RNomics: a computational search for box C/D snoRNA genes in the D. melanogaster genome.

Motivation: In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly C/D and H/ACA snoRNAs), which act as guides in the maturation or post-transcriptional modifications of target RNA molecules. Since in Drosophila melanogaster (Dm) only few examples of snoRNAs have been identified so far by cDNA libraries screening, integration of the molecular data with in silico identification of these types of genes could throw light on their organization in the Dm genome. Results: We have performed a computational screening of the Dm genome for C/D snoRNA genes, followed by experimental validation of the putative candidates. Few of the 26 confirmed snoRNAs had been recognized by cDNA library analysis. Organization of the Dm genome was also found to be more variegated than previously suspected, with snoRNA genes nested in both the introns and exons of protein-coding genes. This finding suggests that the presence of additional mechanisms of snoRNA biogenesis based on the alternative production of overlapping mRNA/snoRNA molecules. Availability: Additional information is available at http://www. bioinformatica.unito.it/bioinformatics/snoRNA

The coding/non-coding overlapping architecture of the gene encoding the Drosophila pseudouridine synthase

BACKGROUND: In eukaryotic cells, each molecule of H/ACA small nucleolar RNA (snoRNA) assembles with four evolutionarily conserved core proteins to compose a specific ribonucleoprotein particle. One of the four core components has pseudouridine synthase activity and catalyzes the conversion of a selected uridine to pseudouridine. Members of the pseudouridine synthase family are highly conserved. In addition to catalyzing pseudouridylation of target RNAs, they carry out a variety of essential functions related to ribosome biogenesis and, in mammals, to telomere maintenance. To investigate further the molecular mechanisms underlying the expression of pseudouridine synthase genes, we analyzed the transcriptional activity of the Drosophila member of this family in great detail. RESULTS: The Drosophila gene for pseudouridine synthase, minifly/Nop60b (mfl), encodes two novel mRNAs ending at a downstream poly(A) site. One species is characterized only by an extended 3'-untranslated region (3'UTR), while a minor mRNA encodes a variant protein that represents the first example of an alternative subform described for any member of the family to date. The rare spliced variant is detected mainly in females and is predicted to have distinct functional properties. We also report that a cluster comprising four isoforms of a C/D box snoRNA and two highly related copies of a small ncRNA gene of unknown function is intron-encoded at the gene-variable 3'UTRs. Because this arrangement, the alternative 3' ends allow mfl not only to produce two distinct protein subforms, but also to release different ncRNAs. Intriguingly, accumulation of all these intron-encoded RNAs was found to be sex-biased and quantitatively modulated throughout development and, within the ovaries, the ncRNAs of unknown function were found not ubiquitously expressed. CONCLUSION: Our results expand the repertoire of coding/non-coding transcripts derived from the gene encoding Drosophila pseudouridine synthase. This gene exhibits a complex and interlaced organization, and its genetic information may be expressed as different protein subforms and/or ncRNAs that may potentially contribute to its biological functions

Expression of human Cfdp1 gene in Drosophila reveals new insights into the function of the evolutionarily conserved BCNT protein family

The Bucentaur (BCNT) protein family is widely distributed in eukaryotes and is characterized by a highly conserved C-terminal domain. This family was identified two decades ago in ruminants, but its role(s) remained largely unknown. Investigating cellular functions and mechanism of action of BCNT proteins is challenging, because they have been implicated in human craniofacial development. Recently, we found that YETI, the D. melanogaster BCNT, is a chromatin factor that participates to H2A.V deposition. Here we report the effects of in vivo expression of CFDP1, the human BCNT protein, in Drosophila melanogaster. We show that CFDP1, similarly to YETI, binds to chromatin and its expression results in a wide range of abnormalities highly reminiscent of those observed in Yeti null mutants. This indicates that CFDP1 expressed in flies behaves in a dominant negative fashion disrupting the YETI function. Moreover, GST pull-down provides evidence indicating that 1) both YETI and CFDP1 undergo homodimerization and 2) YETI and CFDP1 physically interact each other by forming inactive heterodimers that would trigger the observed dominant-negative effect. Overall, our findings highlight unanticipated evidences suggesting that homodimerization mediated by the BCNT domain is integral to the chromatin functions of BCNT proteins

