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1.
Adv Biol Regul ; 91: 100991, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37802761

ABSTRACT

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.


Subject(s)
Phospholipids , Transcription Factors , Female , Humans , Phospholipids/genetics , Ligands , Steroidogenic Factor 1/genetics , Steroidogenic Factor 1/metabolism , Transcription Factors/metabolism , Receptors, Cytoplasmic and Nuclear , DNA
2.
Front Pain Res (Lausanne) ; 4: 1113039, 2023.
Article in English | MEDLINE | ID: mdl-37575637

ABSTRACT

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.

3.
Genes (Basel) ; 14(7)2023 07 22.
Article in English | MEDLINE | ID: mdl-37510397

ABSTRACT

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.


Subject(s)
Keratoderma, Palmoplantar , Humans , Keratoderma, Palmoplantar/genetics , Phenotype , Codon, Nonsense , Inheritance Patterns , Gene Expression Profiling , Membrane Proteins/genetics , Genes, Tumor Suppressor
4.
Sci Data ; 10(1): 169, 2023 03 27.
Article in English | MEDLINE | ID: mdl-36973275

ABSTRACT

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.


Subject(s)
Biodiversity , Fresh Water , Animals , Cuba , Insecta
5.
Int J Mol Sci ; 24(2)2023 Jan 16.
Article in English | MEDLINE | ID: mdl-36675256

ABSTRACT

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.


Subject(s)
Cardiomyopathies , Cardiomyopathy, Hypertrophic , Mitochondrial Diseases , Humans , Cardiomyopathies/genetics , Mitochondrial Diseases/genetics , Electron Transport Complex I/genetics , Cardiomyopathy, Hypertrophic/genetics , Cardiomyopathy, Hypertrophic/pathology , Mutation , Pedigree
6.
Rev. cuba. pediatr ; 94(3)sept. 2022. ilus
Article in Spanish | LILACS, CUMED | ID: biblio-1409151

ABSTRACT

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)


Subject(s)
Humans , Infant, Newborn , Prenatal Diagnosis , Clinical Clerkship , Esophageal Atresia/classification , Esophageal Atresia/etiology , Esophageal Atresia/epidemiology
7.
Mol Genet Metab ; 131(3): 349-357, 2020 11.
Article in English | MEDLINE | ID: mdl-33153867

ABSTRACT

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.


Subject(s)
Genetic Predisposition to Disease , Mitochondrial Diseases/genetics , NADH Dehydrogenase/genetics , Oxidative Phosphorylation , Child , Female , Fibroblasts/metabolism , Humans , Male , Metabolism, Inborn Errors/genetics , Metabolism, Inborn Errors/pathology , Mitochondria/genetics , Mitochondria/pathology , Mitochondrial Diseases/pathology , Siblings , Exome Sequencing
8.
Mol Genet Metab ; 131(3): 341-348, 2020 11.
Article in English | MEDLINE | ID: mdl-33093004

ABSTRACT

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.


Subject(s)
Electron Transport Complex I/deficiency , Electron Transport Complex I/genetics , Mitochondrial Diseases/genetics , Uniparental Disomy/genetics , Electron Transport Complex I/metabolism , Female , Genetic Predisposition to Disease , Homozygote , Humans , Infant , Mitochondrial Diseases/metabolism , Mitochondrial Diseases/pathology , Mutation/genetics , RNA Splicing/genetics , Uniparental Disomy/pathology
9.
Genes (Basel) ; 11(8)2020 07 26.
Article in English | MEDLINE | ID: mdl-32722639

ABSTRACT

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.


Subject(s)
Apoptosis Regulatory Proteins/genetics , Fibroblasts/pathology , Leigh Disease/pathology , Mutation , NADH, NADPH Oxidoreductases/genetics , Oxidative Phosphorylation , Child, Preschool , Computational Biology , Female , Fibroblasts/metabolism , Humans , Leigh Disease/genetics , Leigh Disease/metabolism , Male , Pedigree , Phenotype
10.
Acta méd. peru ; 37(1): 11-18, ene.-mar. 2020. tab, graf
Article in Spanish | LILACS-Express | LILACS | ID: biblio-1141968

