Bioinformatic interrogation of expression array data to identify nutritionally regulated genes potentially modulated by DNA methylation

DNA methylation occurs at CpG dinucleotide sites within the genome and is recognised as one of the mechanisms involved in regulation of gene expression. CpG sites are relatively underrepresented in the mammalian genome, but occur densely in regions called CpG islands (CGIs). CGIs located in the promoters of genes inhibit transcription when methylated by impeding transcription factor binding. Due to the malleable nature of DNA methylation, environmental factors are able to influence promoter CGI methylation patterns and thus influence gene expression. Recent studies have provided evidence that nutrition (and other environmental exposures) can cause altered CGI methylation but, with a few exceptions, the genes influenced by these exposures remain largely unknown. Here we describe a novel bioinformatics approach for the analysis of gene expression microarray data designed to identify regulatory sites within promoters of differentially expressed genes that may be influenced by changes in DNA methylation

Geophysical Characterization, Redox Zonation, and Contaminant Distribution at a Groundwater/Surface Water Interface

Three transects along a groundwater/surface water interface were characterized for spatial distributions of chlorinated aliphatic hydrocarbons and geochemical conditions to evaluate the natural bioremediation potential of this environmental system. Partly on the basis of ground penetrating radar measurements, a conductive sediment layer was detected from the shore out to at least 300 m offshore which exhibited gradients in redox pairs and contaminant profiles. The cis-Dichloroethene and 1-chloroethene were predominant in the presence of elevated methane and ferrous iron concentrations and depressed sulfate and aquifer solids-bound iron concentrations. The shallow monitoring points were generally hypoxic to aerobic and exhibited values of specific conductance reflective of near-shore lake water, indicating reoxygenation of the contaminant plume due to wave infiltration. The barge transect yielded trace contaminant concentrations and showed evidence of sulfate reduction. These analyses contributed to the understanding of processes affecting contaminant fate and transport at near-shore mixing zones

Multivariate analysis of 3D ToF-SIMS images: method validation and application to cultured neuronal networks

Advanced data analysis tools are crucial for the application of ToF-SIMS analysis to biological samples. Here, we demonstrate that by using a training set approach principal components analysis (PCA) can be performed on large 3D ToF-SIMS images of neuronal cell cultures. The method readily provides access to sample component information and significantly improves the images’ signal-to-noise ratio (SNR)

Influence of environment on the corrosion of glass–metal connections

'Glass sensors' of the eighteenth century Backer glass and the sixteenth century enamel from Limoges have been chosen for a series of experiments. Combinations of these materials with different base materials such as copper and bronze has been investigated. To create surface changes on the 'glass sensor', a corrosion process was induced in a controlled environment. A variety of corrosive agents such as hydrochloric acid, sulfuric acid, water and formaldehyde were used. The sample immersed in the corrosive solution was exposed alternately to light and high temperature for a total of 38 weeks. During this period, macroscopic and microscopic observations were made and series of tests such as SEM/EDS and Raman spectroscopy were performed on the surface of the samples. ICP-MS methods were used to determine the change in the chemical composition of the solutions where the samples had corroded. The primary aim of this study was to identify the impact of a number of external corrosive variables such as temperature, humidity and local environment to identify the most damaging environments for glass–metal objects. The obtained results showed the chemical and physical phenomena acting on the surface of the glass, metal or in the place of their joints. Information obtained on this study was used to explain the influence of the environment on the surface of glass–metal materials. Results can be used in the design of conservation work as well as for sustainable conservation

Improving Darwin Core for research and management of alien species

To improve the suitability of the Darwin Core standard for the research and management of alien species, the standard needs to express the native status of organisms, how well established they are and how they came to occupy a location. To facilitate this, we propose: 1. To adopt a controlled vocabulary for the existing Darwin Core term dwc:establishmentMeans 2. To elevate the pathway term from the Invasive Species Pathways extension to become a new Darwin Core term dwc:pathway maintained as part of the Darwin Core standard 3. To adopt a new Darwin Core term dwc:degreeOfEstablishment with an associated controlled vocabulary These changes to the standard will allow users to clearly state whether an occurrence of a species is native to a location or not, how it got there (pathway), and to what extent the species has become a permanent feature of the location. By improving Darwin Core for capturing and sharing these data, we aim to improve the quality of occurrence and checklist data in general and to increase the number of potential uses of these data

Microbicide excipients can greatly increase susceptibility to genital herpes transmission in the mouse

<p>Abstract</p> <p>Background</p> <p>Several active ingredients proposed as vaginal microbicides have been shown paradoxically to <it>increase </it>susceptibility to infection in mouse genital herpes (HSV-2) vaginal susceptibility models and in clinical trials. In addition, "inactive ingredients" (or excipients) used in topical products to formulate and deliver the active ingredient might also cause epithelial toxicities that increase viral susceptibility. However, excipients have not previously been tested in susceptibility models.</p> <p>Methods</p> <p>Excipients commonly used in topical products were formulated in a non-toxic vehicle (the "HEC universal placebo"), or other formulations as specified. Twelve hours after exposure to the excipient or a control treatment, mice were challenged with a vaginal dose of HSV-2, and three days later were assessed for infection by vaginal lavage culture to assess susceptibility.</p> <p>Results</p> <p>The following excipients markedly increased susceptibility to HSV-2 after a single exposure: 5% glycerol monolaurate (GML) formulated in K-Y^®Warming Jelly, 5% GML as a colloidal suspension in phosphate buffered saline, K-Y Warming Jelly alone, and both of its humectant/solvent ingredients (neat propylene glycol and neat PEG-8). For excipients formulated in the HEC vehicle, 30% glycerin significantly increased susceptibility, and a trend toward increased HSV-2 susceptibility was observed after 10% glycerin, and 0.1% disodium EDTA, but not after 0.0186% disodium EDTA. The following excipients did not increase susceptibility: 10% propylene glycol, 0.18%, methylparaben plus 0.02% propylparaben, and 1% benzyl alcohol.</p> <p>Conclusions</p> <p>As reported with other surfactants, the surfactant/emulsifier GML markedly increased susceptibility to HSV-2. Glycerin at 30% significantly increased susceptibility, and, undiluted propylene glycol and PEG-8 greatly increased susceptibility.</p

Grain Surface Models and Data for Astrochemistry

AbstractThe cross-disciplinary field of astrochemistry exists to understand the formation, destruction, and survival of molecules in astrophysical environments. Molecules in space are synthesized via a large variety of gas-phase reactions, and reactions on dust-grain surfaces, where the surface acts as a catalyst. A broad consensus has been reached in the astrochemistry community on how to suitably treat gas-phase processes in models, and also on how to present the necessary reaction data in databases; however, no such consensus has yet been reached for grain-surface processes. A team of ∼25 experts covering observational, laboratory and theoretical (astro)chemistry met in summer of 2014 at the Lorentz Center in Leiden with the aim to provide solutions for this problem and to review the current state-of-the-art of grain surface models, both in terms of technical implementation into models as well as the most up-to-date information available from experiments and chemical computations. This review builds on the results of this workshop and gives an outlook for future directions