Browsing by Author "Silva, Raquel M."
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- Biomarcadores de genotoxicidade em imagiologia medico-dentária: uma revisão sistemáticaPublication . Alonso, Susana; Correia, Maria José; Silva, Raquel M.; Santos, Luís SilvaObjetivos: As técnicas de diagnóstico imagiológico são largamente utilizadas em Medicina Dentária, contribuindo para a elevada exposição global a radiação ionizante verificada nas sociedades modernas. Considerando o bem caracterizado risco genotóxico associado à exposição à radiação ionizante, é altamente desejável a identificação de biomarcadores fiáveis para a biomonitorização dos efeitos genotóxicos da exposição a baixas doses de radiação ionizante em imagiologia dentária. Com este objetivo, foi realizada uma revisão sistemática, de acordo com as diretrizes PRISMA. Materiais e métodos: Revisão sistemática realizada através da metodologia PRISMA, tendo por base os critérios PICO. A busca foi realizada nos bancos de dados PubMed e Web of Science, usando uma expressão de busca baseada nos seguintes termos MeSH: (Mouth mucosa) AND ((Chromosome Aberrations) OR (Cytogenetic Analysis) OR (Cytogenetics) OR (DNA damage) OR (Mutagenicity Tests)) AND ((Dental radiography) OR ((Dentistry) AND (Diagnostic imaging))). Resultados: As pesquisas nas bases de dados devolveram 246 registos, tendo sido incluídos 30 nesta revisão sistemática. 14 (46,7% ) destes estudos apresentaram evidência significativa (p<0,05) de genotoxicidade em células esfoliadas da mucosa oral após irradiação em contexto de diagnóstico dentário imagiológico (comparação pós-exposição versus pré-exposição). A frequência de micronúcleos aos 7-15 dias após a exposição foi claramente o biomarcador mais frequentemente utilizado (26 estudos), tendo sido observados resultados significativos em apenas 38,5% destes estudos. O enrev port estomatol med dent cir maxilofac. 2022;64(S1) :1-53 33 saio Comet foi efetuado em 3 outros estudos, todos com resultados significativos. Um estudo utilizou os níveis de expressão de gH2AX e pChk2, enquanto outro utilizou os níveis de 8-oxo-dG e de quebra de cadeia dupla como biomarcadores de genotoxicidade, ambos com resultados positivos. Conclusões: Estes resultados sugerem que o uso de técnicas imagiológicas em Medicina Dentária pode resultar em danos no ADN e que outros biomarcadores, para além da frequência de micronúcleos, podem ser mais adequados para demonstrar esses danos em futuros estudos de biomonitorização. São necessários mais estudos para confirmar estes resultados.
- Essential genetic findings in neurodevelopmental disordersPublication . Cardoso, Ana R.; Lopes-Marques, Mónica; Silva, Raquel M.; Serrano, Catarina; Amorim, António; Prata, Maria J.; Azevedo, LuísaNeurodevelopmental disorders (NDDs) represent a growing medical challenge in modern societies. Ever-increasing sophisticated diagnostic tools have been continuously revealing a remarkably complex architecture that embraces genetic mutations of distinct types (chromosomal rearrangements, copy number variants, small indels, and nucleotide substitutions) with distinct frequencies in the population (common, rare, de novo). Such a network of interacting players creates difficulties in establishing rigorous genotype-phenotype correlations. Furthermore, individual lifestyles may also contribute to the severity of the symptoms fueling a large spectrum of gene-environment interactions that have a key role on the relationships between genotypes and phenotypes.Herein, a review of the genetic discoveries related to NDDs is presented with the aim to provide useful general information for the medical community.
- Exosomal aβ-binding proteins identified by “in silico” analysis represent putative blood-derived biomarker candidates for alzheimer´s diseasePublication . Martins, Tânia Soares; Marçalo, Rui; Ferreira, Maria; Vaz, Margarida; Silva, Raquel M.; Rosa, Ilka Martins; Vogelgsang, Jonathan; Wiltfang, Jens; Silva, Odete A. B. da Cruz e; Henriques, Ana GabrielaThe potential of exosomes as biomarker resources for diagnostics and even for therapeutics has intensified research in the field, including in the context of Alzheimer´s disease (AD). The search for disease biomarkers in peripheral biofluids is advancing mainly due to the easy access it offers. In the study presented here, emphasis was given to the bioinformatic identification of putative exosomal candidates for AD. The exosomal proteomes of cerebrospinal fluid (CSF), serum and plasma, were obtained from three databases (ExoCarta, EVpedia and Vesiclepedia), and complemented with additional exosomal proteins already associated with AD but not found in the databases. The final biofluids’ proteomes were submitted to gene ontology (GO) enrichment analysis and the exosomal Aβ-binding proteins that can constitute putative candidates were identified. Among these candidates, gelsolin, a protein known to be involved in inhibiting Abeta fibril formation, was identified, and it was tested in human samples. The levels of this Aβ-binding protein, with anti-amyloidogenic properties, were assessed in serum-derived exosomes isolated from controls and individuals with dementia, including AD cases, and revealed altered expression patterns. Identification of potential peripheral biomarker candidates for AD may be useful, not only for early disease diagnosis but also in drug trials and to monitor disease progression, allowing for a timely therapeutic intervention, which will positively impact the patient’s quality of life.
