RNA framework: An all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

RNA is emerging as a key regulator of a plethora of biological processes. While its study has remained elusive for decades, the recent advent of high-throughput sequencing technologies provided the unique opportunity to develop novel techniques for the study of RNA structure and post-transcriptional modifications. Nonetheless, most of the required downstream bioinformatics analyses steps are not easily reproducible, thus making the application of these techniques a prerogative of few laboratories. Here we introduce RNA Framework, an all-in-one toolkit for the analysis of most NGS-based RNA structure probing and post-transcriptional modification mapping experiments. To prove the extreme versatility of RNA Framework, we applied it to both an in-house generated DMS-MaPseq dataset, and to a series of literature available experiments. Notably, when starting from publicly available datasets, our software easily allows replicating authors' findings. Collectively, RNA Framework provides the most complete and versatile toolkit to date for a rapid and streamlined analysis of the RNA epistructurome. RNA Framework is available for download at: http://www.rnaframework.com

classical and molecular cytogenetic studies in some cattle breeds

Numerical autosome aberrations have a few importance in the animal breeding since the carriers show generally abnormal body conformation. For this reason, these abnormalities are systematically eliminated from the animal population by the breeders during the animal breeding. Numerical sex chromosome abnormalities are more tolerate by species, since genes are present in single copy (one of two X-chromosome is genetically inactive), and the carriers show usually normal body conformation. For this reason these abnormalities escape the normal breeding selection

Sequential cross-species chromosome painting among river buffalo, cattle, sheep and goat: a useful tool for chromosome abnormalities diagnosis within the family Bovidae.

The main goal of this study was to develop a comparative multi-colour Zoo-FISH on domestic ruminants metaphases using a combination of whole chromosome and sub-chromosomal painting probes obtained from the river buffalo species (Bubalus bubalis, 2n = 50,XY). A total of 13 DNA probes were obtained through chromosome microdissection and DOP-PCR amplification, labelled with two fluorochromes and sequentially hybridized on river buffalo, cattle (Bos taurus, 2n = 60,XY), sheep (Ovis aries, 2n = 54,XY) and goat (Capra hircus, 2n = 60,XY) metaphases. The same set of paintings were then hybridized on bovine secondary oocytes to test their potential use for aneuploidy detection during in vitro maturation. FISH showed excellent specificity on metaphases and interphase nuclei of all the investigated species. Eight pairs of chromosomes were simultaneously identified in buffalo, whereas the same set of probes covered 13 out 30 chromosome pairs in the bovine and goat karyotypes and 40% of the sheep karyotype (11 out of 27 chromosome pairs). This result allowed development of the first comparative M-FISH karyotype within the domestic ruminants. The molecular resolution of complex karyotypes by FISH is particularly useful for the small chromosomes, whose similarity in the banding patterns makes their identification very difficult. The M-FISH karyotype also represents a practical tool for structural and numerical chromosome abnormalities diagnosis. In this regard, the successful hybridization on bovine secondary oocytes confirmed the potential use of this set of probes for the simultaneous identification on the same germ cell of 12 chromosome aneuploidies. This is a fundamental result for monitoring the reproductive health of the domestic animals in relation to management errors and/or environmental hazards

Comparative mapping of the fragile histidine triad (FHIT) gene in cattle, river buffalo, sheep and goat by FISH and assignment to BTA22 by RH-mapping: a comparison with HSA3

Common fragile sites can be damaged by exposure to a variety of carcinogens. The fragile histidine triad (FHIT) gene, including the most active human chromosomal fragile site (FRA3B) at chromosome band HSA3p14.2,1 has been proposed as a tumour suppressor gene for a variety of tumours.2 The most common response to carcinogen exposure is deletions at the FHIT locus that alter the gene structure and function. In this study we assign the FHIT gene in cattle, river buffalo, sheep and goat chromosomes by comparative fluorescence in situ hybridization (FISH)-mapping. In addition, the assignment to BTA22 was confirmed by typing the marker across a bovine radiation hybrid (RH) panel

