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Research Items (66)
Identifying 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.
Sheep (Ovis aries) saliva is a fluid with properties relevant for the evaluation of individual wellbeing/disease states. It can be used for individual monitoring and to aid in intervention decisions. The total protein profile is characteristic of a species and of individuals in different physiological conditions. Profile data for each subject can be integrated with clinical and environmental data to stratify individuals and analyze their health status. SalivaPrint is an algorithm which enables pattern identification in the protein profile of different individuals and identify proteins which are present in higher or lower quantities.
At SalivaTec we are interested in using this fluid in diagnostics and patient stratification and have been analyzing saliva from several individuals characterizes as to their oral and systemic health.
Background and Aim SalivaTec 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. Methods The strategy followed starts with an in silico analysis of the data in SalivaTecDB which identifies the potential molecules representing molecular mechanisms involved in the conditions under study. Additionally, a protein profile is obtained for each individual by capillary electrophoresis, generating a “SalivaPrint” of each subject which enables the selection of representatives from each group. These molecules are quantified in saliva using different xMAP® Multiplex immunoassay kits from Biorad® and Millipore®. Results Results for the quantification of cytokines in using Bio-Plex Pro™ Human Th17 Cytokine Panel 15-Plex and Bio-Plex Pro™ Human Chemokine MIP-1α/CCL3 and Bio-Plex Pro™ Human Chemokine MCP-4/CCL13 all from Biorad® and Milliplex HSTCMAG-28SK-03.Hu. High Sens. T Cell Mag from Millipore® are presented. We also discuss results for the quantification of Oxytocin, Orexin A, β-Endorphin and Substance P using Milliplex HNPMAG-35K kit from Millipore®, as well as the quantification of MMP9 using the Biorad kit Bio-Plex Pro™ Human. All quantifications were performed in saliva samples following the manufacturer’s instructions for serum samples, since there were no specific recommendations for saliva. Conclusions xMAP ® Multiplex technology, enables the detection and quantification of salivary molecular markers in reduced sample volumes, empowering the use of saliva as a noninvasive biological informative fluid. However, the application of the commercially available kits to saliva is not yet well standardized since most kits are optimized for serum or plasma. Furthermore, the comparison of the results to those reported in the literature is hampered by the fact that different descriptive statistics are used by most authors. Additionally, values of the same molecules seem to vary widely between studies, which raises the question of reproducibility between labs.
- Aug 2017
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.
A realidade da saúde oral avliada por meio clínicos vs. o autoreporte da perceção da saude oral numa população geriátrica do programa ”Viseu Sénior”.
Abstract Objectives: Dental implants are one of the most frequently used treatment options for tooth replacement. Approximately 30% of patients with dental implants develop peri-implantitis, which is an oral inflammatory disease1-4. Our goal was to examine a group of patients with different degrees of periodontal disease including peri-implantitis and use protein profiles to stratify them. Methods: Oral health from 78 patients was examined and unstimulated whole saliva was collected and processed according the standard operating procedure described by Rosa and colleagues (2016)5. Statistical analysis was performed to determine which were the molecular weights more relevant to the stratification. Results: The study group was composed of healthy, mucositis, gingivitis, and peri-implantitis patients. In the protein profiles analyzed there were over 490 bands corresponding to specific molecular weights. Some of the bands are frequently found in different individuals while others seem to be more specific some of them occurring in only one individual. Conversely, some individuals have up to 48 bands while others have only 6. The average number of bands per individual is 11. Conclusion: It is possible to stratify patients relative to their oral health by analyzing their total protein profile which might be a useful tool for periimplantar disease management, diagnosis and prognosis. Keywords: peri-implantitis; protein profile; protein molecular weight References 1. Al-Radha, A. S. D., Pal, A., Pettemerides, A. P., & Jenkinson, H. F. (2012). Molecular analysis of microbiota associated with peri-implant diseases.Journal of dentistry, 40(11), 989-998. 2. Albrektsson T, Isidor F. Consensus report of session IV. In: Lang NP, Karring T (eds). Proceedings of the 1st European Workshop on Periodontology. London: Quintessence, 1994: 365–369. 3. Al-Sabbagh, M. (2014). Complications in Implant Dentistry, An Issue of Dental Clinics of North America (Vol. 59, No. 1). Elsevier Health Sciences. 4. Saliva as a diagnostic tool for periodontal disease: current state and future directions WV Giannobile, T Beikler, JS Kinney, CA Ramseier- Periodontology 2000, 2009 5. Rosa, N., Marques, J., Esteves, E., Fernandes, M., Mendes, V. M., Afonso, Â., ... & Barros, M. (2016). Protein Quality Assessment on Saliva Samples for Biobanking Purposes. Biopreservation and biobanking.
