Loading...
22 results
Search Results
Now showing 1 - 10 of 22
- Peri-implantitis- uncovering the molecular mechanisms by a bioinformatics approachPublication . Correia, André; Albino, Rafaela; Barros, Marlene; Rosa, Nuno
- SalivaPRINT Toolkit – protein profile evaluation and phenotype stratificationPublication . Cruz, Igor; Esteves, Eduardo; Fernandes, Mónica; Rosa, Nuno; Correia, Maria José; Arrais, Joel P.; Barros, MarleneThe value of the molecular information obtained from saliva is dependent on the use of in vitro and in silico techniques. The main proteins of saliva when separated by capillary electrophoresis enable the establishment of individual profiles with characteristic patterns reflecting each individual phenotype. Different physiological or pathological conditions may be identified by specific protein profiles. The association of each profile to the particular protein composition provides clues as to which biological processes are compromised in each situation. Patient stratification according to different phenotypes often within a particular disease spectrum is especially important for the management of individuals carrying multiple diseases and requiring personalized interventions. In this work we present the SalivaPRINT Toolkit, which enables the analysis of protein profile patterns and patient phenotyping. Additionally, the SalivaPRINT Toolkit allows the identification of molecular weight ranges altered in a particular condition and therefore potentially involved in the underlying dysregulated mechanisms. This tutorial introduces the use of the SalivaPRINT Toolkit command line interface (https://github.com/salivatec/SalivaPRINT) as an independent tool for electrophoretic protein profile evaluation. It provides a detailed overview of its functionalities, illustrated by the application to the analysis of profiles obtained from a healthy population versus a population affected with inflammatory conditions. Biological significance We present SalivaPRINT, which serves as a patient characterization tool to identify molecular weights related with particular conditions and, from there, find proteins, which may be involved in the underlying dysregulated cellular mechanisms. The proposed analysis strategy has the potential to boost personalized diagnosis. To our knowledge this is the first independent tool for electrophoretic protein profile evaluation and is crucial when a large number of complex electrophoretic profiles needs to be compared and classified.
- #097. Presença de genes de resistência a antibióticos na cavidade oral: uma revisão sistemáticaPublication . Sousa, Sara; Martins, Jorge; Rosa, Nuno; Barros, Marlene; Correia, Maria JoséObjetivos: O uso excessivo e, muitas vezes, desnecessário de antibióticos pode originar a seleção de genes de resistência a antibióticos. Os biofilmes, especificamente os orais, são conglomerados bacterianos que potenciam a preservação dos genes de resistência a antibióticos. Além disso, há estudos que destacam a propagação dos genes de resistência a antibióticos para outros locais do organismo. Deste modo, é de extrema importância compreender quais são os genes de resistência a antibióticos na cavidade oral, como se pode fazer a sua determinação e estimar o seu impacto na ecologia da cavidade oral. Pretendeu‐se verificar: (i) quantos estudos foram realizados in vivo, em amostras com origem na cavidade oral; (ii) que métodos foram utilizados para a deteção dos genes de resistência a antibióticos; (iii) e quais os genes de resistência a antibióticos encontrados. Materiais e métodos: A revisão bibliográfica foi realizada na base de dados PubMed® do NCBI (19‐04‐2016), com a seguinte estratégia: acrescentou‐se sucessivamente cada grupo de palavras‐chave: pesquisa 1 – «antibiotic resistant bacteria» AND «oral biofilm» AND «saliva» AND «mouth»; pesquisa 2 – «antibiotic resistance» AND «oral biofilm» AND «saliva» AND «mouth». Foi obtido um total de 254 artigos científicos, analisados quanto à metodologia utilizada e respetivos resultados. Adicionaram‐se 20 artigos referenciados por um artigo da primeira pesquisa. Desse total de 274, foram excluídos os artigos com objetivo de testar terapias alternativas aos antibióticos, e estudos em Candida, ficando 135 artigos. Destes foram selecionados apenas os estudos realizados na cavidade oral, obtendo‐se 50 artigos, dos quais 30 referem a presença de genes de resistência a antibióticos. Resultados: Dos artigos selecionados a maioria utiliza exclusivamente técnicas de cultivo (46,7%), 6,7% usam a reação de polimerase em cadeia e 3,3% a versão quantitativa da reação da polimerase em cadeia. A título de exemplo, foram encontrados 18 genes de resistência a antibióticos ß‐lactâmicos, na cavidade oral. Conclusões: Dos poucos estudos focados na cavidade oral, verifica‐se a existência de genes de resistência a antibióticos no biofilme oral. É, deste modo, de extrema importância realizar estudos de quantificação de genes de resistência a antibióticos, de forma a conseguir avaliar o impacto no microbioma oral.
- Protein quality assessment on saliva samples for biobanking purposesPublication . Rosa, Nuno; Marques, Jéssica; Esteves, Eduardo; Fernandes, Mónica; Mendes, Vera M.; Afonso, Ângela; Dias, Sérgio; Pereira, Joaquim Polido; Manadas, Bruno; Correia, Maria José; Barros, MarleneBiobank saliva sample quality depends on specific criteria applied to collection, processing, and storage. In spite of the growing interest in saliva as a diagnostic fluid, few biobanks currently store large collections of such samples. The development of a standard operating procedure (SOP) for saliva collection and quality control is fundamental for the establishment of a new saliva biobank, which stores samples to be made available to the saliva research community. Different collection methods were tested regarding total volume of protein obtained, protein content, and protein profiles, and the results were used to choose the best method for protein studies. Furthermore, the impact of the circadian variability and inter- and intraindividual differences, as well as the saliva sample stability at room temperature, were also evaluated. Considering our results, a sublingual cotton roll method for saliva collection proved to produce saliva with the best characteristics and should be applied in the morning, whenever possible. In addition, there is more variability in salivary proteins between individuals than in the same individual for a 5-month period. According to the electrophoretic protein profile, protein stability is guaranteed for 24 hours at room temperature and the protein degradation profile and protein identification were characterized. All this information was used to establish an SOP for saliva collection, processing, and storage in a biobank. We conclude that it is possible to collect saliva using an easy and inexpensive protocol, resulting in saliva samples for protein analysis with sufficient quality for biobanking purposes.
