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1.
Int J Mol Sci ; 24(2)2023 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-36675256

RESUMO

We report a neonatal patient with hypertrophic cardiomyopathy (HCM), lactic acidosis and isolated complex I deficiency. Using a customized next-generation sequencing panel, we identified a novel hemizygous variant c.338G>A in the X-linked NDUFB11 gene that encodes the NADH: ubiquinone oxidoreductase subunit B11 of the mitochondrial respiratory chain (MRC) complex I (CI). Molecular and functional assays performed in the proband's target tissues­skeletal and heart muscle­showed biochemical disturbances of the MRC, suggesting a pathogenic role for this variant. In silico analyses initially predicted an amino acid missense change p.(Arg113Lys) in the NDUFB11 CI subunit. However, we showed that the molecular effect of the c.338G>A variant, which is located at the last nucleotide of exon 2 of the NDUFB11 gene in the canonical 'short' transcript (sized 462 bp), instead causes a splicing defect triggering the up-regulation of the expression of an alternative 'long' transcript (sized 492 bp) that can also be detected in the control individuals. Our results support the hypothesis that the canonical 'short' transcript is required for the proper NDUFB11 protein synthesis, which is essential for optimal CI assembly and activity, whereas the longer alternative transcript seems to represent a non-functional, unprocessed splicing intermediate. Our results highlight the importance of characterizing the molecular effect of new variants in the affected patient's tissues to demonstrate their pathogenicity and association with the clinical phenotypes.


Assuntos
Cardiomiopatias , Cardiomiopatia Hipertrófica , Doenças Mitocondriais , Humanos , Cardiomiopatias/genética , Doenças Mitocondriais/genética , Complexo I de Transporte de Elétrons/genética , Cardiomiopatia Hipertrófica/genética , Cardiomiopatia Hipertrófica/patologia , Mutação , Linhagem
2.
Mol Genet Metab ; 131(3): 349-357, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-33153867

RESUMO

Isolated complex I (CI) deficiency is the most common cause of oxidative phosphorylation (OXPHOS) dysfunction. Whole-exome sequencing identified biallelic mutations in NDUFA8 (c.[293G > T]; [293G > T], encoding for an accessory subunit of CI, in two siblings with a favorable clinical evolution. The individuals reported here are practically asymptomatic, with the exception of slight failure to thrive and some language difficulties at the age of 6 and 9 years, respectively. These observations are remarkable since the vast majority of patients with CI deficiency, including the only NDUFA8 patient reported so far, showed an extremely poor clinical outcome. Western blot studies demonstrated that NDUFA8 protein was strongly reduced in the patients' fibroblasts and muscle extracts. In addition, there was a marked and specific decrease in the steady-state levels of CI subunits. BN-PAGE demonstrated an isolated defect in the assembly and the activity of CI with impaired supercomplexes formation and abnormal accumulation of CI subassemblies. Confocal microscopy analysis in fibroblasts showed rounder mitochondria and diminished branching degree of the mitochondrial network. Functional complementation studies demonstrated disease-causality for the identified mutation as lentiviral transduction with wild-type NDUFA8 cDNA restored the steady-state levels of CI subunits and completely recovered the deficient enzymatic activity in immortalized mutant fibroblasts. In summary, we provide additional evidence of the involvement of NDUFA8 as a mitochondrial disease-causing gene associated with altered mitochondrial morphology, CI deficiency, impaired supercomplexes formation, and very mild progression of the disease.


Assuntos
Predisposição Genética para Doença , Doenças Mitocondriais/genética , NADH Desidrogenase/genética , Fosforilação Oxidativa , Criança , Feminino , Fibroblastos/metabolismo , Humanos , Masculino , Erros Inatos do Metabolismo/genética , Erros Inatos do Metabolismo/patologia , Mitocôndrias/genética , Mitocôndrias/patologia , Doenças Mitocondriais/patologia , Irmãos , Sequenciamento do Exoma
3.
Mol Genet Metab ; 131(3): 341-348, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-33093004

