Variability analysis of HIV-1 gp120 V3 region: IV. Distribution functions for intra- and inter-subtype amino acid hamming distances

Distribution functions for intra- and inter- HIV-1 V3-loop subtypes amino acid Hamming distances were calculated (850 V3-loop sequences from the Los Alamos HIV-1 Database (1996) were used). These functions have pronounced bell-like shape. Such shapes of the histograms for HIV-1 V3 intra- and inter-subtype distriutions are discussed to confirm the applicability of different hierarchical cluster procedures for HIV-1 V3 classification. Two-mode distribution for the subtype E could sertificate that this subtype includes two thinner taxons.     

New perspectives on the actions of sulphonylureas and hyperglycaemic sulphonamides on the pancreatic beta-cell

Sulphonylureas and the hyperglycaemic sulphonamide diazoxide are commonly employed in the therapy of non-insulin-dependent (Type 2) diabetes mellitus and insulinoma, respectively. Stimulatory effects of sulphonylureas on insulin secretion and the inhibitory action of diazoxide are thought to be primarily mediated through modulation of the activity of ATP-sensitive K+ channels (K(+)-ATP channels) in the beta-cell plasma membrane. Certain sulphonylureas are known to be internalised by the pancreatic B-cell. Recent studies suggest that these drugs and diazoxide can influence insulin secretion from electropermeabilized beta-cells in which K(+)-ATP channels and other plasma membrane ion channels are inoperative. This observation suggests that sulphonylureas and diazoxide interact with intracellular sites in the pancreatic B-cell which are directly involved in the regulation of the final stages of exocytosis.     

Morning hypercoagulability and hypofibrinolysis. Diurnal variations in circulating activated factor VII, prothrombin fragment F1+2, and plasmin-plasmin inhibitor complex

The role of percutaneous needle aspiration for therapy of uncomplicated, large amoebic liver abscess (ALA) is not defined. Twenty nine patients of ALA with a cavity larger than 5 cm were randomised to two groups: (i) metronidazole 800 mg tid for 10 days combined with needle aspiration (group A, n = 15) and (ii) metronidazole therapy alone (group B, n = 14). Clinical parameters, viz, fever, pain and abdominal tenderness were recorded daily and graded 0 to 3 (in order of increasing severity). A statistically significant benefit was demonstrated in group A for clinical parameters evaluated. Group A patients took less time to become afebrile from the grade 2 level as compared to group B (3.8 +/- 1.7 days and 5.6 +/- 2.2 days respectively; p < 0.05). Reduction in pain intensity and abdominal tenderness from grade 2 to 1 also occurred earlier in group A (0.7 +/- 0.7 days vs 2.9 +/- 0.9 days for pain, P < 0.001 and 1.7 +/- 0.8 days vs 2.9 +/- 1.2 days for abdominal tenderness, p < 0.001). The mean duration of hospitalization was significantly shorter in group A as compared to group B (5.8 +/- 0.8 days vs 7.4 +/- 1.5 days, p < 0.001). Improvement in haematological and biochemical variables was similar in both groups. We conclude that percutaneous therapeutic needle aspiration of uncomplicated, large ALA hastens clinical recovery.     

Location of type XV collagen in human tissues and its accumulation in the interstitial matrix of the fibrotic kidney

An antipeptide antibody was produced against the carboxyl-terminal noncollagenous domain of human type XV collagen and used to localize this recently described collagen in a number of human tissues. The most conspicuous findings were powerful staining of most of the capillaries and staining of the basement membrane (BM) zones of muscle cells. Not all of the BM zones were positive, however, as shown by the lack of staining in the developing fetal alveoli and some of the tubules in developing kidney. Nor was type XV collagen staining restricted to the BM zones, as some could be observed in the fibrillar collagen matrix of the papillary dermis and placental villi, for example. Interestingly, differences in the expression of type XV collagen could be observed during kidney development, and staining of fetal lung tissue suggested that changes in its expression may also occur during the formation of vascular structures. Another intriguing finding was pronounced renal interstitial type XV collagen staining in patients with kidney fibrosis due to different pathological processes. This suggests that the accumulation of type XV collagen may accompany fibrotic processes. Full-length human type XV collagen chains with an apparent molecular mass of approximately 200 kd were produced in insect cells using a baculovirus expression system. The fact that these had a markedly higher molecular mass than the 100- to 110-kd type XV collagen chains found in homogenates of heart and kidney tissue suggests either proteolytic processing during the synthesis of type XV collagen or an inability to solubilize complete molecules from tissues.     