- New targets for Zika Virus determined by human-viral interactomic: a bioinformatics approachPublication . Esteves, Eduardo; Rosa, Nuno; Correia, Maria José; Arrais, Joel P.; Barros, MarleneIdentifying ZIKV factors interfering with human host pathways represents a major challenge in understanding ZIKV tropism and pathogenesis. The integration of proteomic, gene expression and Protein-Protein Interactions (PPIs) established between ZIKV and human host proteins predicted by the OralInt algorithm identified 1898 interactions with medium or high score (≥0.7). Targets implicated in vesicular traffic and docking were identified. New receptors involved in endocytosis pathways as ZIKV entry targets, using both clathrin-dependent (17 receptors) and independent (10 receptors) pathways, are described. New targets used by the ZIKV to undermine the host's antiviral immune response are proposed based on predicted interactions established between the virus and host cell receptors and/or proteins with an effector or signaling role in the immune response such as IFN receptors and TLR. Complement and cytokines are proposed as extracellular potential interacting partners of the secreted form of NS1 ZIKV protein. Altogether, in this article, 18 new human targets for structural and nonstructural ZIKV proteins are proposed. These results are of great relevance for the understanding of viral pathogenesis and consequently the development of preventive (vaccines) and therapeutic targets for ZIKV infection management.
- #145. Proteoma oral humano: da saliva ao diagnóstico das doenças cardiovascularesPublication . Silva, Rafael; Pinho, Lilibetty; Barros, Marlene; Correia, Maria José; Rosa, Nuno
- SalivaPrint as a non-invasive diagnostic toolPublication . Esteves, Eduardo; Cruz, Igor; Esteves, Ana Cristina; Barros, Marlene; Rosa, NunoCurrently, the molecular diagnosis is based on the quantification of RNA, proteins and metabolites because they present changes in their quantity related to clinical situations. The same molecules are not generally suitable for early diagnosis or to follow clinical evolution, making necessary strategies to evaluate the complete molecular scenario. There are already experimental strategies that allow the determination of total protein profiles from saliva samples (the SalivaPrint). The goal of this work is to identify a profile of saliva proteins (similar to a fingerprint) and, using computational methods, identify how this profiles changes with age and gender. So far it has been possible to collect 79 samples as well as the metadata associated with each sample using an electronic questionnaire developed by us. A total protein profile was obtained and their association with gender was verified using statistical methods. Currently we are developing the Python scripts for automatic data acquiring and normalization. Total protein profiles annotation on a database (SalivaPrintDB) and their integration with the factors that affects them using machine learning strategies can empower the use of the approach proposed on this work as a tool for monitoring the individual's health status.
- The landscape of protein biomarkers proposed for periodontal disease: markers with functional meaningPublication . Rosa, Nuno; Correia, Maria José; Arrais, Joel P.; Costa, Nuno; Oliveira, José Luís; Barros, MarlenePeriodontal disease (PD) is characterized by a deregulated inflammatory response which fails to resolve, activating bone resorption. The identification of the proteomes associated with PD has fuelled biomarker proposals; nevertheless, many questions remain. Biomarker selection should favour molecules representing an event which occurs throughout the disease progress. The analysis of proteome results and the information available for each protein, including its functional role, was accomplished using the OralOme database. The integrated analysis of this information ascertains if the suggested proteins reflect the cell and/or molecular mechanisms underlying the different forms of periodontal disease. The evaluation of the proteins present/absent or with very different concentrations in the proteome of each disease state was used for the identification of the mechanisms shared by different PD variants or specific to such state. The information presented is relevant for the adequate design of biomarker panels for PD. Furthermore, it will open new perspectives and help envisage future studies targeted to unveil the functional role of specific proteins and help clarify the deregulation process in the PD inflammatory response.
- OvinOralOme: Ovis aries oral proteome databasePublication . Esteves, Eduardo; Rosa, Nuno; Correia, M. J.; Vala, Helena; Barros, Marlene
- SalivaTec: using xMAP® Multiplex Technology for saliva researchPublication . Rosa, Nuno; Correia, Maria; Barros, MarleneSalivaTec is an European laboratory using saliva in health research (salivaTec.viseu.ucp.pt). The main goal of SalivaTec is the clarification of molecular mechanisms of disease and the validation of biomarker panels proposed by in silico studies using bioinformatics tools developed in the laboratory. We demonstrate how SalivaTec uses xMAP ® Multiplex technology to quantify different molecules in saliva. These molecules are selected by an in silico analysis of the data deposited in our databases and quantified in samples chosen through the SalivaPrint algorithm, which identifies the molecules varying the most between groups of individuals. xMAP technology allows for the detection of salivary markers with high sensitivity and reliability although some challenges remain in the application of the commercial kits to saliva.
- «
- 1 (current)
- 2
- 3
- »