Question - In quantitative RT-PCR for bacterial quantification is it legitimate to use for quantification standard a fragment obtained by regular PCR?
Thank you. For your answer. Very useful.
Project - Oral microbiome and host health: is the Firmicutes/Bacteroidetes ratio an indicator of oral and systemic health?
In quantitative RT-PCR for bacterial quantification is it legitimate to use for quantification standard a fragment obtained by regular PCR?
Most of the literature uses a fragmente which has been cloned in a plasmid.
Excel file with Protein-Protein Interactions (PPIs) between human and ZIKV, predicted in this work and respective scores. Excel file with the protein quantification data, obtained from the literature, used in the discussion of the results. Interactive network diagram created with Cytoscape (.CYS) freeware software downloadable at cytoscape.org [http://cytoscape.org].
Aim or purpose: To assess the presence or absence of Streptococcus mutans, Streptococcus gordonii and Streptococcus salivarius in the oral biofilm of children in an elementary school and verify the association between Streptococcus gordonii and Streptococcus salivarius and the absence of dental caries. Materials and methods: An oral exam of all children participants in the study was completed complementing data collection with the identification of their oral health status and collection of oral biofilm. Analysis of biological samples by molecular techniques of DNA isolation and identification of three Streptococci bacteria by Polymerase Chain Reaction (PCR) was accomplished. Results: We identified Streptococcus salivarius and Streptococcus gordoni only in the lower inter-incisal region. These species were also present mainly in the first permanent molars without dental caries. On the other side, Streptococcus mutans was found mostly in first permanent molars with dental caries. Conclusions: This preliminary study establishes a possible association between the absence of dental caries and the presence of Streptococcus gordonii and Streptococcus salivarius. Since these two species are described as alkaline producers it is suggested that their presence somehow confers protection against dental caries. These results support new dental caries prevention strategies based on oral biofilm modulation by enrichment with alkalinogenic species.
- Oct 2016
- XXXVI Congresso Anual da SPEMD
O uso excessivo e muitas vezes desnecessário de antibióticos pode originar a seleção de genes de resistência a antibióticos (Moares et al., 2015). 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 (Berendonk et al. 2015). 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.
Most miRNAs have been explored as blood or serum biomarkers. Our group aims at using saliva’s excellent collection and processing advantages to test if the miRNAs proposed as blood or serum biomarkers can be validated in saliva. So far, using bioinformatics tools it has been possible to suggest 9 miRNAs as promising salivary biomarkers for type II diabetes mellitus since they regulate proteins which we have shown to be altered in diabetic patients. Our group intends to validate these biomarkers for type II diabetes mellitus salivary diagnosis. Using the same approach 3 potential salivary biomarkers to aid in Periodontal disease have also been proposed and will be validated.
Neuronal functional protein networks found in the oral proteome are possibly useful to characterize a healthy phenome state and trait. Proteomics have extensively and objectively epitomized the understanding of healthy and pathological physiological states or conditions. Our group aims at the molecular characterization of cognition.
Program managed by the Município de Viseu promoting supervised physical activity for seniors. SalivaTec is a partner monitoring salivary markers of all participants, with the goal of establishing the molecular profile of diabetic patients.
