Combining data sharing with the master–worker paradigm in the common component architecture

Software component technologies are being accepted as an adequate solution for handling the complexity of applications. However, existing software component models tend to be specialized to some types of resource architectures (e.g. in-process, distributed environments, etc.) and/or do not provide a very high level of abstraction. This paper focuses on handling data sharing on operation invocations between components as a solution allowing applications to be efficiently executed on all kinds of resources. In particular, the data sharing pattern appears in master–worker applications, when workers need to access only a part of a large piece of data, either in read or write mode. This approach is applied to the Common Component Architecture model. Its benefits are discussed using an image rendering application.

Salivary oxytocin increases concurrently with testosterone and time away from home among returning Tsimane’ hunters

Oxytocin, testosterone and cortisol can have opposing effects on social behaviour, yet few studies have examined their interactions. We measured changes in salivary oxytocin, testosterone and cortisol among Tsimane’ men returning home after hunting, an ancient context of male status competition, parental investment and cooperation. Contra normal diurnal rhythm, oxytocin increased relative to baseline and this increase was positively associated with duration of the hunt and change in testosterone, but not cortisol, social context, hunting outcome or physical activity. The concurrent increase in endogenous peripheral oxytocin and testosterone is unexpected given their opposing independent effects on social cognition and behaviour, and has not been observed before. We discuss the potential significance of these effects for the biology of pair-bonding, parenting and social foraging in humans and other species.     

Assessing actual contribution of IF1, inhibitor of mitochondrial FoF1, to ATP homeostasis, cell growth, mitochondrial morphology, and cell viability

F(o)F(1)-ATP synthase (F(o)F(1)) synthesizes ATP in mitochondria coupled with proton flow driven by the proton motive force (pmf) across membranes. It has been known that isolated IF1, an evolutionarily well conserved mitochondrial protein, can inhibit the ATP hydrolysis activity of F(o)F(1). Here, we generated HeLa cells with permanent IF1 knockdown (IF1-KD cells) and compared their energy metabolism with control cells. Under optimum growth conditions, IF1-KD cells have lower cellular ATP levels and generate a higher pmf and more reactive oxygen species. Nonetheless, IF1-KD cells and control cells show the same rates of cell growth, glucose consumption, and mitochondrial ATP synthesis. Furthermore, contrary to previous reports, the morphology of mitochondria in IF1-KD cells appears to be normal. When cells encounter sudden dissipation of pmf, the cytoplasmic ATP level in IF1-KD cells drops immediately (~1 min), whereas it remains unchanged in the control cells, indicating occurrence of futile ATP hydrolysis by F(o)F(1) in the absence of IF1. The lowered ATP level in IF1-KD cells then recovers gradually (~10 min) to the original level by consuming more glucose than control cells. The viability of IF1-KD cells and control cells is the same in the absence of pmf. Thus, IF1 contributes to ATP homeostasis, but its deficiency does not affect the growth and survival of HeLa cells. Only when cells are exposed to chemical ischemia (no glycolysis and no respiration) or high concentrations of reactive oxygen species does IF1 exhibit its ability to alleviate cell injury.     

Epifluorescence and atomic force microscopy: Two innovative applications for studying phage-host interactions in Lactobacillus helveticus

Bacteriophages attacking lactic acid bacteria (LAB) still represent a crucial problem in industrial dairy fermentations. The consequences of a phage infection against LAB can lead to fermentation delay, alteration of the product quality and, in most severe cases, the product loss. Phage particles enumeration and phage-host interactions are normally evaluated by conventional plaque count assays, but, in many cases, these methods can be unsuccessful. Bacteriophages of Lactobacillus helveticus, a LAB species widely used as dairy starter or probiotic cultures, are often unable to form lysis plaques, thus impairing their enumeration by plate assay. In this study, we used epifluorescence microscopy to enumerate L. helveticus phage particles from phage-infected cultures and Atomic Force Microscopy (AFM) to visualize both phages and bacteria during the different stages of the lytic cycle. Preliminary, we tested the sensitivity of phage counting by epifluorescence microscopy. To this end, phage particles of ΦAQ113, a lytic phage of L. helveticus isolated from a whey starter culture, were stained by SYBR Green I and enumerated by epifluorescence microscopy. Values obtained by the microscopic method were 10 times higher than plate counts, with a lowest sensitivity limit of ≥ 6 log phage/ml. The interaction of phage ΦAQ113 with its host cell L. helveticus Lh1405 was imaged by AFM after 0, 2 and 5 h from phage-host adsorption. The lytic cycle was followed by epifluorescence microscopy counting and the concomitant cell wall changes were visualized by AFM imaging. Our results showed that these two methods can be combined for a reliable phage enumeration and for studying phage and host morphology during infection processes, thus giving a complete overview of phage-host interactions in L. helveticus strains involved in dairy productions.     

