Long non-coding RNAs, a novel class of regulatory RNAs: identification and characterization in the model species Brachypodium distachyon

Ninety percent of the eukaryotic genome is transcribed although only a small part corresponds to protein coding mRNAs, suggesting that a large proportion of transcribed RNAs do not code for proteins, hence classified as non-coding RNAs (ncRNAs). High-throughput sequencing technology has allowed the identification and characterization of several classes of ncRNAs with key roles in various biological processes. Among ncRNAs, long ncRNAs (lncRNAs) are transcripts typically longer than 200 nucleotides that tend to be expressed at low levels and exhibit tissue-specific/cell-specific or stress responsive expression profiles. LncRNAs have been identified in animals and in plants as well, where they are involved in different regulatory pathways both in development and stress responses, even if the understanding of molecular basis of these mechanisms remains largely unexplored. My thesis project aims at identifying lncRNAs in Brachypodium distachyon (Bd), a wild grass belonging to the Pooideae and a model species for temperate cereals, such as wheat and barley. A whole-genome annotation and a detailed analysis of lncRNAs expression patterns have been performed for the first time in Brachypodium. Moreover the potential lncRNA targets were investigated to highlight new regulatory networks and cross-talk between different RNA molecules. Public and proprietary RNA-Seq data sets from 15 different experiments conducted in the reference inbred line Bd21 were analysed in this study. Public RNA-Seq data from different experiments, including several plant organs, were downloaded from the Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra). Proprietary RNA-Seq libraries were previously produced by the lab from three leaf developmental leaf areas: proliferation, expansion and mature, grown in control and drought stress conditions. For each proprietary RNA-Seq sample, three biological replicates were produced. This dataset is characterized by a total of 705 millions reads, which were subjected to a quality analysis. Each experiment was aligned independently to the Bd21 reference genome (v.2.1) using the spliced read aligner TopHat2 and, successively, for each experiment the transcriptome was de novo assembled using Cufflinks. In order to identify Bd lncRNAs an in house bioinformatic pipeline was used. Briefly, this pipeline applies five filters based on the main lncRNA features: size selection, Open Reading Frame filter, known protein domain filter, Coding Potential Calculator, filter of housekeeping lncRNAs and precursors of small RNAs. Starting from the whole set of loci/isoforms (99141) de novo reconstructed, 2507 bona fide lncRNAs were identified. Bona fide lncRNAs differential expression analysis was taken into account for datasets with replicates, i.e. proprietary libraries from different developing areas of the third leaf. This analysis revealed that several lncRNAs are differentially expressed during leaf cell differentiation and during drought treatment. Some lncRNAs resulted more abundant in specific plant stages, tissues or organs. Moreover, a computational method developed to identify endogenous microRNA target mimic (eTM) allowed to investigate the link between lncRNAs and microRNAs through target mimicry, a regulatory mechanism for miRNA functions in plants in which the decoy RNAs bind to miRNAs via complementary sequences and therefore could interfere with the interaction between miRNAs and their authentic targets

