Papers by Pedro Fernandes
Chronobiology international, Jan 12, 2016
Morning shift sleep restriction has been associated with higher plasma IL-6 levels. The aim of th... more Morning shift sleep restriction has been associated with higher plasma IL-6 levels. The aim of this study was to investigate the effect of sleep duration on salivary IL-6. Sleep duration of morning shift workers was estimated by actigraphy. Workers with "longer sleep duration" (LSD; N = 6) and "shorter sleep duration" (SSD; N = 15) were then compared regarding salivary IL-6 levels determined at 14:00 h, bed and wake times. SSD workers did not show daily variation of IL-6 and presented higher levels at bedtime and 14:00 h compared to LSD workers. In this study, SSD is associated with an increase in salivary IL-6 content.
The Iowa Orthopaedic Journal, 2014
Tuberculosis can be responsible for extensive spinal lesions. Despite the efficacy of medical tre... more Tuberculosis can be responsible for extensive spinal lesions. Despite the efficacy of medical treatment, surgery is indicated to avoid or correct significant deformity, treat spinal instability, prevent neurological compromise, and to eradicate an extensive tuberculous abscess. In this paper we present our experience in the surgical management of spinal tuberculosis complicated with large abscess. Fifteen patients with spinal tuberculosis complicated with extensive abscess were identified; and nine of those patients had extension of the infection into the epidural space. The average age at treatment was 34 years old. Seven patients had thoracic infection, seven patients had lumbar infection and one had thoracolumbar infection. Six patients had neurological deficit at presentation. All patients were surgically treated with abscess debridement, spinal stabilization and concurrent antituberculous chemotherapy. A single anterior surgical approach was used in three cases, a posterior approach was used in four others and a combined approach was performed in eight patients. Surgical management allowed for effective abscess debridement and sspinal stabilization in this cohort. In combination with antituberculous drugs, surgical treatment resulted in infection eradication and bone fusion in all patients at 24 month average follow-up. Satisfactory neurological outcomes with improved American Spinal Injury Association (ASIA) scores were observed in 100% of patients. Surgical treatment for spinal tuberculosis abscess can lead to satisfactory clinical outcomes.
Bioresource technology, Jan 14, 2016
Polyvinyl alcohol (PVA) electrospun nanofibers were produced using an electrospinning technique. ... more Polyvinyl alcohol (PVA) electrospun nanofibers were produced using an electrospinning technique. Key parameters (e.g. collectors, distance from needle tip to collector, among others) that influence the structure and morphology of fibers were optimized. The naringinase entrapped in PVA nanofibers retained over 100% of its initial activity after 212h of operation, at 25°C. Chemical crosslinking with several boronic acids further increased the hydrolysis temperature (up to 85°C) and yielded nanofibers with thermal stability up to 121°C. A mini packed bed reactor (PBR) developed to establish the feasibility for continuous enzymatic operation, ran for 16days at 45°C. Highest naringenin biosynthesis was attained at a flow rate of 10mLh(-1). Highest volumetric (78molL(-1)h(-1)) and specific (26molh(-1)genzyme(-1)) productivities were attained at 30mLh(-1). The activity of NGase in electrospun nanofibers remained constant for almost 16days of operation at 10mLh(-1).
Acta Crystallogr a, 2005
Antimony oxides display a variety of structural arrangements with different stoichiometries resul... more Antimony oxides display a variety of structural arrangements with different stoichiometries resulting from two stable speciations for Sb ions. They commonly occur as minerals with well known crystal structure, but there are still questions regarding stibiconite -a very rare yellow mineral with pyrochlore-type structure and approximate formula Sb
Neuroendocrinology, Jan 9, 2016
The nocturnal production of melatonin by the pineal gland is triggered by sympathetic activation ... more The nocturnal production of melatonin by the pineal gland is triggered by sympathetic activation of adrenoceptors and may be modulated by immunological signals. The effect of glucocorticoids on nocturnal melatonin synthesis is controversial, both stimulatory and inhibitory effects have been reported. During pathophysiological processes, increased sympathetic tonus could result in different patterns of adrenoceptors activation on the pineal gland. Therefore, in this investigation we evaluated whether the pattern of adrenergic stimulation of the pineal gland drives the direction of the glucocorticoid effect on melatonin production. Corticosterone effect on the pineal hormonal production induced by β or β+α1-adrenoceptors activation was evaluated in cultured glands. We also investigated whether the in vivo LPS-induced inhibition of melatonin is dependent on the interaction of glucocorticoids and α1-adrenoceptor in adrenalectomized animals and by the in vivo blockade of glucocorticoid r...