A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome

Abstract Motivation: In eukaryotes, the family of non-coding RNA genes includes a number of genes encoding small nucleolar RNAs (mainly C/D and H/ACA snoRNAs), which act as guides in the maturation or post-transcriptional modifications of target RNA molecules. Since in Drosophila melanogaster (Dm) only few examples of snoRNAs have been identified so far by cDNA libraries screening, integration of the molecular data with in silico identification of these types of genes could throw light on their organization in the Dm genome. Results: We have performed a computational screening of the Dm genome for C/D snoRNA genes, followed by experimental validation of the putative candidates. Few of the 26 confirmed snoRNAs had been recognized by cDNA library analysis. Organization of the Dm genome was also found to be more variegated than previously suspected, with snoRNA genes nested in both the introns and exons of protein-coding genes. This finding suggests that the presence of additional mechanisms of snoRNA biogenesis based on the alternative production of overlapping mRNA/snoRNA molecules. Availability: Additional information is available at http://www.bioinformatica.unito.it/bioinformatics/snoRNA

Efficacy of 1998 <i>vs</i> 2006 first-line antiretroviral regimens for HIV infection: an ordinary clinics retrospective investigation

Purpose: The evidence suggesting increased HAART efficacy over time comes from randomized trials or cohort studies. This retrospective multicenter survey aimed to assess the variation over time in the efficacy and tolerability of first-line HAART regimens in unselected patients treated in ordinary clinical settings. Methods: Retrospective analysis of data of all patients starting first-line HAART regimens in 1998 and 2006 at adhering centers in the Italian CISAI group. Results: For the 543 patients included, mean age was 39.1 ± 9.8y in 1998 and 41.0 ± 10.7y in 2006 (p=0.03), with a similar proportion of males. Baseline mean log10 HIV-RNA was 4.56 ± 0.97 copies/mL in 1998 vs 4.91 ± 0.96 copies/mL in 2006 (p&lt;0.001); baseline mean CD4 T-cell counts were 343 ± 314/mm3 in 1998 vs 244 ± 174/mm3 in 2006 (p&lt;0.001). The following outcomes were significantly improved at 48w in 2006: proportion with undetectable HIV-RNA (86.3% vs 58.0%; p&lt;0.001); mean increase in CD4 T-cells count (252 ± 225 vs 173 ± 246; p&lt;0.001); HAART modification (20.1% vs 29.2%; p=0.02); HAART interruption (7.3% vs 14.6%; p=0.01); proportion reporting optimal adherence (92.2% vs 82.7%, p=0.03). No differences were observed in the prevalence of grade 3-4 WHO toxicities (26.4% vs 26.6%; p=0.9). Multivariate logistic regression showed that being treated in 1998 remained an independent predictor of virological failure after several adjustments, including adherence. Conclusions: Our data from patients not included in clinical trials or cohort studies provide an additional line of evidence that the effectiveness of HAART significantly improved in 2006. Treated patients, however, were significantly older and more frequently late HIV presenters in 2006 than in 1998.</br

Prospezioni sismiche, geoelettriche ed elettromagnetiche ad alta risoluzione in prossimità della foce del Fiume Volturno

Nell’ambito dell’Obiettivo Realizzativo 2.3 “Sviluppo e allestimento di sensoristica e sistemi innovativi per osservazioni dell’iterazione terra-aria per la qualità dell’aria e degli ecosistemi agro-forestali” del progetto PON I-AMICA (Infrastruttura di Alta tecnologia per il Monitoraggio Integrato Climatico-Ambientale), l’Istituto per l’Ambiente Marino Costiero del Consiglio Nazionale delle Ricerche (CNR-I.A.M.C.) di Napoli, coordinato dal dott. Vincenzo Di Fiore, ha eseguito delle prospezioni sismiche, geoelettriche ed elettromagnetiche in un’area prospiciente la foce del Fiume Volturno. Tali indagini hanno avuto come obiettivo: La valutazione dell’intrusione nelle falde acquifere di componenti idrosaline provenienti dalla vicina area costiera; Lo studio, con risoluzione metrica, della porzione superficiale (0 - 80 metri di profondità) del sottosuolo al fine di caratterizzare, in termini di spessori e di velocità di propagazione, le serie riflettive che caratterizzano l’area in esame

Application of X-Band Wave Radar for Coastal Dynamic Analysis: Case Test of Bagnara Calabra (South Tyrrhenian Sea, Italy)

