ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data

ProfCom is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of ‘complex functions’. A ‘Complex function’ is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes. ProfCom provides a user friendly dialog-driven web page submission available for several model organisms and supports most available gene identifiers. In addition, the web service interface allows the submission of any kind of annotation data. ProfCom is freely available at http://webclu.bio.wzw.tum.de/profcom/

A Study of Euclidean K-Ary Gcd Algorithm

The problem of computing the greatest common divisor GCD of natural numbers is one of the most common problems that is solved in modern computational mathematics and its applications. At the moment, many algorithms are known to solve this problem, but every day the requirements for the effectiveness of such algorithms become more stringent. As a result, there is a need to create new algorithms that are more efficient in time and number of the operations performed. Besides, they must allow the possibility of their transformation into modern programming languages while maintaining the efficiency of the algorithm.This article presents an analysis of the realization features and the results of testing the speed of three GCD computation algorithms: the classical Euclidean algorithm, the Sorenson k-ary algorithm, and the approximating k-ary algorithm developed by the second of the authors in MicrosoftVisualStudio in C #. Qualitative and quantitative data on the effectiveness of these algorithms in terms of time and number of the steps within the main cycle are have been obtained.The concluding part of the article contains the analysis of the results obtained, their representation in the diagrams, and gives the recommendations on the choice of the parameters of the methods

Predicting global habitat suitability for stony corals on seamounts

Aim Globally, species distribution patterns in the deep sea are poorly resolved, with spatial coverage being sparse for most taxa and true absence data missing. Increasing human impacts on deep-sea ecosystems mean that reaching a better understanding of such patterns is becoming more urgent. Cold-water stony corals (Order Scleractinia) form structurally complex habitats (dense thickets or reefs) that can support a diversity of other associated fauna. Despite their widely accepted ecological importance, records of scleractinian corals on seamounts are patchy and simply not available for most of the global ocean. The objective of this paper is to model the global distribution of suitable habitat for stony corals on seamounts. Location Seamounts worldwide. Methods We compiled a database containing all accessible records of scleractinian corals on seamounts. Two modelling approaches developed for presence-only data were used to predict global habitat suitability for seamount scleractinians: maximum entropy modelling (Maxent) and environmental niche factor analysis (ENFA). We generated habitat-suitability maps and used a cross-validation process with a threshold-independent metric to evaluate the performance of the models. Results Both models performed well in cross-validation, although the Maxent method consistently outperformed ENFA. Highly suitable habitat for seamount stony corals was predicted to occur at most modelled depths in the North Atlantic, and in a circumglobal strip in the Southern Hemisphere between 20° and 50° S and shallower than around 1500 m. Seamount summits in most other regions appeared much less likely to provide suitable habitat, except for small near-surface patches. The patterns of habitat suitability largely reflect current biogeographical knowledge. Environmental variables positively associated with high predicted habitat suitability included the aragonite saturation state, and oxygen saturation and concentration. By contrast, low levels of dissolved inorganic carbon, nitrate, phosphate and silicate were associated with high predicted suitability. High correlation among variables made assessing individual drivers difficult. Main conclusions Our models predict environmental conditions likely to play a role in determining large-scale scleractinian coral distributions on seamounts, and provide a baseline scenario on a global scale. These results present a first-order hypothesis that can be tested by further sampling. Given the high vulnerability of cold-water corals to human impacts, such predictions are crucial tools in developing worldwide conservation and management strategies for seamount ecosystems. © 2009 Blackwell Publishing Ltd

Применение песен в обучении иностранным языкам

Целью данного исследования является изучение и анализ существующих методик обучения английскому языку с помощью песен для последующего описания наиболее эффективной методики обучения. Для достижения поставленной цели были выявлены преимущества использования музыки и песен во время обучения иностранным языкам на примере английского, и сформирована полная методика обучения с помощью песен.The purpose of this research is to investigate and analyse existing methods of teaching English by listening to songs in order to provide a more detailed description of the most effective teaching method. To accomplish the purpose, the benefits of using music and songs during the teaching of foreign languages in English were examined, and the comprehensive method of teaching using songs was developed

