A computational approach for identifying pathogenicity islands in prokaryotic genomes

BACKGROUND: Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs. RESULTS: We present a computational method for detecting potential PAIs in complete prokaryotic genomes by combining sequence similarities and abnormalities in genomic composition. We first collected 207 GenBank accessions containing either part or all of the reported PAI loci. In sequenced genomes, strips of PAI-homologs were defined based on the proximity of the homologs of genes in the same PAI accession. An algorithm reminiscent of sequence-assembly procedure was then devised to merge overlapping or adjacent genomic strips into a large genomic region. Among the defined genomic regions, PAI-like regions were identified by the presence of homolog(s) of virulence genes. Also, GIs were postulated by calculating G+C content anomalies and codon usage bias. Of 148 prokaryotic genomes examined, 23 pathogenic and 6 non-pathogenic bacteria contained 77 candidate PAIs that partly or entirely overlap GIs. CONCLUSION: Supporting the validity of our method, included in the list of candidate PAIs were thirty four PAIs previously identified from genome sequencing papers. Furthermore, in some instances, our method was able to detect entire PAIs for those only partial sequences are available. Our method was proven to be an efficient method for demarcating the potential PAIs in our study. Also, the function(s) and origin(s) of a candidate PAI can be inferred by investigating the PAI queries comprising it. Identification and analysis of potential PAIs in prokaryotic genomes will broaden our knowledge on the structure and properties of PAIs and the evolution of bacterial pathogenesis

High-resolution analysis of condition-specific regulatory modules in Saccharomyces cerevisiae

A novel approach for identifying condition-specific regulatory modules in yeast reveals functionally distinct coregulated submodules

Towards pathogenomics: a web-based resource for pathogenicity islands

Pathogenicity islands (PAIs) are genetic elements whose products are essential to the process of disease development. They have been horizontally (laterally) transferred from other microbes and are important in evolution of pathogenesis. In this study, a comprehensive database and search engines specialized for PAIs were established. The pathogenicity island database (PAIDB) is a comprehensive relational database of all the reported PAIs and potential PAI regions which were predicted by a method that combines feature-based analysis and similarity-based analysis. Also, using the PAI Finder search application, a multi-sequence query can be analyzed onsite for the presence of potential PAIs. As of April 2006, PAIDB contains 112 types of PAIs and 889 GenBank accessions containing either partial or all PAI loci previously reported in the literature, which are present in 497 strains of pathogenic bacteria. The database also offers 310 candidate PAIs predicted from 118 sequenced prokaryotic genomes. With the increasing number of prokaryotic genomes without functional inference and sequenced genetic regions of suspected involvement in diseases, this web-based, user-friendly resource has the potential to be of significant use in pathogenomics. PAIDB is freely accessible at

Percutaneous transthoracic localization of pulmonary nodules under C-arm cone-beam CT virtual navigation guidance

PURPOSEWe aimed to describe our initial experience with percutaneous transthoracic localization (PTL) of pulmonary nodules using a C-arm cone-beam CT (CBCT) virtual navigation guidance system.METHODSFrom February 2013 to March 2014, 79 consecutive patients (mean age, 61±10 years) with 81 solid or ground-glass nodules (mean size, 12.36±7.21 mm; range, 4.8–25 mm) underwent PTLs prior to video-assisted thoracoscopic surgery (VATS) excision under CBCT virtual navigation guidance using lipiodol (mean volume, 0.18±0.04 mL). Their procedural details, radiation dose, and complication rates were described.RESULTSAll 81 target nodules were successfully localized within 10 mm (mean distance, 2.54±3.24 mm) from the lipiodol markings. Mean number of CT acquisitions was 3.2±0.7, total procedure time was 14.6±5.14 min, and estimated radiation exposure during the localization was 5.21±2.51 mSv. Postprocedural complications occurred in 14 cases (17.3%); complications were minimal pneumothorax (n=10, 12.3%), parenchymal hemorrhage (n=3, 3.7%), and a small amount of hemoptysis (n=1, 1.2%). All target nodules were completely resected; pathologic diagnosis included invasive adenocarcinoma (n=53), adenocarcinoma-in-situ (n=10), atypical adenomatous hyperplasia (n=4), metastasis (n=7), and benign lesions (n=7).CONCLUSIONPTL procedures can be performed safely and accurately under the guidance of a CBCT virtual navigation system

Effects of a dielectric barrier discharge (DBD) on characteristics of polyaniline nanoparticles synthesized by a solution plasma process with an Ar gas bubble channel

The quality of polyaniline nanoparticles (PANI NPs) synthesized in plasma polymerization depends on the discharge characteristics of a solution plasma process (SPP). In this paper, the low temperature dielectric barrier discharge (DBD) is introduced to minimize the destruction of aniline molecules induced by the direct current (DC) spark discharge. By adopting the new electrode structure coupled with a gas channel, a low temperature DBD is successfully implemented in a SPP, for the first time, thus inducing an effective interaction between the Ar plasma and aniline monomer. We examine the effects of a low temperature DBD on characteristics of polyaniline nanoparticles synthesized by a SPP with an Ar gas bubble channel. As a result, both carbonization of aniline monomer and erosion of the electrode are significantly reduced, which is confirmed by analyses of the synthesized PANI NPs. © 2020 by the authors.1

Dokaz protutijela protiv velikog metilja Fasciola hepatica u goveda na otoku Ulleung, Koreja.