ABSTRACT

RESUMEN Objetivo: extraer y evaluar la actividad antiviral de los compuestos de Chondracanthus chamissoi y Chlorella peruviana contra DENV-2 en células Vero-76. Materiales y métodos: se extrajeron el carragenano de Chondracanthus chamissoi, los carbohidratos solubles de Chondracanthus chamissoi y Chlorella peruviana y se realizó la prueba de toxicidad en células VERO-76 y la evaluación de la actividad antiviral. Resultados: se obtuvieron carragenanos de la fase de esporofito y gametofito de Chondracanthus chamissoi, los mismos que fueron identificados, mediante infrarrojo, como k-carragenano. Por cromatografía se identificaron nueve azúcares (ribosa, xilosa, arabinosa, fructuosa, manosa, galactosa, sucrosa, maltosa y lactosa) en la muestra de carbohidratos solubles de Chondracanthus chamissoi fase gametofito y cuatro azucares (glucosa, sucrosa, maltosa y lactosa) en la de Chlorella peruviana. Los compuestos de Chondracanthus chamissoi y la solución de carbohidratos solubles de Chlorella peruviana no presentaron efecto citotóxico; los carbohidratos del extracto crudo de Chlorella peruviana sí los tuvieron. Todas las fracciones del extracto crudo de Chondracanthus chamissoi fase gametofítica fueron positivas por la prueba de reducción del número de placas(50) a la dilución 1:5. El k-carragenano de Chondracanthus chamissoi en ambas fases y los extractos crudos de carbohidratos solubles de Chondracanthus chamissoi, Chlorella peruviana y la solución de carbohidratos solubles de Chlorella peruviana inhibieron el crecimiento del virus dengue, pero no los carbohidratos del extracto crudo de la Chlorella peruviana. Conclusiones: los compuestos obtenidos de Chondracanthus chamissoi y Chlorella peruviana presentan actividad antiviral contra DENV-2 por lo cual es necesario continuar los estudios del potencial antiviral de estos compuestos fraccionados y purificados.


ABSTRACT Objective: to extract and determine the antiviral activity of compounds from Chondracanthus chamissoi and Chlorella peruviana against DENV-2 in Vero-76 cells. Materials and methods: carrageenan from Chondracanthus chamissoi and soluble carbohydrates from Chlorella peruviana were extracted, and toxicity tests in VERO-76 cells and antiviral activity were determined. Results: carrageenan from Chondracanthus chamissoi sporophyte and gametophyte phases were obtained, the compound was identified as k-carrageenan using infrared light. Nine sugars (ribose, xylose, arabinose, fructose, mannose, galactose, sucrose, maltose, and lactose) were identified using chromatography in the soluble carbohydrate mix from Chondracanthus chamissoi, and four sugars (glucose, sucrose, maltose, and lactose) from Chlorella peruviana were identified. Compounds from Chondracanthus chamissoi and Chlorella peruviana soluble carbohydrate solutions did not show any cytotoxic effect, carbohydrates from the raw extract from Chlorella peruviana did have this effect. All fractions from the raw extract from the gametophyte phase from Chondracanthus chamissoi were positive in the plate reduction test at 1:5 dilution. K-carrageenan from Chondracanthus chamissoi in both phases, as well as the crude extracts of soluble carbohydrates from Chondracanthus chamissoi and Chlorella peruviana as well as the soluble carbohydrate solution from Chlorella peruviana inhibited growth of dengue virus, but that was not the case with the carbohydrates of the raw extract from Chlorella peruviana. Conclusions: compounds obtained from Chondracanthus chamissoi and Chlorella peruviana show antiviral activity against DENV-2, so it is necessary to continue studies aiming to determine the antiviral potential of these fractioned and purified compounds.

11.
Mol Genet Metab ; 128(4): 452-462, 2019 12.
Article in English | MEDLINE | ID: mdl-31727539

ABSTRACT

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.


Subject(s)
ATPases Associated with Diverse Cellular Activities/genetics , Cerebellum/abnormalities , Genes, Recessive , Genetic Predisposition to Disease , Membrane Proteins/genetics , Mitochondrial Proteins/genetics , Mutation , Nervous System Malformations/genetics , Nervous System Malformations/pathology , ATPases Associated with Diverse Cellular Activities/chemistry , Alleles , Amino Acid Substitution , Cerebellum/diagnostic imaging , Cerebellum/pathology , Child , Child, Preschool , Developmental Disabilities/diagnostic imaging , Developmental Disabilities/genetics , Developmental Disabilities/pathology , Female , Genetic Association Studies , Genotype , Humans , Infant , Male , Membrane Proteins/chemistry , Mitochondria/genetics , Mitochondria/metabolism , Mitochondria/ultrastructure , Mitochondrial Proteins/chemistry , Models, Molecular , Nervous System Malformations/diagnostic imaging , Pedigree , Protein Conformation , Structure-Activity Relationship , Ultrasonography/methods , Exome Sequencing
12.
Neuron ; 103(3): 395-411.e5, 2019 08 07.
Article in English | MEDLINE | ID: mdl-31201122

ABSTRACT

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.