RESUMO

Uniparental disomy (UPD) is an underestimated cause of autosomal recessive disorders. In this study, we aim to raise awareness about the possibility of UPD in mitochondrial disorders - where it is a hardly described event -, by functionally characterizing a novel variant in a structural subunit of complex I (CI) of the mitochondrial oxidative phosphorylation system. Using next-generation sequencing, we identified a new intronic homozygous c.350 + 5G > A variant in the NDUFS4 gene in a one-year-old girl (being alive at the age of 7) belonging to a non-consanguineous family presenting with encephalopathy, psychomotor delay, lactic acidosis and a single CI deficiency, a less severe phenotype than those previously reported in most NDUFS4 patients. One parent lacked the variant, and microsatellite genotyping showed complete paternal uniparental isodisomy of the non-imprinted chromosome 5. We demonstrated in patient's skeletal muscle and fibroblasts splicing abnormalities, low expression of NDUFS4, undetectable NDUFS4 protein, defects in cellular respiration (decreased oxygen consumption and ATP production), and impaired assembly or stability of mitochondrial supercomplexes containing CI. Our findings support that c.350 + 5G > A variant is pathogenic, and reinforce that UPD, although rare, should be considered as a possible cause of mitochondrial diseases in order to provide accurate genetic counselling.


Assuntos
Complexo I de Transporte de Elétrons/deficiência , Complexo I de Transporte de Elétrons/genética , Doenças Mitocondriais/genética , Dissomia Uniparental/genética , Complexo I de Transporte de Elétrons/metabolismo , Feminino , Predisposição Genética para Doença , Homozigoto , Humanos , Lactente , Doenças Mitocondriais/metabolismo , Doenças Mitocondriais/patologia , Mutação/genética , Splicing de RNA/genética , Dissomia Uniparental/patologia
4.
Mol Genet Metab ; 128(4): 452-462, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31727539

RESUMO

Lethal neonatal encephalopathies are heterogeneous congenital disorders that can be caused by mitochondrial dysfunction. Biallelic large deletions in the contiguous ATAD3B and ATAD3A genes, encoding mitochondrial inner membrane ATPases of unknown function, as well as compound heterozygous nonsense and missense mutations in the ATAD3A gene have been recently associated with fatal neonatal cerebellar hypoplasia. In this work, whole exome sequencing (WES) identified the novel homozygous variant c.1217 T > G in ATAD3A, predicting a p.(Leu406Arg) substitution, in four siblings from a consanguineous family presenting with fatal neonatal cerebellar hypoplasia, seizures, axial hypotonia, hypertrophic cardiomyopathy, hepatomegaly, congenital cataract, and dysmorphic facies. Biochemical phenotypes of the patients included hyperlactatemia and hypocholesterolemia. Healthy siblings and parents were heterozygous for this variant, which is predicted to introduce a polar chain within the catalytic domain of ATAD3A that shortens its beta-sheet structure, presumably affecting protein stability. Accordingly, patient's fibroblasts with the homozygous variant displayed a specific reduction in ATAD3A protein levels associated with profound ultrastructural alterations of mitochondrial cristae and morphology. Our findings exclude the causative role of ATAD3B on this severe phenotype, expand the phenotypical spectrum of ATAD3A pathogenic variants and emphasize the vital role of ATAD3A in mitochondrial biogenesis.


Assuntos
ATPases Associadas a Diversas Atividades Celulares/genética , Cerebelo/anormalidades , Genes Recessivos , Predisposição Genética para Doença , Proteínas de Membrana/genética , Proteínas Mitocondriais/genética , Mutação , Malformações do Sistema Nervoso/genética , Malformações do Sistema Nervoso/patologia , ATPases Associadas a Diversas Atividades Celulares/química , Alelos , Substituição de Aminoácidos , Cerebelo/diagnóstico por imagem , Cerebelo/patologia , Criança , Pré-Escolar , Deficiências do Desenvolvimento/diagnóstico por imagem , Deficiências do Desenvolvimento/genética , Deficiências do Desenvolvimento/patologia , Feminino , Estudos de Associação Genética , Genótipo , Humanos , Lactente , Masculino , Proteínas de Membrana/química , Mitocôndrias/genética , Mitocôndrias/metabolismo , Mitocôndrias/ultraestrutura , Proteínas Mitocondriais/química , Modelos Moleculares , Malformações do Sistema Nervoso/diagnóstico por imagem , Linhagem , Conformação Proteica , Relação Estrutura-Atividade , Ultrassonografia/métodos , Sequenciamento do Exoma
5.
Hum Mutat ; 39(10): 1338-1343, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30011114

