Mouse large-scale phenotyping initiatives: overview of the European Mouse Disease Clinic (EUMODIC) and of the Wellcome Trust Sanger Institute Mouse Genetics Project

Two large-scale phenotyping efforts, the European Mouse Disease Clinic (EUMODIC) and the Wellcome Trust Sanger Institute Mouse Genetics Project (SANGER-MGP), started during the late 2000s with the aim to deliver a comprehensive assessment of phenotypes or to screen for robust indicators of diseases in mouse mutants. They both took advantage of available mouse mutant lines but predominantly of the embryonic stem (ES) cells resources derived from the European Conditional Mouse Mutagenesis programme (EUCOMM) and the Knockout Mouse Project (KOMP) to produce and study 799 mouse models that were systematically analysed with a comprehensive set of physiological and behavioural paradigms. They captured more than 400 variables and an additional panel of metadata describing the conditions of the tests. All the data are now available through EuroPhenome database (www.europhenome.org) and the WTSI mouse portal (http://www.sanger.ac.uk/mouseportal/), and the corresponding mouse lines are available through the European Mouse Mutant Archive (EMMA), the International Knockout Mouse Consortium (IKMC), or the Knockout Mouse Project (KOMP) Repository. Overall conclusions from both studies converged, with at least one phenotype scored in at least 80?% of the mutant lines. In addition, 57?% of the lines were viable, 13?% subviable, 30?% embryonic lethal, and 7?% displayed fertility impairments. These efforts provide an important underpinning for a future global programme that will undertake the complete functional annotation of the mammalian genome in the mouse model.     

Identifying differentially expressed subnetworks with MMG

BACKGROUND: Mixture model on graphs (MMG) is a probabilistic model that integrates network topology with (gene, protein) expression data to predict the regulation state of genes and proteins. It is remarkably robust to missing data, a feature particularly important for its use in quantitative proteomics. A new implementation in C and interfaced with R makes MMG extremely fast and easy to use and to extend. AVAILABILITY: The original implementation (Matlab) is still available from http://www.dcs.shef.ac.uk/~guido/; the new implementation is available from http://wrightlab.group.shef.ac.uk/people_noirel.htm, from CRAN, and has been submitted to BioConductor, http://www.bioconductor.org/.     

Abundance matters: role of albumin in diabetes,a proteomics perspective

Introduction: Human serum albumin (HSA) is a multifaceted protein with vital physiological functions. It is the most abundant plasma protein with inherent capability to bind to diverse ligands, and thus susceptible to various post-translational modifications (PTMs) which alter its structure and functions. One such PTM is glycation, a non-enzymatic reaction between reducing sugar and protein leading to formation of heterogeneous advanced glycation end products (AGEs). Glycated albumin (GA) concentration increases significantly in diabetes and is implicated in development of secondary complications.

Areas covered: In this review, we discuss in depth, formation of GA and its consequences, approaches used for characterization and quantification of GA, milestones in GA proteomics, clinical relevance of GA as a biomarker, significance of maintaining abundant levels of albumin and future perspectives.

Expert commentary: Elevated GA levels are associated with development of insulin resistance as well as secondary complications, in healthy and diabetic individuals respectively. Mass spectrometry (MS) based approaches aid in precise characterization and quantification of GA including early and advanced glycated peptides, which can be useful in prediction of the disease status. Thus GA has evolved to be one of the best candidates in the pursuit of diagnostic markers for prediction of prediabetes and diabetic complications.     

ontoCAT: an R package for ontology traversal and search

MOTIVATION: There exist few simple and easily accessible methods to integrate ontologies programmatically in the R environment. We present ontoCAT-an R package to access ontologies in widely used standard formats, stored locally in the filesystem or available online. The ontoCAT package supports a number of traversal and search functions on a single ontology, as well as searching for ontology terms across multiple ontologies and in major ontology repositories. AVAILABILITY: The package and sources are freely available in Bioconductor starting from version 2.8: http://bioconductor.org/help/bioc-views/release/bioc/html/ontoCAT.html or via the OntoCAT website http://www.ontocat.org/wiki/r. CONTACT: natalja@ebi.ac.uk; natalja@ebi.ac.uk.     

