Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser

BACKGROUND: To facilitate efficient selection and the prioritization of candidate complex disease susceptibility genes for association analysis, increasingly comprehensive annotation tools are essential to integrate, visualize and analyze vast quantities of disparate data generated by genomic screens, public human genome sequence annotation and ancillary biological databases. We have developed a plug-in package for Ensembl called "Statistical Viewer" that facilitates the analysis of genomic features and annotation in the regions of interest defined by linkage analysis. RESULTS: Statistical Viewer is an add-on package to the open-source Ensembl Genome Browser and Annotation System that displays disease study-specific linkage and/or association data as 2 dimensional plots in new panels in the context of Ensembl's Contig View and Cyto View pages. An enhanced upload server facilitates the upload of statistical data, as well as additional feature annotation to be displayed in DAS tracts, in the form of Excel Files. The Statistical View panel, drawn directly under the ideogram, illustrates lod score values for markers from a study of interest that are plotted against their position in base pairs. A module called "Get Map" easily converts the genetic locations of markers to genomic coordinates. The graph is placed under the corresponding ideogram features a synchronized vertical sliding selection box that is seamlessly integrated into Ensembl's Contig- and Cyto- View pages to choose the region to be displayed in Ensembl's "Overview" and "Detailed View" panels. To resolve Association and Fine mapping data plots, a "Detailed Statistic View" plot corresponding to the "Detailed View" may be displayed underneath. CONCLUSION: Features mapping to regions of linkage are accentuated when Statistic View is used in conjunction with the Distributed Annotation System (DAS) to display supplemental laboratory information such as differentially expressed disease genes in private data tracks. Statistic View is a novel and powerful visual feature that enhances Ensembl's utility as valuable resource for integrative genomic-based approaches to the identification of candidate disease susceptibility genes. At present there are no other tools that provide for the visualization of 2-dimensional plots of quantitative data scores against genomic coordinates in the context of a primary public genome annotation browser

Atom--Molecule Coherence in a Bose-Einstein Condensate

Coherent coupling between atoms and molecules in a Bose-Einstein condensate (BEC) has been observed. Oscillations between atomic and molecular states were excited by sudden changes in the magnetic field near a Feshbach resonance and persisted for many periods of the oscillation. The oscillation frequency was measured over a large range of magnetic fields and is in excellent quantitative agreement with the energy difference between the colliding atom threshold energy and the energy of the bound molecular state. This agreement indicates that we have created a quantum superposition of atoms and diatomic molecules, which are chemically different species.Comment: 7 pages, 6 figure

Identifying Influenza Viruses with Resequencing Microarrays

Resequencing microarrays rapidly identify influenza viruses

Are Compression Stockings an Effective Treatment for Orthostatic Presyncope?

Syncope, or fainting, affects approximately 6.2% of the population, and is associated with significant comorbidity. Many syncopal events occur secondary to excessive venous pooling and capillary filtration in the lower limbs when upright. As such, a common approach to the management of syncope is the use of compression stockings. However, research confirming their efficacy is lacking. We aimed to investigate the effect of graded calf compression stockings on orthostatic tolerance

A Conjugative 38 kB Plasmid Is Present in Multiple Subspecies of <em>Xylella fastidiosa</em>

<div><p>A ∼38kB plasmid (pXF-RIV5) was present in the Riv5 strain of <em>Xylella fastidiosa</em> subsp. <em>multiplex</em> isolated from ornamental plum in southern California. The complete nucleotide sequence of pXF-RIV5 is almost identical to that of pXFAS01 from <em>X. fastidiosa</em> subsp. <em>fastidiosa</em> strain M23; the two plasmids vary at only 6 nucleotide positions. BLAST searches and phylogenetic analyses indicate pXF-RIV5 and pXFAS01 share some similarity to chromosomal and plasmid (pXF51) sequences of <em>X. fastidiosa</em> subsp. <em>pauca</em> strain 9a5c and more distant similarity to plasmids from a wide variety of bacteria. Both pXF-RIV5 and pXFAS01 encode homologues of a complete Type IV secretion system involved in conjugation and DNA transfer among bacteria. Mating pair formation proteins (Trb) from <em>Yersinia pseudotuberculosis</em> IP31758 are the mostly closely related non-<em>X. fastidiosa</em> proteins to most of the Trb proteins encoded by pXF-RIV5 and pXFAS01. Unlike many bacterial conjugative plasmids, pXF-RIV5 and pXFAS01 do not carry homologues of known accessory modules that confer selective advantage on host bacteria. However, both plasmids encode seven hypothetical proteins of unknown function and possess a small transposon-associated region encoding a putative transposase and associated factor. Vegetative replication of pXF-RIV5 and pXFAS01 appears to be under control of RepA protein and both plasmids have an origin of DNA replication (<em>oriV</em>) similar to that of pRP4 and pR751 from <em>Escherichia coli</em>. In contrast, conjugative plasmids commonly encode TrfA and have an <em>oriV</em> similar to those found in IncP-1 incompatibility group plasmids. The presence of nearly identical plasmids in single strains from two distinct subspecies of <em>X. fastidiosa</em> is indicative of recent horizontal transfer, probably subsequent to the introduction of subspecies <em>fastidiosa</em> to the United States in the late 19^th century.</p> </div

Genetic map of pXF-RIV5.

<p>The open reading frames are colored according to presumed function: red, plasmid replication and partition; purple, conjugative transfer (tra); blue, mating pair formation (trb); green, transposon associated; gray, hypothetical proteins of unknown function. The origin of replication (<i>oriV</i>) and the origin of transfer (<i>oriT</i>) are indicated by black circles. An inner circle marks HindIII restriction sites (H) used in subcloning.</p

Structure of <i>oriT</i> and <i>oriV</i>.

<p>A) <i>oriT</i> inverted repeats from pXF-RIV5, pRP4, and pR751 are shown as stem-loop structures to emphasize potential base parings. Unique bases are shown in red; bases conserved in at least two structures are shown in black. Red arrows indicate experimentally determined cleavage sites in pRP4 and pR751 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052131#pone.0052131-Pansegrau1" target="_blank">[21]</a>. B) Tandem repeats in pXF-RIV5 <i>oriV</i> are aligned and the 19-bp core is shown in red. Residues that vary from the consensus are shown in gray. Nucleotides shown (34333 – 34503) are contiguous.</p