Determination of single-pore conductance from noise analysis. Influence of distribution in pore-amplitudes

For pores which can adopt only the open and closed states, the influence of the amplitude distribution of the single-pore conductance (γ, open state) on the covariance function is derived. It is shown that reliable mean values of γ (E(γ)) can be derived from noise analysis only if the variance in the amplitude distribution (σ_γ²) is known. In the past, σ_γ² was set always to zero, leading to an overestimation of E(γ). In the case of gramicidin-doped lipid bilayer membranes, this overestimation amounts to as much as 15% of the true value of E(γ).     

Validation of a novel noninvasive cardiac index of left ventricular contractility in patients

Although there are several excellent indexes of myocardial contractility, they require accurate measurement of pressure via left ventricular (LV) catheterization. Here we validate a novel noninvasive contractility index that is dependent only on lumen and wall volume of the LV chamber in patients with normal and compromised LV ejection fraction (LVEF). By analysis of the myocardial chamber as a thick-walled sphere, LV contractility index can be expressed as maximum rate of change of pressure-normalized stress (d sigma*/dt(max), where sigma* = sigma/P and sigma and P are circumferential stress and pressure, respectively). To validate this parameter, d sigma*/dt(max) was determined from contrast cine-ventriculography-assessed LV cavity and myocardial volumes and compared with LVEF, dP/dt(max), maximum active elastance (E(a,max)), and single-beat end-systolic elastance [E(es(SB))] in 30 patients undergoing clinically indicated LV catheterization. Patients with different tertiles of LVEF exhibit statistically significant differences in d sigma*/dt(max). There was a significant correlation between d sigma*/dt(max) and dP/dt(max) (d sigma*/dt(max) = 0.0075 dP/dt(max) - 4.70, r=0.88, P<0.01), E(a,max) (d sigma*/dt(max) = 1.20E(a,max) + 1.40, r=0.89, P<0.01), and E(es(SB)) [d sigma*/dt(max)=1.60 E(es(SB)) + 1.20, r=0.88, P<0.01]. In 30 additional individuals, we determined sensitivity of the parameter to changes in preload (intravenous saline infusion, n = 10 subjects), afterload (sublingual glyceryl trinitrate, n = 10 subjects), and increased contractility (intravenous dobutamine, n=10 patients). We confirmed that the index is not dependent on load but is sensitive to changes in contractility. In conclusion, d sigma*/dt(max) is equivalent to dP/dt(max), E(a,max), and E(es(SB)) as an index of myocardial contractility and appears to be load independent. In contrast to other measures of contractility, d sigma*/dt(max) can be assessed with noninvasive cardiac imaging and, thereby, should have more routine clinical applicability.     

Analytic computation of the expectation of the linkage disequilibrium coefficient r2

The squared correlation coefficient r(2) (sometimes denoted Delta(2)) is a measure of linkage disequilibrium that is widely used, but computing its expectation E[r(2)] in the population has remained an intriguing open problem. The expectation E[r(2)] is often approximated by the standard linkage deviation sigma(d)(2), which is a ratio of two expectations amenable to analytic computation. In this paper, a method of computing the population-wide E[r(2)] is introduced for a model with recurrent mutation, genetic drift and recombination. The approach is algebraic and is based on the diffusion process approximation. In the limit as the population-scaled recombination rate rho approaches infinity, it is shown rigorously that the asymptotic behavior of E[r(2)] is given by 1/rho+O(rho(-2)), which, incidentally, is the same as that of sigma(d)(2). A computer software that computes E[r(2)] numerically is available upon request.     

Isolation and sequence analysis of rpoH genes encoding sigma 32 homologs from gram negative bacteria: conserved mRNA and protein segments for heat shock regulation.