Chromosome analyses in dairy cows exposed to dioxins and dioxin-like PCBs using the SCE test

Peripheral blood cultures were performed to study the sister chromatid exchanges (SCE) in samples from 15 cows (Valdostana x Piedmontese crossbreds) showing average milk values of dioxins+furans+PCBs higher (18.56 pg/g of fat as WHO-TEQ) than those permitted (6.0 pg/g of dioxins+furans+PCBs as WHO-TEQ) and the results were compared with samples from 16 Valdostana dairy cows (1.75 pg/g of fat as WHO-TEQ) used as control. Significant (P<0.01) higher mean number of SCE/cell (7.10±2.8) were found in cows showing higher levels of dioxins and PCB compared to those achieved in the controls (SCE/cell=5.24±2.51)

An advanced sheep (Ovis aries, 2n = 54) cytogenetic map and assignment of 88 new autosomal loci by fluorescence in situ hybridization and R-banding

Presented herein is an updated sheep cytogenetic map that contains 452 loci (291 type I and 161 type II) assigned to specific chromosome bands or regions on standard R-banded ideograms. This map, which significantly extends our knowledge of the physical organization of the ovine genome, includes new assignments for 88 autosomal loci, including 74 type I loci (known genes) and 14 type II loci (SSRs/microsatellite marker/STSs), by FISH-mapping and R-banding. Comparison of the ovine map to the cattle and goat cytogenetic maps showed that common loci were located within homologous chromosomes and chromosome bands, confirming the high level of conservation of autosomes among ruminant species. Eleven loci that were FISH-mapped in sheep (B3GAT2, ASCC3, RARSL, BRD2, POLR1C, PPP2R5D, TNRC5, BAT2, BAT4, CDC5L and OLA-DRA) are unassigned in cattle and goat. Eleven other loci (D3S32, D1S86, BMS2621, SFXN5, D5S3, D5S68, CSKB1, D7S49, D9S15, D9S55 and D29S35) were assigned to specific ovine chromosome (OAR) bands but have only been assigned to chromosomes in cattle and goat

SiO2nanoparticles modulate the electrical activity of neuroendocrine cells without exerting genomic effects

Engineered silica nanoparticles (NPs) have attracted increasing interest in several applications, and particularly in the field of nanomedicine, thanks to the high biocompatibility of this material. For their optimal and controlled use, the understanding of the mechanisms elicited by their interaction with the biological target is a prerequisite, especially when dealing with cells particularly vulnerable to environmental stimuli like neurons. Here we have combined different electrophysiological approaches (both at the single cell and at the population level) with a genomic screening in order to analyze, in GT1-7 neuroendocrine cells, the impact of SiO2NPs (50\u2009\ub1\u20093\u2009nm in diameter) on electrical activity and gene expression, providing a detailed analysis of the impact of a nanoparticle on neuronal excitability. We find that 20\u2009\ub5g\u2009mL-1NPs induce depolarization of the membrane potential, with a modulation of the firing of action potentials. Recordings of electrical activity with multielectrode arrays provide further evidence that the NPs evoke a temporary increase in firing frequency, without affecting the functional behavior on a time scale of hours. Finally, NPs incubation up to 24\u2009hours does not induce any change in gene expression

New Materials and Technologies for Durability and Conservation of Building Heritage

The increase in concrete structures’ durability is a milestone to improve the sustainability of buildings and infrastructures. In order to ensure a prolonged service life, it is necessary to detect the deterioration of materials by means of monitoring systems aimed at evaluating not only the penetration of aggressive substances into concrete but also the corrosion of carbon-steel reinforcement. Therefore, proper data collection makes it possible to plan suitable restoration works which can be carried out with traditional or innovative techniques and materials. This work focuses on building heritage and it highlights the most recent findings for the conservation and restoration of reinforced concrete structures and masonry buildings