Journal of Computational Chemistry, Jan 30, 2004
2Ј-Azido-2Ј-deoxyribonucleoside 5Ј-diphosphates are mechanism-based inhibitors of Ribonucleotide ... more 2Ј-Azido-2Ј-deoxyribonucleoside 5Ј-diphosphates are mechanism-based inhibitors of Ribonucleotide Reductase. Considerable effort has been made to elucidate their mechanism of inhibition, which is still controversial and not fully understood. Previous studies have detected the formation of a radical intermediate when the inhibitors interact with the enzyme, and several authors have proposed possible structures for this radical. We have conducted a theoretical study of the possible reactions involved, which allowed us to identify the structure of the new radical among the several proposals. A new reactional path is also proposed that is the most kinetically favored to yield this radical and ultimately inactivate the enzyme. The energetic involved in this mechanism, both for radical formation and radical decay, as well as the calculated Hyperfine Coupling Constants for the radical intermediate, are in agreement with the correspondent experimental values. This mechanistic alternative is fully coherent with remaining experimental data.
Brief Bioinform 2013, 2013
Embnet News, 2009
Another round of meetings of the ELIXIR project, now in the last stretch of the preparatory phase... more Another round of meetings of the ELIXIR project, now in the last stretch of the preparatory phase, prior to the presentation of the project proposal to the EU, took place in Copenhagen, on May 18th -21st 2009.
Acta Medica Portuguesa, Aug 30, 2013
Acta Med Port 2013 Jul-Aug;26(4):349-356 RESUMO Introdução: A espondilodiscite de etiologia tuber... more Acta Med Port 2013 Jul-Aug;26(4):349-356 RESUMO Introdução: A espondilodiscite de etiologia tuberculosa é responsável por mais de 40% do universo destas infeções. Enquanto a quimioterapia tuberculostática se mantém como gold-standard da terapêutica desta patologia, o tratamento cirúrgico tem lugar em situações muito específicas. Neste trabalho apresentam-se os resultados de 33 doentes com espondilodiscite tuberculosa operados no nosso serviço durante os últimos 15 anos. Objetivo: Avaliar retrospetivamente doentes com diagnóstico de espondilodiscite tuberculosa operados num período de 15 anos (1996 a 2011); avaliar opções cirúrgicas tomadas e respetivos resultados relativamente à resolução da infeção, controlo da deformidade e evolução da lesão neurológica. Material e Métodos: Análise retrospetiva dos processos clínicos e avaliações imagiológicas de doentes com diagnóstico de espondilodiscite tuberculosa operados entre 1996 e 2011. Foram identificados 33 doentes com idade média de 46,7 anos; 17 doentes apresentavam infeção torácica, 11 lombar e cinco toraco-lombar. O abcesso paravertebral foi identificado em 26 dos casos estudados, existindo extensão intracanalar em 16 doentes. Nove dos doentes avaliados apresentavam lesão neurológica. A abordagem cirúrgica por via anterior foi utilizada em sete casos, a via posterior em 11 e a abordagem combinada foi a preferida em 15 ocasiões. A quimioterapia antibacilar foi mantida em média por 14 meses, com seguimento médio de 24 meses. Resultados: Verificámos cura da infeção em todos os doentes, sendo documentados critérios de fusão óssea, em média, 10,6 meses pós-cirurgia. A abordagem anterior isolada não permitiu obter correção da deformidade inicial, enquanto a via posterior permitiu uma correção média de 12,7º e a via combinada uma correção média de 8,7º. Cinco dos doentes com lesão neurológica melhoraram 2 a 3 níveis na escala ASIA durante o seguimento pós-operatório. Como complicações referem-se 2 casos de infeção superficial da ferida operatória. Discussão e Conclusão: A terapêutica com antibacilares constitui a terapêutica de primeira linha no tratamento da espondilodiscite tuberculosa, existindo indicações específicas para realização de cirurgia. A intervenção cirúrgica, quando indicada, permite corrigir a deformidade assim como a fusão óssea, sendo preferencialmente realizada por via combinada ou posterior. A taxa de complicações foi pouco significativa apesar da introdução de material de osteossíntese. Palavras-chave: Disco Intervertebral; Espondilodiscite Tuberculosa; Procedimentos Ortopédicos.