RESUMO

McArdle disease is a disorder of muscle glycogen metabolism caused by mutations in the PYGM gene, encoding for the muscle-specific isoform of glycogen phosphorylase (M-GP). The activity of this enzyme is completely lost in patients' muscle biopsies, when measured with a standard biochemical test which, does not allow to determine M-GP protein levels. We aimed to determine M-GP protein levels in the muscle of McArdle patients, by studying biopsies of 40 patients harboring a broad spectrum of PYGM mutations and 22 controls. Lack of M-GP protein was found in muscle in the vast majority (95%) of patients, irrespective of the PYGM genotype, including those carrying missense mutations, with few exceptions. M-GP protein biosynthesis is not being produced by PYGM mutations inducing premature termination codons (PTC), neither by most PYGM missense mutations. These findings explain the lack of PYGM genotype-phenotype correlation and have important implications for the design of molecular-based therapeutic approaches.


Assuntos
Estudos de Associação Genética , Doença de Depósito de Glicogênio Tipo V/genética , Mutação de Sentido Incorreto , Adolescente , Adulto , Idoso , Alelos , Biópsia , Feminino , Genótipo , Glicogênio Fosforilase Muscular/genética , Doença de Depósito de Glicogênio Tipo V/diagnóstico , Humanos , Masculino , Pessoa de Meia-Idade , Isoformas de Proteínas , Adulto Jovem
6.
BMC Genomics ; 18(Suppl 8): 819, 2017 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-29143597

RESUMO

BACKGROUND: We recently described the genotype/phenotype features of all Spanish patients diagnosed with McArdle disease as of January 2011 (n = 239, prevalence of ~1/167,000) (J Neurol Neurosurg Psychiatry 2012;83:322-8). Several caveats were however identified suggesting that the prevalence of the disease is actually higher. METHODS: We have now updated main genotype/phenotype data, as well as potential associations within/between them, of all Spanish individuals currently diagnosed with McArdle disease (December 2016). RESULTS: Ninety-four new patients (all Caucasian) have been diagnosed, yielding a prevalence of ~1/139,543 individuals. Around 55% of the mutated alleles have the commonest PYGM pathogenic mutation p.R50X, whereas p.W798R and p.G205S account for 10 and 9% of the allelic variants, respectively. Seven new mutations were identified: p.H35R, p.R70C, p.R94Q, p.L132WfsX163, p.Q176P, p.R576Q, and c.244-3_244-2CA. Almost all patients show exercise intolerance, the second wind phenomenon and high serum creatine kinase activity. There is, however, heterogeneity in clinical severity, with 8% of patients being asymptomatic during normal daily life, and 21% showing limitations during daily activities and fixed muscle weakness. A major remaining challenge is one of diagnosis, which is often delayed until the third decade of life in 72% of new patients despite the vast majority (86%) reporting symptoms before 20 years. An important development is the growing proportion of those reporting a 4-year improvement in disease severity (now 34%) and following an active lifestyle (50%). Physically active patients are more likely to report an improvement after a 4-year period in the clinical course of the disease than their inactive peers (odds ratio: 13.98; 95% confidence interval: 5.6, 34.9; p < 0.001). Peak oxygen uptake is also higher in the former (20.7 ± 6.0 vs. 16.8 ± 5.3 mL/kg/min, p = 0.0013). Finally, there is no association between PYGM genotype and phenotype manifestation of the disease. CONCLUSIONS: The reported prevalence of McArdle disease grows exponentially despite frequent, long delays in genetic diagnosis, suggesting that many patients remain undiagnosed. Until a genetic cure is available (which is not predicted in the near future), current epidemiologic data support that adoption of an active lifestyle is the best medicine for these patients.