We performed a cross-sectional study to estimate the seroprevalence of Fasciola hepatica in herds of cattle on Ulleung island, Korea. Blood samples were collected from randomly selected cattle and the sera were separated and analysed with an ELISA to detect antibodies against F. hepatica. The positive samples were classified as mildly, moderately or strongly positive. Out of 405 cattle sera assessed, 38 (9.4%) were seropositive for antibodies against F. hepatica. From these, 2.5% each were moderately or strongly positive and 4.4% were mildly positive. A significantly higher seroprevalence (P<0.05) was observed in young animals (<2 y old, 15.3%) compared to adults (≥2 y old, 5.4%), while no significant difference in seropositivity was found between male and female animals. This is the the first report of F. hepatica seroprevalence in cattle herds in Korea. These findings may be used to establish a base-line of information for future investigations focused on the significance of F. hepatica in Korea.Provedeno je presječno istraživanje radi procjene seroprevalencije invadiranosti velikim metiljem Fasciola hepatica u stadima goveda na otoku Ulleung u Koreji. Uzorci krvi bili su uzeti od nasumce odabranih goveda, a odvojeni uzorci seruma bili su pretraženi imunoenzimnim testom na prisutnost protutijela specifičnih za velikog metilja. Pozitivni uzorci bili su svrstani u skupine: slabo, umjereno i jako pozitivni. Od 405 pretraženih uzoraka seruma, 38 (9,4%) je bilo pozitivnih na protutijela specifična za metilj F. hepatica. Od toga je 2,5% uzoraka bilo umjereno ili jako pozitivno, a 4,4% slabo pozitivno. Značajno veća seroprevalencija (P<0,05) ustanovljena je u mladih životinja (u dobi manjoj od dvije godine, 15,3%) u usporedbi s odraslima (≥2 godine, 5,4%), dok nije ustanovljena značajna razlika u seropozitivnosti između mužjaka i ženki. Ovo je prvo izvješće o seroprevalenciji velikog metilja u stadima goveda u Koreji. Nalazi mogu biti od koristi za buduća istraživanja o značenju velikog metilja F. hepatica u Koreji

Dokaz protutijela protiv velikog metilja Fasciola hepatica u goveda na otoku Ulleung, Koreja.

We performed a cross-sectional study to estimate the seroprevalence of Fasciola hepatica in herds of cattle on Ulleung island, Korea. Blood samples were collected from randomly selected cattle and the sera were separated and analysed with an ELISA to detect antibodies against F. hepatica. The positive samples were classified as mildly, moderately or strongly positive. Out of 405 cattle sera assessed, 38 (9.4%) were seropositive for antibodies against F. hepatica. From these, 2.5% each were moderately or strongly positive and 4.4% were mildly positive. A significantly higher seroprevalence (P<0.05) was observed in young animals (<2 y old, 15.3%) compared to adults (≥2 y old, 5.4%), while no significant difference in seropositivity was found between male and female animals. This is the the first report of F. hepatica seroprevalence in cattle herds in Korea. These findings may be used to establish a base-line of information for future investigations focused on the significance of F. hepatica in Korea.Provedeno je presječno istraživanje radi procjene seroprevalencije invadiranosti velikim metiljem Fasciola hepatica u stadima goveda na otoku Ulleung u Koreji. Uzorci krvi bili su uzeti od nasumce odabranih goveda, a odvojeni uzorci seruma bili su pretraženi imunoenzimnim testom na prisutnost protutijela specifičnih za velikog metilja. Pozitivni uzorci bili su svrstani u skupine: slabo, umjereno i jako pozitivni. Od 405 pretraženih uzoraka seruma, 38 (9,4%) je bilo pozitivnih na protutijela specifična za metilj F. hepatica. Od toga je 2,5% uzoraka bilo umjereno ili jako pozitivno, a 4,4% slabo pozitivno. Značajno veća seroprevalencija (P<0,05) ustanovljena je u mladih životinja (u dobi manjoj od dvije godine, 15,3%) u usporedbi s odraslima (≥2 godine, 5,4%), dok nije ustanovljena značajna razlika u seropozitivnosti između mužjaka i ženki. Ovo je prvo izvješće o seroprevalenciji velikog metilja u stadima goveda u Koreji. Nalazi mogu biti od koristi za buduća istraživanja o značenju velikog metilja F. hepatica u Koreji

5-Deoxy-Δ 12,14 -Prostaglandin J 2 Down-Regulates Activin-Induced Activin Receptor, Smad, and Cytokines Expression via Suppression of NF-B and MAPK Signaling in HepG2 Cells

15-Deoxy-Δ 12,14 -prostaglandin J 2 (15d-PGJ 2 ) and activin are implicated in the control of apoptosis, cell proliferation, and inflammation in cells. We examined both the mechanism by which 15d-PGJ 2 regulates the transcription of activin-induced activin receptors (ActR) and Smads in HepG2 cells and the involvement of the nuclear factor-B (NF-B) and mitogen-activated protein kinase (MAPK) pathways in this regulation. Activin A (25 ng/mL) inhibited HepG2 cell proliferation, whereas 15d-PGJ 2 (2 M and 5 M) had no effect. Activin A and 15d-PGJ 2 showed different regulatory effects on ActR and Smad expression, NF-B p65 activity and MEK/ERK phosphorylation, whereas they both decreased IL-6 production and increased IL-8 production. When costimulated with 15d-PGJ 2 and activin, 15d-PGJ 2 inhibited the activin-induced increases in ActR and Smad expression, and decreased activin-induced IL-6 production. However, it increased activin-induced IL-8 production. In addition, 15d-PGJ 2 inhibited activininduced NF-B p65 activity and activin-induced MEK/ERK phosphorylation. These results suggest that 15d-PGJ 2 suppresses activin-induced ActR and Smad expression, down-regulates IL-6 production, and up-regulates IL-8 production via suppression of NF-B and MAPK signaling pathway in HepG2 cells. Regulation of ActR and Smad transcript expression and cytokine production involves NF-B and the MAPK pathway via interaction with 15d-PGJ 2 /activin/Smad signaling