GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions

We live in an age of access to more information than ever before. This can be a double-edged sword. Increased access to information allows for more informed and empowered researchers, while information overload becomes an increasingly serious risk. Thus, there is a need for intelligent information retrieval systems that can summarize relevant and reliable textual sources to satisfy a user's query. Question answering is a specialized type of information retrieval with the aim of returning precise short answers to queries posed as natural language questions. We present a review and comparison of three biomedical question answering systems: askHERMES (http://www.askhermes.org/), EAGLi (http://eagl.unige.ch/EAGLi/), and HONQA (http://services.hon.ch/cgi-bin/QA10/qa.pl).     

Developing a quantitative index as a pragmatic aid to assessing implementation of European Union Birds Directive site protection measures for individual species

Capsule: A multi-element index is developed to help support decisions with respect to the establishment and review of national networks of European Union (EU) Special Protection Areas (SPAs).

Aims: To develop an index based on biological criteria which can be used to assess the sufficiency of protected area network coverage for national populations of individual bird species.

Methods: A Site Provision Index (SPI) was derived from data on species’ national and international distribution, population size, habitat use and site-fidelity. It was tested against the results of past UK policy and independent expert judgement.

Results: Index values were calculated for all regularly occurring UK birds for which the EU Birds Directive indicates that SPA provision should be considered. Index values and expert opinion on the percentage of populations of species expected to be found in a national network of protected areas were highly correlated. Indices also strongly correlated with existing provision of SPA protection for populations. Residuals from this regression relationship highlight objectively those species where consideration of further SPA provision may be necessary.

Conclusion: The SPI can provide a decision-support tool, through a form of gap analysis, to help identify where there is a significant difference between current protected area provision for a species and the level of provision that might be expected relative to other species with similar distribution and ecology.     

A first test of unattended,acoustic recorders for monitoring Capercaillie Tetrao urogallus lekking activity

Capsule: Automated acoustic recording can be used as a valuable survey technique for Capercaillie Tetrao urogallus leks, improving the quality and quantity of field data for this endangered bird species. However, more development work and testing against traditional methods are needed to establish optimal working practices.

Aims: This study aims to determine whether Capercaillie vocalizations can be recognized in lek recordings, whether this can be automated using readily available software, and whether the number of calls resulting varies with location, weather conditions, date and time of day.

Methods: Unattended recording devices and semi-automated call classification software were used to record and analyse the display calls of Capercaillie at three known lek sites in Scotland over a two-week period.

Results: Capercaillie calls were successfully and rapidly identified within a data set that included the vocalizations of other bird species and environmental noise. Calls could be readily recognized to species level using a combination of unsupervised software and manual analysis. The number of calls varied by time and date, by recorder/microphone location at the lek site, and with weather conditions. This information can be used to better target future acoustic monitoring and improve the quality of existing traditional lek surveys.

Conclusion: Bioacoustic methods provide a practical and cost-effective way to determine habitat occupancy and activity levels by a vocally distinctive bird species. Following further testing alongside traditional counting methods, it could offer a significant new approach towards more effective monitoring of local population levels for Capercaillie and other species of conservation concern.     

SynView: a GBrowse-compatible approach to visualizing comparative genome data

SUMMARY: We present SynView, a simple and generic approach to dynamically visualize multi-species comparative genome data. It is a light-weight application based on the popular and configurable web-based GBrowse framework. It can be used with a variety of databases and provides the user with a high degree of interactivity. The tool is written in Perl and runs on top of the GBrowse framework. It is in use in the PlasmoDB (http://www.PlasmoDB.org) and the CryptoDB (http://www.CryptoDB.org) projects and can be easily integrated into other cross-species comparative genome projects. AVAILABILITY: The program and instructions are freely available at http://www.ApiDB.org/apps/SynView/ CONTACT: jkissing@uga.edu.     

Understanding the molecular consequences of inherited muscular dystrophies: advancements through proteomic experimentation

Introduction: Proteomic techniques offer insights into the molecular perturbations occurring in muscular-dystrophies (MD). Revisiting published datasets can highlight conserved downstream molecular alterations, which may be worth re-assessing to determine whether their experimental manipulation is capable of modulating disease severity.

Areas covered: Here, we review the MD literature, highlighting conserved molecular insights warranting mechanistic investigation for therapeutic potential. We also describe a workflow currently proving effective for efficient identification of biomarkers & therapeutic targets in other neurodegenerative conditions, upon which future MD proteomic investigations could be modelled.