Um olhar sobre o conceito de paisagem cultural: o caso de Urussanga/SC

Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro Tecnológico, Programa de Pós-Graduação em Urbanismo História e Arquitetura da Cidade, Florianópolis, 2015.Este estudo busca compreender quais são os conceitos e metodologias utilizadas atualmente para o reconhecimento de paisagens culturais e analisar o município de Urussanga, no sul de Santa Catarina com vistas a classifica-la como possível paisagem cultural. Esse novo termo ganhou força nas últimas décadas e hoje se encontra difundido não só entre os órgãos encarregados da proteção ao patrimônio, mas também entre os estudiosos do tema. Apesar de sua grande difusão, o conceito adotado por órgãos como o Iphan ainda é muito generalista. Através de revisão bibliográfica buscou-se compreender como se deu a evolução do entendimento patrimonial, a partir do final século XVIII até os dias atuais. Analisou-se então o conceito de paisagem cultural adotado pela UNESCO a partir de 1992, e a metodologia criada para que seja feita a análise da paisagem para seu possível reconhecimento como patrimônio. Posteriormente, buscou-se compreender como é a abordagem conceitual e metodológica dada pelo Iphan no Brasil através da análise de suas publicações e da legislação atual. As análises demonstram um grande esforço por parte da UNESCO em criar uma metodologia que consiga atender ao máximo das diferentes situações encontradas no mundo. Porém, observa-se uma limitação de classificação das paisagens culturais, inclusive no âmbito urbano, existindo dificuldades para serem reconhecidas utilizando a metodologia atual. Já no caso brasileiro, o que se vê é uma grande abrangência conceitual e falta de uma metodologia a ser seguida para as análises das possíveis paisagens culturais, o que parece resultar numa generalização do conceito, correndo-se o risco de  tudo ser paisagem cultural . Nota-se, portanto a necessidade de uma melhor definição conceitual e desenvolvimento de uma metodologia para que as paisagens culturais sejam mais bem definidas, reconhecidas e consequentemente protegidas. Busca-se então definir uma metodologia adequada para analisar o objeto de estudo, a cidade de Urussanga. No final do século XIX houve o movimento colonizador do sul do estado com a chegada de imigrantes europeus, nesse caso italianos, que iniciam então a formação de pequenas vilas que darão origem aos municípios da região de Criciúma. Como resultado dessa interação do imigrante com a paisagem, hoje se encontram conjuntos edificados de características particulares, hábitos e tradições que ainda se mantém vivos. Todas essas características conferem à Urussanga, seja no âmbito urbano ou rural, uma ambiência única. Analisa-se então, sob o olhar desse novo termo patrimonial, a ambiência da cidade buscando identificá-la como possível paisagem cultural.Abstract : This paper aims to understand wich concepts e methodologies are currently uses to recognize cultural landscapes and analyse the city of Urussanga, in the south of Santa Catarina intending to classify it as possible cultural ladscape. This new term has gained strength in the last decades e today it s spread not only among the organizations responsible for protecting the heritage, but also among scholars of the theme. Despite its great spread, the concept adopted by organizations such as IPHAN is still very general. Through bibliographical revision it sought to understand how was the evolution of heritage understanding, from the late eighteenth century to nowadays. Then it was analyzed the concept of cultural landscape adopted by UNESCO since 1992, and the methodology created to analyze landscapes for their possible recognition as heritage. Later, it was sought to understand how is the conceptual and methodological approach given by Iphan in Brazil by analyzing their publications and current legislation. The analysis show a great effort by UNESCO in creating a methodology that can reach most of the diferent situations encountered in the world. However, there is a limitation for the classification of cultural landscapes, including in the urban context, finding difficulties to be recognized using the current methodology. In Brazil, what is observed is a wide conceptual scope and lack of methodology to be followed for the analysis of possible cultural landscapes, which seems to result in a generalization of the concept itself, risking that "everything is cultural landscape". It is noticed, therefore, the need for a better conceptual definition and the development of a methodology so that cultural landscapes can be better defined, recognized and protected. It was sought to define a adequate methodology to analyze the object of study, the city of Urussanga. In the late nineteenth century there was the colonizer movement of southern state with the arrival of European immigrants, in this case italians, which initiated the formation of small villages that give rise to the cities of Criciúma region. As a result of the interaction of the immigrant with the landscape, today is found building collections of specific characteristics, habits and traditions that still remains alive. All these features give Urussanga, whether in urban or rural areas, a unique setting. Then it s analyzed, under the eyes of this new heritage term, the city's ambience seeking to identify it as a possible cultural landscape

Aplicação da avaliação ultraestrutural de espermatozoides na rotina da andrologia

ResumoA microscopia eletrônica de espermatozoides é uma ferramenta complementar da análise seminal que pode contribuir na interpretação clínica da astenozoospermia grave e da teratozoospermia e na investigação de infertilidade idiopática. Reportamos um caso de paciente com varicocele, submetido à varicocelectomia, com análise seminal ultraestrutural por microscopia eletrônica.AbstractElectron microscopy of sperm is a complementary tool to semen analysis that can contribute to the clinical interpretation of severe astenozoospermia, teratozoospermia and idiopathic infertility investigation. We report a patient with varicocele, submitted to varicocelectomy, with seminal ultrastructural analysis by electron microscopy

Hypofractionated radiotherapy after conservative surgery may increase low-intermediate grade late fibrosis in breast cancer patients