Caderno De Estudos Geoambientais Cadegeo, Apr 15, 2014
O presente trabalho tem como objetivo apresentar uma metodologia para classificar, de forma autom... more O presente trabalho tem como objetivo apresentar uma metodologia para classificar, de forma automática, fragmentos florestais do município de São José de Ubá (RJ), utilizando técnicas de processamento digital de imagens e mineração de dados em imagens ETM+/Landsat 7. Primeiramente, foi feita a restauração das imagens ETM+ para eliminar o aspecto borrado das imagens. Em seguida, usouse o método IHS (Intensity/Hue/Saturation) de fusão entre as bandas 3, 4 e 5 (com resolução de 30 m) e a banda pancromática (com resolução de 15 m) por permitir a adição de um alto grau de detalhe nas bandas origenais. O passo seguinte foi a aplicação de um filtro 5x5 de coocorrência sobre as bandas fusionadas que gerou 24 imagens referentes aos atributos texturais das bandas fusionadas. Posteriormente, coletou-se amostras de pixels das 3 bandas fusionadas e das 24 imagens geradas das duas classes estabelecidas: "Floresta" e "Não Floresta". Depois, essas amostras foram exportadas para o formato ASCII e foram inseridas em um software de mineração de dados que gerou uma árvore de decisão, a partir do algoritmo C4.5, utilizada na classificação. Obteve-se, como resultado, um mapa de fragmentos florestais com Kappa igual a 0,765. É possível observar que o município sofreu um processo de fragmentação florestal, possuindo aproximadamente 27,28% de cobertura vegetal. Nota-se que as áreas mais preservadas estão ao longo das margens de rios e em relevos declivosos das fronteiras oeste e sul/sudeste. Finalmente, pode-se concluir que a metodologia desenvolvida foi eficaz para alcançar o objetivo deste estudo. Palavras-chave: Sensoriamento Remoto, Geoprocessamento, Vegetação.
Journal of enzyme inhibition and medicinal chemistry, Jan 18, 2016
Farnesyltransferase is one of the enzyme targets for the development of drugs for diseases, inclu... more Farnesyltransferase is one of the enzyme targets for the development of drugs for diseases, including cancer, malaria, progeria, etc. In the present study, the structure-based pharmacophore models have been developed from five complex structures (1LD7, 1NI1, 2IEJ, 2ZIR and 2ZIS) obtained from the protein data bank. Initially, molecular dynamic (MD) simulations were performed for the complexes for 10 ns using AMBER 12 software. The conformers of the complexes (75) generated from the equilibrated protein were undergone protein-ligand interaction fingerprint (PLIF) analysis. The results showed that some important residues, such as LeuB96, TrpB102, TrpB106, ArgB202, TyrB300, AspB359 and TyrB361, are predominantly present in most of the complexes for interactions. These residues form side chain acceptor and surface (hydrophobic or π-π) kind of interactions with the ligands present in the complexes. The structure-based pharmacophore models were generated from the fingerprint bits obtained...
Food Technology and Biotechnology, Dec 20, 2011
In response to the growing demand for the consumption of natural, healthy and low--calorie food, ... more In response to the growing demand for the consumption of natural, healthy and low--calorie food, a large number of so-called alternative sugars has emerged since the early 80s, among them fructose. This sugar is a ketohexose, known as D-fructose or levulose, and is considered the sweetest sugar found in nature. Currently, fructose is mostly produced through the acid hydrolysis of sucrose, or through the multi-enzymatic hydrolysis of starch. Processes involving specific enzymes like inulinases, acting on widely available fructose polysaccharides such as inulin, have been studied as alternatives to the current approaches, in order to reduce time, complexity and costs involved in this process. Fructose syrup is used worldwide, mainly because of its sweetening power and functional properties. The present work aims to provide an overview of the properties of fructose and of the present and envisaged production processes, within the scope of a biotechnological approach.
