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Fogliano Redipuglia, Italy

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.

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.

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.

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.

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