Derivation and characterisation of hESC lines from supernumerary embryos, experience from Odense, Denmark

The derivation and characterisation of human embryonic stem cells provides a source of pluripotent stem cells with potential for clinical applications. Utilising locally sourced embryos from two IVF clinics, we derived and characterised five new cell lines for use in a non-clinical setting. Analysis of clinical data showed that the majority of embryos (94.5%) failed to reach the blastocyst stage of development and of all embryos, regardless of developmental status, 248 embryos were needed to create one stem cell line. From the number of embryos (69) which developed to the blastocyst stage 8.7% developed into cell lines. Using outgrowth of the whole blastocyst, we derived five new, unreported cell lines in Odense, Denmark between 2005 and 2006. Characterisation was carried out using RT-PCR, staining, karyotyping, EB formation and teratoma formation. The KMEB hESC lines will, in the future, be made available through the UK Stem Cell Bank (http://www.ukstemcellbank.org.uk/).     

The design of Jemboss: a graphical user interface to EMBOSS

DESIGN: Jemboss is a graphical user interface (GUI) for the European Molecular Biology Open Software Suite (EMBOSS). It is being developed at the MRC UK HGMP-RC as part of the EMBOSS project. This paper explains the technical aspects of the Jemboss client-server design. The client-server model optionally allows that a Jemboss user have an account on the remote server. The Jemboss client is written in Java and is downloaded automatically to a user's workstation via Java Web Start using the HTML protocol. The client then communicates with the remote server using SOAP (Simple Object Access Protocol). A Tomcat server listens on the remote machine and communicates the SOAP requests to a Jemboss server, again written in Java. This Java server interprets the client requests and executes them through Java Native Interface (JNI) code written in the C language. Another C program having setuid privilege, jembossctl, is called by the JNI code to perform the client requests under the user's account on the server. The commands include execution of EMBOSS applications, file management and project management tasks. Jemboss allows the use of JSSE for encryption of communication between the client and server. The GUI parses the EMBOSS Ajax Command Definition language for form generation and maximum input flexibility. Jemboss interacts directly with the EMBOSS libraries to allow dynamic generation of application default settings. RESULTS: This interface is part of the EMBOSS distribution and has attracted much interest. It has been set up at many other sites globally as well as being used at the HGMP-RC for registered users. AVAILABILITY: The software, EMBOSS and Jemboss, is freely available to academics and commercial users under the GPL licence. It can be downloaded from the EMBOSS ftp server: http://www.uk.embnet.org/Software/EMBOSS/, ftp://ftp.uk.embnet.org/pub/EMBOSS/. Registered HGMP-RC users can access an installed server from: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/     

Water Footprint Symposium: where next for water footprint and water assessment methodology?

Recognizing the need for a comprehensive review of the tools and metrics for the quantification and assessment of water footprints, and allowing for the opportunity for open discussion on the challenges and future of water footprinting methodology, an international symposium on water footprint was organized. The Water Footprint Symposium was held in December 2013 at the University of Leeds, UK. In particular, four areas were highlighted for discussion: water footprint and agriculture, quantification of water footprint, industrial water footprint, and from theory to practice. Discussion was organized to focus on the “prioritization of water footprint research & applications to practical sectors”. The concept of water footprinting has helped to better communicate water management and assessment among different research and user communities. Significant research progress has been made in the relations between water footprint and agriculture, quantification of water footprint, industrial water footprint, and the transition from theory to practice. Future water footprint research needs to further enhance assessment accuracy, improve sustainability assessment methodology, develop databases, address uncertainties, and prioritize application by government and in practical sectors. More information on the symposium can be found on the water@leeds website: http://www.wateratleeds.org/conferences/2013/water-footprint-symposium.     

Cardiovascular GO Annotation Initiative Year 1 Report: Why Cardiovascular GO?

Gene Ontology (GO) vocabularies are an established standard for linking functional information to genes and gene products (www.geneontology.org/). A recent collaboration between University College London and the European Bioinformatics Institute is providing GO annotation to human cardiovascular-associated genes (http://www.ucl.ac.uk/medicine/cardiovascular-genetics/geneontology.html). This report outlines the aims of this collaboration and summarizes how the cardiovascular community can help improve the quality and quantity of GO annotations. This new initiative is funded by the British Heart Foundation and fully supported by the GO Consortium.     