Assuntos
Genótipo , Doença de Depósito de Glicogênio Tipo V/genética , Fenótipo , Idoso , Idoso de 80 Anos ou mais , Humanos , Masculino , Pessoa de Meia-Idade , Espanha
7.
Genet Med ; 18(11): 1128-1135, 2016 11.
Artigo em Inglês | MEDLINE | ID: mdl-26913921

RESUMO

PURPOSE: McArdle disease is a metabolic disorder caused by pathogenic mutations in the PYGM gene. Timely diagnosis can sometimes be difficult with direct genomic analysis, which requires additional studies of cDNA from muscle transcripts. Although the "nonsense-mediated mRNA decay" (NMD) eliminates tissue-specific aberrant transcripts, there is some residual transcription of tissue-specific genes in virtually all cells, such as peripheral blood mononuclear cells (PBMCs). METHODS: We studied a subset of the main types of PYGM mutations (deletions, missense, nonsense, silent, or splicing mutations) in cDNA from easily accessible cells (PBMCs) in 12 McArdle patients. RESULTS: Analysis of cDNA from PBMCs allowed detection of all mutations. Importantly, the effects of mutations with unknown pathogenicity (silent and splicing mutations) were characterized in PBMCs. Because the NMD mechanism does not seem to operate in nonspecific cells, PBMCs were more suitable than muscle biopsies for detecting the pathogenicity of some PYGM mutations, notably the silent mutation c.645G>A (p.K215=), whose effect in the splicing of intron 6 was unnoticed in previous muscle transcriptomic studies. CONCLUSION: We propose considering the use of PBMCs for detecting mutations that are thought to cause McArdle disease, particularly for studying their actual pathogenicity.Genet Med 18 11, 1128-1135.


Assuntos
Glicogênio Fosforilase Muscular/sangue , Doença de Depósito de Glicogênio Tipo V/sangue , Doença de Depósito de Glicogênio Tipo V/genética , Patologia Molecular/métodos , Adolescente , Adulto , Códon sem Sentido/genética , Feminino , Glicogênio Fosforilase Muscular/genética , Doença de Depósito de Glicogênio Tipo V/patologia , Humanos , Leucócitos Mononucleares , Masculino , Pessoa de Meia-Idade , Splicing de RNA/genética , Deleção de Sequência/genética , Adulto Jovem
8.
J Struct Biol ; 190(3): 348-59, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25913484

RESUMO

Image formation in bright field electron microscopy can be described with the help of the contrast transfer function (CTF). In this work the authors describe the "CTF Estimation Challenge", called by the Madrid Instruct Image Processing Center (I2PC) in collaboration with the National Center for Macromolecular Imaging (NCMI) at Houston. Correcting for the effects of the CTF requires accurate knowledge of the CTF parameters, but these have often been difficult to determine. In this challenge, researchers have had the opportunity to test their ability in estimating some of the key parameters of the electron microscope CTF on a large micrograph data set produced by well-known laboratories on a wide set of experimental conditions. This work presents the first analysis of the results of the CTF Estimation Challenge, including an assessment of the performance of the different software packages under different conditions, so as to identify those areas of research where further developments would be desirable in order to achieve high-resolution structural information.


Assuntos
Substâncias Macromoleculares/química , Microscopia Eletrônica/métodos , Algoritmos , Processamento de Imagem Assistida por Computador/métodos , Software
9.
Adv Biol Regul ; 91: 100991, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37802761

RESUMO

Steroidogenic Factor-1 (SF-1, NR5A1) is a member of the nuclear receptor superfamily of ligand-regulated transcription factors, consisting of a DNA-binding domain (DBD) connected to a transcriptional regulatory ligand binding domain (LBD) via an unstructured hinge domain. SF-1 is a master regulator of development and adult function along the hypothalamic pituitary adrenal and gonadal axes, with strong pathophysiological association with endometriosis and adrenocortical carcinoma. SF-1 was shown to bind and be regulated by phospholipids, one of the most interesting aspects of SF-1 regulation is the manner in which SF-1 interacts with phospholipids: SF-1 buries the phospholipid acyl chains deep in the hydrophobic core of the SF-1 protein, while the lipid headgroups remain solvent-exposed on the exterior of the SF-1 protein surface. Here, we have reviewed several aspects of SF-1 structure, function and physiology, touching on other transcription factors that help regulate SF-1 target genes, non-canonical functions of SF-1, the DNA-binding properties of SF-1, the use of mass spectrometry to identify lipids that associate with SF-1, how protein phosphorylation regulates SF-1 and the structural biology of the phospholipid-ligand binding domain. Together this review summarizes the form and function of Steroidogenic Factor-1 in physiology and in human disease, with particular emphasis on adrenal cancer.