Cardosin A enzyme has been demonstrated to have similar activity and cleavage site of MMP 1 (Duarte et al., 2007). Moreover, according to Muller et al., 2007, MMP 1 is up regulated on good healers during 1st week post wound (inflammation state). After that the proportion is reversed by increasing TIMP 1 activity. Based on these results we can infer that this exogenous enzyme will support the MMP activity during the first phase of diabetic wound healing. SalivaTec has the know-how for the isolation and characterization of cardosins. We are able to produce it in large scale with the support of Instituto Poliécnico de Viseu. There is the interest to motivate colleagues from other institutions to include this enzyme in materials with a potential treatment of the diabetic foot.
Estudos recentes têm evidenciado a relação entre a periodontite crónica e as doenças cardiovasculares. A plausibilidade biológica para esta associação baseia-se no facto de os pacientes com periodontite crónica apresentarem níveis aumentados de marcadores inflamatórios, os quais estão implicados na inflamação sistémica. O objetivo deste trabalho é contribuir para identificação de proteínas salivares com potencial para serem biomarcadores de doenças cardiovasculares tendo em conta o seu enquadramento molecular em ambas as patologias.
Introdução: As ciências Ómicas fazem parte das rotinas de investigação e diagnóstico em saúde humana. No entanto, a sua aplicação às ciências veterinárias ainda está no inicio, havendo, contudo, um aumento crescente de publicações dedicadas à proteómica, principalmente de animais com interesse económico. A quantidade de informação acumulada com estas tecnologias de alto rendimento cria a necessidade de desenvolver bases de dados em que os resultados são anotados e disponibilizados à comunidade científica. Estes dados são essenciais à compreensão dos mecanismos fisopatológicos presentes, mas também ao desenvolvimento de novas ferramentas de diagnóstico, prognóstico e terapêutica. Objetivo: Este trabalho tem por objetivo apresentar a base de dados OvisOme e demonstrar como pode ser utilizada para compreender os mecanismos fisiopatológicos de algumas das doenças que afetam as ovelhas.
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 poster is to present the OvisOme database and to demosntrate how it can be used to understand the molecular mechanisms urderlying sheep disease.
Biobank 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.
A Biobank is an organized collection of biological samples, which is a key resource for academic research and translational medicine. Threfore, the quality control of the samples is fundamental to ensure the quality of the proteins preserved on the samples. Thus the aim of this study was to establish quality control standards for saliva samples to be stored in the Biobank. For the quality assessment of the samples, several factors were studied: total saliva volume, protein concentration, circadian intra and inter-individual variability in protein content and protein degradation throughout storage.
Saliva sample quality for Biobank storage depends on specific criteria applied to the collection, processing and storage. The two main concerns of a Biobank are the quality and preservation of the samples. Both are dependent on the way the sample is collected, processed and stored. Through a simple and inexpensive protocol, we can get saliva samples for analysis of protein and DNA of sufficient quality, for storage in a Biobank.
The relationship between consciousness and neural activity, i.e., between mental and brain states, has been widely studied. However, the relation between consciousness and its biochemical markers is still undetermined. Altered states of consciousness (ASC), can be a learning process for the achievement of subjective states of happiness. Clinical hypnosis and guided meditation are fast learning techniques, leading to the desired subjective state. This subjective state of happiness has saliva molecular biomark-ers and can be correlated with psychological assessments. Therefore, it is proposed a new approach of altered state of consciousness induction, associated with subjective states of happiness, using a specific methodology and analysis, named The Pursuit of Happiness model. This model: (1) Studies the use of a hypnotic induction technique, named The Way of Happiness, to achieve states and traits of consciousness associated happiness. (2) Proposes, in parallel, a biomedical analysis named: States and Traits of Consciousness: Saliva Molecular Biomarkers. (3) Correlates the objective saliva molecular biomarkers with the subjective psychological assessments. (4) Develops a Knowledge Discovery Database with data-mining algorithms and bioinformatics tools to discover patterns that relates ASC, subjective states of happiness , saliva molecular biomarkers, peak experiences and self-consciousness.