ProServer: a simple, extensible Perl DAS server

SUMMARY: The increasing size and complexity of biological databases has led to a growing trend to federate rather than duplicate them. In order to share data between federated databases, protocols for the exchange mechanism must be developed. One such data exchange protocol that is widely used is the Distributed Annotation System (DAS). For example, DAS has enabled small experimental groups to integrate their data into the Ensembl genome browser. We have developed ProServer, a simple, lightweight, Perl-based DAS server that does not depend on a separate HTTP server. The ProServer package is easily extensible, allowing data to be served from almost any underlying data model. Recent additions to the DAS protocol have enabled both structure and alignment (sequence and structural) data to be exchanged. ProServer allows both of these data types to be served. AVAILABILITY: ProServer can be downloaded from http://www.sanger.ac.uk/proserver/ or CPAN http://search.cpan.org/~rpettett/. Details on the system requirements and installation of ProServer can be found at http://www.sanger.ac.uk/proserver/.     

Response to: the nature of evidence for and against epigenetic inheritance

We thank Dr. Nadeau for his interest in our work. Dr. Nadeau has raised concerns about the experimental approach (mouse strains, route of administration, lack of phenotypic assessment) and about the validity of our conclusions. We will respond to each of these concerns point-by point.Please see related article: www.dx.doi.org/10.1186/s13059-015-0709-y     

ToxoDB: accessing the Toxoplasma gondii genome

ToxoDB (http://ToxoDB.org) provides a genome resource for the protozoan parasite Toxoplasma gondii. Several sequencing projects devoted to T. gondii have been completed or are in progress: an EST project (http://genome.wustl.edu/est/index.php?toxoplasma=1), a BAC clone end-sequencing project (http://www.sanger.ac.uk/Projects/T_gondii/) and an 8X random shotgun genomic sequencing project (http://www.tigr.org/tdb/e2k1/tga1/). ToxoDB was designed to provide a central point of access for all available T. gondii data, and a variety of data mining tools useful for the analysis of unfinished, un-annotated draft sequence during the early phases of the genome project. In later stages, as more and different types of data become available (microarray, proteomic, SNP, QTL, etc.) the database will provide an integrated data analysis platform facilitating user-defined queries across the different data types.     

The effect of a haptic biofeedback system on postural control in patients with stroke: An experimental pilot study

Background: Impaired balance in patients with hemiparesis caused by stroke is frequently related to deficits in the central integration of afferent inputs, and traditional rehabilitation reinforces excessive visual reliance by focusing on visual compensation.

Objective: The present study investigated whether a balance task involving a haptic biofeedback (BF) system, which provided supplementary vibrotactile sensory cues associated with center-of-foot-pressure displacement, improved postural control in patients with stroke.

Methods: Seventeen stroke patients were assigned to two groups: the Vibrotactile BF and Control groups. During the balance task (i.e., standing on a foam mat), participants in the Vibrotactile BF group tried to stabilize their postural sway while wearing the BF system around the pelvic girdle. In the Control group, participants performed an identical postural task without the BF system.

Results: Pre- and post-test measurements of postural control using a force plate revealed that the stability of bipedal posture in the Vibrotactile BF group was markedly improved compared with that in the Control group.

Conclusions: A balance task involving a vibrotactile BF system improved postural stability in patients with stroke immediately. This confirms the potential of a haptic-based BF system for balance training, both in routine clinical practice and in everyday life.     

PartiGene--constructing partial genomes

Expressed sequence tags (ESTs) offer a low-cost approach to gene discovery and are being used by an increasing number of laboratories to obtain sequence information for a wide variety of organisms. The challenge lies in processing and organizing this data within a genomic context to facilitate large scale analyses. Here we present PartiGene, an integrated sequence analysis suite that uses freely available public domain software to (1) process raw trace chromatograms into sequence objects suitable for submission to dbEST; (2) place these sequences within a genomic context; (3) perform customizable first-pass annotation of the data; and (4) present the data as HTML tables and an SQL database resource. PartiGene has been used to create a number of non-model organism database resources including NEMBASE (http://www.nematodes.org) and LumbriBase (http://www.earthworms.org/). The packages are readily portable, freely available and can be run on simple Linux-based workstations. AVAILABILITY: PartiGene is available from http://www.nematodes.org/PartiGene and also forms part of the EST analysis software, associated with the Natural Environmental Research Council (UK) Bio-Linux project (http://envgen.nox.ac.uk/biolinux.html).     

