Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2

ABSTRACT: BACKGROUND: The analysis of complex diseases is an important problem in human genetics. Because multifactoriality isexpected to play a pivotal role, many studies are currently focused on collecting information on the geneticand environmental factors that potentially influence these diseases. However, there is still a lack of efficientand thoroughly tested statistical models that can be used to identify implicated features and theirinteractions. Simulations using large biologically realistic data sets with known gene-gene andgene-environment interactions that influence the risk of a complex disease are a convenient and useful wayto assess the performance of statistical methods. RESULTS: The Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and oneenvironmental factor and also allows for epistatic interactions. GENS2 is based on data with realisticpatterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to besimulated or on number of non-predisposing genetic/environmental factors to be considered. The GENS2tool is able to simulate gene-environment and gene-gene interactions. To make the Simulator more intuitive,the input parameters are expressed as standard epidemiological quantities. GENS2 is written in Pythonlanguage and takes advantage of operators and modules provided by the simuPOP simulation environment.It can be used through a graphical or a command-line interface and is freely available fromhttp://sourceforge.net/projects/gensim. The software is released under the GNU General Public Licenseversion 3.0. CONCLUSIONS: Data produced by GENS2 can be used as a benchmark for evaluating statistical tools designed for theidentification of gene-gene and gene-environment interactions.     

Ultrastructural effects of PCMS on mycelial-yeast transition in Histoplasma capsulatum.

The Yeast phase of Histoplasma capsulatum has stringent growth requirements. Transition from mycelium to yeast takes place only in the presence of cysteine and can be blocked by the -SH groups inhibitor p-chloromercury-phenylsulfonic acid (PCMS). Ultrastructural studies show lysis and degeneration of PCMS treated mycelium grown at 37 degrees C for 24 hours. Only 50% of PCMS treated mycelium appear degenerate when grown at 34 degrees C for 24 hours. The remaining cells have normal morphology with only slight changes in the cell wall structure. The effect of PCMS is permanent and hereditary. Mice injected with PCMS treated mycelium do not develop disease and are resistant to virulent strains of H. capsulatum when challenged.     

Dicarboxyamylose and dicarboxycellulose,stereoregular polyelectrolytes: physicochemical characterization and interaction with divalent cations

2,3-Dicarboxyamylose (DCA) and 2,3-dicarboxycellulose (DCC) have been obtained by splitting with periodate of all the C(2)C(3) bonds of amylose and cellulose, and further oxidation (with chlorite) of the corresponding polydialdehydes. Small, but reproducible, differences of ¹³C chemical shifts in dicate that DCA and DCC retained the different configuration at C-1 of the original polysaccharides, therefore being stereoisomers. The potentiometric and conductimetric titration curves of DCA and DCC and the pH-dependence of their ¹H n.m.r. spectra are those of typical polydicarboxylates. Interaction of DCA and DCC (Na salts) with divalent cations is clearly indicated by inflexions in conductimetric titration curves with Ca²⁺, Mg²⁺, Cu²⁺ and Fe²⁺, and by variation in specific optical rotation.     

Glycogen metabloism in the developing chick glycogen body: functional significance of the direct oxidative pathway.

Glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, and glucose-6-phosphatase were quantitatively determined for the first time in glycogen body tissue from late embryonic and neonatal chicks. For comparative purposes, the activities of these enzymes were examined also in liver and skeletal muscle from pre- and post-hatched chicks. The present data show that both the embryonic and neonatal glycogen body lack glucose-6-phosphatase, but contain relatively high levels of glucose-6-phosphate dehydrogenase. The activity of each dehydrogenase in either embryonic or neonatal glycogen body tissue is two- to five-fold greater than that found in muscle or liver from pre- or post-hatched chicks. The relatively high activities observed for both dehydrogenases in the glycogen body, together with the absence of glucose-6-phosphatase activity in that tissue, suggest that the direct oxidative pathway (pentose phosphate cycle) of glucose metabolism is a functionally significant route for glycogen utilization in the glycogen body. It is hypothesized that the glycogen body is metabolically linked to lipid synthesis and myelin formation in the central nervous system of the avian embryo.     