Descrever o perfil clínico-epidemiológico dos acidentes ofídicos ocorridos na ilha de Colares, Pará, Brasil. O estudo consistiu em uma investigação epidemiológica transversal a partir da análise de todos os casos de envenenamento por serpentes peçonhentas atendidos no Hospital Municipal e notificados ao Sistema Nacional de Notificações e Agravos (SINAN) do Ministério da Saúde, entre janeiro de 2007 e dezembro de 2011. Os dados obtidos a partir das fichas de notificação foram analisados utilizando-se estatística descritiva simples no Microsoft Excel (versão 2007). Foram notificados ao SINAN 94 casos de acidentes ofídicos, sendo observada maior concentração dos envenenamentos no primeiro semestre de cada ano, período em que ocorrem os maiores índices pluviométricos para a região. A maioria dos acidentes aconteceu na zona rural (85,11%), durante a realização dos trabalhos braçais (55,32%), com maior incidência em homens (73,40%), predominantemente provocados por serpentes do gênero Bothrops (69,62%). Foram identificadas falhas no protocolo de soroterapia, sendo verificada sua utilização em dois casos cujas serpentes não eram peçonhentas e não administrado em dois casos confirmados de acidentes ofídicos envolvendo serpentes peçonhentas. O pé foi a região mais acometida (51,06%) e a dor, edema e manifestações vagais foram os sinais mais frequentes. Estes resultados demonstram que o município de Colares segue o perfil dos acidentes ofídicos de outras localidades rurais amazônicas, sendo necessária maior atenção dos profissionais de saúde quanto ao preenchimento das fichas de notificação e aos protocolos terapêuticos dispensados às vítimas.
To describe the clinical and epidemiological profile of snakebites occurred on the island of Colares, Pará, Brazil. The study consisted of a cross-epidemiological research based on the analysis of all cases of poisoning by venomous snakes treated at City Hospital and served on the National System Notifications and Disability (SINAN) and conducted to the Ministry of Health between January 2007 and December 2011. Data obtained from the notification records were analyzed using simple descriptive statistics in Microsoft Excel (2007 version). Ninety-four cases of snakebites were reported to SINAN and the highest frequency occurred in the first half of each year, a period in which most precipitation occurs in the region. Most accidents occurred in rural areas (85.11%), while performing manual labor (55.32%), with higher incidence in men (73.40%), with predominance of accidents caused by snakes of the genus (Bothrops) (69.62%). Failures were identified in the protocol of serum therapy, as it was used in two cases in which the snakes were not venomous and not used in two other cases involving poisonous snakes. Regarding clinical aspects, the foot was the most affected region (51.06%) while pain, edema and vagal manifestations were the most frequent signs. These results demonstrate that the municipality of necklaces follows the profile of snakebites other Amazonian rural areas. Greater attention is needed from health professionals when filling in the notification forms and when following therapeutic protocols of snakebite victims.
- Jan 2015
- X Jornadas de Medicina Dentária - Universidade Católica Portuguesa
Ao nível das bolsas periodontais o biolfime apresenta um microbioma complexo em que se estabelece uma rede de interações quer com o hospedeiro quer entre os microrganismos. Tradicionalmente é aceite que há um conjunto de bactérias associadas à doença periodontal como Porphyromonas gingivalis, Prevotella intermedia, Aggregatibacter actinomycetemcomitans, Tannerella forsythia e Treponema denticola. No entanto, o projeto do microbioma humano em conjunto com outros estudos, têm revelado a presença de bactérias que por não serem cultiváveis eram desconhecidas. Uma dessas é a bactéria gram positiva Filifactor alocis que deve ser tida como um microrganismo importante na doença periodontal pois está presente em número aumentado nos pacientes com doença periodontal crónica (1). OBJETIVO Utilizar o algoritmo OralInt para prever que interação é estabelecida a nível molecular entre Filifactor alocis e os toll-like receptor (TLR) do hospedeiro.