The rpoH genes encoding homologs of Escherichia coli sigma 32 (heat shock sigma factor) were isolated and sequenced from five gram negative proteobacteria (gamma or alpha subgroup): Enterobacter cloacae (gamma), Serratia marcescens (gamma), Proteus mirabilis (gamma), Agrobacterium tumefaciens (alpha) and Zymomonas mobilis (alpha). Comparison of these and three known genes from E.coli (gamma), Citrobacter freundii (gamma) and Pseudomonas aeruginosa (gamma) revealed marked similarities that should reflect conserved function and regulation of sigma 32 in the heat shock response. Both the sequence complementary to part of 16S rRNA (the 'downstream box') and a predicted mRNA secondary structure similar to those involved in translational control of sigma 32 in E.coli were found for the rpoH genes from the gamma, but not the alpha, subgroup, despite considerable divergence in nucleotide sequence. Moreover, a stretch of nine amino acid residues Q(R/K)(K/R)LFFNLR, designated the 'RpoH box', was absolutely conserved among all sigma 32 homologs, but absent in other sigma factors; this sequence overlapped with the segment of polypeptide thought to be involved in DnaK/DnaJ chaperone-mediated negative control of synthesis and stability of sigma 32. In addition, a putative sigma E (sigma 24)-specific promoter was found in front of all rpoH genes from the gamma, but not alpha, subgroup. These results suggest that the regulatory mechanisms, as well as the function, of the heat shock response known in E.coli are very well conserved among the gamma subgroup and partially conserved among the alpha proteobacteria.     

Survismeter--type I and II for surface tension, viscosity measurements of liquids for academic, and research and development studies

For centuries surface tension (gamma) and viscosity (eta) data have been measured with individual instruments consuming much time and materials. Thus the two different types of survismeters have been designed and made of borosil glass material for surface tension and viscosity data to rationalize frictional and cohesive forces, respectively. Friccohesity (sigma (sm(-1), second per meter)) is derived from Fric of frictional and cohesity of cohesive forces of the liquid respectively, and denoted by rational coefficient a eta/gamma (sigma). The values of the friccohesity are correlated to the dipole moment of liquids and their plot gives a standard calibration curve along with an equation of the curve with definite values of the coefficients, the friccohesity values are put on the calibration curve to retrieve the dipole moment values. Here, the sigma values for each of dimethylformamide, dimethylsulfoxide and acetronitrile solvents along with their 0.05, 0.10 and 0.20 mol kg(-1) aqueous solutions, respectively, were determined at 293.15K and plotted against their dipole moment values for standard calibration curve. The range of the dipole moment values for calibration curve is pre-decided and the sigma values for homogenous solutions of compositions below their saturation point can be measured with +/-1 x 10(-5)sm(-1).     

Antimicrobial peptides activate the Vibrio cholerae sigmaE regulon through an OmpU-dependent signalling pathway

Vibrio cholerae, an enteric pathogen, is subject to assault by several membrane-acting, host gut-derived antimicrobial peptides (AP). We previously found that a major V. cholerae outer membrane protein, OmpU, confers resistance to polymyxin B and to a bioactive peptide (P2) derived from the human bactericidal/permeability-increasing protein. Here, we report that the alternative sigma factor sigma(E) also plays a critical role in determining V. cholerae resistance to AP and that OmpU and sigma(E) lie in the same pathway. In fact, we found that OmpU is a key determinant of basal sigma(E) expression. We also found that sublethal AP exposure activates sigma(E) and the sigma(E)-mediated periplasmic stress response. sigma(E) is not activated by P2 in V. cholerae cells lacking OmpU or DegS, a periplasmic protease that controls sigma(E) activity. The lack of AP-elicited sigma(E) activation in a strain harbouring a point mutation in OmpU's putative DegS-binding residues provides support for a link between OmpU and DegS-mediated activation of sigma(E). We propose that AP-induced membrane perturbations change the conformation of OmpU to trigger a DegS-dependent sigma(E)-activating cascade. Thus, OmpU appears to act as a sensor component in a signal transduction pathway.     

The structural basis for unidirectional rotation of thermoalkaliphilic F1-ATPase

The ATP synthase of the thermoalkaliphilic Bacillus sp. TA2.A1 operates exclusively in ATP synthesis direction. In the crystal structure of the nucleotide-free alpha(3)beta(3)gamma epsilon subcomplex (TA2F(1)) at 3.1 A resolution, all three beta subunits adopt the open beta(E) conformation. The structure shows salt bridges between the helix-turn-helix motif of the C-terminal domain of the beta(E) subunit (residues Asp372 and Asp375) and the N-terminal helix of the gamma subunit (residues Arg9 and Arg10). These electrostatic forces pull the gamma shaft out of the rotational center and impede rotation through steric interference with the beta(E) subunit. Replacement of Arg9 and Arg10 with glutamines eliminates the salt bridges and results in an activation of ATP hydrolysis activity, suggesting that these salt bridges prevent the native enzyme from rotating in ATP hydrolysis direction. A similar bending of the gamma shaft as in the TA2F(1) structure was observed by single-particle analysis of the TA2F(1)F(o) holoenzyme.     