Selecting control genes for RT-QPCR using public microarray data

Background: Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely used techniques for expression profiling of selected genes. In order to obtain results that are comparable across assays, a stable normalization strategy is required. In general, the normalization of PCR measurements between different samples uses one to several control genes (e. g. housekeeping genes), from which a baseline reference level is constructed. Thus, the choice of the control genes is of utmost importance, yet there is not a generally accepted standard technique for screening a large number of candidates and identifying the best ones. Results: We propose a novel approach for scoring and ranking candidate genes for their suitability as control genes. Our approach relies on publicly available microarray data and allows the combination of multiple data sets originating from different platforms and/or representing different pathologies. The use of microarray data allows the screening of tens of thousands of genes, producing very comprehensive lists of candidates. We also provide two lists of candidate control genes: one which is breast cancer-specific and one with more general applicability. Two genes from the breast cancer list which had not been previously used as control genes are identified and validated by RT-QPCR. Open source R functions are available at http://www.isrec.isb-sib.ch/similar to vpopovic/research/ Conclusion: We proposed a new method for identifying candidate control genes for RT-QPCR which was able to rank thousands of genes according to some predefined suitability criteria and we applied it to the case of breast cancer. We also empirically showed that translating the results from microarray to PCR platform was achievable

HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors

<p>Abstract</p> <p>Background</p> <p>Protein domain classification is an important step in metagenomic annotation. The state-of-the-art method for protein domain classification is profile HMM-based alignment. However, the relatively high rates of insertions and deletions in homopolymer regions of pyrosequencing reads create frameshifts, causing conventional profile HMM alignment tools to generate alignments with marginal scores. This makes error-containing gene fragments unclassifiable with conventional tools. Thus, there is a need for an accurate domain classification tool that can detect and correct sequencing errors.</p> <p>Results</p> <p>We introduce HMM-FRAME, a protein domain classification tool based on an augmented Viterbi algorithm that can incorporate error models from different sequencing platforms. HMM-FRAME corrects sequencing errors and classifies putative gene fragments into domain families. It achieved high error detection sensitivity and specificity in a data set with annotated errors. We applied HMM-FRAME in Targeted Metagenomics and a published metagenomic data set. The results showed that our tool can correct frameshifts in error-containing sequences, generate much longer alignments with significantly smaller E-values, and classify more sequences into their native families.</p> <p>Conclusions</p> <p>HMM-FRAME provides a complementary protein domain classification tool to conventional profile HMM-based methods for data sets containing frameshifts. Its current implementation is best used for small-scale metagenomic data sets. The source code of HMM-FRAME can be downloaded at <url>http://www.cse.msu.edu/~zhangy72/hmmframe/</url> and at <url>https://sourceforge.net/projects/hmm-frame/</url>.</p

The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets

<p>Abstract</p> <p>Background</p> <p>Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS) makes it an obvious target for such development. While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting, processing and presenting publicly submitted GC/MS metabolomics datasets for public re-analysis.</p> <p>Description</p> <p>Here, we present MetabolomeExpress, a new File Transfer Protocol (FTP) server and web-tool for the online storage, processing, visualisation and statistical re-analysis of publicly submitted GC/MS metabolomics datasets. Users may search a quality-controlled database of metabolite response statistics from publicly submitted datasets by a number of parameters (eg. metabolite, species, organ/biofluid etc.). Users may also perform meta-analysis comparisons of multiple independent experiments or re-analyse public primary datasets via user-friendly tools for t-test, principal components analysis, hierarchical cluster analysis and correlation analysis. They may interact with chromatograms, mass spectra and peak detection results via an integrated raw data viewer. Researchers who register for a free account may upload (via FTP) their own data to the server for online processing via a novel raw data processing pipeline.</p> <p>Conclusions</p> <p>MetabolomeExpress <url>https://www.metabolome-express.org</url> provides a new opportunity for the general metabolomics community to transparently present online the raw and processed GC/MS data underlying their metabolomics publications. Transparent sharing of these data will allow researchers to assess data quality and draw their own insights from published metabolomics datasets.</p

g:Profiler—a web server for functional interpretation of gene lists (2011 update)

