DNA Methylation variability among individuals is related to CpGs cluster density and evolutionary signatures

Background: In recent years, epigenetics has gained a central role in the understanding of the process of natural selection. It is now clear how environmental impacts on the methylome could promote methylation variability with direct effects on disease etiology as well as phenotypic and genotypic variations in evolutionary processes. To identify possible factors influencing inter-individual methylation variability, we studied methylation values standard deviation of 166 healthy individuals searching for possible associations with genomic features and evolutionary signatures. Results: We analyzed methylation variability values in relation to CpG cluster density and we found a strong association between them (p-value <2.2×10-16). Furthermore, we found that genes related to CpGs with high methylation variability values were enriched for immunological pathways; instead, those associated with low ones were enriched for pathways related to basic cellular functions. Finally, we found an association between methylation variability values and signals of both ancient (p-value <2.2×10-16) and recent selective pressure (p-value <1×10-4). Conclusion: Our results indicate the presence of an intricate interplay between genetics, epigenetic code and evolutionary constraints in humans

Additional file 1: of DNA Methylation variability among individuals is related to CpGs cluster density and evolutionary signatures

additional information about CEU population and bootstrap analyses. (PDF 557 kb

ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons

Background CpG sites in an individual molecule may exist in a binary state (methylated or unmethylated) and each individual DNA molecule, containing a certain number of CpGs, is a combination of these states defining an epihaplotype. Classic quantification based approaches to study DNA methylation are intrinsically unable to fully represent the complexity of the underlying methylation substrate. Epihaplotype based approaches, on the other hand, allow methylation profiles of cell populations to be studied at the single molecule level. For such investigations, next-generation sequencing techniques can be used, both for quantitative and for epihaplotype analysis. Currently available tools for methylation analysis lack output formats that explicitly report CpG methylation profiles at the single molecule level and that have suited statistical tools for their interpretation. Results Here we present ampliMethProfiler, a python-based pipeline for the extraction and statistical epihaplotype analysis of amplicons from targeted deep bisulfite sequencing of multiple DNA regions. Conclusions ampliMethProfiler tool provides an easy and user friendly way to extract and analyze the epihaplotype composition of reads from targeted bisulfite sequencing experiments. ampliMethProfiler is written in python language and requires a local installation of BLAST and (optionally) QIIME tools. It can be run on Linux and OS X platforms. The software is open source and freely available at http://amplimethprofiler.sourceforge.net. Keyword

Modelling DNA methylation by analyzing the individual configurations of single molecules

DNA methylation is often analyzed by reporting the average methylation degree of each cytosine. In this study, we used a single molecule methylation analysis in order to look at the methylation conformation of individual molecules. Using D-aspartate oxidase as a model gene, we performed an in-depth methylation analysis through the developmental stages of three different mouse tissues (brain, lung, and gut), where this gene undergoes opposite methylation destiny. This approach allowed us to track both methylation and demethylation processes at high resolution. The complexity of these dynamics was markedly simplified by introducing the concept of methylation classes (MCs), defined as the number of methylated cytosines per molecule, irrespective of their position. The MC concept smooths the stochasticity of the system, allowing a more deterministic description. In this framework, we also propose a mathematical model based on the Markov chain. This model aims to identify the transition probability of a molecule from one MC to another during methylation and demethylation processes. The results of our model suggest that: 1) both processes are ruled by a dominant class of phenomena, namely, the gain or loss of one methyl group at a time; and 2) the probability of a single CpG site becoming methylated or demethylated depends on the methylation status of the whole molecule at that time

Analysis of risk factors for central venous catheter-related complications: a prospective observational study in pediatric patients with bone sarcomas

