CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data

Summary: CARPET (Collection of Automated Routine Programs for Easy Tiling) is a set of Perl, Python and R scripts, integrated on the Galaxy2 web-based platform, for the analysis of ChIP-chip and expression tiling data, both for standard and custom chip designs. CARPET allows rapid experimental data entry, simple quality control, normalization, easy identification and annotation of enriched ChIP-chip regions, detection of the absolute or relative transcriptional status of genes assessed by expression tiling experiments and, more importantly, it allows the integration of ChIP-chip and expression data. Results can be visualized instantly in a genomic context within the UCSC genome browser as graph-based custom tracks through Galaxy2. All generated and uploaded data can be stored within sessions and are easily shared with other users. Availability: http://bio.ifom-ieo-campus.it/galaxy Contacts: [email protected] lucilla.luzi@if om-ieo-campus.i

the tempio della consolazione in todi integrated geomatictechniques for a monument description including structuraldamage evolution in time

The Tempio della Consolazione in Todi (16th cent.) has always been one of the most significant symbols of the Umbrian landscape. Since the first times after its completion (1606) the structure has exhibited evidences of instability, due to foundation subsiding and/or seismic activity. Structural and geotechnical countermeasures have been undertaken on the Tempio and its surroundings from the 17th century until recent times. Until now a truly satisfactory analysis of the overall deformation and attitude of the building has not been performed, since the existing surveys record the overhangs of the pillars, the crack pattern or the subsidence over limited time spans. Describing the attitude of the whole church is in fact a complex operation due to the architectural character of the building, consisting of four apses (three polygonal and one semicircular) covered with half domes, which surround the central area with the large dome. The present research aims to fill the gap of knowledge with a global study based on geomatic techniques for an accurate 3D reconstruction of geometry and attitude, integrated with a historical research on damage and interventions and a geotechnical analysis. The geomatic survey results from the integration of different techniques: GPS-GNSS for global georeferencing, laser scanning and digital photogrammetry for an accurate 3D reconstruction, high precision total station and geometric leveling for a direct survey of deformations and cracks, and for the alignment of the laser scans. The above analysis allowed to assess the dynamics of the cracks occurred in the last 25 years by a comparison with a previous survey. From the photographic colour associated to the point cloud was also possible to map the damp patches showing on the domes intrados, mapping their evolution over the last years

Roles of Noncoding RNAs in Islet Biology.

The discovery that most mammalian genome sequences are transcribed to ribonucleic acids (RNA) has revolutionized our understanding of the mechanisms governing key cellular processes and of the causes of human diseases, including diabetes mellitus. Pancreatic islet cells were found to contain thousands of noncoding RNAs (ncRNAs), including micro-RNAs (miRNAs), PIWI-associated RNAs, small nucleolar RNAs, tRNA-derived fragments, long non-coding RNAs, and circular RNAs. While the involvement of miRNAs in islet function and in the etiology of diabetes is now well documented, there is emerging evidence indicating that other classes of ncRNAs are also participating in different aspects of islet physiology. The aim of this article will be to provide a comprehensive and updated view of the studies carried out in human samples and rodent models over the past 15 years on the role of ncRNAs in the control of α- and β-cell development and function and to highlight the recent discoveries in the field. We not only describe the role of ncRNAs in the control of insulin and glucagon secretion but also address the contribution of these regulatory molecules in the proliferation and survival of islet cells under physiological and pathological conditions. It is now well established that most cells release part of their ncRNAs inside small extracellular vesicles, allowing the delivery of genetic material to neighboring or distantly located target cells. The role of these secreted RNAs in cell-to-cell communication between β-cells and other metabolic tissues as well as their potential use as diabetes biomarkers will be discussed. © 2020 American Physiological Society. Compr Physiol 10:893-932, 2020

Small RNAs derived from tRNA fragmentation regulate the functional maturation of neonatal β cells.

tRNA-derived fragments (tRFs) are an emerging class of small non-coding RNAs with distinct cellular functions. Here, we studied the contribution of tRFs to the regulation of postnatal β cell maturation, a critical process that may lead to diabetes susceptibility in adulthood. We identified three tRFs abundant in neonatal rat islets originating from 5' halves (tiRNA-5s) of histidine and glutamate tRNAs. Their inhibition in these islets reduced β cell proliferation and insulin secretion. Mitochondrial respiration was also perturbed, fitting with the mitochondrial enrichment of nuclear-encoded tiRNA-5 <sup>HisGTG</sup> and tiRNA-5 <sup>GluCTC</sup> . Notably, tiRNA-5 inhibition reduced Mpc1, a mitochondrial pyruvate carrier whose knock down largely phenocopied tiRNA-5 inhibition. tiRNA-5 <sup>HisGTG</sup> interactome revealed binding to Musashi-1, which was essential for the mitochondrial enrichment of tiRNA-5 <sup>HisGTG</sup> . Finally, tiRNA-5s were dysregulated in the islets of diabetic and diabetes-prone animals. Altogether, tiRNA-5s represent a class of regulators of β cell maturation, and their deregulation in neonatal islets may lead to diabetes susceptibility in adulthood

Assessment of the application for renewal of authorisation of GalliPro ® (Bacillus subtilis DSM 17299) for chickens for fattening

