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28 results on '"Bertoldi, Loris"'

3. The fecal bacterial microbiota is not useful for discriminating between lymphoplasmacytic enteritis and low-grade intestinal T-cell lymphoma in cats nor for predicting therapeutic response

Author

Benvenuti, Elena, primary, Ferriani, Riccardo, additional, Gianella, Paola, additional, Ruggiero, Pietro, additional, Cagnasso, Federica, additional, Borrelli, Antonio, additional, Benvenuto, Giuseppe, additional, Bertoldi, Loris, additional, and Bottero, Enrico, additional

Published
2024
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4. New Insights into Pediatric Kidney Transplant Rejection Biomarkers: Tissue, Plasma and Urine MicroRNAs Compared to Protocol Biopsy Histology

Author

Carraro, Andrea, primary, De Gaspari, Piera, additional, Antoniello, Benedetta, additional, Marzenta, Diana, additional, Vianello, Emanuele, additional, Bussolati, Benedetta, additional, Tritta, Stefania, additional, Collino, Federica, additional, Bertoldi, Loris, additional, Benvenuto, Giuseppe, additional, Vedovelli, Luca, additional, Benetti, Elisa, additional, and Negrisolo, Susanna, additional

Published
2024
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5. Whole-Genome Sequencing of Two Canine Herpesvirus 1 (CaHV-1) Isolates and Clinicopathological Outcomes of Infection in French Bulldog Puppies

Author

Rocchigiani, Angela Maria, primary, Bertoldi, Loris, additional, Coradduzza, Elisabetta, additional, Lostia, Giada, additional, Pintus, Davide, additional, Scivoli, Rosario, additional, Cancedda, Maria Giovanna, additional, Fiori, Mariangela Stefania, additional, Bechere, Roberto, additional, Murtino, Anna Pina, additional, Pala, Giovanni, additional, Cardeti, Giusy, additional, Macioccu, Simona, additional, Dettori, Maria Antonietta, additional, Pintore, Antonio, additional, Ligios, Ciriaco, additional, and Puggioni, Giantonella, additional

Published
2024
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8. RNAseq analysis of olfactory neuroepithelium cytological samples in individuals with Down syndrome compared to euploid controls: a pilot study

Author

Brozzetti, Lorenzo, primary, Scambi, Ilaria, additional, Bertoldi, Loris, additional, Zanini, Alice, additional, Malacrida, Giorgio, additional, Sacchetto, Luca, additional, Baldassa, Lucia, additional, Benvenuto, Giuseppe, additional, Mariotti, Raffaella, additional, Zanusso, Gianluigi, additional, and Cecchini, Maria Paola, additional

Published
2022
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11. Co-Infection by Leptospira montravelensis and Leptospira interrogans Serovar Pomona in Urine Samples of Donkeys and Pigs in Sardinia, Italy.

Author

Piredda, Ivana, Bertoldi, Loris, Pedditzi, Aureliana, Pintore, Pierangela, Palmas, Bruna, and Chisu, Valentina

Subjects
*LEPTOSPIRA interrogans, *LEPTOSPIRA, *DONKEYS, *MIXED infections, *ZOONOSES, *SWINE, *SWINE farms
Abstract

Simple Summary: Leptospirosis is one of the most neglected zoonotic diseases in the world and humans can easily acquire the pathogen after exposure to water, soil, or mud contaminated with urine from infected animals. In September 2018, a leptospirosis outbreak caused by a pathogenic Leptospira genospecies interrogans was identified in one farm in North Sardinia, Italy. In addition, culture and isolation of a saprophytic Leptospira genospecies montravelensis from two urine samples (from one pig and one donkey) was reported for the first time, indicating that co-infection with more than one strain of Leptospira in the same reservoir host is possible. These results provide new information on the epidemiology of leptospirosis and on the genotypes circulating in Sardinia, emphasizing the conducting of active surveillance of leptospirosis in humans and animals. Saprophytic leptospires are spirochetes enclosed within the non-pathogenic clade of the genus Leptospira, which in turn is subdivided into two subclades S1 and S2. To date, the microorganisms included in these subclades have been isolated from the environment in various parts of the world, and are believed to have no known animal reservoirs. After a case of Leptospira interrogans serovar Pomona was notified to the owner of a farm in Sardinia, all of the farm animals (11 pigs and 3 donkeys) were examined for the presence of Leptospira. Sera of all tested animals resulted positive for antibodies to Leptospira using a microscopic agglutination test (MAT). Moreover, nine (82%) kidney samples from pigs and three urine samples collected from donkeys (100%) tested positive for Leptospira DNA after qPCR. Results obtained after MLST analysis and sequencing of rrs, rpoB, and secY genes, performed on six Leptospira strains isolated in culture, revealed the presence of the genomospecies L. interrogans serovar Pomona in the kidney samples. Conversely, whole - genome sequencing combined with mean nucleotide identity revealed the presence of the saprophytic L. montravelensis in the urine samples. Our results report, for the first time, the isolation of a saprophytic species from mammalian urine, suggesting a new ecological specialization for these bacteria, with a possible transition from free-living to a symbiotic lifestyle. Further studies will have to be conducted to understand the evolution of virulence of these bacteria, potential infectivity, and possible public health implications. [ABSTRACT FROM AUTHOR]