Sea state knowledge has a key role in evaluation of coastal erosion, the assessment of vulnerability and potential in coastal zone utilization, and development of numerical models to predict its evolution. X-band radar measurements were conducted to observe the spatial and temporal variation of the sea-state parameters along a 3 km long sandy-gravelly pocket beaches forming a littoral cell on Bagnara Calabra. We produced a sequence of 1000 images of the sea state extending offshore up to 1 mile. The survey has allowed monitoring the coastline, the directional wave spectra, the sea surface current fields, and the significant wave heights and detecting strong rip currents which cause scours around the open inlets and affect the stability of the submerged reef-type breakwaters. The possibility to validate the data acquired with other datasets (e.g., LaMMA Consortium) demonstrates the potential of the X-band radar technology as a monitoring tool to advance the understanding of the linkages between sea conditions, nearshore sediment dynamics, and coastal change. This work proves the possibility to obtain relevant information (e.g., wave number, period, and direction) for evaluation of local erosion phenomena and of morphological changes in the nearshore and surf zone

Molecular and Functional Characterization of the Odorant Receptor2 (OR2) in the Tiger Mosquito Aedes albopictus

In mosquitoes, the olfactory system plays a crucial role in many types of behavior, including nectar feeding, host preference selection and oviposition. Aedes albopictus, known also as the tiger mosquito, is an anthropophilic species, which in the last few years, due to its strong ecological plasticity, has spread throughout the world. Although long considered only a secondary vector of viruses, the potential of its vector capacity may constitute a threat to public health. Based on the idea that an improved understanding of the olfactory system of mosquitoes may assist in the development of control methods that interfere with their behavior, we have undertaken a study aimed at characterizing the A. albopictus Odorant Receptors. Here we report the identification, cloning and functional characterization of the AalOR2 ortholog, that represents the first candidate member of the odorant receptor (OR) family of proteins from A. albopictus. AalOR2 is expressed in the larval heads and antennae of adults. Our data indicate that A. albopictus OR2 (AalOR2) shares a high degree of identity with other mosquito OR2 orthologs characterized to date, confirming that OR2 is one of the most conserved mosquito ORs. Our data indicate that AalOR2 is narrowly tuned to indole, and inhibited by (-)-menthone. In agreement with this results, these two compounds elicit two opposite effects on the olfactory-based behavior of A. albopictus larvae, as determined through a larval behavioral assay. In summary, this work has led to the cloning and de-orphaning of the first Odorant Receptor in the tiger mosquito A. albopictus. In future control strategies this receptor may be used as a potential molecular target

Monitoraggio integrato di un'area marino-costiera: la foce del fiume Volturno (Mar Tirreno centrale)

Vengono presentati i risultati dell’attività di monitoraggio svolta nel corso del progetto PONa3_00363 I-AMICA (Infrastruttura di Alta tecnologia per il Monitoraggio Integrato Climatico-Ambientale; www.i-amica.it/i-amica/), nell’ambito delle attività relative all’Obiettivo Realizzativo 4.4 (Processi di interfaccia biosfera-idrosfera e funzionalità degli ecosistemi costieri). L’attività, che ha avuto come scopo l’acquisizione di conoscenze avanzate sulle dinamiche e/o variazioni nel tempo degli ecosistemi marino-costieri in relazione ai processi fisici, chimici e biologici che caratterizzano il loro habitat, si è sviluppata attraverso la sperimentazione di nuove metodologie di monitoraggio in relazione alle specifiche caratteristiche dell’area marino-costiera prospiciente la foce del fiume Volturno (Golfo di Gaeta). In particolare, oltre che sulle tecniche di monitoraggio classiche, lo studio si è principalmente focalizzato sulla acquisizione ed interpretazione di dati ambientali sia in colonna d’acqua che nei sedimenti a fondo mare e sulla identificazione di specie e/o associazioni di specie significative (bio-indicatori) da un punto di vista ambientale ed indicative dello stato di salute del sistema costiero. Poiché il sistema costiero rappresenta una struttura naturale complessa e delicata, la cui evoluzione è il risultato di delicati equilibri fisici, chimici e biologici, fortemente condizionabili dagli interventi antropici, l’attività di monitoraggio è stata integrata da studi sulla variazione della linea di costa, da studi sismostratigrafici della piana deltizia, sedimentologici e morfo-batimetrici dei fondali.Published1-714A. Oceanografia e climaJCR Journa