- Identification and characterization of Candida spp. from denture stomatitis patientsPublication . Carvalho, Gonçalo; Lourenço, Juliana; Abrantes, Ana; Fernandes, Mónica; Correia, Maria José; Duarte, Ana Sofia; Silva, Raquel M.
- Merging microarray studies to identify a common gene expression signature to several structural heart diseasesPublication . Fajarda, Olga; Duarte-Pereira, Sara; Silva, Raquel M.; Oliveira, José LuísBackground: Heart disease is the leading cause of death worldwide. Knowing a gene expression signature in heart disease can lead to the development of more efficient diagnosis and treatments that may prevent premature deaths. A large amount of microarray data is available in public repositories and can be used to identify differentially expressed genes. However, most of the microarray datasets are composed of a reduced number of samples and to obtain more reliable results, several datasets have to be merged, which is a challenging task. The identification of differentially expressed genes is commonly done using statistical methods. Nonetheless, these methods are based on the definition of an arbitrary threshold to select the differentially expressed genes and there is no consensus on the values that should be used. Results: Nine publicly available microarray datasets from studies of different heart diseases were merged to form a dataset composed of 689 samples and 8354 features. Subsequently, the adjusted p-value and fold change were determined and by combining a set of adjusted p-values cutoffs with a list of different fold change thresholds, 12 sets of differentially expressed genes were obtained. To select the set of differentially expressed genes that has the best accuracy in classifying samples from patients with heart diseases and samples from patients with no heart condition, the random forest algorithm was used. A set of 62 differentially expressed genes having a classification accuracy of approximately 95% was identified. Conclusions: We identified a gene expression signature common to different cardiac diseases and supported our findings by showing their involvement in the pathophysiology of the heart. The approach used in this study is suitable for the identification of gene expression signatures, and can be extended to different diseases.
- Methodology to identify a gene expression signature by merging microarray datasetsPublication . Fajarda, Olga; Almeida, João Rafael; Duarte-Pereira, Sara; Silva, Raquel M.; Oliveira, José LuísA vast number of microarray datasets have been produced as a way to identify differentially expressed genes and gene expression signatures. A better understanding of these biological processes can help in the diagnosis and prognosis of diseases, as well as in the therapeutic response to drugs. However, most of the available datasets are composed of a reduced number of samples, leading to low statistical, predictive and generalization power. One way to overcome this problem is by merging several microarray datasets into a single dataset, which is typically a challenging task. Statistical methods or supervised machine learning algorithms are usually used to determine gene expression signatures. Nevertheless, statistical methods require an arbitrary threshold to be defined, and supervised machine learning methods can be ineffective when applied to high-dimensional datasets like microarrays. We propose a methodology to identify gene expression signatures by merging microarray datasets. This methodology uses statistical methods to obtain several sets of differentially expressed genes and uses supervised machine learning algorithms to select the gene expression signature. This methodology was validated using two distinct research applications: one using heart failure and the other using autism spectrum disorder microarray datasets. For the first, we obtained a gene expression signature composed of 117 genes, with a classification accuracy of approximately 98%. For the second use case, we obtained a gene expression signature composed of 79 genes, with a classification accuracy of approximately 82%. This methodology was implemented in R language and is available, under the MIT licence, at https://github.com/bioinformatics-ua/MicroGES.