Published
2023
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12. Clinical evaluation and microbiota analysis in 9 dogs with antibiotic‐responsive enteropathy: A prospective comparison study

Author

Bottero, Enrico, primary, Ferriani, Riccardo, additional, Benvenuti, Elena, additional, Ruggiero, Pietro, additional, Astorina, Simona, additional, Giraldi, Marco, additional, Bertoldi, Loris, additional, Benvenuto, Giuseppe, additional, Sattin, Eleonora, additional, Gianella, Paola, additional, and Suchodolski, Jan S., additional

Published
2022
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18. Very-Low-Calorie Ketogenic Diets With Whey, Vegetable, or Animal Protein in Patients With Obesity: A Randomized Pilot Study

Author

Basciani, Sabrina, primary, Camajani, Elisabetta, additional, Contini, Savina, additional, Persichetti, Agnese, additional, Risi, Renata, additional, Bertoldi, Loris, additional, Strigari, Lidia, additional, Prossomariti, Giancarlo, additional, Watanabe, Mikiko, additional, Mariani, Stefania, additional, Lubrano, Carla, additional, Genco, Alfredo, additional, Spera, Giovanni, additional, and Gnessi, Lucio, additional

Published
2020
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20. SAMHD1‐deficient fibroblasts from Aicardi‐Goutières Syndrome patients can escape senescence and accumulate mutations

Author

Franzolin, Elisa, primary, Coletta, Sara, additional, Ferraro, Paola, additional, Pontarin, Giovanna, additional, D'Aronco, Giulia, additional, Stevanoni, Martina, additional, Palumbo, Elisa, additional, Cagnin, Stefano, additional, Bertoldi, Loris, additional, Feltrin, Erika, additional, Valle, Giorgio, additional, Russo, Antonella, additional, Bianchi, Vera, additional, and Rampazzo, Chiara, additional

Published
2019
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21. Bioinformatics for personal genomics: development and application of bioinformatic procedures for the analysis of genomic data

Author

Bertoldi, Loris

Subjects
variant analysis, next generation sequencing, data analysis, BIO/11 Biologia molecolare, variant annotation, genomics, variant prioritization, variant annotation, variant analysis, next generation sequencing, whole exome sequencing, data analysis, bioinformatics, genomics, Settore BIO/11 - Biologia Molecolare, bioinformatics, variant prioritization, whole exome sequencing
Abstract

In the last decade, the huge decreasing of sequencing cost due to the development of high-throughput technologies completely changed the way for approaching the genetic problems. In particular, whole exome and whole genome sequencing are contributing to the extraordinary progress in the study of human variants opening up new perspectives in personalized medicine. Being a relatively new and fast developing field, appropriate tools and specialized knowledge are required for an efficient data production and analysis. In line with the times, in 2014, the University of Padua funded the BioInfoGen Strategic Project with the goal of developing technology and expertise in bioinformatics and molecular biology applied to personal genomics. The aim of my PhD was to contribute to this challenge by implementing a series of innovative tools and by applying them for investigating and possibly solving the case studies included into the project. I firstly developed an automated pipeline for dealing with Illumina data, able to sequentially perform each step necessary for passing from raw reads to somatic or germline variant detection. The system performance has been tested by means of internal controls and by its application on a cohort of patients affected by gastric cancer, obtaining interesting results. Once variants are called, they have to be annotated in order to define their properties such as the position at transcript and protein level, the impact on protein sequence, the pathogenicity and more. As most of the publicly available annotators were affected by systematic errors causing a low consistency in the final annotation, I implemented VarPred, a new tool for variant annotation, which guarantees the best accuracy (>99%) compared to the state-of-the-art programs, showing also good processing times. To make easy the use of VarPred, I equipped it with an intuitive web interface, that allows not only a graphical result evaluation, but also a simple filtration strategy. Furthermore, for a valuable user-driven prioritization of human genetic variations, I developed QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. The prioritization is achieved by a global positive selection process that promotes the emergence of the most reliable variants, rather than filtering out those not satisfying the applied criteria. QueryOR has been used to analyze the two case studies framed within the BioInfoGen project. In particular, it allowed to detect causative variants in patients affected by lysosomal storage diseases, highlighting also the efficacy of the designed sequencing panel. On the other hand, QueryOR simplified the recognition of LRP2 gene as possible candidate to explain such subjects with a Dent disease-like phenotype, but with no mutation in the previously identified disease-associated genes, CLCN5 and OCRL. As final corollary, an extensive analysis over recurrent exome variants was performed, showing that their origin can be mainly explained by inaccuracies in the reference genome, including misassembled regions and uncorrected bases, rather than by platform specific errors.