BACKGROUND:: The incidence of central venous catheter (CVC)-related complications reported in pediatric sarcoma patients is not established as reports in available literature are limited. The analysis of risk factors is part of the strategy to reduce the incidence of CVC complications. OBJECTIVE:: The objective of this study was to determine the incidence of CVC complications in children with bone sarcomas and if defined clinical variables represent a risk factor. METHODS:: During an 8-year period, 155 pediatric patients with bone sarcomas were prospectively followed up for CVC complications. Incidence and correlation with clinical features including gender, age, body mass index, histology, disease stage, and use of thromboprophylaxis with low-molecular-weight heparin were analyzed. RESULTS:: Thirty-three CVC complications were recorded among 42 687 CVC-days (0.77 per 1000 CVC-days). No correlation between the specific clinical variables and the CVC complications was found. A high incidence of CVC-related sepsis secondary to gram-negative bacteria was observed. CONCLUSIONS:: The analysis of CVC complications and their potential risk factors in this sizable and relatively homogeneous pediatric population with bone sarcomas has led to the implementation of a multimodal approach by doctors and nurses to reduce the incidence and morbidity of the CVC-related infections, particularly those related to gram-negative bacteria. IMPLICATIONS FOR PRACTICE:: As a result of this joint medical and nursing study, a multimodal approach that included equipping faucets with water filters, the reeducation of doctors and nurses, and the systematic review of CVC protocol was implemented. \ua9 2014 Wolters Kluwer Health Lippincott Williams & Wilkins

Dietary intake and major food sources of polyphenols in people with type 2 diabetes: The TOSCA.IT Study