Assuntos
Fosfolipídeos , Fatores de Transcrição , Feminino , Humanos , Fosfolipídeos/genética , Ligantes , Fator Esteroidogênico 1/genética , Fator Esteroidogênico 1/metabolismo , Fatores de Transcrição/metabolismo , Receptores Citoplasmáticos e Nucleares , DNA
10.
Acta Crystallogr D Biol Crystallogr ; 69(Pt 5): 695-700, 2013 May.
Artigo em Inglês | MEDLINE | ID: mdl-23633578

RESUMO

Electron microscopy is a valuable tool for elucidating the three-dimensional structures of macromolecular complexes. As the field matures and the number of solved structures increases, the existence of infrastructures that keep this information organized and accessible is crucial. At the same time, standards and clearly described conventions facilitate software maintenance, benefit interoperability with other packages and allow data interchange. This work describes three developments promoting integrative biology, standardization and workflow processing, namely PeppeR, the EMX initiative and Scipion.


Assuntos
Disseminação de Informação , Microscopia Eletrônica/métodos , Software , Algoritmos , Processamento de Imagem Assistida por Computador/métodos
11.
Front Pain Res (Lausanne) ; 4: 1113039, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37575637

RESUMO

Castration is a stressful and painful procedure that can impact swine welfare negatively. The objectives of this study were to (1) evaluate the effect of one incision compared to two incisions and the use of a topical vapocoolant (VAPO; ethyl chloride; a topical anesthetic) applied before castration and (2) evaluate the most effective combination in reducing pain in objective 1 and the use of Metacam®; meloxicam before castration on measures of performance, behavior, and physiology. Study 1 consisted of six treatment groups (N = 27 pigs per treatment) and included: nothing (NO); sham castrated (SH); one incision castration (C1); one incision castration plus VAPO (C1V); two incision castration (C2); two incision castration plus VAPO (C2V). Body weights and blood samples were taken at baseline and other time points after castration. Behavior measures were collected for 24 h after castration. Wound scores were collected daily for 10 days. The C1 pigs and C1V pigs were significantly heavier than the other castrated treatment groups but not different from NO and SH pigs. Vocalizations were louder for C1 and C1V pigs (P = 0.0015). Study 2 (N = 40 pigs per treatment) included: nothing (NO); one incision castration (C1); and one incision castration plus meloxicam administered 15 min before castration (C1M). The same measures (performance, behavior, and physiology) were collected as in Study 1. Performance measures and behavior did not differ among treatment groups. Physiological measures were only different for red blood cells (RBC; P = 0.0304). Pigs in C1 and C1M treatment groups had cortisol concentrations that were greater than the NO treatment group at 15 min post-castration (P < 0.05). The data collected give insight into the benefits of one-incision castration compared to 2-incision castration. However, the data only support a lower-level relief from acute pain associated with castration, as it is evident that pigs still experience stress at 15 min post-castration with or without the use of meloxicam. Further research could potentially identify the correct timing, route and dose for the administration of meloxicam.

12.
Sci Data ; 10(1): 169, 2023 03 27.
Artigo em Inglês | MEDLINE | ID: mdl-36973275

RESUMO

In light of the ongoing freshwater biodiversity crisis, detailed knowledge regarding the spatial distribution of freshwater species is urgently required, especially in biodiversity hotspots. Here we present a database of georeferenced occurrence records of four freshwater invertebrate taxa groups across Cuba, namely flatworms (Platyhelminthes: Tricladida), insects (Ephemeroptera, Odonata, Hemiptera, Trichoptera, Coleoptera, Diptera), crabs and shrimps (Crustacea: Decapoda), and mollusks (Mollusca). We collated the geographic occurrence information from scientific literature, unpublished field records, museum collections and online databases. The database, comprising 6292 records of 457 species at 1075 unique localities, is organized in 32 fields that contain the information about the taxonomic classification of each recorded species, the sex and life stage of collected individuals; the geographic coordinates, location, author and date of the record and a reference to the original data source. This database provides an important basis towards an improved understanding of the spatial distribution of freshwater biodiversity in Cuba.