- Jan 2015
- I Jornadas Científicas da Primavera
Todos os organismos apresentam algum sistema de defesa contra agentes patogénicos. No ser humano a família dos Toll-like receptors (TLRs) é umas das mais estudadas ao nível dos receptores para detecção de patógenos. Os TLRs são uma família de proteínas membranares expressas em células eucariotas que reconhecem ligandos provenientes de praticamente todos os microrganismos (1). Alguns estudos encontraram uma grande diversidade destes receptores os TLR1 a TLR10 em amostras de saliva (2, 3). Este estudo preliminar visa estabelecer os níveis de expressão de TLRs em pacientes saudáveis, analisando os resultados agrupados por idade e género. A estratégia poderia ser a detecção directa dos TLRs mas alguns destes receptores encontram-se em membranas intracelulares o que dificulta a sua detecção (Figura 1) (1). Assim, será realizada uma abordagem ao nível do transcripto mRNA especificamente para cada TLR através de PCR quantitativo em tempo real (qPCR-RT). Deste modo será possível verificar os níveis de expressão de um conjunto de TLRs que serão a base de comparação para o posterior estudo de pacientes com patologias como periodontite, periimplantite, diabetes e Alzheimer e ainda pacientes multi-comprometidos.
Question - Does anyone have experience or feedback on the usefulness of the QIAcube DNA station?
Thank you. Very usefull.
- Oct 2014
- XXXIV CONGRESSO ANUAL SPEMD
Aims: To evaluate the presence or absence of Streptococcus mutans, Streptococcus gordonii and Streptococcus salivarius in the oral biofilm of children in elementary school and verify the relationship between Streptococcus gordonii and Streptococcus salivarius and the absence of dental caries. Methods: Oral exam of all participant children with the identification of their oral health status and collection of oral biofilm. Analysis of biological samples by molecular techniques of DNA isolation and identification of three Streptococci bacteria by Polimerase Chain Reaction (PCR). Results: We identified S. salivarius and S. gordoni only in the lower interincisal region. These species were also present mainly in the first permanent non decayed molars. On the contrary, S. mutans was found mostly in decayed first permanent molars. Conclusion: This preliminary study establishes a relationship between the absence of caries and the presence of Streptococcus gordonii and Streptococcus salivarius. Since these two species are described as alkali producers it is suggested that their presence somehow confers protection against caries. These results support new caries prevention strategies based on oral biofilm modulation by enrichment with alkalinogenic species.
Periodontal 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 2 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 de-regulation process in the PD inflammatory response
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.
Introdução: Ferramentas que armazenem e procedam à catalogação das proteínas identificadas em proteomas resultantes de amostras de tecidos diversos recolhidos a partir de indivíduos representativos de situações fisiológicas e patológicas, constituem instrumentos poderosos para a integração da informação já publicada. Muita informação sobre os mecanismos moleculares subjacentes a patologias pode hoje ser gerada a partir de estratégias bioinformáticas. No âmbito de projetos anteriormente desenvolvidos, foi construída uma base de dados, o OralOma dedicada ao armazenamento de toda a informação sobre proteínas presentes na cavidade oral humana. A base de dados é consultável pela ferramenta bioinformática OralCard. Objetivo: O presente trabalho tem como objetivo a criação de uma base de dados, através da aplicação da metodologia desenvolvida para humanos, agora para o armazenamento e catalogação de proteínas presentes na cavidade oral e noutros tecidos de Ovis aries, procurando assim desenvolver um método de diagnóstico em vida, capaz de detetar as principais patologias que grassam nos rebanhos da Serra da Estrela.