patients Abstract Fulltext Metrics Get Permission Cite this article Authors Diges\uf9 C, Deodato F, Macchia G, Cilla S, Pieri M, Zamagni A, Farioli A, Buwenge M, Ferrandina G, Morganti AG Received 12 March 2018 Accepted for publication 23 May 2018 Published 3 October 2018 Volume 2018:10 Pages 143\u2014151 DOI https://doi.org/10.2147/BCTT.S167914 Checked for plagiarism Yes Review by Single-blind Peer reviewer comments 3 Editor who approved publication: Professor Pranela Rameshwar Article has an altmetric score of 2 Cinzia Diges\uf9,1 Francesco Deodato,1 Gabriella Macchia,1 Savino Cilla,2 Martina Pieri,3 Alice Zamagni,4 Andrea Farioli,5 Milly Buwenge,4 Gabriella Ferrandina,6,* Alessio G Morganti4,* 1Radiotherapy Unit, General Oncology Unit, Fondazione Giovanni Paolo II, Campobasso, Italy; 2Medical Physics Unit, Fondazione Giovanni Paolo II, Campobasso, Italy; 3Radiotherapy Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori, Meldola, Italy; 4Radiation Oncology Center, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy; 5Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy; 6Department of Woman and Child Health, Gynecologic Oncology Unit, Fondazione \u201cPoliclinico Universitario A. Gemelli\u201d, IRCSS, Universita\u2019 Cattolica Sacro Cuore, Rome, Italy *These authors contributed equally to this work Aim: To compare late toxicity after postoperative hypofractionated radiotherapy (RT) and standard fractionated RT in patients with early-stage breast carcinoma. Methods: This retrospective study included 447 patients (Modulated Accelerated Radiotherapy [MARA-1]: 317 patients, and control group [CG]: 130 patients). In the CG, the whole breast received 50.4 Gy in 28 fractions (fx) using 3D-radiotherapy, plus a sequential electron boost (10 Gy in 4 fx) to tumor bed. In MARA-1 group, a forward-planned intensity-modulated radiotherapy technique with 40 Gy in 16 fx with a concomitant boost of 4 Gy to breast was used. The primary endpoint was to evaluate late toxicity, and secondary endpoints were acute toxicity, local control, and survival. ClinicalTrials.gov: NCT03461224. Results: Median follow-up was 52 months (range: 3\u2013115 months). Late skin and subcutaneous toxicity were acceptable: 5-year actuarial cumulative incidence of Grade (G) 3 late skin toxicity was 1.5% in CG and 0.0% in MARA-1. Five-year actuarial cumulative incidence of G3 late subcutaneous toxicity was 0.8% in CG and 0.3% in MARA-1. On multivariate analysis, tobacco smoking and planning target volume were associated with an increased risk of late G1 skin toxicity (HR: 2.15, 95% CI: 1.38\u20133.34 and HR: 1.12, 95% CI: 1.07\u20131.18, respectively), whereas patients with a larger planning target volume also showed an increased risk of G1 and G2 late subcutaneous toxicity (HR: 1.14, CI 95%: 1.08\u20131.20 and HR: 1.14, 95% CI: 1.01\u20131.28, respectively). MARA-1 patients also showed an increased risk of late G1 and G2 subcutaneous toxicity (HR: 2.35, 95% CI: 1.61\u20133.41 and HR: 3.07, 95% CI: 1.11\u20138.53, respectively) compared to CG. Conclusion: In this retrospective analysis, postoperative accelerated-hypofractionated RT for early-stage-breast carcinoma was associated with higher incidence of subcutaneous side effects. However, this increase was limited to G1\u2013G2 toxicity. In the future, development of predictive models could help in tailoring dose and fractionation based on the risk of toxicity

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

Lack of SARS-CoV-2 RNA environmental contamination in a tertiary referral hospital for infectious diseases in Northern Italy

