Structure of bacterial communities in diverse freshwater habitats

The structures and dynamics of bacterial communities from raw source water, groundwater, and drinking water before and after filtration were studied in four seasons of a year, with culture-independent methods. Genomic DNA from water samples was analyzed by the polymerase chain reaction?- denaturing gradient gel electrophoresis system and by cloning of the 16S rRNA gene. Water samples exhibited complex denaturing gradient gel electrophoresis genetic profiles composed of many bands, corresponding to a great variety of bacterial taxa. The bacterial communities of different seasons from the four sampling sites clustered into two major groups: (i) water before and after filtration, and (ii) source water and groundwater. Phylogenetic analyses of the clones from the autumn sampling revealed 13 phyla, 19 classes, and 155 operational taxonomic units. Of the clones, 66% showed less than 97% similarities to known bacterial species. Representatives of the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were found at all four sampling sites. Species belonging to the phylum Firmicutes were an important component of the microbial community in filtered water. Representatives of Enterobacteriaceae were not detected, indicating the absence of fecal pollution in the drinking water. Differences were found in the bacterial populations that were sampled from the same sites in different seasons. Each water habitat had a unique bacterial profile. Drinking water harbors diverse and dynamic microbial communities, part of which may be active and resilient to chlorine disinfection. This study provides, for the first time, basic data for uncultivable drinking water bacteria in Israel.     

Meiosis-activating sterol synthesis in rat preovulatory follicle: is it involved in resumption of meiosis?

Meiosis-activating sterol (MAS) was shown to overcome the inhibitory effect of hypoxanthine on spontaneous maturation of mouse oocytes and was suggested to mediate the stimulation of meiosis by gonadotropins. Follicular fluid (FF)-MAS is synthesized by cytochrome P450 lanosterol 14alpha-demethylase (LDM). Follicular LDM was preferentially localized in oocytes by immunohistochemistry. Using [3H]acetate or R-[5-3H]mevalonate as precursors as well as high-performance liquid chromatographic and thin-layer chromatographic separation, we have measured the concentrations of de novo-synthesized lanosterol, FF-MAS, and cholesterol in rat graafian follicles, cumulus-oocyte complexes (COCs), and denuded oocytes (DOs) treated with LH, AY-9944 (an inhibitor of Delta14-reductase, which was anticipated to increase FF-MAS levels by inhibiting its metabolism), or both after 8 h of culture. In follicles, both LH and AY-9944 increased the accumulation of FF-MAS as compared to controls. In COCs, AY-9944 caused a marked increase in FF-MAS, but we were unable to detect accumulation of FF-MAS in DOs. Neither the endogenous increases in FF-MAS accumulation nor the addition of FF-MAS to the culture medium could overcome the inhibition on resumption of meiosis by phosphodiesterase inhibitors. Compared to LH-induced resumption of meiosis in follicles, that induced by AY-9944 was much delayed. These results call into question any role of FF-MAS as an obligatory mediator of LH activity on germinal vesicle breakdown. The discrepancy between the positive staining for LDM in oocytes and our inability to detect de novo synthesized FF-MAS in DOs may relate to the sensitivity of the methodology employed and either the number of oocytes used or a deficiency in LDM synthetic activity in such oocytes. Further studies are required to confirm any of these alternatives.     

Semiparametric estimation of marginal hazard function from case-control family studies

Estimating marginal hazard function from the correlated failure time data arising from case-control family studies is complicated by noncohort study design and risk heterogeneity due to unmeasured, shared risk factors among the family members. Accounting for both factors in this article, we propose a two-stage estimation procedure. At the first stage, we estimate the dependence parameter in the distribution for the risk heterogeneity without obtaining the marginal distribution first or simultaneously. Assuming that the dependence parameter is known, at the second stage we estimate the marginal hazard function by iterating between estimation of the risk heterogeneity (frailty) for each family and maximization of the partial likelihood function with an offset to account for the risk heterogeneity. We also propose an iterative procedure to improve the efficiency of the dependence parameter estimate. The simulation study shows that both methods perform well under finite sample sizes. We illustrate the method with a case-control family study of early onset breast cancer.     

The splicing machinery is a genetic modifier of disease severity

Disease severity correlates with the level of correctly spliced RNA transcribed from genes carrying splicing mutations and with the ratio of alternatively spliced isoforms. Hence, a role for splicing regulation as a genetic modifier has been suggested. Here we discuss recent experiments that provide direct evidence that changes in the level of splicing factors modulate the splicing pattern of disease-associated genes. Importantly, modulation of the splicing pattern led to regulation of the protein function and modification of disease severity.     

