Differential gene body methylation and reduced expression of cell adhesion and neurotransmitter receptor genes in adverse maternal environment

Early life adversity, including adverse gestational and postpartum maternal environment, is a contributing factor in the development of autism, attention deficit hyperactivity disorder (ADHD), anxiety and depression but little is known about the underlying molecular mechanism. In a model of gestational maternal adversity that leads to innate anxiety, increased stress reactivity and impaired vocal communication in the offspring, we asked if a specific DNA methylation signature is associated with the emergence of the behavioral phenotype. Genome-wide DNA methylation analyses identified 2.3% of CpGs as differentially methylated (that is, differentially methylated sites, DMSs) by the adverse environment in ventral-hippocampal granule cells, neurons that can be linked to the anxiety phenotype. DMSs were typically clustered and these clusters were preferentially located at gene bodies. Although CpGs are typically either highly methylated or unmethylated, DMSs had an intermediate (20-80%) methylation level that may contribute to their sensitivity to environmental adversity. The adverse maternal environment resulted in either hyper or hypomethylation at DMSs. Clusters of DMSs were enriched in genes that encode cell adhesion molecules and neurotransmitter receptors; some of which were also downregulated, indicating multiple functional deficits at the synapse in adversity. Pharmacological and genetic evidence links many of these genes to anxiety.

TissueInfo: high-throughput identification of tissue expression profiles and specificity

We describe TissueInfo, a knowledge-based method for the high-throughput identification of tissue expression profiles and tissue specificity. TissueInfo defines a set of tissue information calculations that can be computed for large numbers of genes, expressed sequence tags (ESTs) or proteins. Tissue information records that result from the TissueInfo calculations are used to generate tables suitable for data mining and for the selection of genes according to a given expression profile or specificity. When benchmarked against a test set of 116 proteins and literature information, TissueInfo was found to be accurate for 69% of identified tissue specificities and for 80% of expression profiles. The accuracy of the identifications can be increased if query sequences for which little information is available from dbEST are ignored. Thus, with 80% coverage, TissueInfo achieves an accuracy of 76% for specificity and 89% for expression. For the same set of proteins, the curated tissue specificity offered in SWISS-PROT was accurate in 78% of cases. TissueInfo can be useful for the selection of clones for custom microarrays, selection of training sets for ab initio identification of tissue information, gene discovery and genome-wide predictions. Further information about the program can be found at http://icb.mssm.edu/tissueinfo.

Tas1r3, encoding a new candidate taste receptor, is allelic to the sweet responsiveness locus Sac

The ability to taste the sweetness of carbohydrate-rich foodstuffs has a critical role in the nutritional status of humans. Although several components of bitter transduction pathways have been identified, the receptors and other sweet transduction elements remain unknown. The Sac locus in mouse, mapped to the distal end of chromosome 4 (refs. 7-9), is the major determinant of differences between sweet-sensitive and -insensitive strains of mice in their responsiveness to saccharin, sucrose and other sweeteners. To identify the human Sac locus, we searched for candidate genes within a region of approximately one million base pairs of the sequenced human genome syntenous to the region of Sac in mouse. From this search, we identified a likely candidate: T1R3, a previously unknown G protein-coupled receptor (GPCR) and the only GPCR in this region. Mouse Tas1r3 (encoding T1r3) maps to within 20,000 bp of the marker closest to Sac (ref. 9) and, like human TAS1R3, is expressed selectively in taste receptor cells. By comparing the sequence of Tas1r3 from several independently derived strains of mice, we identified a specific polymorphism that assorts between taster and non-taster strains. According to models of its structure, T1r3 from non-tasters is predicted to have an extra amino-terminal glycosylation site that, if used, would interfere with dimerization.

Clustalnet: the joining of Clustal and CORBA

MOTIVATION

Performing sequence alignment operations from a different program than the original sequence alignment code, and/or through a network connection, is often required. Interactive alignment editors and large-scale biological data analysis are common examples where such a flexibility is important. Interoperability between the alignment engine and the client should be obtained regardless of the architectures and programming languages of the server and client.

RESULTS

Clustalnet, a Clustal alignment CORBA server is described, which was developed on the basis of Clustalw. This server brings the robustness of the algorithms and implementations of Clustal to a new level of reuse. A Clustalnet server object can be accessed from a program, transparently through the network. We present interfaces to perform the alignment operations and to control these operations via immutable contexts. The interfaces that select the contexts do not depend on the nature of the operation to be performed, making the design modular. The IDL interfaces presented here are not specific to Clustal and can be implemented on top of different sequence alignment algorithm implementations.