- Microbial DNA extraction methods for microbial screening - saliva vs biofilm comparisonPublication . Gomes, Ana T. P. C.; Pinto, Marla; Abrantes, Patrícia; Almeida, Rita; Mendes, Karina; Duarte, Ana S.; Silva, Raquel M.; Rosa, Nuno; Correia, Maria; Barros, Marlene
- Molecular mechanisms of ischemia and glutamate excitotoxicityPublication . Neves, Diogo; Salazar, Ivan L.; Almeida, Ramiro D.; Silva, Raquel M.Excitotoxicity is classically defined as the neuronal damage caused by the excessive release of glutamate, and subsequent activation of excitatory plasma membrane receptors. In the mammalian brain, this phenomenon is mainly driven by excessive activation of glutamate receptors (GRs). Excitotoxicity is common to several chronic disorders of the Central Nervous System (CNS) and is considered the primary mechanism of neuronal loss of function and cell death in acute CNS diseases (e.g. ischemic stroke). Multiple mechanisms and pathways lead to excitotoxic cell damage including pro-death signaling cascade events downstream of glutamate receptors, calcium (Ca2+) overload, oxidative stress, mitochondrial impairment, excessive glutamate in the synaptic cleft as well as altered energy metabolism. Here, we review the current knowledge on the molecular mechanisms that underlie excitotoxicity, emphasizing the role of Nicotinamide Adenine Dinucleotide (NAD) metabolism. We also discuss novel and promising therapeutic strategies to treat excitotoxicity, highlighting recent clinical trials. Finally, we will shed light on the ongoing search for stroke biomarkers, an exciting and promising field of research, which may improve stroke diagnosis, prognosis and allow better treatment options.
- Molecular techniques and target selection for the identification of Candida spp. in oral samplesPublication . Magalhães, Joana; Correia, Maria José; Silva, Raquel M.; Esteves, Ana Cristina; Alves, Artur; Duarte, Ana SofiaCandida species are the causative agent of oral candidiasis, with medical devices being platforms for yeast anchoring and tissue colonization. Identifying the infectious agent involved in candidiasis avoids an empirical prescription of antifungal drugs. The application of high-throughput technologies to the diagnosis of yeast pathogens has clear advantages in sensitivity, accuracy, and speed. Yet, conventional techniques for the identification of Candida isolates are still routine in clinical and research settings. Molecular approaches are the focus of intensive research, but conversion into clinic settings requires overcoming important challenges. Several molecular approaches can accurately identify Candida spp.: Polymerase Chain Reaction, Microarray, High-Resolution Melting Analysis, Multi-Locus Sequence Typing, Restriction Fragment Length Polymorphism, Loop-mediated Isothermal Amplification, Matrix Assisted Laser Desorption Ionization-mass spectrometry, and Next Generation Sequencing. This review examines the advantages and disadvantages of the current molecular methods used for Candida spp. Identification, with a special focus on oral candidiasis. Discussion regarding their application for the diagnosis of oral infections aims to identify the most rapid, affordable, accurate, and easy-to-perform molecular techniques to be used as a point-of-care testing method. Special emphasis is given to the difficulties that health care professionals need to overcome to provide an accurate diagnosis.
- Neuroprotection by mitochondrial NAD against glutamate-induced excitotoxicityPublication . Paiva, Bruna S.; Neves, Diogo; Tomé, Diogo; Costa, Filipa J.; Bruno, Inês C.; Trigo, Diogo; Silva, Raquel M.; Almeida, Ramiro D.Excitotoxicity is a pathological process that occurs in many neurological diseases, such as stroke or epilepsy, and is characterized by the extracellular accumulation of high concentrations of glutamate or other excitatory amino acids (EAAs). Nicotinamide adenine dinucleotide (NAD) depletion is an early event following excitotoxicity in many in vitro and in vivo excitotoxic-related models and contributes to the deregulation of energy homeostasis. However, the interplay between glutamate excitotoxicity and the NAD biosynthetic pathway is not fully understood. To address this question, we used a primary culture of rat cortical neurons and found that an excitotoxic glutamate insult alters the expression of the NAD biosynthetic enzymes. Additionally, using a fluorescent NAD mitochondrial sensor, we observed that glutamate induces a significant decrease in the mitochondrial NAD pool, which was reversed when exogenous NAD was added. We also show that exogenous NAD protects against the glutamate-induced decrease in mitochondrial membrane potential (MMP). Glutamate excitotoxicity changed mitochondrial retrograde transport in neurites, which seems to be reversed by NAD addition. Finally, we show that NAD and NAD precursors protect against glutamate-induced cell death. Together, our results demonstrate that glutamate-induced excitotoxicity acts by compromising the NAD biosynthetic pathway, particularly in the mitochondria. These results also uncover a potential role for mitochondrial NAD as a tool for central nervous system (CNS) regenerative therapies.