The oral cavity is a complex ecosystem where human chemical compounds coexist with a particular microbiota. However, shifts in the normal composition of this microbiota may result in the onset of oral ailments, such as periodontitis and dental caries. In addition, it is known that the microbial colonization of the oral cavity is mediated by protein-protein interactions (PPIs) between the host and microorganisms. Nevertheless, this kind of PPIs is still largely undisclosed. To elucidate these interactions, we have created a computational prediction method that allows us to obtain a first model of the Human-Microbial oral interactome. We collected high-quality experimental PPIs from five major human databases. The obtained PPIs were used to create our positive dataset and, indirectly, our negative dataset. The positive and negative datasets were merged and used for training and validation of a naive Bayes classifier. For the final prediction model, we used an ensemble methodology combining five distinct PPI prediction techniques, namely: literature mining, primary protein sequences, orthologous profiles, biological process similarity, and domain interactions. Performance evaluation of our method revealed an area under the ROC-curve (AUC) value greater than 0.926, supporting our primary hypothesis, as no single set of features reached an AUC greater than 0.877. After subjecting our dataset to the prediction model, the classified result was filtered for very high confidence PPIs (probability >= 1-10-7), leading to a set of 46,579 PPIs to be further explored. We believe this dataset holds not only important pathways involved in the onset of infectious oral diseases, but also potential drug-targets and biomarkers. The dataset used for training and validation, the predictions obtained and the network final network are available at http://bioinformatics.ua.pt/software/oralint.
The human oral cavity is a complex ecosystem where multiple interactions occur and whose comprehension is critical in understanding several disease mechanisms. In order to comprehend the composition of the oral cavity at a molecular level, it is necessary to compile and integrate the biological information resulting from specific techniques, especially from proteomic studies of saliva. The objective of this work was to compile and curate a specific group of proteins related to the oral cavity, providing a tool to conduct further studies of the salivary proteome. In this paper we present a platform that integrates in a single endpoint all available information for proteins associated with the oral cavity. The proposed tool allows researchers in biomedical sciences to explore microorganisms, proteins and diseases, constituting a unique tool to analyse meaningful interactions for oral health.
The objective of this study is to demonstrate the molecular action of Porphyromonas gingivalis cysteine proteases such as gingipains (R1, R2 and K) upon human molecules.Materials and methodsUsing the information on protein structure and function available in international databases (UniProtKB and Merops Database), the molecular interactions already described between gingipains and host molecules were clarified.ResultsPossible cleavage sites were identified in host-produced elastase inhibitors and in pro-Matrix MetalloProteinase (MMP)1. Analysis of the results leads to the suggestion that the elastase inhibitor alpha1-antitrypsin is also degraded by interpain A, a cystein protease of Prevotella intermedia sharing a high homology with the PrtT and periodontain of P. gingivalis.Conclusion The information obtained suggests a synergistic molecular mechanism by which cysteine proteases of different bacteria can be responsible for the clinical manifestations of periodontal disease, and illustrates the use of bioinformatics to establish and predict molecular mechanisms.
The human oral cavity is a complex ecosystem where multiple interactions occur and whose comprehension is critical to understand several disease mechanisms. In order to comprehend the composition of the oral cavity at a molecular level, it is needed to compile and integrate the biological information resulting from specific techniques, especially from proteomic studies of saliva. The objective for this work was to compile and curate a specific group of proteins related to the oral cavity, providing a tool to conduct further studies over the salivary proteome. Despite previous efforts to identify the protein components of saliva in healthy individuals and in several oral and systemic disorders, a resource compiling and reviewing all of these proteins is still lacking. In this paper we present a platform that integrates in a single endpoint all available information for proteins associated with the oral cavity. The proposed tool allows researchers in the biomedical sciences to explore organisms, proteins and diseases, constituting a unique tool to analyse meaningful interactions for oral health.
