Simulation of rod ejection accident byPARCS code

This paper describes reactor core model used for simulating REA. The model was designed in PARCS utilizing graphical interface SNAP. The data for model were given from benchmark NEACPR L-335. The PARCS model used integrated thermal hydraulic block for calculation. The results and solution is shown in the paper. Thermal hydraulic calculation can also be provided by external system code TRACE. The PARCS model is prepared to couple with TRACE model for giving more accurate calculation

Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays

<p>Abstract</p> <p>Background</p> <p>Syphilis spirochete <it>Treponema pallidum </it>ssp. <it>pallidum </it>remains the enigmatic pathogen, since no virulence factors have been identified and the pathogenesis of the disease is poorly understood. Increasing rates of new syphilis cases per year have been observed recently.</p> <p>Results</p> <p>The genome of the SS14 strain was sequenced to high accuracy by an oligonucleotide array strategy requiring hybridization to only three arrays (Comparative Genome Sequencing, CGS). Gaps in the resulting sequence were filled with targeted dideoxy-terminators (DDT) sequencing and the sequence was confirmed by whole genome fingerprinting (WGF). When compared to the Nichols strain, 327 single nucleotide substitutions (224 transitions, 103 transversions), 14 deletions, and 18 insertions were found. On the proteome level, the highest frequency of amino acid-altering substitution polymorphisms was in novel genes, while the lowest was in housekeeping genes, as expected by their evolutionary conservation. Evidence was also found for hypervariable regions and multiple regions showing intrastrain heterogeneity in the <it>T. pallidum </it>chromosome.</p> <p>Conclusion</p> <p>The observed genetic changes do not have influence on the ability of <it>Treponema pallidum </it>to cause syphilitic infection, since both SS14 and Nichols are virulent in rabbit. However, this is the first assessment of the degree of variation between the two syphilis pathogens and paves the way for phylogenetic studies of this fascinating organism.</p

Complete Genome Sequence of Treponema paraluiscuniculi, Strain Cuniculi A: The Loss of Infectivity to Humans Is Associated with Genome Decay

Treponema paraluiscuniculi is the causative agent of rabbit venereal spirochetosis. It is not infectious to humans, although its genome structure is very closely related to other pathogenic Treponema species including Treponema pallidum subspecies pallidum, the etiological agent of syphilis. In this study, the genome sequence of Treponema paraluiscuniculi, strain Cuniculi A, was determined by a combination of several high-throughput sequencing strategies. Whereas the overall size (1,133,390 bp), arrangement, and gene content of the Cuniculi A genome closely resembled those of the T. pallidum genome, the T. paraluiscuniculi genome contained a markedly higher number of pseudogenes and gene fragments (51). In addition to pseudogenes, 33 divergent genes were also found in the T. paraluiscuniculi genome. A set of 32 (out of 84) affected genes encoded proteins of known or predicted function in the Nichols genome. These proteins included virulence factors, gene regulators and components of DNA repair and recombination. The majority (52 or 61.9%) of the Cuniculi A pseudogenes and divergent genes were of unknown function. Our results indicate that T. paraluiscuniculi has evolved from a T. pallidum-like ancestor and adapted to a specialized host-associated niche (rabbits) during loss of infectivity to humans. The genes that are inactivated or altered in T. paraluiscuniculi are candidates for virulence factors important in the infectivity and pathogenesis of T. pallidum subspecies

Whole Genome Sequences of Three Treponema pallidum ssp. pertenue Strains: Yaws and Syphilis Treponemes Differ in Less than 0.2% of the Genome Sequence

Spirochete Treponema pallidum ssp. pertenue (TPE) is the causative agent of yaws while strains of Treponema pallidum ssp. pallidum (TPA) cause syphilis. Both yaws and syphilis are distinguished on the basis of epidemiological characteristics and clinical symptoms. Neither treponeme can reproduce outside the host organism, which precludes the use of standard molecular biology techniques used to study cultivable pathogens. In this study, we determined high quality whole genome sequences of TPE strains and compared them to known genetic information for T. pallidum ssp. pallidum strains. The genome structure was identical in all three TPE strains and also between TPA and TPE strains. The TPE genome length ranged between 1,139,330 bp and 1,139,744 bp. The overall sequence identity between TPA and TPE genomes was 99.8%, indicating that the two pathogens are extremely closely related. A set of 34 TPE genes (3.5%) encoded proteins containing six or more amino acid replacements or other major sequence changes. These genes more often belonged to the group of genes with predicted virulence and unknown functions suggesting their involvement in infection differences between yaws and syphilis

Genomic epidemiology of syphilis reveals independent emergence of macrolide resistance across multiple circulating lineages.

Syphilis is a sexually transmitted infection caused by Treponema pallidum subspecies pallidum and may lead to severe complications. Recent years have seen striking increases in syphilis in many countries. Previous analyses have suggested one lineage of syphilis, SS14, may have expanded recently, indicating emergence of a single pandemic azithromycin-resistant cluster. Here we use direct sequencing of T. pallidum combined with phylogenomic analyses to show that both SS14- and Nichols-lineages are simultaneously circulating in clinically relevant populations in multiple countries. We correlate the appearance of genotypic macrolide resistance with multiple independently evolved SS14 sub-lineages and show that genotypically resistant and sensitive sub-lineages are spreading contemporaneously. These findings inform our understanding of the current syphilis epidemic by demonstrating how macrolide resistance evolves in Treponema subspecies and provide a warning on broader issues of antimicrobial resistance

Simulation of rod ejection accident byPARCS code

This paper describes reactor core model used for simulating REA. The model was designed in PARCS utilizing graphical interface SNAP. The data for model were given from benchmark NEACPR L-335. The PARCS model used integrated thermal hydraulic block for calculation. The results and solution is shown in the paper. Thermal hydraulic calculation can also be provided by external system code TRACE. The PARCS model is prepared to couple with TRACE model for giving more accurate calculation