Functional interpretation of candidate gene lists is an essential task in modern biomedical research. Here, we present the 2011 update of g:Profiler (http://biit.cs.ut.ee/gprofiler/), a popular collection of web tools for functional analysis. g:GOSt and g:Cocoa combine comprehensive methods for interpreting gene lists, ordered lists and list collections in the context of biomedical ontologies, pathways, transcription factor and microRNA regulatory motifs and protein–protein interactions. Additional tools, namely the biomolecule ID mapping service (g:Convert), gene expression similarity searcher (g:Sorter) and gene homology searcher (g:Orth) provide numerous ways for further analysis and interpretation. In this update, we have implemented several features of interest to the community: (i) functional analysis of single nucleotide polymorphisms and other DNA polymorphisms is supported by chromosomal queries; (ii) network analysis identifies enriched protein–protein interaction modules in gene lists; (iii) functional analysis covers human disease genes; and (iv) improved statistics and filtering provide more concise results. g:Profiler is a regularly updated resource that is available for a wide range of species, including mammals, plants, fungi and insects

Magnesium administration provokes motor unit survival, after sciatic nerve injury in neonatal rats

BACKGROUND: We examined the time course of the functional alterations in two types of muscles following sciatic nerve crush in neonatal rats and the neuroprotective effect of Mg(2+). METHODS: The nerve crush was performed on the 2(nd )postnatal day. MgSO(4)*7H(2)O was administered daily for two weeks. Animals were examined for the contractile properties and for the number of motor units of extensor digitorum longus and soleus muscles at three postnatal stages and adulthood. Four experimental groups were included in this study: i) controls, ii) axotomized rats, iii) magnesium treated controls and iv) axotomized and Mg(2+)-treated rats. RESULTS: Axotomy resulted in 20% MU survival in EDL and 50% in soleus. In contrast, magnesium treatment resulted in a significant motor unit survival (40% survival in EDL and 80% in soleus). The neuroprotective effects of Mg(2+ )were evident immediately after the Mg(2+)-treatment. Immature EDL and soleus muscles were slow and fatigueable. Soleus gradually became fatigue resistant, whereas, after axotomy, soleus remained fatigueable up to adulthood. EDL gradually became fastcontracting. Tetanic contraction in axotomized EDL was just 3,3% of the control side, compared to 15,2% in Mg(2+)-treated adult rats. The same parameter for axotomized soleus was 12% compared to 97% in Mg(2+)-treated adult rats. CONCLUSIONS: These results demonstrate that motoneuron death occurs mostly within two weeks of axotomy. Magnesium administration rescues motoneurons and increases the number of motor units surviving into adulthood. Fast and slow muscles respond differently to axotomy and to subsequent Mg(2+ )treatment in vivo

