Quantitative NME microscopy of iron transport in methanogenic aggregates

Transport of micronutrients (iron, cobalt, nickel, etc.) within biofilms matrixes such as methanogenic granules is of high importance, because these are either essential or toxic for the microorganisms living inside the biofilm. The present study demonstrates quantitative measurements of metal transport inside these biofilms using T1 weighted 3D RARE. It is shown that iron(II)-EDTA diffusion within the granule is independent of direction or the inner structure of the granules. Assuming position dependence of the spin-lattice relaxivity, Fick’s law for diffusion in a sphere can be applied to simulate the diffusion within the methanogenic granules under investigation. A relatively low diffusion coefficient of 2.5*10-11 m2·s-1 was obtained for iron diffusion within the methanogenic granul

Graph-based analysis and visualization of experimental results with ONDEX

Motivation: Assembling the relevant information needed to interpret the output from high-throughput, genome scale, experiments such as gene expression microarrays is challenging. Analysis reveals genes that show statistically significant changes in expression levels, but more information is needed to determine their biological relevance. The challenge is to bring these genes together with biological information distributed across hundreds of databases or buried in the scientific literature (millions of articles). Software tools are needed to automate this task which at present is labor-intensive and requires considerable informatics and biological expertise. Results: This article describes ONDEX and how it can be applied to the task of interpreting gene expression results. ONDEX is a database system that combines the features of semantic database integration and text mining with methods for graph-based analysis. An overview of the ONDEX system is presented, concentrating on recently developed features for graph-based analysis and visualization. A case study is used to show how ONDEX can help to identify causal relationships between stress response genes and metabolic pathways from gene expression data. ONDEX also discovered functional annotations for most of the genes that emerged as significant in the microarray experiment, but were previously of unknown function

Monitoring herpetofauna in a managed forest landscape: effects of habitat types and census techniques

We surveyed the herpetofaunal (amphibian and reptile) communities inhabiting five types of habitat on a managed landscape. We conducted monthly surveys during 1997 in four replicate plots of each habitat type using several different methods of collection. Communities of the two wetland habitats (bottomland wetlands and isolated upland wetlands) were clearly dissimilar from the three terrestrial communities (recent clearcut, pine plantation, and mixed pine–hardwood forest). Among the three terrestrial habitats, the total herpetofaunal communities were dissimilar (P\u3c0.10), although neither faunal constituent group alone (amphibians and squamate reptiles) varied significantly with regard to habitat. Three survey techniques used in the terrestrial habitats were not equally effective in that they resulted in the collection of different subsets of the total herpetofauna. The drift fence technique revealed the presence of more species and individuals in every habitat and was the only one to detect species dissimilarity among habitats. Nonetheless, coverboards contributed to measures of abundance and revealed species not detected by other techniques. We suggest that a combination of census techniques be used when surveying and monitoring herpetofaunal communities in order to maximize the detection of species

Dynamics, cation conformation and rotamers in guanidinium ionic liquids with ether groups

Ionic liquids are modern materials with a broad range of applications, including electrochemical devices, the exploitation of sustainable resources and chemical processing. Expanding the chemical space to include novel ion classes allows for the elucidation of novel structure-property relationships and fine tuning for specific applications. We prepared a set of ionic liquids based on the sparsely investigated pentamethyl guanidinium cation with a 2-ethoxy-ethyl side chain in combination with a series of frequently used anions. The resulting properties are compared to a cation with a pentyl side chain lacking ether functionalization. We measured the thermal transitions and transport properties to estimate the performance and trends of this cation class. The samples with imide-type anions form liquids at ambient temperature, and show good transport properties, comparable to imidazolium or ammonium ionic liquids. Despite the dynamics being significantly accelerated, ether functionalization of the cation favors the formation of crystalline solids. Single crystal structure analysis, ab initio calculations and variable temperature nuclear magnetic resonance measurements (VT-NMR) revealed that cation conformations for the ether- and alkyl-chain-substituted are different in both the solid and liquid states. While ether containing cations adopt compact, curled structures, those with pentyl side chains are linear. The Eyring plot revealed that the curled conformation is accompanied by a higher activation energy for rotation around the carbon-nitrogen bonds, due to the coordination of the ether chain as observed by VT-NMR

An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow

<p>Abstract</p> <p>Background</p> <p>Genomic analysis, particularly for less well-characterized organisms, is greatly assisted by performing comparative analyses between different types of genome maps and across species boundaries. Various providers publish a plethora of on-line resources collating genome mapping data from a multitude of species. Datasources range in scale and scope from small bespoke resources for particular organisms, through larger web-resources containing data from multiple species, to large-scale bioinformatics resources providing access to data derived from genome projects for model and non-model organisms. The heterogeneity of information held in these resources reflects both the technologies used to generate the data and the target users of each resource. Currently there is no common information exchange standard or protocol to enable access and integration of these disparate resources. Consequently data integration and comparison must be performed in an <it>ad hoc </it>manner.</p> <p>Results</p> <p>We have developed a simple generic XML schema (GenomicMappingData.xsd – GMD) to allow export and exchange of mapping data in a common lightweight XML document format. This schema represents the various types of data objects commonly described across mapping datasources and provides a mechanism for recording relationships between data objects. The schema is sufficiently generic to allow representation of any map type (for example genetic linkage maps, radiation hybrid maps, sequence maps and physical maps). It also provides mechanisms for recording data provenance and for cross referencing external datasources (including for example ENSEMBL, PubMed and Genbank.). The schema is extensible via the inclusion of additional datatypes, which can be achieved by importing further schemas, e.g. a schema defining relationship types. We have built demonstration web services that export data from our ArkDB database according to the GMD schema, facilitating the integration of data retrieval into Taverna workflows.</p> <p>Conclusion</p> <p>The data exchange standard we present here provides a useful generic format for transfer and integration of genomic and genetic mapping data. The extensibility of our schema allows for inclusion of additional data and provides a mechanism for typing mapping objects via third party standards. Web services retrieving GMD-compliant mapping data demonstrate that use of this exchange standard provides a practical mechanism for achieving data integration, by facilitating syntactically and semantically-controlled access to the data.</p

Theoretical analysis of electronic processes occurring during ultrafast demagnetization of cobalt triggered by X-ray photons tuned to Co L3_3 resonance

Magnetization dynamics triggered with ultrashort laser pulses has been attracting significant attention, with strong focus on the dynamics excited by VIS/NIR pulses. Only recently, strong magnetic response in solid materials induced by intense X-ray pulses from free-electron lasers (FELs) has been observed. The exact mechanisms that trigger the X-ray induced demagnetization are not yet fully understood. They are subject of on-going experimental and theoretical investigations. Here, we present a theoretical analysis of electronic processes occurring during demagnetization of Co multilayer system irradiated by X-ray pulses tuned to L$_3$-absorption edge of cobalt. We show that, similarly as in the case of X-ray induced demagnetization at M-edge of Co, electronic processes play a predominant role in the demagnetization until the pulse fluence does not exceed the structural damage threshold. The impact of electronic processes can reasonably well explain the available experimental data, without a need to introduce the mechanism of stimulated elastic forward scattering.Comment: 10 pages, 4 figures (7 panels), 57 references; pdfRevTeX class; double column formatting; two appendices and 18 references added; author-created version submitted to and accepted in Physical Review B journal. arXiv admin note: text overlap with arXiv:2202.1384