Time course of release of catecholamines from individual vesicles during exocytosis at adrenal medullary cells

The time course of extrusion of the vesicular contents during exocytosis has been examined at adrenal medullary cells with carbon-fiber microelectrodes. Two electrochemical techniques were used: cyclic voltammetry and amperometry. Spikes obtained by amperometry had a faster time course than those measured by cyclic voltammetry, consistent with the different concentration profiles established by each technique. However, the experimental data obtained with both techniques were temporally broadened with respect to dispersion of an instantaneous point source by diffusion. Measurements with the electrode firmly pressed against the cell surface established that the temporal broadening is a result of a rate-limiting kinetic step associated with extrusion of the vesicular contents at the cell surface. The data do not support a rate-limiting process due to restricted efflux from a small pore. When combined with previous results, the data suggest that the rate-limiting step for chemical secretion from adrenal medullary cells during exocytosis is the dissociation of catecholamines from the vesicular matrix at the surface of the cell

Branch-recombinant Gaussian processes for analysis of perturbations in biological time series.

MOTIVATION: A common class of behaviour encountered in the biological sciences involves branching and recombination. During branching, a statistical process bifurcates resulting in two or more potentially correlated processes that may undergo further branching; the contrary is true during recombination, where two or more statistical processes converge. A key objective is to identify the time of this bifurcation (branch or recombination time) from time series measurements, e.g. by comparing a control time series with perturbed time series. Gaussian processes (GPs) represent an ideal framework for such analysis, allowing for nonlinear regression that includes a rigorous treatment of uncertainty. Currently, however, GP models only exist for two-branch systems. Here, we highlight how arbitrarily complex branching processes can be built using the correct composition of covariance functions within a GP framework, thus outlining a general framework for the treatment of branching and recombination in the form of branch-recombinant Gaussian processes (B-RGPs). RESULTS: We first benchmark the performance of B-RGPs compared to a variety of existing regression approaches, and demonstrate robustness to model misspecification. B-RGPs are then used to investigate the branching patterns of Arabidopsis thaliana gene expression following inoculation with the hemibotrophic bacteria, Pseudomonas syringae DC3000, and a disarmed mutant strain, hrpA. By grouping genes according to the number of branches, we could naturally separate out genes involved in basal immune response from those subverted by the virulent strain, and show enrichment for targets of pathogen protein effectors. Finally, we identify two early branching genes WRKY11 and WRKY17, and show that genes that branched at similar times to WRKY11/17 were enriched for W-box binding motifs, and overrepresented for genes differentially expressed in WRKY11/17 knockouts, suggesting that branch time could be used for identifying direct and indirect binding targets of key transcription factors. AVAILABILITY AND IMPLEMENTATION: https://github.com/cap76/BranchingGPs. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Evaluating Process Quality Based on Change Request Data – An Empirical Study of the Eclipse Project

Abstract. The information routinely collected in change request management systems contains valuable information for monitoring of the process quality. However this data is currently utilized in a very limited way. This paper presents an empirical study of the process quality in the product portfolio of the Eclipse project. It is based on a systematic approach for the evaluation of process quality characteristics using change request data. Results of the study offer insights into the development process of Eclipse. Moreover the study allows assessing applicability and limitations of the proposed approach for the evaluation of process quality

Challenges in Survey Research

While being an important and often used research method, survey research has been less often discussed on a methodological level in empirical software engineering than other types of research. This chapter compiles a set of important and challenging issues in survey research based on experiences with several large-scale international surveys. The chapter covers theory building, sampling, invitation and follow-up, statistical as well as qualitative analysis of survey data and the usage of psychometrics in software engineering surveys.Comment: Accepted version of chapter in the upcoming book on Contemporary Empirical Methods in Software Engineering. Update includes revision of typos and additional figures. Last update includes fixing two small issues and typo

The rice transcription factor OsWRKY47 is a positive regulator of the response to water deficit stress

OsWRKY47 is a divergent rice transcription factor belonging to the group II of the WRKY family. A transcriptomic analysis of the drought response of transgenic rice plants expressing PSARK::IPT, validated by qPCR, indicated that OsWRKY47 expression was induced under drought stress in PSARK::IPT plants. A PCR-assisted site selection assay (SELEX) of recombinant OsWRKY47 protein showed that the preferred sequence bound in vitro is (G/T)TTGACT. Bioinformatics analyses identified a number of gene targets of OsWRKY47; among these two genes encode a Calmodulin binding protein and a Cys-rich secretory protein. Using Oswrk47 knockout mutants and transgenic rice overexpressing OsWRKY47 we show that the transcription of these putative targets were regulated by OsWRKY47. Phenotypic analysis carried out with transgenic rice plants showed that Oswrky47 mutants displayed higher sensitivity to drought and reduced yield, while plants overexpressing OsWRKY47 were more tolerant.Fil: Raineri, Jesica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; ArgentinaFil: Wang, Songhu. Chinese Academy of Sciences; República de China. University of California at Davis; Estados UnidosFil: Peleg, Zvi. The Hebrew University of Jerusalem; Israel. University of California at Davis; Estados UnidosFil: Blumwald, Eduardo. University of California at Davis; Estados UnidosFil: Chan, Raquel Lia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentin