Characterization of Chromosomal Inversions Using Anti-Parallel Probes

A method for the characterization of chromosomal inversions using anti-parallel probes is described. Reporter species are attached to oligonucleotide strands designed such that they may hybridize to portions of only one of a pair of single-stranded sister chromatids which may be prepared by the CO-FISH procedure. If an inversion has occurred, these marker probes will be detected on the second sister chromatid at the same location as the inversion on the first chromatid. Further, one or more reporter species are replaced with anti-parallel probes that hybridize at known locations along the second sister chromatid such that the position and size of the inversion may be identified/estimated

The Spatial Correlation of Bent-Tail Galaxies and Galaxy Clusters

We have completed a deep radio continuum survey covering 86 square degrees of the Spitzer-South Pole Telescope deep field to test whether bent-tail galaxies are associated with galaxy clusters. We present a new catalogue of 22 bent-tail galaxies and a further 24 candidate bent-tail galaxies. Surprisingly, of the 8 bent-tail galaxies with photometric redshifts, only two are associated with known clusters. While the absence of bent-tail sources in known clusters may be explained by effects such as sensitivity, the absence of known clusters associated with most bent-tail galaxies casts doubt upon current models of bent-tail galaxies.Comment: Accepted by MNRA

Snap2Diverse: Coordinating Information Visualizations and Virtual Environments

The field of Information Visualization is concerned with improving with how users perceive, understand, and interact with visual representations of data sets. Immersive Virtual Environments (VEs) excel at providing researchers and designers a greater comprehension of the spatial features and relations of their data, models, and scenes. This project addresses the intersection of these two fields where information is visualized in a virtual environment. Specifically we are interested in visualizing abstract information in relation to spatial information in the context of a virtual environment. We describe a set of design issues for this type of integrated visualization and demonstrate a coordinated, multiple-views system supporting 2D and 3D visualization tasks such as overview, navigation, details-on-demand, and brushing-and-linking selection. Software architecture issues are discussed with details of our implementation applied to the domain of chemical information and visualization. Lastly, we subject our system to an informal usability evaluation and identify usability issues with interaction and navigation that may guide future work in these situations

Complete genome sequence of Salmonella enterica serovar Typhimurium U288

Salmonella enterica serovar Typhimurium U288 has firmly established itself within the United Kingdom pig production industry. The prevalence of this highly pathogenic multidrug-resistant serovar at such a critical point in the food chain is therefore of great concern. To enhance our understanding of this microorganism, whole-genome and plasmid sequencing was performed

Salmonella Typhimurium-specific bacteriophage ΦSH19 and the origins of species specificity in the Vi01-like phage family

<p>Abstract</p> <p>Background</p> <p>Whole genome sequencing of bacteriophages suitable for biocontrol of pathogens in food products is a pre-requisite to any phage-based intervention procedure. Trials involving the biosanitization of <it>Salmonella </it>Typhimurium in the pig production environment identified one such candidate, ΦSH19.</p> <p>Results</p> <p>This phage was sequenced and analysis of its 157,785 bp circular dsDNA genome revealed a number of interesting features. ΦSH19 constitutes another member of the recently-proposed <it>Myoviridae </it>Vi01-like family of phages, containing <it>S</it>. Typhi-specific Vi01 and <it>Shigella</it>-specific SboM-AG3. At the nucleotide level ΦSH19 is highly similar to phage Vi01 (80-98% pairwise identity over the length of the genome), with the major differences lying in the region associated with host-range determination. Analyses of the proteins encoded within this region by ΦSH19 revealed a cluster of three putative tail spikes. Of the three tail spikes, two have protein domains associated with the pectate lyase family of proteins (Tsp2) and P22 tail spike family (Tsp3) with the prospect that these enable <it>Salmonella </it>O antigen degradation. Tail spike proteins of Vi01 and SboM-AG3 are predicted to contain conserved right-handed parallel β-helical structures but the internal protein domains are varied allowing different host specificities.</p> <p>Conclusions</p> <p>The addition or exchange of tail spike protein modules is a major contributor to host range determination in the Vi01-like phage family.</p

Detection of chromosomal inversions using non-repetitive nucleic acid probes

A method for the identification of chromosomal inversions is described. Single-stranded sister chromatids are generated, for example by CO-FISH. A plurality of non-repetitive, labeled probes of relatively small size are hybridized to portions of only one of a pair of single-stranded sister chromatids. If no inversion exists, all of the probes will hybridize to a first chromatid. If an inversion has occurred, these marker probes will be detected on the sister chromatid at the same location as the inversion on the first chromatid

The complete plasmid sequences of Salmonella enterica serovar Typhimurium U288.