Distribution of estramustine in the BT4C rat glioma model

When maintained under continuous selection with the folate inhibitor, methotrexate, cultured Aedes albopicfus mosquito cells amplify an 200 kb region of DNA containing the dihydrofolate reductase gene. To determine whether the amplicon contained additional coding regions, Southern blots of cosmid clones containing amplicon DNA were probed separately with reverse-transcribed mRNA from methotrexate-sensitive and methotrexate-resistant cells. Cosmid pWED118 contained five EcoRI fragments (A, B, C, F, G) ranging in size from 2 to 5 kb that hybridized with cDNA from resistant cells. Of these, fragments B and F also hybridized to probe representing mRNA from sensitive cells, and all but fragment G hybridized to repetitive DNA from wild-type cells. Fragment G, which appeared to encode a low copy number gene in wild-type cells that subsequently became part of the dihydrofolate reductase amplicon in methotrexate-resistant cells, hybridized strongly to a 7 kb band and more weakly to bands measuring 9 and 3 kb on Northern blots containing RNA from resistant cells. Fragment G contained a 1203 bp open reading frame, encoding 401 amino acids homologous to synaptic vesicle protein SV2, a member of a transmembrane transporter family expressed in neural and endocrine cells. The region of homology included the six N-terminal transmembrane domains, an internal cytoplasmic loop, a seventh transmembrane domain, and most of an intravesicular loop. This partial sequence, which appears to correspond to a truncated gene generated during formation of the dihydrofolate reductase amplicon, provides a useful basis for more extensive characterization of an important gene family that may be the target of novel insecticides.     

Screening of compounds interacting with HIV-1 proteinase using optical biosensor technology

A high-resolution optical biosensor assay for screening of low-molecular-weight compounds, using an immobilized protein target, has been developed. HIV-1 proteinase was immobilized on the sensor surface by direct amine coupling and a variety of inhibitors and noninteracting reference drugs were applied to the sensor surface in a continuous flow of buffer. The procedure did not require intrinsic reporter groups, substrates, inhibitors, or other ligands for detection. By using a reference protein, the signal could be corrected for the relatively large background signal caused by differences in dimethyl sulfoxide concentration between running and sample buffers. Substances binding with high affinity (Ki in nM range) required efficient regeneration of the sensor surface and washing of the injection system between sample cycles to get consistent results. Analysis was simplified by using report points, extracted during both association and dissociation phases, and a simple graphical display of data. The optimized assay could correctly distinguish HIV-1 inhibitors from other compounds in a randomized series, indicate differences in their interaction kinetics, and reveal artifacts due to nonspecific signals, incomplete regeneration, or carryover. The method is expected to be generally applicable to secondary screening of low-molecular-weight compound libraries with proteins as targets.     

Prevalence of hyperapobetalipoproteinemia and other lipoprotein phenotypes in men (aged < or = 50 years) and women (< or = 60 years) with coronary artery disease

The prevalence and clinical characteristics of hyperapobetalipoproteinemia (hyperapoB) and other phenotypes of dyslipoproteinemia were examined in 99 men (aged < or = 50 years) and 104 women (< or = 60 years) undergoing elective diagnostic coronary arteriography. HyperapoB was the most common phenotype (34%) associated with premature coronary artery disease (CAD). Only 20.2% of patients with CAD had a normal lipoprotein phenotype. The significant odds ratios for CAD were as follows: hypertriglyceridemic hyperapoB 17.45 (p < 0.0001), type IV 6.54 (p = 0.0001), type IIa 4.73 (p = 0.008), normotriglyceridemic hyperapoB 2.54 (p = 0.03) and type IIb 8.73 (p = 0.05). The strong association of hypertriglyceridemic hyperapoB with CAD reflected the multiplicative effect of increased low-density lipoprotein apolipoprotein B and endogenous hypertriglyceridemia, and was independent of the effects of age, sex, diabetes mellitus, systemic hypertension, body mass index and cigarette smoking. The ratio of apolipoprotein B to A-1 was better than those of low-density to high-density lipoprotein cholesterol and total to high-density lipoprotein cholesterol at discriminating dyslipidemic phenotypes from normal. Obesity was increased approximately 1.5 to two-fold in the hypertriglyceridemic phenotypes, diabetes was more prevalent in hypertriglyceridemic hyperapoB (6.8-fold; p < 0.001) and type IV (4.4-fold; p = 0.02), and hypertension was increased 1.5- to twofold in most dyslipidemic groups. The data indicate that hyperapoB and endogenous hypertriglyceridemia both contribute to the risk of premature CAD.     

Cluster analysis and display of genome-wide expression patterns

A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression. The output is displayed graphically, conveying the clustering and the underlying expression data simultaneously in a form intuitive for biologists. We have found in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function, and we find a similar tendency in human data. Thus patterns seen in genome-wide expression experiments can be interpreted as indications of the status of cellular processes. Also, coexpression of genes of known function with poorly characterized or novel genes may provide a simple means of gaining leads to the functions of many genes for which information is not available currently.