Expert commentary: Studying disease models can be useful for identifying biomarkers and model specific degenerative cascades, but rarely offer translatable mechanistic insights into disease pathology. Conversely, direct analysis of human samples undergoing degeneration presents challenges derived from complex chronic degenerative molecular processes. This requires a carefully planed & reproducible experimental paradigm accounting for patient selection through to grouping by disease severity and ending with proteomic data filtering and processing.     

A novel microRNA miR-1165-3p as a potential diagnostic biomarker for allergic asthma

Context: A further examination of a novel miRNA,miR-1165-3p as a biomarker for asthma, which was previously implicated in helper T cells (Th2) in a murine asthma model.

Objective: To determine whether serum miR-1165-3p can serve as a potential diagnostic biomarker for allergic asthma.

Methods: Serum miR-1165-3p was quantified via quantitative real-time PCR (qRT-PCR) in asthmatic and control samples. Serum miR-1165-3p levels were compared between groups and the clinical diagnostic abilities of miR-1165-3p were evaluated. The analyses utilized included a student’s t test, one-way ANOVA, and the generation of receiver operating characteristic (ROC) curves.

Results: Serum miRNA-1165-3p levels were significantly elevated in asthmatics when compared to the healthy controls. Furthermore, the sensitivity and specificity of serum miR-1165-3p were found to be 83% and 68.2%. Additionally, serum miR-1165-3p levels were also found to be significantly elevated in patients with allergic rhinitis (AR) or allergic bronchopulmonary aspergillosis (ABPA).

Conclusions: This study showed that serum miR-1165-3p can potentially be utilized as a noninvasive biomarker that is able to aid in the diagnosis and characterization of allergic asthma.     

Proteomics and pulse azidohomoalanine labeling of newly synthesized proteins: what are the potential applications?

Introduction: Measuring the immediate changes in cells that arise from changing environmental conditions is crucial to understanding the underlying mechanisms involved. These changes can be measured with metabolic stable isotope fully labeled proteomes, but requires looking for changes in the midst of a large background. In addition, labeling efficiency can be an issue in primary and fully differentiated cells.

Area covered: Azidohomoalanine (AHA), an analog of methionine, can be accepted by cellular translational machinery and incorporated into newly synthesized proteins (NSPs). AHA-NSPs can be coupled to biotin via CuAAC-mediated click-chemistry and enriched using avidin-based affinity purification. Thus, AHA-containing proteins or peptides can be enriched and efficiently separated from the whole proteome. In this review, we describe the development of mass spectrometry (MS) based AHA strategies and discuss their potential to measure proteins involved in immune response, secretome, gut microbiome, and proteostasis as well as their potential for clinical uses.

Expert commentary: AHA strategies have been used to identify synthesis activity and to compare two biological conditions in various biological model organisms. In combination with instrument development, improved sample preparation and fractionation strategies, MS-based AHA strategies have the potential for broad application, and the methods should translate into clinical use.     

XEMBL: distributing EMBL data in XML format

Data in the EMBL Nucleotide Sequence Database is traditionally available in a flat file format that has a number of known shortcomings. With XML rapidly emerging as a standard data exchange format that can address some problems of flat file formats by defining data structure and syntax, there is now a demand to distribute EMBL data in an XML format. XEMBL is a service tool that employs CORBA servers to access EMBL data, and distributes the data in XML format via a number of mechanisms. AVAILABILITY: Use of the XEMBL service is free of charge at http://www.ebi.ac.uk/xembl/, and can be accessed via web forms, CGI, and a SOAP-enabled service. SUPPLEMENTARY INFORMATION: Information on the EMBL Nucleotide Sequence Database is available at http://www.ebi.ac.uk/embl/. The EMBL Object Model is available at http://corba.ebi.ac.uk/models/. Information on the EMBL CORBA servers is at http://corba.ebi.ac.uk/     

A grid layout algorithm for automatic drawing of biochemical networks

MOTIVATION: Visualization is indispensable in the research of complex biochemical networks. Available graph layout algorithms are not adequate for satisfactorily drawing such networks. New methods are required to visualize automatically the topological architectures and facilitate the understanding of the functions of the networks. RESULTS: We propose a novel layout algorithm to draw complex biochemical networks. A network is modeled as a system of interacting nodes on squared grids. A discrete cost function between each node pair is designed based on the topological relation and the geometric positions of the two nodes. The layouts are produced by minimizing the total cost. We design a fast algorithm to minimize the discrete cost function, by which candidate layouts can be produced efficiently. A simulated annealing procedure is used to choose better candidates. Our algorithm demonstrates its ability to exhibit cluster structures clearly in relatively compact layout areas without any prior knowledge. We developed Windows software to implement the algorithm for CADLIVE. AVAILABILITY: All materials can be freely downloaded from http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/ SUPPLEMENTARY INFORMATION: http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/     

Future breeding and foraging sites of a southern edge population of the locally endangered Black Guillemot Cepphus grylle

Capsule: One of the southernmost populations of the Black Guillemot Cepphus grylle is currently endangered, and the risk may be exacerbated by climate change.