GalliPro \uae is the trade name for a feed additive based on viable cells of a strain of Bacillus subtilis intended for use as a zootechnical additive (gut flora stabiliser) in feed for chickens for fattening. The product is currently authorised for use in chickens for fattening. This opinion concerns the renewal of this authorisation. Bacillus subtilis is considered by EFSA to be suitable for the qualified presumption of safety (QPS) approach to establish the safety for the target species, consumers and the environment. The identity of the strain present in the additive was established and evidence was provided on the lack of toxigenic potential as well as acquired antibiotic resistance determinants to antibiotics of human and veterinary importance. Accordingly, this strain is presumed safe for the target species, consumers of products derived from animals fed the additive and the environment. Since no concerns are expected from other components of the additive, GalliPro \uae is considered safe for the target species, consumers and the environment. The applicant has provided evidence that the additive currently in the market complies with the existing conditions of authorisation. The FEEDAP Panel confirms its previous conclusions that GalliPro \uae is safe for the target species; consumers of products from animals fed the additive and the environment. GalliPro \uae should be considered a potential respiratory sensitiser. In the absence of data, the FEEDAP Panel cannot conclude on the potential of GalliPro \uae for skin and eyes irritancy and dermal sensitisation

A circular RNA generated from an intron of the insulin gene controls insulin secretion.

Fine-tuning of insulin release from pancreatic β-cells is essential to maintain blood glucose homeostasis. Here, we report that insulin secretion is regulated by a circular RNA containing the lariat sequence of the second intron of the insulin gene. Silencing of this intronic circular RNA in pancreatic islets leads to a decrease in the expression of key components of the secretory machinery of β-cells, resulting in impaired glucose- or KCl-induced insulin release and calcium signaling. The effect of the circular RNA is exerted at the transcriptional level and involves an interaction with the RNA-binding protein TAR DNA-binding protein 43 kDa (TDP-43). The level of this circularized intron is reduced in the islets of rodent diabetes models and of type 2 diabetic patients, possibly explaining their impaired secretory capacity. The study of this and other circular RNAs helps understanding β-cell dysfunction under diabetes conditions, and the etiology of this common metabolic disorder

Rab3D is critical for secretory granule maturation in PC12 cells.

Neuropeptide- and hormone-containing secretory granules (SGs) are synthesized at the trans-Golgi network (TGN) as immature secretory granules (ISGs) and complete their maturation in the F-actin-rich cell cortex. This maturation process is characterized by acidification-dependent processing of cargo proteins, condensation of the SG matrix and removal of membrane and proteins not destined to mature secretory granules (MSGs). Here we addressed a potential role of Rab3 isoforms in these maturation steps by expressing their nucleotide-binding deficient mutants in PC12 cells. Our data show that the presence of Rab3D(N135I) decreases the restriction of maturing SGs to the F-actin-rich cell cortex, blocks the removal of the endoprotease furin from SGs and impedes the processing of the luminal SG protein secretogranin II. This strongly suggests that Rab3D is implicated in the subcellular localization and maturation of ISGs

A circular RNA generated from an intron of the insulin gene controls insulin secretion

Fine-tuning of insulin release from pancreatic β-cells is essential to maintain blood glucose homeostasis. Here, we report that insulin secretion is regulated by a circular RNA containing the lariat sequence of the second intron of the insulin gene. Silencing of this intronic circular RNA in pancreatic islets leads to a decrease in the expression of key components of the secretory machinery of β-cells, resulting in impaired glucose- or KCl-induced insulin release and calcium signaling. The effect of the circular RNA is exerted at the transcriptional level and involves an interaction with the RNA-binding protein TAR DNA-binding protein 43 kDa (TDP-43). The level of this circularized intron is reduced in the islets of rodent diabetes models and of type 2 diabetic patients, possibly explaining their impaired secretory capacity. The study of this and other circular RNAs helps understanding β-cell dysfunction under diabetes conditions, and the etiology of this common metabolic disorder

Safety and efficacy of B‐Act® (Bacillus licheniformis DSM 28710) for chickens for fattening and chickens reared for laying

The additive B-Act\uae is a preparation containing viable spores of a strain of Bacillus licheniformis. The additive is intended for use in feed for chickens for fattening and chickens reared for laying at the proposed dose of 1.6 9 109 colony-forming unit (CFU)/kg complete feedingstuffs. B. licheniformis is considered by EFSA to be suitable for the qualified presumption of safety approach for establishing safety. As the identity of the active agent was established and the lack of toxigenic potential and resistance to antibiotics of human or veterinary clinical significance were demonstrated, the additive is presumed safe for the target species, consumers and the environment. In the absence of data, no conclusion can be drawn on the skin/eye irritation or skin sensitisation potential. The dustiness of the preparations tested indicated a potential for users to be exposed via inhalation. B-Act\uae should be considered to have the potential to be a respiratory sensitiser. B-Act\uae at the recommended dose 1.6 9 109 CFU/kg feed has some potential to improve the feed to gain ratio of chickens for fattening. This conclusion can be extended to chickens reared for laying when used at the same dose. B. licheniformis DSM 28710 is compatible with decoquinate, diclazuril, halofuginone, nicarbazin, robenidine hydrochloride, lasalocid A sodium, maduramicin ammonium, monensin sodium, narasin and salinomycin sodium