Browsing by Author "Esteves, Eduardo"
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- #095 Avaliação da saúde oral e sua relação com o SalivaPrint – variação com idade e géneroPublication . André, Marta; Esteves, Eduardo; Correia, Bruna; Fernandes, Mónica; Rosa, Nuno
- #107 Identificação molecular de espécies de Candida em lesões de estomatite protéticaPublication . Ribeiro, Adriana; Fernandes, Mónica; Esteves, Eduardo; Barros, Marlene; Veiga, Nélio; Correia, Maria JoséObjetivos: O fungo Candida é parte integrante do microbioma oral e geralmente estabelece uma relação comensal com o hospedeiro. No entanto, desequilíbrios no ecossistema oral podem levar à proliferação deste microrganismo levando a micoses orais. Os fatores de risco para o desenvolvimento de candidíases orais incluem a idade e a utilização de prótese, fatores que muitas vezes levam ao aparecimento de um tipo específico de micose oral designado por estomatite protética. Objetivos: Verificar, por métodos moleculares independentes de cultura, quais as espécies de Candida associadas a lesões compatíveis com estomatite protética. Materiais e métodos: Foram observados 177 participantes com mais de 60 anos. A observação clínica da cavidade oral foi seguida da recolha de uma amostra de saliva estimulada e zaragatoa de lesões suspeitas de estomatite protética. O DNA isolado foi analisado pela reação de polimerase em cadeia com primers específicos para 6 espécies de Candida: albicans, tropicalis, glabrata, parapsilopsis krusei e dublinensis. Resultados: Do total de indivíduos na amostra 47,5% usava prótese dentária e cerca de um terço destes (31%) apresentava lesões compatíveis com estomatite protética. A grande maioria das lesões (77%) estava colonizada com Candida e 65% das amostras apresentava mais que uma espécie. As espécies mais abundantes foram Candida tropicalis e albicans com 69% e 62% das amostras respetivamente. Conclusões: Foi possível verificar que na amostra analisada as lesões de estomatite protética são frequentes entre os utilizadores de próteses e que estas lesões são maioritariamente colonizadas por Candida albicans e C. tropicalis. Estes resultados podem ser relevantes no que concerne aos fatores de virulência presentes e terapêuticas a aplicar.
- # 39. Identificação de biomarcadores salivares de doença periodontal em pacientes com gengivitePublication . Serra, Beatriz Patrício; Esteves, Eduardo; Fernandes, Mónica; Rosa, Nuno; Barros, Marlene; Correia, Maria José
- An analysis of protein patterns present in the saliva of diabetic patients using pairwise relationship and hierarchical clusteringPublication . Soares, Airton; Esteves, Eduardo; Rosa, Nuno; Esteves, Ana Cristina; Lins, Anthony; Bastos-Filho, Carmelo J. A.Molecular diagnosis is based on the quantification of RNA, proteins, or metabolites whose concentration can be correlated to clinical situations. Usually, these molecules are not suitable for early diagnosis or to follow clinical evolution. Large-scale diagnosis using these types of molecules depends on cheap and preferably noninvasive strategies for screening. Saliva has been studied as a noninvasive, easily obtainable diagnosis fluid, and the presence of serum proteins in it enhances its use as a systemic health status monitoring tool. With a recently described automated capillary electrophoresis-based strategy that allows us to obtain a salivary total protein profile, it is possible to quantify and analyze patterns that may indicate disease presence or absence. The data of 19 persons with diabetes and 58 healthy donors obtained by capillary electrophoresis were transformed, treated, and grouped so that the structured values could be used to study individuals’ health state. After Pairwise Relationships and Hierarchical Clustering analysis were observed that amplitudes of protein peaks present in the saliva of these individuals could be used as differentiating parameters between healthy and unhealthy people. It indicates that these characteristics can serve as input for a future computational intelligence algorithm that will aid in the stratification of individuals that manifest changes in salivary proteins.