Published
2018

22. Genetic Analyses in Dent Disease and Characterization of CLCN5 Mutations in Kidney Biopsies.

Author

Gianesello, Lisa, Ceol, Monica, Bertoldi, Loris, Terrin, Liliana, Priante, Giovanna, Murer, Luisa, Peruzzi, Licia, Giordano, Mario, Paglialonga, Fabio, Cantaluppi, Vincenzo, Musetti, Claudio, Valle, Giorgio, Del Prete, Dorella, and Anglani, Franca

Subjects
RENAL biopsy, PROXIMAL kidney tubules, MOLECULAR weights, DISEASES, ENDOCYTOSIS
Abstract

Dent disease (DD), an X-linked renal tubulopathy, is mainly caused by loss-of-function mutations in CLCN5 (DD1) and OCRL genes. CLCN5 encodes the ClC-5 antiporter that in proximal tubules (PT) participates in the receptor-mediated endocytosis of low molecular weight proteins. Few studies have analyzed the PT expression of ClC-5 and of megalin and cubilin receptors in DD1 kidney biopsies. About 25% of DD cases lack mutations in either CLCN5 or OCRL genes (DD3), and no other disease genes have been discovered so far. Sanger sequencing was used for CLCN5 gene analysis in 158 unrelated males clinically suspected of having DD. The tubular expression of ClC-5, megalin, and cubilin was assessed by immunolabeling in 10 DD1 kidney biopsies. Whole exome sequencing (WES) was performed in eight DD3 patients. Twenty-three novel CLCN5 mutations were identified. ClC-5, megalin, and cubilin were significantly lower in DD1 than in control biopsies. The tubular expression of ClC-5 when detected was irrespective of the type of mutation. In four DD3 patients, WES revealed 12 potentially pathogenic variants in three novel genes (SLC17A1, SLC9A3, and PDZK1), and in three genes known to be associated with monogenic forms of renal proximal tubulopathies (SLC3A, LRP2, and CUBN). The supposed third Dent disease-causing gene was not discovered. [ABSTRACT FROM AUTHOR]

Published
2020
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25. QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

Author

Bertoldi, Loris, primary, Forcato, Claudio, additional, Vitulo, Nicola, additional, Birolo, Giovanni, additional, De Pascale, Fabio, additional, Feltrin, Erika, additional, Schiavon, Riccardo, additional, Anglani, Franca, additional, Negrisolo, Susanna, additional, Zanetti, Alessandra, additional, D’Avanzo, Francesca, additional, Tomanin, Rosella, additional, Faulkner, Georgine, additional, Vezzi, Alessandro, additional, and Valle, Giorgio, additional

Published
2017
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26. Whole-exome sequencing in radically resected gastric cancer (GC): Analysis of patients (pts) with poor prognostic factors from the Italian Trial of Adjuvant Chemotherapy Adenocarcinoma (ITACA-S) trial.

Author

Di Bartolomeo, Maria, primary, Andrea, Devecchi, additional, Canevari, Silvana, additional, Pellegrinelli, Alessandro, additional, Pietrantonio, Filippo, additional, Martinetti, Antonia, additional, Paoli, Alessandro, additional, Penso, Donata, additional, Valle, Giorgio, additional, Disciglio, Vittoria, additional, Bertoldi, Loris, additional, Feltrin, Erika, additional, Rosati, Gerardo, additional, De Vita, Fernando, additional, Dominoni, Francesca, additional, De Braud, Filippo G., additional, Berenato, Rosa, additional, Niger, Monica, additional, Miceli, Rosalba, additional, and De Cecco, Loris, additional

Published
2017
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