Biomedical subjects

B Neelam

Publications and source records attributed to B Neelam.

6 recordsLinked to original sources

PubMed2001

The sequence of the human genome.

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Algorithms↗

PubMed2000

Palladium(II) complexes of NS donor ligandsderived from S-methyl-dithiocarbazate, S-benzyldithiocarbazateand thiosemicarbazide as antiamoebic agents.

Synthesis of palladium(II) complexes of the type [PdLCl(2)] (where L = Schiff bases derived from 2-acetylpyridine and S-methyldithiocarbazate, S-benzyldithiocarbazate or thiosemicarbazide) have been isolated by the reaction of [Pd(DMSO)(2)C1(2)] and respective ligands. The complexes have been characterized by elemental analyses, IR, 1H-NMR, electronic spectra and thermogravimetric analysis. It is concluded that the thionic sulphur and the azomethine nitrogen atoms of the ligands are bonded to the metal ion. Assessment of antiamoebic activity against Entamoeba histolytica (strain HK-9) was done by using a microdilution method. [Pd(2-Acpy-SMDT)C1(2)] and Pd(2-Acpy-SBDT)C1(2)] have shown greater activity, whereas [Pd(2-Acpy-TSC)C1(2)] showed similar activity as metronidazole in vitro.

Amebicides↗

PubMed1999

VacA seropositivity is not associated with the development of gastric cancer in a Japanese population.

OBJECTIVES: Infection with Helicobacter pylori strains producing vacuolating cytotoxin (VacA) is associated with enhanced gastric mucosal damage and the development of gastric mucosal atrophy. The aim of this study was to investigate whether VacA seropositivity is associated with increasing risk of gastric cancer in Japanese populations which have much higher incidence of gastric cancer than Western populations. METHODS: Serum sample was collected from 81 patients with gastric cancer and 81 sex- and age-matched endoscopically evaluated control subjects. Histologically, 62 cancers were of the intestinal type and 76 were early gastric cancer. H. pylori and VacA IgG antibodies were assayed by Western blotting using Chiron Diagnostics' Recombinant Immunoblot Assay (RIBAa). RESULTS: VacA seropositivity was 68% (55/81) in patients with gastric cancer and 70% (57/81) in controls. The odds ratio for the risk of gastric cancer in VacA seropositives was 0.89 (95% CI 0.46-1.74). In H. pylori seropositive patients and their control subjects (matched H. pylori-positive controls), VacA seropositivity was the same 80.6% (50/62). The odds ratio for the risk of gastric cancer in H. pylori-positive patients if VacA seropositive was 1.00 (95% CI 0.41-2.44). The mean relative intensity of VacA antibody titre was 3.01+/-0.18 in the 55 VacA seropositive cancer patients and 3.09+/-0.17 in the 57 VacA seropositive control subjects (difference not significant). CONCLUSION: These results suggest that VacA seropositivity is not associated with increasing risk of gastric cancer in Japanese populations.

Antibodies, Bacterial↗

PubMed1999

Multiple genes in the left half of the cag pathogenicity island of Helicobacter pylori are required for tyrosine kinase-dependent transcription of interleukin-8 in gastric epithelial cells.

Helicobacter pylori strains that contain the cag pathogenicity island (PAI) elicit increased synthesis of gastric C-X-C chemokines, promote neutrophilic infiltration into the gastric epithelium, and stimulate the synthesis of interleukin-8 (IL-8) in cultured gastric epithelial cells. To investigate the effects of cag PAI genes on the transcription of the IL-8 gene, the Kato-3 gastric epithelial cell line was stably transfected with plasmid DNA containing the IL-8 gene promoter fused to a luciferase reporter gene. The resulting reporter cell line, L5F11, was used to monitor the effects of infection in cell culture by H. pylori 26695 and isogenic derivatives with null mutations in genes in the cag PAI on transcription of the IL-8 gene. We found that null mutations in eight open reading frames, including homologs of the Agrobacterium virB9, virB10, and virB11 genes, in the left half of the cag PAI abrogated the induction of IL-8 gene transcription. Further studies with the L5F11 cell line showed that IL-8 gene transcription induced by H. pylori was blocked by the protein tyrosine kinase inhibitor herbimycin A but not by the protein kinase C inhibitor calphostin C or by the protein kinase G inhibitor KT5823. IL-8 gene transcription in L5F11 cells could also be induced by the cytokine tumor necrosis factor alpha (TNF-alpha) without exposure to H. pylori. This TNF-alpha-induced IL-8 transcription was inhibited by the protein kinase A inhibitor H7, which had no significant effect on H. pylori-induced IL-8 transcription. These studies show that multiple genes in the left half of the cag PAI are essential for the transcription of the IL-8 gene in gastric epithelial cells and that this depends on protein tyrosine kinase activation.

1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine↗

PubMed1998

Structure-function studies of ligand-induced epidermal growth factor receptor dimerization.

We present a novel 96-well assay which we have applied to a structure-function study of epidermal growth factor receptor dimerization. The basis of the assay lies in the increased probability of EGFRs being captured as dimers by a bivalent antibody when they are immobilized in the presence of a cognate ligand. Once immobilized, the antibody acts as a tether, retaining the receptor in its dimeric state with a resultant 5-7-fold increase in binding of a radiolabeled ligand probe. When the assay was applied to members of the EGF ligand family, murine EGF, transforming growth factor alpha, and heparin-binding EGF-like growth factor were comparable with human EGF (EC50 = 2nM); betacellulin, which has a broader receptor specificity, was slightly less effective. In contrast, amphiregulin (AR1-84), which has a truncated C-tail and lacks a conserved leucine residue, was ineffective unless used at >1 microM. We further probed the involvement of the C-tail and the conserved leucine residue in receptor dimerization by comparing the activities of two genetically modified EGFs (the chimera mEGF/TGFalpha44-50 and the EGF point mutant L47A) and a C-terminally extended form of AR (AR1-90) with those of two other unrelated EGF mutants (I23T and L15A). The potency of these ligands was in the order EGF > I23T > mEGF/TGFalpha44-50 > L47A = L15A >> AR1-90 > AR1-84. Although AR was much worse than predicted from its affinity, this defect could be partially rectified by co-localization of the immobilizing antibody with heparin. Thus, it seems likely that AR cannot dimerize the EGFR unless other accessory molecules are present to stabilize its functional association with the EGFR.

Cell Line↗

PubMed1993

The effect of iron limitation on the growth of Aeromonas salmonicida.

The effects of the iron-chelating agents ethylenediamine dihydroxyphenylacetic acid (EDDA), 2,2'-dipyridyl (Dipy) and 8-hydroxyquinoline (8HQ) on the growth of Aeromonas salmonicida were examined. In these studies, EDDA caused a small decrease in growth, whereas Dipy and 8HQ reduced cell growth by 50 and 90%, respectively. The extracellular products contained a greater proportion of the major protease (70 kD) when cells were grown in the presence of the chelating agents. Analysis of the outer membrane proteins showed that the chelating agents caused a marked increase in the proportion of proteins in the 70-90 kD range. The effects of Dipy were compared for a number of strains of A. salmonicida.

2,2'-Dipyridyl↗