Salmonella enterica Serovar Typhimurium U288 is an emerging pathogen of pigs. The strain contains three plasmids of diverse origin that encode traits that are of concern for food security and safety, these include antibiotic resistant determinants, an array of functions that can modify cell physiology and permit genetic mobility. At 148,711 bp, pSTU288-1 appears to be a hybrid plasmid containing a conglomerate of genes found in pSLT of S. Typhimurium LT2, coupled with a mosaic of horizontally-acquired elements. Class I integron containing gene cassettes conferring resistance against clinically important antibiotics and compounds are present in pSTU288-1. A curious feature of the plasmid involves the deletion of two genes encoded in the Salmonella plasmid virulence operon (spvR and spvA) following the insertion of a tnpA IS26-like element coupled to a blaTEM gene. The spv operon is considered to be a major plasmid-encoded Salmonella virulence factor that is essential for the intracellular lifecycle. The loss of the positive regulator SpvR may impact on the pathogenesis of S. Typhimurium U288. A second 11,067 bp plasmid designated pSTU288-2 contains further antibiotic resistance determinants, as well as replication and mobilization genes. Finally, a small 4675 bp plasmid pSTU288-3 was identified containing mobilization genes and a pleD-like G-G-D/E-E-F conserved domain protein that modulate intracellular levels of cyclic di-GMP, and are associated with motile to sessile transitions in growth

The ATLAS-SPT radio survey of cluster galaxies

Using a high-performance computing cluster to mosaic 4,787 pointings, we have imaged the 100 sq. deg. South Pole Telescope (SPT) deep-field at 2.1 GHz using the Australian Telescope Compact Array to an rms of 80 mJy and a resolution of 8". Our goal is to generate an independent sample of radio-selected galaxy clusters to study how the radio properties compare with cluster properties at other wavelengths, over a wide range of redshifts in order to construct a timeline of their evolution out to z ~ 1:3. A preliminary analysis of the source catalogue suggests there is no spatial correlation between the clusters identified in the SPT-SZ catalogue and our wide-angle tail galaxies

Detection of Chromosomal Inversions Using Non-Repetitive Nucleic Acid Probes

A method and a kit for the identification of chromosomal inversions are described. Single-stranded sister chromatids are generated, for example by CO-FISH. A plurality of non-repetitive, labeled probes of relatively small size are hybridized to portions of only one of a pair of single-stranded sister chromatids. If no inversion exists, all of the probes will hybridize to a first chromatid. If an inversion has occurred, these marker probes will be detected on the sister chromatid at the same location as the inversion on the first chromatid

WFPC2 Observations of the Hubble Deep Field-South

The Hubble Deep Field-South observations targeted a high-galactic-latitude field near QSO J2233-606. We present WFPC2 observations of the field in four wide bandpasses centered at roughly 300, 450, 606, and 814 nm. Observations, data reduction procedures, and noise properties of the final images are discussed in detail. A catalog of sources is presented, and the number counts and color distributions of the galaxies are compared to a new catalog of the HDF-N that has been constructed in an identical manner. The two fields are qualitatively similar, with the galaxy number counts for the two fields agreeing to within 20%. The HDF-S has more candidate Lyman-break galaxies at z > 2 than the HDF-N. The star-formation rate per unit volume computed from the HDF-S, based on the UV luminosity of high-redshift candidates, is a factor of 1.9 higher than from the HDF-N at z ~ 2.7, and a factor of 1.3 higher at z ~ 4.Comment: 93 pages, 25 figures; contains very long table