Interactive construction of residue-based diagrams of proteins: the RbDe web service

We announce the Residue-based Diagram Editor (RbDe) web service that allows online construction of residue-based diagrams and the creation of stored diagram libraries. The service has been tuned for the construction of snake-like diagrams (for transmembrane proteins) but can be used to render any protein for which defined secondary structure data or hypotheses are available. RbDe is freely available through the Internet from our web site: http://transport.physbio. mssm.edu/rbde/RbDe.html. Licenses for intranet uses can be obtained upon request.

Visualisation and integration of G protein-coupled receptor related information help the modelling: description and applications of the Viseur program

G Protein-Coupled Receptors (GPCRs) constitute a superfamily of receptors that forms an important therapeutic target. The number of known GPCR sequences and related information increases rapidly. For these reasons, we are developing the Viseur program to integrate the available information related to GPCRs. The Viseur program allows one to interactively visualise and/or modify the sequences, transmembrane areas, alignments, models and results of mutagenesis experiments in an integrated environment. This integration increases the ease of modelling GPCRs: visualisation and manipulation improvements enable easier databank interrogation and interpretation. Unique program features include: (i) automatic construction of 'Snake-like' diagrams or hyperlinked GPCR molecular models to HTML or VRML and (ii) automatic access to a mutagenesis data server through the Internet. The novel algorithms or methods involved are presented, followed by the overall complementary features of the program. Finally, we present two applications of the program: (i) an automatic construction of GPCR snake-like diagrams for the GPCRDB WWW server, and (ii) a preparation of the modelling of the 5HT receptor subtypes. The interest of the direct access to mutagenesis results through an alignment and a molecular model are discussed. The Viseur program, which runs on SGI workstations, is freely available and can be used for preparing the modelling of integral membrane proteins or as an alignment editor tool.

Schematic representation of residue-based protein context-dependent data: an application to transmembrane proteins

An algorithmic method for drawing residue-based schematic diagrams of proteins on a 2D page is presented and illustrated. The method allows the creation of rendering engines dedicated to a given family of sequences, or fold. The initial implementation provides an engine that can produce a 2D diagram representing secondary structure for any transmembrane protein sequence. We present the details of the strategy for automating the drawing of these diagrams. The most important part of this strategy is the development of an algorithm for laying out residues of a loop that connects to arbitrary points of a 2D plane. As implemented, this algorithm is suitable for real-time modification of the loop layout. This work is of interest for the representation and analysis of data from (1) protein databases, (2) mutagenesis results, or (3) various kinds of protein context-dependent annotations or data.

Multiple sequence alignment in HTML: colored, possibly hyperlinked, compact representations

Protein sequence alignments are widely used in protein structure prediction, protein engineering, modeling of proteins, etc. This type of representation is useful at different stages of scientific activity: looking at previous results, working on a research project, and presenting the results. There is a need to make it available through a network (intranet or WWW), in a way that allows biologists, chemists, and noncomputer specialists to look at the data and carry on research--possibly in a collaborative research. Previous methods (text-based, Java-based) are reported and their advantages are discussed. We have developed two novel approaches to represent the alignments as colored, hyper-linked HTML pages. The first method creates an HTML page that uses efficiently the image cache mechanism of a WWW browser, thereby allowing the user to browse different alignments without waiting for the images to be loaded through the network, but only for the first viewed alignment. The generated pages can be browsed with any HTML2.0-compliant browser. The second method that we propose uses W3C-CSS1-style sheets to render alignments. This new method generates pages that require recent browsers to be viewed. We implemented these methods in the Viseur program and made a WWW service available that allows a user to convert an MSF alignment file in HTML for WWW publishing. The latter service is available at http:@www.lctn.u-nancy.fr/viseur/services.htm l.

GPCRDB: an information system for G protein-coupled receptors

The GPCRDB is a G protein-coupled receptor (GPCR) database system aimed at the collection and dissemination of GPCR related data. It holds sequences, mutant data and ligand binding constants as primary (experimental) data. Computationally derived data such as multiple sequence alignments, three dimensional models, phylogenetic trees and two dimensional visualization tools are added to enhance the database's usefulness. The GPCRDB is an EU sponsored project aimed at building a generic molecular class specific database capable of dealing with highly heterogeneous data. GPCRs were chosen as test molecules because of their enormous importance for medical sciences and due to the availability of so much highly heterogeneous data. The GPCRDB is available via the WWW at http://www.gpcr.org/7tm