- CanisOme - the protein signatures of Canis lupus familiaris diseasesPublication . Fernandes, Mónica; Rosa, Nuno; Esteves, Eduardo; Correia, Maria José; Arrais, Joel; Ribeiro, Paulo; Vala, Helena; Barros, MarleneAlthough the applications of Proteomics in Human Biomedicine have been explored for some time now, in animal and veterinary research, the potential of this resource has just started to be explored, especially when companion animal health is considered. In the last years, knowledge on the Canis lupus familiaris proteome has been accumulating in the literature and a resource compiling all this information and critically reviewing it was lacking. This article presents such a resource for the first time. CanisOme is a database of all proteins identified in Canis lupus familiaris tissues, either in health or in disease, annotated with information on the proteins present on the sample and on the donors. This database reunites information on 549 proteins, associated with 63 dog diseases and 33 dog breeds. Examples of how this information may be used to produce new hypothesis on disease mechanisms is presented both through the functional analysis of the proteins quantified in canine cutaneous mast cell tumors and through the study of the interactome of C. lupus familiaris and Leishmania infantum. Therefore, the usefulness of CanisOme for researchers looking for protein biomarkers in dogs and interested in a comprehensive analysis of disease mechanisms is demonstrated. Biological significance: This paper presents CanisOme, a database of proteomic studies with relevant protein annotation, allowing the enlightenment of disease mechanisms and the discovery of novel disease biomarkers for C. lupus familiaris. This knowledge is important not only for the improvement of animal health but also for the use of dogs as models for human health studies.
- COVID-19 salivary protein profile: unravelling molecular aspects of SARS-CoV-2 infectionPublication . Esteves, Eduardo; Mendes, Vera M.; Manadas, Bruno; Lopes, Rafaela; Bernardino, Liliana; Correia, Maria José; Barros, Marlene; Esteves, Ana Cristina; Rosa, NunoCOVID-19 is the most impacting global pandemic of all time, with over 600 million infected and 6.5 million deaths worldwide, in addition to an unprecedented economic impact. Despite the many advances in scientific knowledge about the disease, much remains to be clarified about the molecular alterations induced by SARS-CoV-2 infection. In this work, we present a hybrid proteomics and in silico interactomics strategy to establish a COVID-19 salivary protein profile. Data are available via ProteomeXchange with identifier PXD036571. The differential proteome was narrowed down by the Partial Least-Squares Discriminant Analysis and enrichment analysis was performed with FunRich. In parallel, OralInt was used to determine interspecies Protein-Protein Interactions between humans and SARS-CoV-2. Five dysregulated biological processes were identified in the COVID-19 proteome profile: Apoptosis, Energy Pathways, Immune Response, Protein Metabolism and Transport. We identified 10 proteins (KLK 11, IMPA2, ANXA7, PLP2, IGLV2-11, IGHV3-43D, IGKV2-24, TMEM165, VSIG10 and PHB2) that had never been associated with SARS-CoV-2 infection, representing new evidence of the impact of COVID-19. Interactomics analysis showed viral influence on the host immune response, mainly through interaction with the degranulation of neutrophils. The virus alters the host’s energy metabolism and interferes with apoptosis mechanisms.
- MODeLING.Vis: a graphical user interface toolbox developed for machine learning and pattern recognition of biomolecular dataPublication . Martins, Jorge Emanuel; D’Alimonte, Davide; Simões, Joana; Sousa, Sara; Esteves, Eduardo; Rosa, Nuno; Correia, Maria José; Simões, Mário; Barros, MarleneMany scientific publications that affect machine learning have set the basis for pattern recognition and symmetry. In this paper, we revisit the concept of “Mind-life continuity” published by the authors, testing the symmetry between cognitive and electrophoretic strata. We opted for machine learning to analyze and understand the total protein profile of neurotypical subjects acquired by capillary electrophoresis. Capillary electrophoresis permits a cost-wise solution but lacks modern proteomic techniques’ discriminative and quantification power. To compensate for this problem, we developed tools for better data visualization and exploration in this work. These tools permitted us to examine better the total protein profile of 92 young adults, from 19 to 25 years old, healthy university students at the University of Lisbon, with no serious, uncontrolled, or chronic diseases affecting the nervous system. As a result, we created a graphical user interface toolbox named MODeLING.Vis, which showed specific expected protein profiles present in saliva in our neurotypical sample. The developed toolbox permitted data exploration and hypothesis testing of the biomolecular data. In conclusion, this analysis offered the data mining of the acquired neuroproteomics data in the molecular weight range from 9.1 to 30 kDa. This molecular weight range, obtained by pattern recognition of our dataset, is characteristic of the small neuroimmune molecules and neuropeptides. Consequently, MODeLING.Vis offers a machine-learning solution for probing into the neurocognitive response.
- 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.
- OvinOralOme: Ovis aries oral proteome databasePublication . Esteves, Eduardo; Rosa, Nuno; Correia, M. J.; Vala, Helena; Barros, Marlene
- OvinOralOme: Ovis aries oral proteome databasePublication . Esteves, Eduardo; Rosa, Nuno; Correia, M. J.; Vala, Helena; Barros, MarleneThe present study aims to develop a database transferring the methodology used in humans to the storage and cataloguing of 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 stock in Serra da Estrela region.