Gas transfer through clay barriers

Gas transport through clay-rocks can occur by different processes that can be basically subdivided into pressure-driven flow of a bulk gas phase and transport of dissolved gas either by molecular diffusion or advective water flow (Figure 1, Marschall et al., 2005). The relative importance of these transport mechanisms depends on the boundary conditions and the scale of the system. Pressure-driven volume flow (“Darcy flow”) of gas is the most efficient transport mechanism. It requires, however, pressure gradients that are sufficiently large to overcome capillary forces in the typically water-saturated rocks (purely gas-saturated argillaceous rocks are not considered in the present context). These pressure gradients may form as a consequence of the gravity field (buoyancy, compaction) or by gas generation processes (thermogenic, microbial, radiolytic). Dissolved gas may be transported by water flow along a hydraulic gradient. This process is not affected by capillary forces but constrained by the solubility of the gas. It has much lower transport efficiency than bulk gas phase flow. Molecular diffusion of dissolved gas, finally, is occurring essentially without constraints, ubiquitously and perpetually. Effective diffusion distances are, however, proportional to the square root of time, which limits the relevance of this transport process to the range of tens to hundreds of metres on a geological time scale (millions of years). 2 Process understanding and the quantification of the controlling parameters, like diffusion coefficients, capillary gas breakthrough pressures and effective gas permeability coefficients, is of great importance for up-scaling purposes in different research disciplines and applications. During the past decades, gas migration through fully water-saturated geological clay-rich barriers has been investigated extensively (Thomas et al., 1968, Pusch and Forsberg, 1983; Horseman et al., 1999; Galle, 2000; Hildenbrand et al., 2002; Marschall et al., 2005; Davy et al., 2009; Harrington et al., 2009, 2012a, 2014). All of these studies aimed at the analysis of experimental data determined for different materials (rocks of different lithotype, composition, compaction state) and pressure/temperature conditions. The clay-rocks investigated in these studies, ranged from unconsolidated to indurated clays and shales, all characterised by small pores (2-100 nm) and very low hydraulic conductivity (K < 10-12 m·s-1) or permeability coefficients (k < 10-19 m²). Studies concerning radioactive waste disposal include investigations of both the natural host rock formation and synthetic/engineered backfill material at a depth of a few hundred meters (IAEA, 2003, 2009). Within a geological disposal facility, hydrogen is generated by anaerobic corrosion of metals and through radiolysis of water (Rodwell et al., 1999; Yu and Weetjens, 2009). Additionally, methane and carbon dioxide are generated by microbial degradation of organic wastes (Rodwell et al., 1999; Ortiz et al., 2002; Johnson, 2006; Yu and Weetjens, 2009). The focus of carbon capture and storage (CCS) studies is on the analysis of the long-term sealing efficiency of lithologies above depleted reservoirs or saline aquifers, typically at larger depths (hundreds to thousands of meters). During the last decade, several studies were published on the sealing integrity of clay-rocks to carbon dioxide (Hildenbrand et al., 2004; Li et al., 2005; Hangx et al., 2009; Harrington et al., 2009; Skurtveit et al., 2012; Amann-Hildenbrand et al., 2013). In the context of petroleum system analysis, a significant volume of research has been undertaken regarding gas/oil expulsion mechanisms from sources rocks during burial history (Tissot & Pellet, 1971; Appold & Nunn, 2002), secondary migration (Luo et al., 2008) and the capillary sealing capacity of caprocks overlying natural gas accumulations (Berg, 1975; Schowalter, 1979; Krooss, 1992; Schlömer and Kross, 2004; Li et al., 2005; Berne et al., 2010). Recently, more attention has been paid to investigations of the transport efficiency of shales in the context of oil/gas shale production (Bustin et al., 2008; Eseme et al., 2012; Amann-Hildenbrand et al., 2012; Ghanizadeh et al., 2013, 2014). Analysis of the migration mechanisms within partly unlithified strata becomes important when explaining the 3 origin of overpressure zones, sub-seafloor gas domes and gas seepages (Hovland & Judd, 1988; Boudreau, 2012). The conduction of experiments and data evaluation/interpretation requires a profound process understanding and a high level of experience. The acquisition and preparation of adequate samples for laboratory experiments usually constitutes a major challenge and may have serious impact on the representativeness of the experimental results. Information on the success/failure rate of the sample preparation procedure should therefore be provided. Sample specimens “surviving” this procedure are subjected to various experimental protocols to derive information on their gas transport properties. The present overview first presents the theoretical background of gas diffusion and advective flow, each followed by a literature review (sections 2 and 3). Different experimental methods are described in sections 4.1 and 4.2. Details are provided on selected experiments performed at the Belgian Nuclear Research Centre (SCK-CEN, Belgium), Ecole Centrale de Lille (France), British Geological Survey (UK), and at RWTH-Aachen University (Germany) (section 4.3). Experimental data are discussed with respect to different petrophysical parameters outlined above: i) gas diffusion, ii) evolution of gas breakthrough, iii) dilation-controlled flow, and iv) effective gas permeability after breakthrough. These experiments were conducted under different pressure and temperature conditions, depending on sample type, burial depth and research focus (e.g. radioactive waste disposal, natural gas exploration, or carbon dioxide storage). The interpretation of the experimental results can be difficult and sometimes a clear discrimination between different mechanisms (and the controlling parameters) is not possible. This holds, for instance, for gas breakthrough experiments where the observed transport can be interpreted as intermittent, continuous, capillary- or dilation-controlled flow. Also, low gas flow rates through samples on the length-scale of centimetres can be equally explained by effective two-phase flow or diffusion of dissolved gas