none200nononeVitale, M.; Masulli, M.; Rivellese, A.A.; Bonora, E.; Cappellini, F.; Nicolucci, A.; Squatrito, S.; Antenucci, D.; Barrea, A.; Bianchi, C.; Bianchini, F.; Fontana, L.; Fornengo, P.; Giorgino, F.; Gnasso, A.; Mannucci, E.; Mazzotti, A.; Nappo, R.; Palena, A.P.; Pata, P.; Perriello, G.; Potenziani, S.; Radin, R.; Ricci, L.; Romeo, F.; Santini, C.; Scarponi, M.; Serra, R.; Timi, A.; Turco, A.A.; Vedovato, M.; Zavaroni, D.; Grioni, S.; Riccardi, G.; Vaccaro, O; Rivellese, Angela Albarosa; Cocozza, Sara; Auciello, Stefania; Turco, Anna Amelia; Bonora, Enzo; Cigolini, Massimo; Pichiri, Isabella; Brangani, Corinna; Tomasetto, Elena; Perriello, Gabriele; Timi, Alessia; Squatrito, Sebastiano; Sinagra, Tiziana; Longhitano, Sara; Tropea, Vanessa; Ballardini, Giorgio; Babini, Anna Carla; Ripani, Raffaella; Gregori, Giovanna; Dolci, Maria; Bruselli, Laura; Salutini, Isabella; Mori, Mary; Baccetti, Fabio; Lapolla, Annunziata; Sartore, Giovanni; Burlina, Silvia; Chilelli, Nino Cristiano; Buzzetti, Raffaella; Venditti, Chiara; Potenziani, Stella; Carlone, Angela; Galluzzo†, Aldo; Giordano, Carla; Torregrossa, Vittoria; Corsi, Laura; Cuneo, Giacomo; Corsi, Simona; Tizio, Biagio; Clemente, Gennaro; Citro, Giuseppe; Natale, Maria; Salvatore, Vita; Di Cianni, Graziano; Lacaria, Emilia; Russo, Laura; Iannarelli, Rossella; de Gregorio, Antonella; Sciarretta, Filomena; D’Andrea, Settimio; Montani, Valeria; Cannarsa, Emanuela; Dolcetti, Katia; Cordera, Renzo; Bonabello, Laura Affinito; Mazzucchelli, Chiara; Giorda, Carlo Bruno; Romeo, Francesco; Bonetto, Caterina; Antenucci, Daniela; Baldassarre, Maria Pompea Antonia; Iovine, Ciro; Nappo, Rossella; Ciano, Ornella; Dall’Aglio, Elisabetta; Mancastroppa, Giovanni; Grimaldi, Franco; Tonutti, Laura; Boemi, Massimo; D’Angelo, Federica; Leotta, Sergio; Fontana, Lucia; Lauro, Davide; Rinaldi, Maria Elena; Cignarelli, Mauro; la Macchia, Olga; Fariello, Stefania; Tomasi, Franco; Zamboni, Chiara; Dozio, Nicoletta; Trevisan, Roberto; Scaranna, Cristiana; Del Prato, Stefano; Miccoli, Roberto; Bianchi, Cristina; Garofolo, Monia; Pugliese, Giuseppe; Salvi, Laura; Rangel, Graziela; Vitale, Martina; Anichini, Roberto; Tedeschi, Anna; Corsini, Elisa; Cucinotta, Domenico; Di Benedetto, Antonino; Giunta, Loretta; Ruffo, Maria Concetta; Bossi, Antonio Carlo; Carpinter, Rita; Dotta, Francesco; Ceccarelli, Elena; Bartolo, Paolo Di; Caselli, Chiara; Luberto, Alessandra; Santini, Costanza; Mazzotti, Arianna; Calbucci, Giovanni; Consoli, Agostino; Ginestra, Federica; Calabrese, Maria; Zogheri, Alessia; Ricci, Lucia; Giorgino, Francesco; Laviola, Luigi; Ippolito, Claudia; Tarantino, Lucia; Avogaro, Angelo; Vedovato, Monica; Gnasso, Agostino; Carallo, Claudio; Scicchitano, Caterina; Zavaroni, Donatella; Livraga, Stefania; Perin, Paolo Cavallo; Forrnengo, Paolo; Prinzis, Tania; de Cosmo, Salvatore; Palena, Antonio Pio; Bacci, Simonetta; Mannucci, Edoardo; Lamanna, Caterina; Pata, Pietro; Lettina, Gabriele; Aiello, Antimo; Barrea, Angelina; Lalli, Carlo; Scarponi, Maura; Franzetti, Ivano; Radin, Raffaella; Serra, Rosalia; Petrachi, Francesca; Asprino, Vincenzo; Capra, Claudio; Cigolini, Massimo; Forte, Elisa; Potenziani, Stella; Reggiani, Giulio Marchesini; Forlani, Gabriele; Montesi, Luca; Mazzella, Natalia; Piatti, Pier Marco; Monti, Lucilla; Stuccillo, Michela; Auletta, Pasquale; Petraroli, Ettore; Capobianco, Giuseppe; Romano, Geremia; Cutolo, Michele; de Simone, Giosetta; Caiazzo, Gennaro; Nunziata, Peppe; Sorrentino, Susy; Amelia, Umberto; Calatola, Pasqualino; Capuano, GelsominaVitale, M.; Masulli, M.; Rivellese, A. A.; Bonora, Enzo; Cappellini, F.; Nicolucci, A.; Squatrito, S.; Antenucci, D.; Barrea, A.; Bianchi, C.; Bianchini, FRANCESCA