BMR Genomics

Padova, Italy

BMR Genomics

Padova, Italy
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Plebani R.,University of Chieti Pescara | Oliver G.R.,Almac Diagnostics | Trerotola M.,University of Chieti Pescara | Trerotola M.,Thomas Jefferson University | And 9 more authors.
Neoplasia (United States) | Year: 2012

mRNA chimeras from chromosomal translocations often play a role as transforming oncogenes. However, cancer transcriptomes also contain mRNA chimeras that may play a role in tumor development, which arise as transcriptional or post-transcriptional events. To identify such chimeras, we developed a deterministic screening strategy for long-range sequence analysis. High-throughput, long-read sequencing was then performed on cDNA libraries from major tumor histotypes and corresponding normal tissues. These analyses led to the identification of 378 chimeras, with an unexpectedly high frequency of expression (≈ 2 × 10-5 of all mRNA). Functional assays in breast and ovarian cancer cell lines showed that a large fraction of mRNA chimeras regulates cell replication. Strikingly, chimeras were shown to include both positive and negative regulators of cell growth, which functioned as such in a cell-type-specific manner. Replication-controlling chimeras were found to be expressed by most cancers from breast, ovary, colon, uterus, kidney, lung, and stomach, suggesting a widespread role in tumor development. © 2012 Neoplasia Press, Inc. All rights reserved.


Angione C.,University of Teesside | Lio P.,University of Cambridge | Pucciarelli S.,University of Camerino | Can B.,Epigenetiks Genetik Biyoinformatik Yazilim A.S | And 6 more authors.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2016

Biological systems show impressive adaptations at extreme environments. In extreme environments, directional selection pressure mechanisms acting upon mutational events often produce functional and structural innovations. Examples are the antifreeze proteins in Antarctic fish and their lack of hemoglobin, and the thermostable properties of TAQ polymerase from thermophilic organisms. During the past decade, more than 4000 organisms have been part of genome-sequencing projects. This has enabled the retrieval of information about evolutionary relationships among all living organisms, and has increased the understanding of complex phenomena, such as evolution, adaptation, and ecology. Bioinformatics tools have allowed us to perform genome annotation, crosscomparison, and to understand the metabolic potential of living organisms. In the last few years, research in bioinformatics has started to migrate from the analysis of genomic sequences and structural biology problems to the analysis of genotype-phenotype mapping. We believe that the analysis of multi-omic information, particularly metabolic and transcriptomic data of organisms living in extreme environments, could provide important and general insights into the how natural selection in an ecosystem shapes the molecular constituents. Here we present a review of methods with the aim to bridge the gap between theoretical models, bioinformatics analysis and experimental settings. The amount of data suggests that bioinformatics could be used to investigate whether the adaptation is generated by interesting molecular inventions.We therefore review and discuss the methodology and tools to approach this challenge. © Springer International Publishing Switzerland 2016.


Sattin E.,BMR Genomics | Andreani N.A.,University of Padua | Carraro L.,University of Padua | Lucchini R.,Instituto Zooprofilattico Sperimentale delle Venezie | And 6 more authors.
Frontiers in Microbiology | Year: 2016

In the past, milk whey was only a by-product of cheese production, but currently, it has a high commercial value for use in the food industries. However, the regulation of whey management (i.e., storage and hygienic properties) has not been updated, and as a consequence, its microbiological quality is very challenging for food safety. The Next Generation Sequencing (NGS) technique was applied to several whey samples used for Ricotta production to evaluate the microbial community composition in depth using both RNA and DNA as templates for NGS library construction. Whey samples demonstrating a high microbial and aerobic spore load contained mostly Firmicutes; although variable, some samples contained a relevant amount of Gammaproteobacteria. Several lots of whey acquired as raw material for Ricotta production presented defective organoleptic properties. To define the volatile compounds in normal and defective whey samples, a headspace gas chromatography/mass spectrometry (GC/MS) analysis was conducted. The statistical analysis demonstrated that different microbial communities resulted from DNA or cDNA library sequencing, and distinguishable microbiota composed the communities contained in the organoleptic-defective whey samples. © 2016 Sattin, Andreani, Carraro, Lucchini, Fasolato, Telatin, Balzan, Novelli, Simionati and Cardazzo.