A candidíase oral é uma infecção micótica oportunista, comum na cavidade oral, causada pela proliferação anormal de Candida, sendo a mais comum a Candida albicans. Estes microrganismos são comensais do tracto gastrointestinal, vaginal e pele, estando presentes em 20-50% da população dentada saudável. As espécies Candida non-albicans, têm vindo a aumentar a sua representatividade, alterando o padrão epidemiológico da etiologia da candidíase. A nível mundial a candidiase apresenta uma elevada incidência e prevalência devido à multiplicidade de factores predisponentes, locais e sistémicos, que facilitam a conversão da Candida da forma comensal para a parasitária. Na última década as infecções por Candida tornaram-se a oitava causa de infecções invasivas na Europa. Nos países em vias de desenvolvimento constata-se uma maior prevalência de infecções candidiásicas, devido aos recursos hospitalares deficitários, e ao desconhecimento da patologia. Nos países desenvolvidos têm aumentado os casos de candidíase oral, e diminuído os casos de candidíase invasiva. A candidíase invasiva é a infecção fúngica mais comum, sendo a candidíase oral a infecção candidiásica superficial mais frequente. Para além da sua alta prevalência em pacientes VIH positivos, é considerada um marcador de má terapêutica antiviral, ou de risco mortal. É a lesão oral mais comum em pacientes pediátricos com essa síndrome. Em Portugal, a mortalidade regista valores aproximados aos países europeus, cerca de 39,3%. A alta mortalidade registada em Portugal, e a considerável incidência de fungémia nosocomial, têm consequências inevitáveis na Saúde Pública, impondo elevados custos económicos ao Serviço Nacional de Saúde, bem como destaca a necessidade de dados epidemiológicos nacionais regulares, até agora inexistentes. Tem-se verificado um aumento da candidíase oral nos países desenvolvidos, ainda que a prevalência de candidíase invasiva tenha diminuído. Nos países em vias de desenvolvimento constata-se uma prevalência crescente de infecções candidiásicas superficiais e invasivas. A evolução e alteração constante da epidemiologia das infecções candidiásicas, aumentam o desafio das técnicas de diagnóstico, terapêutica e estratégias profilácticas.
New endosymbiotic diatom isolations from previously unsampled field sites are reported. Nitzschia laevis was the most commonly isolated diatom from populations of Amphistegina lobifera collected at both the North Beach in the Gulf of Eilat and at Sifnos, Greece. Nitzschia frustulum var. symbiotica (as emended by Lee et al., 2000) was the second most abundant species of diatoms found in the Amphistegina examined from the North Beach, Gulf of Eilat, (31%) and Sifnos, Greece, (28%) and the most abundant diatom species present in the specimens examined from Coconut Beach, Lizard Island, Great Barrier Reef. New observations are not entirely in consonance with previous observations, but one general conclusion has not changed: a small number of diatom species (~20) are involved in the endosymbiotic phenomenon and certain species are dominant in every population. A rare, yet to be described, nitzschioid diatom was found and figured.
- Nov 2003
A species of Amphidinium bloomed in a mariculture sedimentation pond that was used to grow bivalves near the Gulf of Eilat, Israel. Its overall length averaged 13 μm, the hypocone was 11 μm, and its width was 8μm. It has a ventral ridge. The sulcus begins at the longitudinal flagellar pore and does not project forward in the apex toward the transverse flagellar pore and left margin of the cingulum. The sulcus is a very shallow groove that projects variably about a third of the body length toward the antapex. The cingulum is a deep groove as it circles the cell from the left ventral side to the dorsal side and then becomes very shallow on the right ventral side as it arches posterior toward the longitudinal flagellar pore. Using a modified method for studying dinoflagellate chromosomes in the SEM, we observed 31 chromosomes. The plastid is dorsal and peripheral with 6 ventrally projecting peripheral digital lobes that wrap around the sides of the ventral and posterior nucleus. Amphidinium eilatiensis n. sp. is morphologically closest to Amphidinium carterae and Amphidinium rhynchocephalum, but it does not have the obvious thecal plates or polygonal units described for the former species. Instead, it has a series of spicules, bumps, and ridges on its surface. It differs from A. rhynchocephalum by two morphological characters: surface morphology and gross plastid architecture.