Human combinatorial Fab library yielding specific and functional antibodies against the human fibroblast growth factor receptor 3

The human combinatorial antibody library Fab 1 (HuCAL-Fab 1) was generated by transferring the heavy and light chain variable regions from the previously constructed single-chain Fv library (Knappik, A., Ge, L., Honegger, A., Pack, P., Fischer, M., Wellnhofer, G., Hoess, A., W?lle, J., Plückthun, A., and Virnek?s, B. (2000) J. Mol. Biol. 296, 57-86), diversified in both complementarity-determining regions 3 into a novel Fab display vector, yielding 2.1 x 10(10) different antibody fragments. The modularity has been retained in the Fab display and screening plasmids, ensuring rapid conversion into various antibody formats as well as antibody optimization using prebuilt maturation cassettes. HuCAL-Fab 1 was challenged against the human fibroblast growth factor receptor 3, a potential therapeutic antibody target, against which, to the best of our knowledge, no functional antibodies could be generated so far. A unique screening mode was designed utilizing recombinant functional proteins and cell lines differentially expressing fibroblast growth factor receptor isoforms diversified in expression and receptor dependence. Specific Fab fragments with subnanomolar affinities were isolated by selection without any maturation steps as determined by fluorescence flow cytometry. Some of the selected Fab fragments completely inhibit target-mediated cell proliferation, rendering them the first monoclonal antibodies against fibroblast growth factor receptors having significant function blocking activity. This study validates HuCAL-Fab 1 as a valuable source for the generation of target-specific antibodies for therapeutic applications.     

Interactions of quinidine and lidocaine with rat brain and heart muscarinic receptors

We have studied the effect of quinidine and lidocaine on binding to rat brain and cardiac muscarinic receptors. Both drugs had a higher affinity to brain stem and cardiac receptors, as compared with cerebral cortex, coinciding with the distribution of high-affinity agonist binding sites in the above tissues. The effects of the drugs on muscarinic antagonist and agonist binding did not fit simple competition to one receptor site, suggesting either preferential binding to high affinity agonist binding sites, or allosteric interactions. Batrachotoxin, which opens voltage sensitive sodium channels, had an opposite effect on agonist binding. The possibility of allosteric interactions between the muscarinic receptors and a site analogous to the sodium channel is discussed.     

An ion-site interaction model for sodium currents in the giant axon

The time and voltage dependence of sodium currents in the Myxicola giant axon were examined as functions of the external sodium concentration. The results were incompatible with a model of free diffusion through a gated channel, but lent themselves to analysis in terms of a model involving a positive cooperative homotropic reaction in which Na⁺ interacts with two allosteric sites - a regulatory site and a transfer site - at the ‘sodium channel’. The time-dependent solution of the rate equations describing the kinetics of the transfer reaction was derived as an expression describing the sodium current as a function of time membrane potential and external sodium concentration. This function was used to test the validity of the model by its ability to predict the nerve excitability properties. The predicted i-v and i-t curves fitted the experimental results (p < 0.005 and p < 0.05, respectively). The computed parameters of these functions are consistent with other experimental results. The possibility of a noncooperative reaction was rejected.     

CFTR Haplotype Analysis Reveals Genetic Heterogeneity in the Etiology of Congenital Bilateral Aplasia of the Vas Deferens

Congenital bilateral aplasia of the vas deferens (CBAVD) was suggested to be a mild form of cystic fibrosis (CF). Mutation analysis of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in males with CBAVD revealed that in some males CBAVD is caused by two defective CFTR alleles. The genetic basis of CBAVD in the other males and its association with CF remained unclear. We undertook this study to test the hypothesis of commonality of CBAVD and CF by haplotype analysis, in the CFTR locus, of males suffering from CBAVD and of their families. According to the hypothesis of commonality of CBAVD and CF, two brothers with CBAVD are expected to carry the same two CFTR alleles, while their fertile brothers are expected to carry at least one different allele. Eleven families were studied, of which two families, with unidentified CFTR mutations, did not support this hypothesis. In these families two brothers with CBAVD inherited different CFTR alleles. Their fertile brothers inherited the same CFTR alleles as their brothers with CBAVD. These results provide evidence for genetic heterogeneity in CBAVD. Though in some families CBAVD is associated with two CFTR mutations, we suggest that in others it is caused by other mechanisms, such as mutations at other loci or homozygosity or heterozygosity for partially penetrant CFTR mutations.