Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections

<p>Abstract</p> <p>Background</p> <p>The recent emergence of the H5N1 influenza virus from avian reservoirs has raised concern about future influenza strains of high virulence emerging that could easily infect humans. We analyzed differential gene expression of lung epithelial cells to compare the response to H5N1 infection with a more benign infection with Respiratory Syncytial Virus (RSV). These gene expression data are then used as seeds to find important nodes by using a novel combination of the Gene Ontology database and the Human Network of gene interactions. Additional analysis of the data is conducted by training support vector machines (SVM) with the data and examining the orientations of the optimal hyperplanes generated.</p> <p>Results</p> <p>Analysis of gene clustering in the Gene Ontology shows no significant clustering of genes unique to H5N1 response at 8 hours post infection. At 24 hours post infection, however, a number of significant gene clusters are found for nodes representing "immune response" and "response to virus" terms. There were no significant clusters of genes in the Gene Ontology for the control (Mock) or RSV experiments that were unique relative to the H5N1 response. The genes found to be most important in distinguishing H5N1 infected cells from the controls using SVM showed a large degree of overlap with the list of significantly regulated genes. However, though none of these genes were members of the GO clusters found to be significant.</p> <p>Conclusions</p> <p>Characteristics of H5N1 infection compared to RSV infection show several immune response factors that are specific for each of these infections. These include faster timescales within the cell as well as a more focused activation of immunity factors. Many of the genes that are found to be significantly expressed in H5N1 response relative to the control experiments are not found to cluster significantly in the Gene Ontology. These genes are, however, often closely linked to the clustered genes through the Human Network. This may suggest the need for more diverse annotations of these genes and verification of their action in immune response.</p

Complete genome sequence of Deinococcus maricopensis type strain (LB-34T)

Deinococcus maricopensis (Rainey and da Costa 2005) is a member of the genus Deinococcus, which is comprised of 44 validly named species and is located within the deeply branching bacterial phylum Deinococcus–Thermus. Strain LB-34T was isolated from a soil sample from the Sonoran Desert in Arizona. Various species of the genus Deinococcus are characterized by extreme radiation resistance, with D. maricopensis being resistant in excess of 10 kGy. Even though the genomes of three Deinococcus species, D. radiodurans, D. geothermalis and D. deserti, have already been published, no special physiological characteristic is currently known that is unique to this group. It is therefore of special interest to analyze the genomes of additional species of the genus Deinococcus to better understand how these species adapted to gamma- or UV ionizing-radiation. The 3,498,530 bp long genome of D. maricopensis with its 3,301 protein-coding and 66 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project

Complete genome sequence of Odoribacter splanchnicus type strain (1651/6T)

Odoribacter splanchnicus (Werner et al. 1975) Hardham et al. 2008 is the type species of the genus Odoribacter, which belongs to the family Porphyromonadaceae in the order ‘Bacteroidales’. The species is of interest because members of the Odoribacter form an isolated cluster within the Porphyromonadaceae. This is the first completed genome sequence of a member of the genus Odoribacter and the fourth sequence from the family Porphyromonadaceae. The 4,392,288 bp long genome with its 3,672 protein-coding and 74 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project

Persistent urogenital sinus with recto-vaginal fistula: the new variant in which the anus is normally positioned and literature review

Abstract Background Persistent urogenital sinus is a rare cloacal anomaly in which the urinary and genital tracts cannot be differentiated during embryonic development. However, the presence of concomitant recto-urogenital sinus or recto-vaginal fistula is much rarer. In the literature, only two cases with accompanying fistula have been presented so far. Case presentation We present the diagnosis and treatment management of a persistent urogenital sinus case with recto-vaginal fistula. We also aimed to reveal the difference between our patient, who is the 3rd case in the literature, and the other two and the described cloacal anomalies. By performing total urogenital sinus mobilization and fistula repair, the three systems were separated from each other, and both a functional and cosmetic appearance was obtained. Conclusion It should be kept in mind that there may be different variants other than the defined cloacal malformations. In patients with cloacal malformation, cystoscopy and rectoscopy should be performed to reveal the anatomy before reconstructive surgery in order to avoid any unexpected situation