Journal of Agricultural and Food Chemistry, Oct 13, 2010
Polyphenols are plant secondary metabolites commonly present in the human diet that possess the a... more Polyphenols are plant secondary metabolites commonly present in the human diet that possess the ability to bind and inhibit digestive proteins. In the present study, kinetic measurements of porcine pancreatic elastase (PPE) activity were determined using Suc-(Ala)(3)-p-nitroanilide as substrate and polyphenolic compounds as inhibitors. A positive relationship between the degree of polyphenol polymerization and the capacity of the polyphenols to inhibit PPE was observed. Procyanidins with a molecular weight of at least 1154 Da were necessary to observe a significant inhibitory ability. Kinetic parameters were also calculated and confirmed that the inhibition is reversible and competitive. Molecular docking and dynamics simulations demonstrated that the tetramer structure has a higher affinity to the enzyme due the establishment of more contact points with the amino acids present in its active site. Hydrogen bond interactions and hydrophobic effects established between the polyphenol groups and the side chain of residues stabilize and favor the binding mode of this procyanidin. This work is relevant to the study of the antinutritional effects caused by dietary tannins on the digestive enzymes' activity, reducing food digestibility and the absorption of nutrients. In general, the elastase model studied herein allows a better understanding of the inhibitory ability of polyphenol compounds.
The Journal of Physical Chemistry B, May 21, 2003
The enzymatic conversion of pyruvate into formate by the radical enzyme pyruvate formate lyase is... more The enzymatic conversion of pyruvate into formate by the radical enzyme pyruvate formate lyase is studied using density functional theory with the hybrid B3LYP functional. The residues glycine 734, cysteine 418, and cysteine 419 are known to be fundamental for the reaction to ...
The Journal of Physical Chemistry a, Sep 1, 2009
Gas-phase optimization of single biological molecules and of small active-site biological models ... more Gas-phase optimization of single biological molecules and of small active-site biological models has become a standard approach in first principles computational enzymology. The important role played by the surrounding environment (solvent, enzyme, both) is normally only accounted for through higher-level single point energy calculations performed using a polarizable continuum model (PCM) and an appropriate dielectric constant with the gas-phase-optimized geometries. In this study we analyze this widely used approximation, by comparing gas-phase-optimized geometries with geometries optimized with different PCM approaches (and considering different dielectric constants) for a representative data set of 20 very important biological molecules--the 20 natural amino acids. A total of 323 chemical bonds and 469 angles present in standard amino acid residues were evaluated. The results show that the use of gas-phase-optimized geometries can in fact be quite a reasonable alternative to the use of the more computationally intensive continuum optimizations, providing a good description of bond lengths and angles for typical biological molecules, even for charged amino acids, such as Asp, Glu, Lys, and Arg. This approximation is particularly successful if the protonation state of the biological molecule could be reasonably described in vacuum, a requirement that was already necessary in first principles computational enzymology.
Journal of Pineal Research, 2016
Adenosine triphosphate (ATP) is released onto the pinealocyte, along with noradrenaline, from sym... more Adenosine triphosphate (ATP) is released onto the pinealocyte, along with noradrenaline, from sympathetic neurons and triggers P2Y1 receptors that enhance β-adrenergic-induced N-acetylserotonin (NAS) synthesis. Nevertheless, the biotransformation of NAS into melatonin, which occurs due to the subsequent methylation by acetylserotonin O-methyltransferase (ASMT; EC 2.1.1.4), has not yet been evaluated in the presence of purinergic stimulation. We therefore evaluated the effects of purinergic signaling on melatonin synthesis induced by β-adrenergic stimulation. ATP increased NAS levels, but, surprisingly, inhibited melatonin synthesis in an inverse, concentration-dependent manner. Our results demonstrate that enhanced NAS levels, which depend on phospholipase C (PLC) activity (but not the induction of gene transcription), are a post-translational effect. By contrast, melatonin reduction is related to an ASMT inhibition of expression at both the gene transcription and protein levels. These results were independent of nuclear factor-kappa B (NF-kB) translocation. Neither the P2Y1 receptor activation nor the PLC-mediated pathway was involved in the decrease in melatonin, indicating that ATP regulates pineal metabolism through different mechanisms. Taken together, our data demonstrate that purinergic signaling differentially modulates NAS and melatonin synthesis and point to a regulatory role for ATP as a cotransmitter in the control of ASMT, the rate-limiting enzyme in melatonin synthesis. The endogenous production of melatonin regulates defense responses; therefore, understanding the mechanisms involving ASMT regulation might provide novel insights into the development and progression of neurological disorders since melatonin presents anti-inflammatory, neuroprotective, and neurogenic effects.
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Papers by Pedro Fernandes