Assuntos
Biodiversidade , Água Doce , Animais , Cuba , Insetos
13.
Genes (Basel) ; 14(7)2023 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-37510397

RESUMO

Hereditary palmoplantar keratodermas (PPKs) are a clinically and genetically heterogeneous group of disorders characterized by excessive epidermal thickening of palms and soles. Several genes have been associated with PPK including PERP, a gene encoding a crucial component of desmosomes that has been associated with dominant and recessive keratoderma. We report a patient with recessive erythrokeratoderma (EK) in which whole exome sequencing (WES) prioritized by human phenotype ontology (HPO) terms revealed the presence of the novel variant c.153C > A in the N-terminal region the PERP gene. This variant is predicted to have a nonsense effect, p.(Cys51Ter), resulting in a premature stop codon. We demonstrated a marked reduction in gene expression in cultured skin fibroblasts obtained from the patient. Despite the PERP gene is expressed at low levels in fibroblasts, our finding supports a loss-of-function (LoF) mechanism for the identified variant, as previously suggested in recessive EK. Our study underscores the importance of integrating HPO analysis when using WES for molecular genetic diagnosis in a clinical setting, as it facilitates continuous updates regarding gene-clinical feature associations.


Assuntos
Ceratodermia Palmar e Plantar , Humanos , Ceratodermia Palmar e Plantar/genética , Fenótipo , Códon sem Sentido , Padrões de Herança , Perfilação da Expressão Gênica , Proteínas de Membrana/genética , Genes Supressores de Tumor
14.
Genes (Basel) ; 11(8)2020 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-32722639

RESUMO

Leigh syndrome (LS) usually presents as an early onset mitochondrial encephalopathy characterized by bilateral symmetric lesions in the basal ganglia and cerebral stem. More than 75 genes have been associated with this condition, including genes involved in the biogenesis of mitochondrial complex I (CI). In this study, we used a next-generation sequencing (NGS) panel to identify two novel biallelic variants in the NADH:ubiquinone oxidoreductase subunit A13 (NDUFA13) gene in a patient with isolated CI deficiency in skeletal muscle. Our patient, who represents the second family report with mutations in the CI NDUFA13 subunit, presented with LS lesions in brain magnetic resonance imaging, mild hypertrophic cardiomyopathy, and progressive spastic tetraparesis. This phenotype manifestation is different from that previously described in the first NDUFA13 family, which was predominantly characterized by neurosensorial symptoms. Both in silico pathogenicity predictions and oxidative phosphorylation (OXPHOS) functional findings in patient's skin fibroblasts (delayed cell growth, isolated CI enzyme defect, decreased basal and maximal oxygen consumption and as well as ATP production, together with markedly diminished levels of the NDUFA13 protein, CI, and respirasomes) suggest that these novel variants in the NDUFA13 gene are the underlying cause of the CI defect, expanding the genetic heterogeneity of LS.


Assuntos
Proteínas Reguladoras de Apoptose/genética , Fibroblastos/patologia , Doença de Leigh/patologia , Mutação , NADH NADPH Oxirredutases/genética , Fosforilação Oxidativa , Pré-Escolar , Biologia Computacional , Feminino , Fibroblastos/metabolismo , Humanos , Doença de Leigh/genética , Doença de Leigh/metabolismo , Masculino , Linhagem , Fenótipo
15.
Elife ; 82019 04 26.
Artigo em Inglês | MEDLINE | ID: mdl-31025934

RESUMO

Biophysical modeling of neuronal networks helps to integrate and interpret rapidly growing and disparate experimental datasets at multiple scales. The NetPyNE tool (www.netpyne.org) provides both programmatic and graphical interfaces to develop data-driven multiscale network models in NEURON. NetPyNE clearly separates model parameters from implementation code. Users provide specifications at a high level via a standardized declarative language, for example connectivity rules, to create millions of cell-to-cell connections. NetPyNE then enables users to generate the NEURON network, run efficiently parallelized simulations, optimize and explore network parameters through automated batch runs, and use built-in functions for visualization and analysis - connectivity matrices, voltage traces, spike raster plots, local field potentials, and information theoretic measures. NetPyNE also facilitates model sharing by exporting and importing standardized formats (NeuroML and SONATA). NetPyNE is already being used to teach computational neuroscience students and by modelers to investigate brain regions and phenomena.