none140noNAnoneColaneri M.; Seminari E.; Piralla A.; Zuccaro V.; Di Filippo A.; Baldanti F.; Bruno R.; Mondelli M.U.; Brunetti E.; Di Matteo A.; Maiocchi L.; Pagnucco L.; Mariani B.; Ludovisi S.; Lissandrin R.; Parisi A.; Sacchi P.; Patruno S.F.A.; Michelone G.; Gulminetti R.; Zanaboni D.; Novati S.; Maserati R.; Orsolini P.; Vecchia M.; Sciarra M.; Asperges E.; Sambo M.; Biscarini S.; Lupi M.; Roda S.; Chiara Pieri T.; Gallazzi I.; Sachs M.; Valsecchi P.; Perlini S.; Alfano C.; Bonzano M.; Briganti F.; Crescenzi G.; Giulia Falchi A.; Guarnone R.; Guglielmana B.; Maggi E.; Martino I.; Pettenazza P.; Pioli di Marco S.; Quaglia F.; Sabena A.; Salinaro F.; Speciale F.; Zunino I.; De Lorenzo M.; Secco G.; Dimitry L.; Cappa G.; Maisak I.; Chiodi B.; Sciarrini M.; Barcella B.; Resta F.; Moroni L.; Vezzoni G.; Scattaglia L.; Boscolo E.; Zattera C.; Michele Fidel T.; Vincenzo C.; Vignaroli D.; Bazzini M.; Iotti G.; Mojoli F.; Belliato M.; Perotti L.; Mongodi S.; Tavazzi G.; Marseglia G.; Licari A.; Brambilla I.; Daniela B.; Antonella B.; Patrizia C.; Giulia C.; Giuditta C.; Marta C.; Rossana D.; Milena F.; Bianca M.; Roberta M.; Enza M.; Stefania P.; Maurizio P.; Elena P.; Antonio P.; Francesca R.; Antonella S.; Maurizio Z.; Guy A.; Laura B.; Ermanna C.; Giuliana C.; Luca D.; Gabriella F.; Gabriella G.; Alessia G.; Viviana L.; Claudia L.; Valentina M.; Simona P.; Marta P.; Alice B.; Giacomo C.; Irene C.; Alfonso C.; Di Martino R.; Di Napoli A.; Alessandro F.; Guglielmo F.; Loretta F.; Federica G.; Alessandra M.; Federica N.; Giacomo R.; Beatrice R.; Maria S.I.; Monica T.; Nepita Edoardo V.; Calvi M.; Tizzoni M.; Nicora C.; Triarico A.; Petronella V.; Marena C.; Muzzi A.; Lago P.; Comandatore F.; Bissignandi G.; Gaiarsa S.; Rettani M.; Bandi C.Colaneri, M.; Seminari, E.; Piralla, A.; Zuccaro, V.; Di Filippo, A.; Baldanti, F.; Bruno, R.; Mondelli, M. U.; Brunetti, E.; Di Matteo, A.; Maiocchi, L.; Pagnucco, L.; Mariani, B.; Ludovisi, S.; Lissandrin, R.; Parisi, A.; Sacchi, P.; Patruno, S. F. A.; Michelone, G.; Gulminetti, R.; Zanaboni, D.; Novati, S.; Maserati, R.; Orsolini, P.; Vecchia, M.; Sciarra, M.; Asperges, E.; Sambo, M.; Biscarini, S.; Lupi, M.; Roda, S.; Chiara Pieri, T.; Gallazzi, I.; Sachs, M.; Valsecchi, P.; Perlini, S.; Alfano, C.; Bonzano, M.; Briganti, F.; Crescenzi, G.; Giulia Falchi, A.; Guarnone, R.; Guglielmana, B.; Maggi, E.; Martino, I.; Pettenazza, P.; Pioli di Marco, S.; Quaglia, F.; Sabena, A.; Salinaro, F.; Speciale, F.; Zunino, I.; De Lorenzo, M.; Secco, G.; Dimitry, L.; Cappa, G.; Maisak, I.; Chiodi, B.; Sciarrini, M.; Barcella, B.; Resta, F.; Moroni, L.; Vezzoni, G.; Scattaglia, L.; Boscolo, E.; Zattera, C.; Michele Fidel, T.; Vincenzo, C.; Vignaroli, D.; Bazzini, M.; Iotti, G.; Mojoli, F.; Belliato, M.; Perotti, L.; Mongodi, S.; Tavazzi, G.; Marseglia, G.; Licari, A.; Brambilla, I.; Daniela, B.; Antonella, B.; Patrizia, C.; Giulia, C.; Giuditta, C.; Marta, C.; D'Alterio, Rossana; Milena, F.; Bianca, M.; Roberta, M.; Enza, M.; Stefania, P.; Maurizio, P.; Elena, P.; Antonio, P.; Francesca, R.; Antonella, S.; Maurizio, Z.; Guy, A.; Laura, B.; Ermanna, C.; Giuliana, C.; Luca, D.; Gabriella, F.; Gabriella, G.; Alessia, G.; Viviana, L.; Meisina, Claudia; Valentina, M.; Simona, P.; Marta, P.; Alice, B.; Giacomo, C.; Irene, C.; Alfonso, C.; Di Martino, R.; Di Napoli, A.; Alessandro, F.; Guglielmo, F.; Loretta, F.; Federica, G.; Albertini, Alessandra; Federica, N.; Giacomo, R.; Beatrice, R.; Maria, S. I.; Monica, T.; Nepita Edoardo, V.; Calvi, M.; Tizzoni, M.; Nicora, C.; Triarico, A.; Petronella, V.; Marena, C.; Muzzi, A.; Lago, P.; Comandatore, F.; Bissignandi, G.; Gaiarsa, S.; Rettani, M.; Bandi, C

Clinical characteristics of coronavirus disease (COVID-19) early findings from a teaching hospital in Pavia, North Italy, 21 to 28 February 2020

We describe clinical characteristics, treatments and outcomes of 44 Caucasian patients with coronavirus disease (COVID-19) at a single hospital in Pavia, Italy, from 21\u201328 February 2020, at the beginning of the outbreak in Europe. Seventeen patients developed severe disease, two died. After a median of 6 days, 14 patients were discharged from hospital. Predictors of lower odds of discharge were age>65 years, antiviral treatment and for severe disease, lactate dehydrogenase >300 mg/dL