ANTONIA; Fontana, L.; Fornengo, P.; Giorgino, FRANCESCO LIBERO; Gnasso, A.; Mannucci, E.; Mazzotti, Alfredo; Nappo, R.; Palena, A. P.; Pata, P.; Perriello, G.; Potenziani, S.; Radin, R.; Ricci, Laura; Romeo, Francesco; Santini, C.; Scarponi, M.; Serra, Roberto; Timi, A.; Turco, A. A.; Vedovato, M.; Zavaroni, D.; Grioni, S.; Riccardi, Giovanna; Vaccaro, O; Rivellese, Angela Albarosa; Cocozza, Sara; Auciello, Stefania; Turco, Anna Amelia; Bonora, Enzo; Cigolini, Massimo; Pichiri, Isabella; Brangani, Corinna; Tomasetto, Elena; Perriello, Gabriele; Timi, Alessia; Squatrito, Sebastiano; Sinagra, Tiziana; Longhitano, Sara; Tropea, Vanessa; Ballardini, Giorgio; Babini, Anna Carla; Ripani, Raffaella; Gregori, Giovanna; Dolci, Maria; Bruselli, Laura; Salutini, Isabella; Mori, Mary; Baccetti, Fabio; Lapolla, Annunziata; Sartore, Giovanni; Burlina, Silvia; Chilelli, NINO CRISTIANO; Buzzetti, Raffaella; Venditti, Chiara; Potenziani, Stella; Carlone, Angela; Galluzzo†, Aldo; Giordano, Carla; Torregrossa, Vittoria; Corsi, Laura; Cuneo, Giacomo; Corsi, Simona; Tizio, Biagio; Clemente, Gennaro; Citro, Giuseppe; Natale, Maria; Salvatore, Vita; Di Cianni, Graziano; Lacaria, Emilia; Russo, Laura; Iannarelli, Rossella; de Gregorio, Antonella; Sciarretta, Filomena; D’Andrea, Settimio; Montani, Valeria; Cannarsa, Emanuela; Dolcetti, Katia; Cordera, Renzo; Bonabello, Laura Affinito; Mazzucchelli, Chiara; Giorda, Carlo Bruno; Romeo, Francesco; Bonetto, Caterina; Antenucci, Daniela; Baldassarre, Maria Pompea Antonia; Iovine, Ciro; Nappo, Rossella; Ciano, Ornella; Dall’Aglio, Elisabetta; Mancastroppa, Giovanni; Grimaldi, Franco; Tonutti, Laura; Boemi, Massimo; D’Angelo, Federica; Leotta, Sergio; Fontana, Lucia; Lauro, Davide; Rinaldi, Maria Elena; Cignarelli, Mauro; la Macchia, Olga; Fariello, Stefania; Tomasi, Franco; Zamboni, Chiara; Dozio, Nicoletta; Trevisan, Roberto; Scaranna, Cristiana; Del Prato, Stefano; Miccoli, Roberto; Bianchi, Cristina; Garofolo, Monia; Pugliese, Giuseppe; Salvi, Laura; Rangel, Graziela; Vitale, Martina; Anichini, Roberto; Tedeschi, Anna; Corsini, Elisa; Cucinotta, Domenico; Di Benedetto, Antonino; Giunta, Loretta; Ruffo, Maria Concetta; Bossi, Antonio Carlo; Carpinter, Rita; Dotta, Francesco; Ceccarelli, Elena; Bartolo, Paolo Di; Caselli, Chiara; Luberto, Alessandra; Santini, Costanza; Mazzotti, Arianna; Calbucci, Giovanni; Consoli, Agostino; Ginestra, Federica; Calabrese, Maria; Zogheri, Alessia; Ricci, Lucia; Giorgino, FRANCESCO LIBERO; Laviola, Luigi; Ippolito, Claudia; Tarantino, Lucia; Avogaro, Angelo; Vedovato, Monica; Gnasso, Agostino; Carallo, Claudio; Scicchitano, Caterina; Zavaroni, Donatella; Livraga, Stefania; Perin, Paolo Cavallo; Forrnengo, Paolo; Prinzis, Tania; de Cosmo, Salvatore; Palena, Antonio Pio; Bacci, Simonetta; Mannucci, Edoardo; Lamanna, Caterina; Pata, Pietro; Lettina, Gabriele; Aiello, Antimo; Barrea, Angelina; Lalli, Carlo; Scarponi, Maura; Franzetti, Ivano; Radin, Raffaella; Serra, Rosalia; Petrachi, Francesca; Asprino, Vincenzo; Capra, Claudio; Cigolini, Massimo; Forte, Elisa; Potenziani, Stella; Reggiani, Giulio Marchesini; Forlani, Gabriele; Montesi, Luca; Mazzella, Natalia; Piatti, Pier Marco; Monti, Lucilla; Stuccillo, Michela; Auletta, Pasquale; Petraroli, Ettore; Capobianco, Giuseppe; Romano, Geremia; Cutolo, Michele; de Simone, Giosetta; Caiazzo, Gennaro; Nunziata, Peppe; Sorrentino, Susy; Amelia, Umberto; Calatola, Pasqualino; Capuano, Gelsomin