Assuntos
Encéfalo/anatomia & histologia , Encéfalo/fisiologia , Biologia Computacional/métodos , Rede Nervosa/anatomia & histologia , Rede Nervosa/fisiologia , Simulação por Computador , Modelos Neurológicos
16.
Neuron ; 103(3): 395-411.e5, 2019 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-31201122

RESUMO

Computational models are powerful tools for exploring the properties of complex biological systems. In neuroscience, data-driven models of neural circuits that span multiple scales are increasingly being used to understand brain function in health and disease. But their adoption and reuse has been limited by the specialist knowledge required to evaluate and use them. To address this, we have developed Open Source Brain, a platform for sharing, viewing, analyzing, and simulating standardized models from different brain regions and species. Model structure and parameters can be automatically visualized and their dynamical properties explored through browser-based simulations. Infrastructure and tools for collaborative interaction, development, and testing are also provided. We demonstrate how existing components can be reused by constructing new models of inhibition-stabilized cortical networks that match recent experimental results. These features of Open Source Brain improve the accessibility, transparency, and reproducibility of models and facilitate their reuse by the wider community.


Assuntos
Encéfalo/fisiologia , Biologia Computacional/normas , Simulação por Computador , Modelos Neurológicos , Neurônios/fisiologia , Encéfalo/citologia , Biologia Computacional/métodos , Humanos , Internet , Redes Neurais de Computação , Sistemas On-Line
17.
Artigo em Inglês | MEDLINE | ID: mdl-30201843

RESUMO

Geppetto is an open-source platform that provides generic middleware infrastructure for building both online and desktop tools for visualizing neuroscience models and data and managing simulations. Geppetto underpins a number of neuroscience applications, including Open Source Brain (OSB), Virtual Fly Brain (VFB), NEURON-UI and NetPyNE-UI. OSB is used by researchers to create and visualize computational neuroscience models described in NeuroML and simulate them through the browser. VFB is the reference hub for Drosophila melanogaster neural anatomy and imaging data including neuropil, segmented neurons, microscopy stacks and gene expression pattern data. Geppetto is also being used to build a new user interface for NEURON, a widely used neuronal simulation environment, and for NetPyNE, a Python package for network modelling using NEURON. Geppetto defines domain agnostic abstractions used by all these applications to represent their models and data and offers a set of modules and components to integrate, visualize and control simulations in a highly accessible way. The platform comprises a backend which can connect to external data sources, model repositories and simulators together with a highly customizable frontend.This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.


Assuntos
Caenorhabditis elegans/fisiologia , Conectoma/métodos , Drosophila melanogaster/fisiologia , Modelos Neurológicos , Fenômenos Fisiológicos do Sistema Nervoso , Neurociências/métodos , Animais , Software
18.
Protein Sci ; 27(1): 269-275, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-28971542

RESUMO

Macromolecular structural determination by Electron Microscopy under cryogenic conditions is revolutionizing the field of structural biology, interesting a large community of potential users. Still, the path from raw images to density maps is complex, and sophisticated image processing suites are required in this process, often demanding the installation and understanding of different software packages. Here, we present Scipion Web Tools, a web-based set of tools/workflows derived from the Scipion image processing framework, specially tailored to nonexpert users in need of very precise answers at several key stages of the structural elucidation process.


Assuntos
Microscopia Crioeletrônica , Processamento de Imagem Assistida por Computador , Internet , Software
19.
Free Radic Biol Med ; 126: 235-248, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30138712

RESUMO

A major challenge in mitochondrial diseases (MDs) is the identification of biomarkers that could inform of the mechanisms involved in the phenotypic expression of genetic defects. Herein, we have investigated the protein signature of metabolism and of the antioxidant response in muscle biopsies of clinically and genetically diagnosed patients with Progressive External Ophthalmoplegia due to single large-scale (PEO-sD) or multiple (PEO-mD) deletions of mtDNA and Mitochondrial Encephalopathy Lactic Acidosis and Stroke-like episode (MELAS) syndrome, and healthy donors. A high-throughput immunoassay technique that quantitates the expression of relevant proteins of glycolysis, glycogenolysis, pentose phosphate pathway, oxidative phosphorylation, pyruvate and fatty acid oxidation, tricarboxylic acid cycle and the antioxidant response in two large independent and retrospectively collected cohorts of PEO-sD, PEO-mD and MELAS patients revealed that despite the heterogeneity of the genetic alterations, the three MDs showed the same metabolic signatures in both cohorts of patients, which were highly divergent from those of healthy individuals. Linear Discriminant Analysis and Support Vector Machine classifier provided a minimum of four biomarkers to discriminate healthy from pathological samples. Regardless of the induction of a large number of enzymes involved in ameliorating oxidative stress, the down-regulation of mitochondrial superoxide dismutase (SOD2) and catalase expression favored the accumulation of oxidative damage in patients' proteins. Down-regulation of SOD2 and catalase expression in MD patients is not due to relevant changes in the availability of their mRNAs, suggesting that oxidative stress regulates the expression of the two enzymes post-transcriptionally. We suggest that SOD2 and catalase could provide specific targets to improve the detoxification of reactive oxygen species that affects muscle proteins in these patients.