Dynamic force spectroscopy of the digoxigenin-antibody complex

Small ligands and their receptors are widely used non-covalent couplers in various biotech applications. One prominent example, the digoxigenin-antibody complex, was often used to immobilize samples for single molecule force measurements by optical trap or AFM. Here, we employed dynamic AFM spectroscopy to demonstrate that a single digoxigenin-antibody bond is likely to fail even under moderate loading rates. This effect potentially could lower the yield of measurements or even obscure the unbinding data of the sample by the rupture events of the coupler. Immobilization by multiple antibody-antigen bonds, therefore, is highly recommended. The analysis of our data revealed a pronounced loading rate dependence of the rupture force, which we analyzed based on the well-established Bell-Evans-model with two subsequent unbinding barriers. We could show that the first barrier has a width of Deltax(1)=1.15 nm and a spontaneous rate of k(off1)=0.015 s(-1) and the second has a width of Deltax(2)=0.35 nm and a spontaneous rate of k(off2)=4.56 s(-1). In the crossover region between the two regimes, we found a marked discrepancy between the predicted bond rupture probability density and the measured rupture force histograms, which we discuss as non-Markovian contribution to the unbinding process.     

Gene-Trait Similarity Regression for Multimarker-Based Association Analysis

Summary .  We propose a similarity-based regression method to detect associations between traits and multimarker genotypes. The model regresses similarity in traits for pairs of "unrelated" individuals on their haplotype similarities, and detects the significance by a score test for which the limiting distribution is derived. The proposed method allows for covariates, uses phase-independent similarity measures to bypass the needs to impute phase information, and is applicable to traits of general types (e.g., quantitative and qualitative traits). We also show that the gene-trait similarity regression is closely connected with random effects haplotype analysis, although commonly they are considered as separate modeling tools. This connection unites the classic haplotype sharing methods with the variance-component approaches, which enables direct derivation of analytical properties of the sharing statistics even when the similarity regression model becomes analytically challenging.     

Lipids on the move: Simulations of membrane pores, domains, stalks and curves

In this review we describe the state-of-the-art of computer simulation studies of lipid membranes. We focus on collective lipid-lipid and lipid-protein interactions that trigger deformations of the natural lamellar membrane state, showing that many important biological processes including self-aggregation of membrane components into domains, the formation of non-lamellar phases, and membrane poration and curving, are now amenable to detailed simulation studies.     

SFMN GeoSearch: An interactive approach to the visualization and exchange of point-based ecological data

Recent advances in computer networks and information technologies have created exciting new possibilities for sharing and analyzing scientific research data. Although individual datasets can be studied efficiently, many scientists are still largely limited to considering data collected by themselves, their students, or closely affiliated research groups. Increasingly widespread high-speed network connections and the existence of large, coordinated research programs suggest the potential for scientists to access and learn from data from outside their immediate research circle. We are developing a web-based application that facilitates the sharing of scientific data within a research network using the now-common “virtual globe” in combination with advanced visualization methods designed for geographically distributed scientific data. Two major components of the system enable the rapid assessment of geographically distributed scientific data: a database built from information submitted by network members, and a module featuring novel and sophisticated geographic data visualization techniques. By enabling scientists to share results with each other and view their shared data through a common virtual-globe interface, the system provides a new platform for important meta-analyses and the analysis of broad-scale patterns. Here we present the design and capabilities of the SFMN GeoSearch platform for the Sustainable Forest Management Network, a pan-Canadian network of forest researchers who have accumulated data for more than a decade. Through the development and dissemination of this new tool, we hope to help scientists, students, and the general public to understand the depth and breadth of scientific data across potentially large areas.