Aims: We evaluated the future vulnerability of the Black Guillemot by predicting the impact of climate change on the geographic distribution of its breeding and foraging range in the Baltic Sea.

Methods: We used MaxEnt, a species distribution modelling technique, to predict the current and future breeding grounds and foraging sites.

Results: We found that although the foraging range is expected to increase in the southern Baltic Sea in future, these areas will no longer be suitable as breeding grounds due to a changing climate, creating a spatial mismatch.

Conclusion: Our predictions indicate where threats to the species may be most severe and can be used to guide conservation planning. We advocate conservation measures which integrate potential future threats and focus on breeding sites across the current and future potential geographic range of the Black Guillemot.     

Web-based kinetic modelling using JWS Online

JWS Online is a repository of kinetic models, describing biological systems, which can be interactively run and interrogated over the Internet. It is implemented using a client-server strategy where the clients, in the form of web browser based Java applets, act as a graphical interface to the model servers, which perform the required numerical computations. AVAILABILITY: The JWS Online website is publicly accessible at http://jjj.biochem.sun.ac.za/ with mirrors at http://www.jjj.bio.vu.nl/ and http://jjj.vbi.vt.edu/     

Quantification of 1-hydroxypyrene, 1- and 2-hydroxynaphthalene, 3-hydroxybenzo[a]pyrene and 6-hydroxynitropyrene by HPLC-MS/MS in human urine as exposure biomarkers for environmental and occupational surveys

Context: Several urinary PAHs metabolites can be detected by HPLC-MS/MS for individual exposure assessment.

Objective: Quantitation of urinary metabolites of four PAHs, selected on the basis of their significance, with reduced costs and high sensitivity.

Materials and methods: HPLC-MS/MS was used and pure standards and isotope-labeled internal analogs of the analytes. Two hundred samples were tested after enzymatic hydrolysis.

Results: Accuracy was higher than 90% and variability lower than 19%; LODs permit to measure 1-hydroxypyrene, 1 and 2-hydroxynaphthalene in all subjects, 6-hydroxynitropyrene in the 65% and 3-hydroxybenzo[a]pyrene in the 70%.

Discussion and conclusion: The method is suitable both for occupational and for environmental studies. This is the first paper reporting urinary levels of 6-hydroxynitropyrene in European subjects, nonoccupationally exposed to nitro-PAHs.     

WiGID: wireless genome information database

WiGID, wireless genome information database, is a new application for mobile internet and can be reached through wireless application protocol (WAP). The main purpose of WiGID is to give easy access to information on completely sequenced genomes. Genome entries in WiGID can be queried by the number of open reading frames (ORFs), genus and species name and year published. Initial search results are linked to information on the full entry. AVAILABILITY: WiGID can be accessed through WAP at http://wigid.cgb.ki.se/index.wml and through the regular internet at http://wigid.cgb.ki.se.     

Impact assessment of risk parameters of underground coal mining on the environment

Coal is an important energy source but it has a significant negative impact on the environmental processes. This paper analyses the impact, measurement, and input of parameters representing potential environmental polluters in the information system (IS).

The methodology of recording and systematization includes the following parameters: coal deposits; climate parameters; roads; rivers; land and surrounding objects; air polluters; water polluters; and soil polluters. Methods for calculating land deformation, air polluter emissions, and noise impact are also presented.

Based on the number and specificity of analyzed data, the paper provides a concept of the IS and an overview of environmental impact of underground coal mine technological units. The concept was used to present the results of a research conducted at the underground coal mine “Soko” in Serbia.

The results of this research can help many potential users realize their goals. Those goals are preventive by nature, since negative environmental impact can be predicted, which enables the environmental protection experts to take appropriate measures.     

Transplanting the leafy liverwort Herbertus hutchinsiae: a suitable conservation tool to maintain oceanic-montane liverwort-rich heath?

Background: Translocating plants for conservation purposes can be a useful tool to enhance existing populations, restore lost populations or create new ones, but has rarely been done for bryophytes, especially liverworts.