Assuntos
DNA Mitocondrial/genética , Síndrome MELAS/metabolismo , Doenças Mitocondriais/metabolismo , Oftalmoplegia Externa Progressiva Crônica/metabolismo , Adolescente , Adulto , Idoso , Antioxidantes/metabolismo , Biomarcadores/metabolismo , Biópsia , Criança , Pré-Escolar , Regulação da Expressão Gênica , Glicólise , Voluntários Saudáveis , Humanos , Síndrome MELAS/genética , Síndrome MELAS/patologia , Pessoa de Meia-Idade , Doenças Mitocondriais/genética , Músculo Esquelético/metabolismo , Músculo Esquelético/patologia , Oftalmoplegia Externa Progressiva Crônica/genética , Oftalmoplegia Externa Progressiva Crônica/patologia , Estresse Oxidativo , Espécies Reativas de Oxigênio , Superóxido Dismutase/genética , Máquina de Vetores de Suporte , Adulto Jovem
20.
Rev. cuba. pediatr ; 94(3)sept. 2022. ilus
Artigo em Espanhol | LILACS, CUMED | ID: biblio-1409151

RESUMO

La atresia esofágica es una de las anomalías congénitas más frecuentes en la práctica quirúrgica neonatal. Se estima que tiene una incidencia de 1 por cada 3500 recién nacidos vivos a nivel mundial. La preparación de guías de actuación y protocolos asistenciales es tendencia en la práctica médica actual. Esta Guía de Práctica Clínica se elaboró respondiendo a la necesidad de protocolizar la atención médico-quirúrgica de la atresia esofágica. En el Centro Territorial de Cirugía Neonatal de Holguín, donde se regionaliza la atención a neonatos de las cinco provincias orientales del país con afecciones congénitas y quirúrgicas de alta complejidad, la atresia esofágica fue la afección quirúrgica más frecuente en los últimos diez años, con una supervivencia ascendente que alcanzó 94,4 por ciento en 2019. La guía que se presenta se aprobó en el Primer Consenso Nacional de Guías de Prácticas Clínicas en Cirugía Pediátrica, en Varadero, Matanzas en 2019. Incluye las principales pautas para el diagnóstico, tratamiento y seguimiento de los pacientes afectados y se considera una herramienta eficiente para mejorar los resultados en la asistencia médica y quirúrgica neonatal(AU)


Esophageal atresia is one of the most common congenital anomalies in neonatal surgical practice. It is estimated to have an incidence of 1 per 3500 live newborns globally. The preparation of action guides and care protocols is a trend in current medical practice. This Clinical Practice Guide was prepared in response to the need to protocolize the medical-surgical care of esophageal atresia. In the Territorial Center for Neonatal Surgery of Holguín, where the care of neonates from the five eastern provinces of the country with congenital and surgical conditions of high complexity is regionalized, esophageal atresia was the most frequent surgical condition in the last ten years, with an ascending survival that reached 94.4 percent in 2019. The guideline presented was approved in the First National Consensus of Clinical Practice Guidelines in Pediatric Surgery, in Varadero, Matanzas in 2019. It includes the main guidelines for the diagnosis, treatment and follow-up of affected patients and is considered an efficient tool to improve outcomes in neonatal medical and surgical care(AU)


Assuntos
Humanos , Recém-Nascido , Diagnóstico Pré-Natal , Estágio Clínico , Atresia Esofágica/classificação , Atresia Esofágica/etiologia , Atresia Esofágica/epidemiologia
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