Antibody Affinity↗