The ModFOLD server for the quality assessment of protein structural models

The reliable assessment of the quality of protein structural models is fundamental to the progress of structural bioinformatics. The ModFOLD server provides access to two accurate techniques for the global and local prediction of the quality of 3D models of proteins. Firstly ModFOLD, which is a fast Model Quality Assessment Program (MQAP) used for the global assessment of either single or multiple models. Secondly ModFOLDclust, which is a more intensive method that carries out clustering of multiple models and provides per-residue local quality assessment. AVAILABILITY: http://www.biocentre.rdg.ac.uk/bioinformatics/ModFOLD/.     

Comet assay for assessment of DNA damage in greenhouse workers exposed to pesticides

Purpose: The main goal of the present study was to determine DNA damage in pesticide-exposed greenhouse workers and pesticides non-exposed controls.

Materials and methods: The DNA damage was measured by alkaline comet assay method (pH?>?13) in 41 greenhouse workers and 45 non-exposed individuals as the control. Pesticide exposure was assessed by duration of working in the greenhouse and pesticide application in the greenhouse time. DNA damage was estimated by arbitrary unit and damage frequency.

Results: Arbitrary unit and damage frequency were consistently significantly higher in greenhouse workers than those of the controls (p?=?0.001). In terms of gender in greenhouse, DNA damage of female workers was significantly higher than those in male workers (p?<?0.05). We found significant correlation between DNA damage and working hours spent. Multiple linear regression analysis showed that working hours in the greenhouse as an indication of pesticide exposure were significantly associated with the DNA damage, which can be attributed to the genotoxic potential of the pesticide mixture.

Conclusions: The comet assay is sensitive to detect the damage exposed to chronic effect of pesticides in greenhouse workers. Significant DNA damage was obtained for the exposed group, which was associated with the pesticide exposure.     

Mapping SNPs to protein sequence and structure data

MOTIVATION: Data on both single nucleotide polymorphisms and disease-related mutations are being collected at ever-increasing rates. To understand the structural effects of missense mutations, we consider both classes under the term single amino acid polymorphisms (SAAPs) and we wish to map these to protein structure where their effects can be analyzed. Our initial aim therefore is to create a completely automatically maintained database of SAAPs mapped to individual residues in the Protein Data Bank (PDB) updated as new mutations or structures become available. RESULTS: We present an integrated pipeline for the automated mapping of SAAP data from HGVbase to individual PDB residues. Achieving this in a completely automated and reliable manner is a complex task. Data extracted from HGVbase are mapped to EMBL entries to confirm whether the mutation occurs in an exon and, if so, where in the sequence it occurs. From there we map to Swiss-Prot entries and thence to the PDB. AVAILABILITY: The resulting database may be accessed over the web at http://www.bioinf.org.uk/saap/ or http://acrmwww.biochem.ucl.ac.uk/saap/ CONTACT: a.martin@biochem.ucl.ac.uk.     

Sequence search algorithm assessment and testing toolkit (SAT)

MOTIVATION: The Sequence Search Algorithm Assessment and Testing Toolkit (SAT) aims to be a complete package for the comparison of different protein homology search algorithms. The structural classification of proteins can provide us with a clear criterion for judgment in homology detection. There have been several assessments based on structural sequences with classifications but a good deal of similar work is now being repeated with locally developed procedures and programs. The SAT will provide developers with a complete package which will save time and produce more comparable performance assessments for search algorithms. The package is complete in the sense that it provides a non-redundant large sequence resource database, a well-characterized query database of proteins domains, all the parsers and some previous results from PSI-BLAST and a hidden markov model algorithm. RESULTS: An analysis on two different data sets was carried out using the SAT package. It compared the performance of a full protein sequence database (RSDB100) with a non-redundant representative sequence database derived from it (RSDB50). The performance measurement indicated that the full database is sub-optimal for a homology search. This result justifies the use of much smaller and faster RSDB50 than RSDB100 for the SAT. AVAILABILITY: A web site is up. The whole packa ge is accessible via www and ftp. ftp://ftp.ebi.ac.uk/pub/contrib/jong/SAT http://cyrah.ebi.ac.uk:1111/Proj/Bio/SAT http://www.mrc-lmb.cam.ac.uk/genomes/SAT In the package, some previous assessment results produced by the package can also be found for reference. CONTACT: jong@ebi.ac.uk