Function suggests nano-structure: towards a unified theory for secretion rate,a statistical mechanics approach

The inventory of secretory granules along the plasma membrane can be viewed as maintained in two restricted compartments. The release-ready pool represents docked granules available for an initial stage of fast, immediate secretion, followed by a second stage of granule set-aside secretion pool, with significantly slower rate. Transmission electron microscopy ultra-structural investigations correlated with electrophysiological techniques and mathematical modelling have allowed the categorization of these secretory vesicle compartments, in which vesicles can be in various states of secretory competence. Using the above-mentioned approaches, the kinetics of single vesicle exocytosis can be worked out. The ultra-fast kinetics, explored in this study, represents the immediately available release-ready pool, in which granules bound to the plasma membrane are exocytosed upon Ca²⁺ influx at the SNARE rosette at the base of porosomes. Formalizing Dodge and Rahamimoff findings on the effect of calcium concentration and incorporating the effect of SNARE transient rosette size, we postulate that secretion rate (rate), the number (X) of intracellular calcium ions available for fusion, calcium capacity (0 ≤ M ≤ 5) and the fusion nano-machine size (as measured by the SNARE rosette size K) satisfy the parsimonious M–K relation rate ≈ C × [Ca²⁺]^min(X,M)e^−K/2.     

Guided Sampling via Weak Motion Models and Outlier Sample Generation for Epipolar Geometry Estimation

The problem of automatic robust estimation of the epipolar geometry in cases where the correspondences are contaminated with a high percentage of outliers is addressed. This situation often occurs when the images have undergone a significant deformation, either due to large rotation or wide baseline of the cameras. An accelerated algorithm for the identification of the false matches between the views is presented. The algorithm generates a set of weak motion models (WMMs). Each WMM roughly approximates the motion of correspondences from one image to the other. The algorithm represents the distribution of the median of the geometric distances of a correspondence to the WMMs as a mixture model of outlier correspondences and inlier correspondences. The algorithm generates a sample of outlier correspondences from the data. This sample is used to estimate the outlier rate and to estimate the outlier pdf. Using these two pdfs the probability that each correspondence is an inlier is estimated. These probabilities enable guided sampling. In the RANSAC process this guided sampling accelerates the search process. The resulting algorithm when tested on real images achieves a speedup of between one or two orders of magnitude. This work was supported partly by grant 01-99-08430 of the Israeli Space Agency through the Ministry of Science Culture and Sports of Israel.     

Optimal design of the inspection buffer for an unreliable process

Placing an inspection buffer immediately after an unreliable process subject to failure protects the process customers from receiving non-conforming products. Such protection is achieved by screening the buffer contents whenever a shift in the process is detected. Previous studies have suggested that, if properly designed, such buffers can reduce overall costs. In this paper we make two types of contributions to the study of inspection buffers. First, we refine the model proposed by Klastorin et al. (1993), by incorporating a more efficient way of sampling, a more realistic objective function and more accurate cost expressions. Second, we provide analytical results to assist in the calculation of the economically optimal buffer size. Specifically, these include conditions for determining whether an inspection buffer is at all justified and a theorem for bounding the search for the optimal buffer size. The performance of the search bound and the sensitivity of the model are examined computationally.     

Bacterial community composition and structure of biofilms developing on nanofiltration membranes applied to wastewater treatment

The structure and microbial communities of biofilms developing on cross-flow nanofiltration (NF) membranes at different temperatures (20, 25 or 34 degrees C) and operation lengths (8h-24days) were studied. Feedwater comprised tertiary quality wastewater effluent or synthetic media mimicking effluents of intermediate quality. After each run, the membranes were autopsied for bacterial enumeration, bacterial community composition and microscopy visualization (SEM, CLSM and AFM/NSOM). Community composition was analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) coupled with sequence analysis of 16S rRNA gene fragments from dominant bands. Deposition of polysaccharides and initial bacterial colonization were observed within 8h, whereas developed biofilms markedly affecting membrane permeability were evident from days 2-3 onwards. Regardless of applied conditions, the heterotrophic plate counts in the biofilm were 3-4x10(6)CFU/cm(2) and the thickness of the biofouling layer was 20-30microm. From a total of 22 sequences obtained from 14 independent experiments, most species identified were Gram negative (19 of 22 sequences). Proteobacteria were found to be a prevalent group in all cases (16 of 22 sequences) and among it, the beta-subclass was the most predominant (8 sequences), followed by the gamma-subclass (5 sequences). Pseudomonas/Burkholderia, Ralstonia, Bacteroidetes and Sphingomonas were the dominant groups found in most cases. Even though the microbial population might be important with respect to biofouling patterns, membrane permeability decline seems to be more substantially influenced by the formation and accumulation of exopolymeric substances (EPS).     

Stem-loop structure in the 5' region of potato virus X genome required for plus-strand RNA accumulation

Computer-generated thermodynamic predictions and solution structure probing indicated two stem-loop structures, stem-loop 1 (SL1; nt 32-106) and stem-loop 2 (SL2; nt 143-183), within the 5' 230 nt of potato virus X (PVX) RNA. Because the existence of SL1 was further supported by covariation analysis of several PVX strains, the functional significance of this structure was investigated by site-directed mutational analysis in a tobacco protoplast system. In general, mutations that reduced genomic plus-strand RNA accumulation similarly affected coat protein accumulation, indicating that subgenomic plus-strand RNA was also affected. In contrast, minus-strand RNA levels remained relatively unchanged. Mutational analysis of the stem C (SC) region of SL1 indicated that pairing was more important than sequence, which was consistent with the covariation analysis. Alterations that increased length and stability of either SC or stem D (SD) were deleterious to plus-strand RNA accumulation. The formation of internal loop C between SC and SD, as well as specific nucleotides within this loop, were also required. Several modifications were made to the terminal GAAA tetraloop, a motif known for enhanced RNA stability. Both GANA and GAAG motifs resulted in wild-type levels of RNA accumulation. However, a UUCG tetraloop was detrimental, indicating that the sequence of this element was important beyond just providing stabilization of the structure. These data indicate that multiple features of SL1 are critical for accumulation of PVX plus-strand RNA.     

Morphological changes of human skin cells exposed to a DC electric field in vitro using a new exposure system

The human skin contains a physiological battery that could be implicated in the healing process, by creating an endogenous electric field. Skin cells undergo morphological changes in response to an external DC electric field (EF). We found that fibroblasts reorient their cell bodies in a manner perpendicular to the EF direction, for normal and above physiological intensities. Actin and tubulin filaments (cytoskeleton proteins) follow the same pattern of reorientation. Keratinocytes tend to elongate in the same direction, although to a lesser extent. The study of the response of human skin cells to an external EF is a first step toward a better understanding of the mechanisms involved in wound healing and eventually toward the improvement of wound repair.