Filamentous actin localized to polar cytoplasmic areas between chloroplasts of the prymnesiophyte Pleurochrysis sp. Phalloidin staining of cells, confocal laser scanning microscopy, and previous electron microscopy (E. K. Hawkins and J. J. Lee, Protoplasma 216: 227-238, 2001) indicate that the location of phalloidin staining coincides with the cellular location of the Golgi apparatus. The results are consistent with the hypothesis that filamentous actin may be involved in biogenesis and polarized secretion of scales.
Previous studies showed that, when specimens of Elphidium excavatum harvested from field collections are fed diatoms, they retain more chloroplasts and survive longer than they do when fed diets of other types of algae. Does the host retain the chloroplasts other types of algae? To answer this question, foraminifera were fed diets of either a chlorophyte or a dinoflagellate and then studied by transmission electron microscopy (TEM). The algae used Amphora coffeiformis (diatom), Amphidinium sp. (dinoflagellate), and Dunaliella salina (green alga) have chloroplasts which are quite distinct from each other at the fine structural level. The experimental foraminifera were harvested directly from the field and thus already had a population of chloroplasts within their cytoplasm when the experiment started. Regardless of the type of alga used in the experimental diet, the ultrastructure of the retained plastids were typical of diatoms: 2-3 thylakoid stacks; a simple internal pyrenoid with a thylakoid crossing it; and a girdle lamella surrounding the outside of the chloroplast. Some of the plastids were undergoing digestion, because they had lost organization and we observed fusion of vesicles (presumed to be lysosomes) with the symbiosome vacuole. Cytoplasm within the inter-chamber canals of the foraminifera contained numerous vacuoles and vesicles, some of which contained algae in the process of digestion, others had isolated plastids. The plastids inside the chambers had protrusions on their edges corresponding to the positions of cannalicular pores connected to the intercameral canals. These pores were plugged by an electron dense material and no cytoplasmic connection was observed between the pores in the test and the intercameral cytoplasm.
Intact plastids are retained by Elphidium excavatum (Foraminifera). There is preferential retention of diatom plastids. Freshly collected specimens of E. excavatum were fed diets of three different axenic cultures of algae for a week, and then starved for 8 weeks to assess the longevity of plastids retained from their diets. The number of plastids retained per individual was assessed weekly with the aid of a confocal laser scanning microscope. Starved individuals served as controls. Since controls already had plastids they retained while they were feeding in the field before they were harvested, we subtracted control values from experimental values to estimate the experimental results. Results indicate that plastids remain in the cytoplasm of Elphidium for at least 8 weeks. When the foraminifera were incubated with 12/12h light/dark cycle, the half-life of diatom plastids was shorter. Although we observed plastids in foraminifera fed chlorophytes or dinoflagellates, the numbers retained were the same or less than starved controls, suggesting that no new plastids had been added to the "symbiont" population during the week of experimental feeding. The half-lives of all retained chloroplasts were longer for hosts that were incubated in the dark (diatom plastids 9.5 weeks; dinoflagellate plastids 4.7 weeks; chlorophyte plastids 8.2 weeks; and plastids [most probably from diatoms] in controls 10.7 weeks). The results are in general accordance with what is known about the kleptochloroplast phenomenon in the ascoglossan mollusk, Elysia chlorotica.
Some foraminifera retain chloroplasts from algae they partly digest. Elphidium excavatum (Terquem) was kept under laboratory cultures for a month and fed monoalgal cultures. The number of chloroplasts retained by this species of foraminifera depended on the algal diet. Higher numbers of chloroplasts were observed when the foraminifera were fed diatom species; the number of chloroplasts retained by each individual was approximately 3.7×104 chloroplasts. Significantly fewer green algal, and dinoflagellate chloroplasts were retained by each individual; the numbers were lower than the starved controls. These results seem to indicate that diatoms are the chloroplast donors for husbandry by E. excavatum.