Short interspersed nuclear element (SINE) sequences in the genome of the human pathogenic fungus Aspergillus fumigatus Af293.

Copyright: © 2016 The Authors. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Citation: Kanhayuwa L, Coutts RHA (2016) Short Interspersed Nuclear Element (SINE) Sequences in the Genome of the Human Pathogenic Fungus Aspergillus fumigatus Af293. PLoS ONE 11(10): e0163215. https://doi.org/10.1371/journal.pone.0163215.Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4-14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140-493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNAArg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3'-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50-65% and 60-75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259-343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity.Peer reviewedFinal Published versio

Identification of a family of SINEs and LINEs in the Pipistrellus kuhli genome: A new structural and functional symbiotic relationship

We initially describe a novel tRNA-derived SINE family, abundantly and randomly distributed in the genome of the bat Pipistrellus kuhli. We present evidence that the LINE retrotransposition machinery is recruited for the creation of a new chimerical retrotranscript constituted by the partial LINE reverse transcriptase ORF2, which is interrupted by the SINE15 retrotransposon. Structural homology between SINE15 and Homo sapiens helix 6 7SL RNA allows us to propose multiple genome partners for SINE retrotransposition, such as SRP proteins and LINE enzymatic machinery. Moreover, on the basis of the LINE and SINE/LINE chimerical transcripts, we propose a mutual relationship between SINE and LINE retrotransposons. © 2007 Elsevier Inc. All rights reserved

Ty1-copia group retrotransposons and the evolution of retroelements in several angiosperm plants: evidence of horizontal transmission.

"The phylogenetic relationships among thirty-seven new Ty1-copia group retrotransposons in seven angiosperm plants were examined by reverse transcriptase and ribonuclease H sequence analysis. Distribution pattern of the retrotransposons of closely related plant species generally reflects a close phylogenetic relationship. In contrast, we found that several retrotransposon sequences from the same genome exhibited a high degree of divergence and had a relatively high degree of identity versus retrotransposon sequences from widely divergent species, including an ancestral phytopathogen fungus. This finding supports the hypothesis that the horizontal transmission from phytopatogen organism to the host flowering plants could have played a role in the evolutionary dynamics of Ty1-copia group retrotransposons.

Patterns of treatment with PDE5 inhibitors in the clinical practice in Italy: longitudinal data from the Erectile Dysfunction Observational Study.

The Erectile Dysfunction Observational Study (EDOS) is a 6-months observational prospective multicentric study enrolling men with erectile dysfunction (ED) who asked, to be started on a treatment or to change a previous treatment. Aims of the study were to analyse the pattern of treatment and compare the efficacy of treatments used. Patients were enrolled during a normal hospital visit and were prescribed a treatment for ED. They were asked at baseline and after 3 and 6 months, to answer a set of questions from the International Index of Erectile Function, Erectile Dysfunction Inventory of Treatment Satisfaction (EDITS) and Short Form of the Psychological and Interpersonal Relationships Scale questionnaires (SF-PAIRS). Clinicians were free to prescribe any therapy for ED available in the market, and to change therapy at any time during the study. Out of 1 338 patients, available for analysis at 6 months, 624 (47%) changed their treatment during the study and 714 (53%) continued with the drug prescribed at baseline. Patients assuming tadalafil had a significantly higher probability of maintaining the same treatment compared to sildenafil or vardenafil. There was no clinically significant difference in terms of efficacy, patient satisfaction, self-confidence and spontaneity between the different inhibitors of PDE5. The 'time concerns' domain score of SF-PAIRS, was statistically better in patients assuming tadalafil. In conclusion sildenafil, vardenafil and tadalafil show similar efficacy in the clinical practice. However, patients receiving tadalafil display a lower risk to discontinue or change the treatment

Patterns of treatment with PDE5 inhibitors in the clinical practice in Italy: longitudinal data from the Erectile Dysfunction Observational Study.

The Erectile Dysfunction Observational Study (EDOS) is a 6-months observational prospective multicentric study enrolling men with erectile dysfunction (ED) who asked, to be started on a treatment or to change a previous treatment. Aims of the study were to analyse the pattern of treatment and compare the efficacy of treatments used. Patients were enrolled during a normal hospital visit and were prescribed a treatment for ED. They were asked at baseline and after 3 and 6 months, to answer a set of questions from the International Index of Erectile Function, Erectile Dysfunction Inventory of Treatment Satisfaction (EDITS) and Short Form of the Psychological and Interpersonal Relationships Scale questionnaires (SF-PAIRS). Clinicians were free to prescribe any therapy for ED available in the market, and to change therapy at any time during the study. Out of 1 338 patients, available for analysis at 6 months, 624 (47%) changed their treatment during the study and 714 (53%) continued with the drug prescribed at baseline. Patients assuming tadalafil had a significantly higher probability of maintaining the same treatment compared to sildenafil or vardenafil. There was no clinically significant difference in terms of efficacy, patient satisfaction, self-confidence and spontaneity between the different inhibitors of PDE5. The 'time concerns' domain score of SF-PAIRS, was statistically better in patients assuming tadalafil. In conclusion sildenafil, vardenafil and tadalafil show similar efficacy in the clinical practice. However, patients receiving tadalafil display a lower risk to discontinue or change the treatment