Control of the expression and compartmentalization of (sigma)G activity during sporulation of Bacillus subtilis by regulators of (sigma)F and (sigma)E

During formation of spores by Bacillus subtilis the RNA polymerase factor sigma(G) ordinarily becomes active during spore formation exclusively in the prespore upon completion of engulfment of the prespore by the mother cell. Formation and activation of sigma(G) ordinarily requires prior activity of sigma(F) in the prespore and sigma(E) in the mother cell. Here we report that in spoIIA mutants lacking both sigma(F) and the anti-sigma factor SpoIIAB and in which sigma(E) is not active, sigma(G) nevertheless becomes active. Further, its activity is largely confined to the mother cell. Thus, there is a switch in the location of sigma(G) activity from prespore to mother cell. Factors contributing to the mother cell location are inferred to be read-through of spoIIIG, the structural gene for sigma(G), from the upstream spoIIG locus and the absence of SpoIIAB, which can act in the mother cell as an anti-sigma factor to sigma(G). When the spoIIIG locus was moved away from spoIIG to the distal amyE locus, sigma(G) became active earlier in sporulation in spoIIA deletion mutants, and the sporulation septum was not formed, suggesting that premature sigma(G) activation can block septum formation. We report a previously unrecognized control in which SpoIIGA can prevent the appearance of sigma(G) activity, and pro-sigma(E) (but not sigma(E)) can counteract this effect of SpoIIGA. We find that in strains lacking sigma(F) and SpoIIAB and engineered to produce active sigma(E) in the mother cell without the need for SpoIIGA, sigma(G) also becomes active in the mother cell.     

Intermediates in the formation of the open complex by RNA polymerase holoenzyme containing the sigma factor sigma 32 at the groE promoter

The interaction of E sigma 32 with the groE promoter at temperatures between 0 degrees C and 37 degrees C was studied using DNase I footprinting and dimethyl sulfate methylation. Three distinct complexes were observed. At 0 degrees C E sigma 32 fully protected sequences between -60 and -5 from DNase I digestion on the top (non-template) strand of the promoter. At 16 degrees C the majority of the E sigma 32 promoter complexes had a DNase I footprint almost identical with that seen at 37 degrees C, protecting the DNA from about -60 to +20; however, little DNA strand separation had occurred, and the changes in sensitivity of guanine residues to dimethyl sulfate methylation caused by E sigma 32 differed from those seen at 37 degrees C. DNA strand separation, and changes in the pattern of protections from and enhancements of methylation by dimethyl sulfate to those characteristic of the open complex, occurred at temperatures between 16 degrees C and 27 degrees C. It is plausible to assume that these temperature-dependent isomerizations are analogous to the time-dependent sequence of intermediates on the pathway to open complex formation at 37 degrees C. Therefore we propose that the formation of an open complex by E sigma 32 at the groE promoter involves three classes of steps: E sigma 32 initially binds to the promoter in a closed complex (RPC1) in which the enzyme interacts with a smaller region of the DNA than in the open complex. E sigma 32 then isomerizes to form a second closed complex (RPC2) in which the enzyme interacts with the same region of the DNA as in the open complex. Finally, a process of local DNA denaturation (strand opening) leads to formation of the open complex (RPO).     

Distensibility characteristics of caval veins and empirical exponential formulae

The stress-strain curves of the vena cava have been measured of vena cava superior, and the intrathoracic and abdominal portions of vena cava inferior excised from dogs. The stress sigma is expressed by the exponential function of the strain gamma as follows: sigma = sigma 0[exp (gamma/gamma 0) - 1] in the longitudinal direction, and sigma = sigma 1[exp(gamma/gamma 1) - 1] + sigma 2 [exp(gamma/gamma 2) - 1] in the circumferential one for all the three kinds of veins. The constants sigma 0, gamma 0, sigma 1, gamma 1, sigma 2 and gamma 2 are determined by a nonlinear least squares method.