A new cytochemical method for ultrastructural detection of liposomes in tissues in vivo

Multilamellar vesicles (MLVs) have been used as drug carriers to increase efficacy or decrease toxicity of a variety of therapeutic agents, including antineoplastics, antibiotics, and immunomodulators. Although analysis of the disposition of encapsulated materials is relatively simple using radiolabels or single enzymes, determining the cellular and subcellular disposition of intact MLVs, i.e., those that still retain their encapsulated materials, is much less straightforward. We have developed a technique that allows demonstration of the uptake of intact MLVs by Kupffer cells. The method is based on co-localization of paired enzymes, glucose oxidase (GO), and horseradish peroxidase (HRP). The rationale for the localization is that H2O2 generated from glucose and oxygen by GO acts as the substrate for the HRP-mediated oxidative polymerization of diaminobenzidine. Therefore, only sites of co-localization of GO and HRP should stain. Mice were injected IV with phosphatidyl choline MLVs encapsulating HRP and GO. Encapsulated enzymes were separated from non-encapsulated by passing the MLVs over a Sepharose 2B column. Control mice were injected with equivalent amounts of free GO. Mice were sacrificed 30 min after injection and liver tissue was fixed in 3% cacodylate-buffered glutaraldehyde for at least 18 hr. Tissues were washed in buffer, then stained in medium containing glucose, diaminobenzidine HCl, and dimethylsulfoxide in 0.1 M cacodylate buffer. In animals injected with MLV-encapsulated GO and HRP, vacuoles in Kupffer cells and some endothelial cells contained electron-dense reaction product. No other cell type, including polymorphonuclear leukocytes, was stained. In control animals no staining was seen. Our results indicate that encapsulation of paired enzymes may be a feasible method to demonstrate the cellular and subcellular disposition of intact liposomes.     

The Proline-rich Antibacterial Peptide Bac7 Binds to and Inhibits in vitro the Molecular Chaperone DnaK

Bac7, a cathelicidin peptide of the proline-rich group, inactivates bacteria in a stereospecific manner by entering target cells without any apparent membrane damage and by binding to as yet unknown intracellular targets. The present study was aimed at detecting these putative intracellular interactors, which might mediate the antibacterial action of this peptide. By using affinity resins functionalized with the N-terminal 1-35 fragment of Bac7, a single protein was specifically retained with high affinity from Escherichia coli cytoplasmic protein lysates. This ligand was identified as the heat shock protein DnaK, the Hsp70 homolog in E. coli. The interaction between the peptide and the chaperone is stereospecific, given that a resin prepared with the all- d enantiomer failed to retain the protein. In vitro, Bac7(1-35) formed a complex with DnaK with an affinity comparable to that of other known high-affinity peptide ligands. In addition, at 10–100 μM concentration, the peptide inhibited the protein refolding activity of the complete DnaK/DnaJ/GrpE/ATP molecular chaperone system in a dose-dependent manner. Despite these results, the in vitro sensitivity to the peptide, under growth permitting conditions, of DnaK-deficient E. coli strains was not significantly affected compared to the wild-type strain. This suggests that, apart from DnaK, other vital targets for the proline-rich AMPs are present in susceptible bacteria. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Marco Scocchi and Christine Lüthy contributed equally to this work.     

Silver Nanoparticle Arrays on a DVD-Derived Template: An easy&cheap SERS Substrate

Commercially available digital versatile discs (DVDs) contain a silver-coated spiral distribution of rectangular-shaped grooves (AgDVD): for the first time, they have been used to produce surface-enhanced Raman scattering (SERS) substrates by electrochemical deposition of silver nanoparticles (AgNPs@AgDVD). The overall procedure only requires cheap and widely available materials and can be easily accomplished. Scanning electron microscopy images of AgNPs@AgDVD revealed that small AgNPs (average diameter about 15 nm) are present within the valleys of AgDVD, whereas over the ridges, the AgNPs are bigger, more densely packed and with a dendrite-like morphology somewhere. The SERS properties of these substrates have been studied in terms of the enhancement factor (EF), point-to-point reproducibility and sample-to-sample repeatability. It turned out that high SERS EF and good reproducibility requirements are both fulfilled. As for repeatability, remarkably better results than typical literature values have been achieved. Such an easy&cheap preparation along with efficient SERS properties make DVD-derived SERS substrates very good candidates for the development of convenient and disposable sensing platforms.