Aims: Here, the leafy liverwort Herbertus hutchinsiae, a representative species of oceanic-montane liverwort-rich heath, was translocated to unoccupied habitat within its current range, to establish whether its restricted distribution is due to habitat or dispersal limitation.

Methods: Feasibility of establishing new populations outside the current distribution range was assessed, to test the suitability of the species for assisted colonisation. Furthermore, transplants were grown at degraded sites where the species had declined to assess potential for restoration.

Results: Although maximal growth rates occurred within-range, transplants grew at all sites, indicating that the species could be dispersal limited; a conclusion supported by distribution modelling.

Conclusions: Assisted colonisation is thus an option for this species to overcome dispersal limitation and to track future climate space. Reinforcement of populations at degraded sites is only recommended if the pressure causing the degradation has been removed. These findings provide an evidence base for practical conservation management.     

Methionine metabolism and multiple sclerosis

Context: Methylation reactions are particularly important in the brain and their inhibition can lead to a number of serious pathologies. Multiple sclerosis is one of the most common neurological disorders caused by interaction of genetic and environmental factors, but little is known about its cause or factors that contribute to the disorder. Although multiple sclerosis is primarily regarded as demyelinating disorder, there are no many articles focusing on methionine determination.

Objective: The aim of this work was to investigate whether serum methionine and its related compounds like homocysteine, cysteine, glutathione and asymmetric dimethylarginine were changed in multiple sclerosis patients.

Materials and methods: Sulphur-containing compounds were determined by using high-performance liquid chromatography with electrochemical detection in a single run for providing more complex view on methionine metabolism and asymmetric dimetylarginine was measured by a commercial enzyme-linked immunosorbent assay kit.

Results: Methionine and glutathione were decreased, but homocysteine, asymmetric dimethylarginine and cysteine were unchanged in patients with multiple sclerosis compared with controls.

Conclusions: Methionine and glutathione seem to be potential biomarkers for prognosis of the disease.     

Prophet, a web-based tool for class prediction using microarray data

Sample classification and class prediction is the aim of many gene expression studies. We present a web-based application, Prophet, which builds prediction rules and allows using them for further sample classification. Prophet automatically chooses the best classifier, along with the optimal selection of genes, using a strategy that renders unbiased cross-validated errors. Prophet is linked to different microarray data analysis modules, and includes a unique feature: the possibility of performing the functional interpretation of the molecular signature found. Availability: Prophet can be found at the URL http://prophet.bioinfo.cipf.es/ or within the GEPAS package at http://www.gepas.org/ Supplementary information: http://gepas.bioinfo.cipf.es/tutorial/prophet.html.     

JNK pathway in osteoarthritis: pathological and therapeutic aspects

Context: Osteoarthritis (OA) is a common chronic degenerative joint disease resulting in physical disability and reduced quality of life. Different biochemical signaling pathways are involved in the progression of OA, including the c-Jun NH2-terminal kinase (JNK) signal transduction pathway.

Objective: In this study, we have reviewed the recent updates on the association of JNK pathway with OA.

Methods: In this review, we have explored the databases like PubMed, Google Scholar, Medline, Scopus, etc., and collected the most relevant papers of JNK signaling pathway involved in the pathogenesis and therapeutics of OA

Results: JNK has been shown by scientific studies to be activated (phosphorylated) in OA that can play a key role in the cartilage destruction. Activation of JNK causes the phosphorylation of c-Jun that causes decreased proteoglycan synthesis and enhanced production of matrix metalloproteinase 13 (MMP-13). Overproduction of MMP-13 by chondrocytes plays a central role in cartilage degeneration in OA. Thus, targeting JNK pathway might be a promising therapeutic application for the prevention and treatment of OA. A number of JNK-inhibitors have been used in vitro and in vivo studies; however, not yet been translated into human use.

Conclusions: This review study indicates that JNK pathway plays an important role in development and progression of OA, and targeting the JNK pathway might be a potential approach for the treatment of OA in future.     

wombsoft: an r package that implements the Wombling method to identify genetic boundary

wombsoft is an r package that analyses individually georeferenced multilocus genotypes for the inferences of genetic boundaries between populations. It is based on the Wombling method that estimates the systemic function by looking for the local variation of the allele frequencies. This study presents an original way of estimating the systemic function, based on the local polynomial regression, and a binomial test to assess the significance of boundaries. The method applies to codominant or dominant markers and allows for missing data. The software r can be downloaded from http://www.r‐project.org/ and wombsoft from http://www‐leca.ujf‐grenoble.fr/logiciels.htm or http://www.r‐project.org/ .