Browsing by Author "Barros, M."
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- CanisTecOme: Canis lupus familiaris proteome databasePublication . Fernandes, M.; Rosa, N.; Correia, M.J.; Vala, Helena; Barros, M.Introduction: The great amount of data generated by the omic sciences can only be explored and conjugated with other data using bioinformatics tools and databases. There is a great number of databases and dedicated bioinformatics tools to explore the proteomes, genomes and transcriptomes of several animals which interact with humans and therefore have an impact on the Health of several populations. Objective: The aim of the present work is the creation of a database with the molecular information available for Canis lupus familiaris. Such a tool will facilitate the identification of molecular mechanisms underlying physiological and physiopathological processes in dogs and therefore generates new opportunities for the design of therapeutical and diagnostic strategies. Methods: The development of this database is based on the manual compilation and review of the proteins identified in different studies using dog samples, with the annotation of the sample characterization and proteomics techniques used. Results: The database obtained is called CanisTecOme and includes proteins identified in proteomic and targeted studies published in the scientific literature from 2000 to 2013. Conclusion: We believe CanisTecOme and its publication with a web interface based on bioinformatics tools to explore the data, such as the OralCard available for the Human and previously developed, is a powerful instrument for the study of the physiology of this species.
- Morphological evaluation of cardoon (Cynara cardunculus L.): assessing biodiversity for applications based on tradition, innovation and sustainabilityPublication . Barracosa, Paulo; Oliveira, Jorge; Barros, M.; Pires, E.Selected cardoon cultivars established in the “Serra da Estrela” region were analysed to evaluate morphological characteristics related principally to the production of cardoon flowers, which are a compulsory ingredient for particular Mediterranean PDO cheese regions. The biodiversity of twelve cardoon cultivars installed in an experimental field were evaluated over three growing seasons using thirty-four morphological descriptors. Statistically significant differences were found between cultivars for twenty-four morphological characteristics which indicate a wide genetic diversity. The relationship among the cultivars and characteristics was analysed using principal component analysis. A three dimensional template was found to be very significant and explained 71% of the total variation. The first component is dominated positively by plant height, diameter of stalk, inflorescence characteristics and flower production, while the second component is positively dominated by leaf characteristics. Cultivars A26, D32 and D33, present a plant architecture simultaneously well adapted for flower production, ease of harvesting and plant biomass. These characterizations and understandings can be useful for a plant breeding programme to develop cultivars for innovative potential applications besides flowers, and also for application by other cheese producers in Mediterranean regions.
- OvinOralOme: Ovis aries oral proteome databasePublication . Esteves, E.; Rosa, N.; Correia, M.J.; Vala, Helena; Barros, M.Introduction: Tools to store and catalog proteins identified in proteome surveys of tissues from subjects representing different physiological and pathological states are powerful instruments to integrate published information. Much of the information on molecular mechanisms can be generated using bioinformatics strategies powered by this tools. Within the scope of previous projects a database named OralOme was built, dedicated to the storage of all the information on the proteins of the human oral cavity. This database is available through the web interface OralCard. Objective: The present study aims the development of a database transferring the methodology used in humans to the storage and cataloguing of the proteins present in the oral cavity and other tissues of Ovis aries. This database will be essential to develop diagnosis methods to be applied to living animals targeting the most prevalent diseases affecting the flocks in Serra da Estrela region. Methods: The development of this database involves the manual compilation and review of the proteins, identified in different studies, relative to Ovis aries, with the annotation of the sample characterization and proteomics techniques used. Results: The database resultant from this work is called OvinOralOme and includes proteins identified in proteomic and directed studies, published in the scientific literature from 2000 to 2013. Conclusion: The creation of OvinOralOme is a valuable instrument for the underlying several pathologies of these animals.
- OvisOme: atualização da base de dados de Ovis ariesPublication . Esteves, E.; Fernandes, M.; Rosa, N.; Correia, M. J.; Vala, Helena; Barros, M.Introduction: The Omics sciences are part of the research and diagnostic routines in human health. However, their application in veterinary sciences is still sparse, albeit the increasing number of proteomics studies published, especially regarding farm animals. The amount of information accumulated by these high throughput techniques, makes the existence of specialized databases fundamental. These databases are essential to store, annotate and make available to the scientific community, all the information gathered by the different omics studies, so that researchers can use it to understand the physio pathological mechanisms underlying sheep diseases, as well as to develop new and improved diagnostic, prognostic and therapeutic strategies. Objetive: The aim of this work is to present the OvisOme database and to demosntrate how it can be used to understand the molecular mechanisms urderlying sheep disease. Methodologies: OvisOme compiles all proteins identified by proteomics studies of Ovis aries. The proteins are annotated as to the sample characterization, the proteomics techniques used and all the data the authors refer regarding the donor sheep’s health. Results: The database currently has 1451 proteins, associated to 8 diseases and 10 breeds. When compared to other proteomics databases, the OvisOme stores and displays more information than other databases not specific for sheep, such as UniProt. Conclusion: OvisOme is a valuable tool for the study of the molecular mechanisms underlying sheep health and disease.
- SalivaPrint: sheep saliva electrophoretic protein profile in a bioinformatics approachPublication . Esteves, E.; Fernandes, M.; Cruz, I.; Esteves, Fernando; Rosa, N.; Correia, M. J.; Vala, Helena; Barros, M.Introduction: Sheep saliva is a fluid with properties relevant for the evaluation of individual wellbeing and disease states. It can be used for individual monitoring and decision aiding in therapeutic intervention. The total protein profile of each subject (SalivaPrint) can be integrated with clinical and environmental data to stratify individuals and analyze their health status. This strategy can also support the discovery of novel biomarkers. This study applies a bioinformatics strategy in order to identify standard protein profiles in healthy sheep. Standard total protein profiles of sheep are compared to human profile. Methods: Saliva samples were collected using an adaptation of the collection method available in Rosa et al 2016.Total protein profile of sheep saliva samples was performed b capillary electrophoretic analysis using the Experion™ technology. An algorithm which is able to identify common molecular weights ranges in a group of electrophoretic profiles was used. The molecular weight ranges identified were then used to discern between sheep and human population. Common molecular weights present in sheep SalivaPrint were then used with OvisOme database to identify proteins. Using AgBase GORetriever tool it was possible to analyze and catalogue their biological process. Results: Sheep and Human SalivaPrints are different and it is possible to discern both species. The SalivaPrints of individuals from the same flock appear to have a higher degree of similarity than individuals of different flocks. Sheep SalivaPrints showed five commonly present molecular weight ranges 7,9-8,9; 8,9-9,8; 12,7-13,6; 17,4 18,4 and 27,928,8 kDa. In this ranges, 14 proteins were identified using OvisOme database. The most representative biological process found was the response to stress (imm ne system process) with the proteins: Cathelicidin-1, Beta 2 microglobulin, Cathelin, Kallirein and Chloride intracellular channel protein. Conclusion: It was possible to conclude that different species have different salivary protein profiles. In addition to this, the total protein profile seem to be highly conserved between flocks. By using SalivaPrint profiles with bioinformatic tools like OvisOme.