Sattin E.,BMR Genomics | Andreani N.A.,University of Padua | Carraro L.,University of Padua | Fasolato L.,University of Padua | And 6 more authors.
Food Microbiology | Year: 2016

Dairy products are perishable and have to be preserved from spoilage during the food chain to achieve the desired shelf-life. Ricotta is a typical Italian soft dairy food produced by heat coagulation of whey proteins and is considered to be a light and healthy product. The shelf-life of Ricotta could be extended, as required by the international food trade market; however, heat resistant microflora causes spoilage and poses issues regarding the safety of the product. Next-generation sequencing (NGS) applied to the Ricotta samples defined the composition of the microbial community in-depth during the shelf-life. The analysis demonstrated the predominance of spore-forming bacteria throughout the shelf-life, mostly belonging to Bacillus, Paenibacillus and Clostridium genera. A strain involved in spoilage and causing a pink discolouration of Ricotta was isolated and characterised as Bacillus mycoides/weihenstephanensis. This is the first report of a food discolouration caused by a toxigenic strain belonging to the Bacillus cereus group that resulted the predominant strain in the community of the defective ricotta. These results suggest that the processing of raw materials to eliminate spores and residual microflora could be essential for improving the quality and the safety of the product and to extend the shelf-life of industrial Ricotta. © 2015 Elsevier Ltd.


Maccagnan A.,University of Padua | Riva M.,BMR Genomics | Feltrin E.,University of Padua | Simionati B.,BMR Genomics | And 3 more authors.
Automated Experimentation | Year: 2010

Background. Laboratory protocols in life sciences tend to be written in natural language, with negative consequences on repeatability, distribution and automation of scientific experiments. Formalization of knowledge is becoming popular in science. In the case of laboratory protocols two levels of formalization are needed: one for the entities and individuals operations involved in protocols and another one for the procedures, which can be manually or automatically executed. This study aims to combine ontologies and workflows for protocol formalization. Results. A laboratory domain specific ontology and the COW (Combining Ontologies with Workflows) software tool were developed to formalize workflows built on ontologies. A method was specifically set up to support the design of structured protocols for biological laboratory experiments. The workflows were enhanced with ontological concepts taken from the developed domain specific ontology. The experimental protocols represented as workflows are saved in two linked files using two standard interchange languages (i.e. XPDL for workflows and OWL for ontologies). A distribution package of COW including installation procedure, ontology and workflow examples, is freely available from http://www.bmr-genomics.it/farm/cow. Conclusions. Using COW, a laboratory protocol may be directly defined by wet-lab scientists without writing code, which will keep the resulting protocol's specifications clear and easy to read and maintain. © 2010 Maccagnan et al; licensee BioMed Central Ltd.


MacCagnan A.,University of Padua | Vardanega T.,University of Padua | Feltriny E.,University of Padua | Valley G.,University of Padua | And 2 more authors.
CEUR Workshop Proceedings | Year: 2010

Software-based Laboratory Information Management Systems can handle samples, plates, instruments, users, potentially up to the automation of whole workflows. One frustrating element of this predicament is that Life Sciences laboratory protocols are normally expressed in natural languages and thus are scarcely amenable to real automation. We want to defeat this major limitation by way of a project combining Model-Driven Engineering, Workflows, Ontologies and Multiagent systems (MAS). This paper describes the latter ingredient. Our MAS has been implemented with JADE and WADE to automatically interpret and execute a structured representation of laboratory protocols expressed in XPDL+OWL. Our work has recently been tested on a real test case and will shortly be deployed in the field.


PubMed | University of Padua and BMR Genomics
Type: | Journal: Food microbiology | Year: 2016

Dairy products are perishable and have to be preserved from spoilage during the food chain to achieve the desired shelf-life. Ricotta is a typical Italian soft dairy food produced by heat coagulation of whey proteins and is considered to be a light and healthy product. The shelf-life of Ricotta could be extended, as required by the international food trade market; however, heat resistant microflora causes spoilage and poses issues regarding the safety of the product. Next-generation sequencing (NGS) applied to the Ricotta samples defined the composition of the microbial community in-depth during the shelf-life. The analysis demonstrated the predominance of spore-forming bacteria throughout the shelf-life, mostly belonging to Bacillus, Paenibacillus and Clostridium genera. A strain involved in spoilage and causing a pink discolouration of Ricotta was isolated and characterised as Bacillus mycoides/weihenstephanensis. This is the first report of a food discolouration caused by a toxigenic strain belonging to the Bacillus cereus group that resulted the predominant strain in the community of the defective ricotta. These results suggest that the processing of raw materials to eliminate spores and residual microflora could be essential for improving the quality and the safety of the product and to extend the shelf-life of industrial Ricotta.

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