Subject(s)
Brain/physiology , Computational Biology/standards , Computer Simulation , Models, Neurological , Neurons/physiology , Brain/cytology , Computational Biology/methods , Humans , Internet , Neural Networks, Computer , Online Systems
13.
Elife ; 82019 04 26.
Article in English | MEDLINE | ID: mdl-31025934

ABSTRACT

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.


Subject(s)
Brain/anatomy & histology , Brain/physiology , Computational Biology/methods , Nerve Net/anatomy & histology , Nerve Net/physiology , Computer Simulation , Models, Neurological
14.
Article in English | MEDLINE | ID: mdl-30201843

ABSTRACT

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'.


Subject(s)
Caenorhabditis elegans/physiology , Connectome/methods , Drosophila melanogaster/physiology , Models, Neurological , Nervous System Physiological Phenomena , Neurosciences/methods , Animals , Software
15.
Free Radic Biol Med ; 126: 235-248, 2018 10.
Article in English | MEDLINE | ID: mdl-30138712

ABSTRACT

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.


Subject(s)
DNA, Mitochondrial/genetics , MELAS Syndrome/metabolism , Mitochondrial Diseases/metabolism , Ophthalmoplegia, Chronic Progressive External/metabolism , Adolescent , Adult , Aged , Antioxidants/metabolism , Biomarkers/metabolism , Biopsy , Child , Child, Preschool , Gene Expression Regulation , Glycolysis , Healthy Volunteers , Humans , MELAS Syndrome/genetics , MELAS Syndrome/pathology , Middle Aged , Mitochondrial Diseases/genetics , Muscle, Skeletal/metabolism , Muscle, Skeletal/pathology , Ophthalmoplegia, Chronic Progressive External/genetics , Ophthalmoplegia, Chronic Progressive External/pathology , Oxidative Stress , Reactive Oxygen Species , Superoxide Dismutase/genetics , Support Vector Machine , Young Adult
16.
Hum Mutat ; 39(10): 1338-1343, 2018 10.
Article in English | MEDLINE | ID: mdl-30011114

ABSTRACT

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.


Subject(s)
Genetic Association Studies , Glycogen Storage Disease Type V/genetics , Mutation, Missense , Adolescent , Adult , Aged , Alleles , Biopsy , Female , Genotype , Glycogen Phosphorylase, Muscle Form/genetics , Glycogen Storage Disease Type V/diagnosis , Humans , Male , Middle Aged , Protein Isoforms , Young Adult
17.
Protein Sci ; 27(1): 269-275, 2018 01.
Article in English | MEDLINE | ID: mdl-28971542

ABSTRACT

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.


Subject(s)
Cryoelectron Microscopy , Image Processing, Computer-Assisted , Internet , Software
18.
BMC Genomics ; 18(Suppl 8): 819, 2017 Nov 14.
Article in English | MEDLINE | ID: mdl-29143597

ABSTRACT

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.


Subject(s)
Genotype , Glycogen Storage Disease Type V/genetics , Phenotype , Aged , Aged, 80 and over , Humans , Male , Middle Aged , Spain
19.
Rev. biol. trop ; 65(2): 807-818, Apr.-Jun. 2017. tab, ilus
Article in Spanish | LILACS-Express | LILACS | ID: biblio-897582

ABSTRACT

ResumenSe conoce poco sobre los patrones de emergencia de los odonatos tropicales. Estudiamos el patrón de emergencia de odonatos en un cuerpo dulceacuícola lótico de Giro, al norte de la ciudad de Santiago de Cuba, entre enero y diciembre 2008. Visitamos la localidad semanalmente, entre 09:00 y 14:00 h y recolectamos las exuvias directamente sobre la vegetación de ribera en una sección fija de 8 x 1 m2. Caracterizamos la variación temporal de la composición específica, la abundancia y la biomasa relativas y el patrón de emergencia de cada especie. Registramos 443 exuvias, pertenecientes a 22 especies, siete de Zygoptera y 15 de Anisoptera. El 50 % de la emergencia anual ocurrió en la temporada poco lluviosa (diciembre a marzo) con el valor más elevado en febrero (25 %). En el caso de las especies con siete o más exuvias por mes, Enallagma coecum y Macrothemis celeno se sincronizaron temporalmente durante la emergencia. También encontramos segregación temporal entre Macrothemis celeno con Protoneura capillaris, Neoneura maria, Progomphus integer y Scapanea frontalis. Estas diferencias se relacionaron con las mayores fluctuaciones anuales de temperatura, humedad relativa y el número de días lluviosos por mes. En general, detectamos asincronía y heterogeneidad en los patrones temporales de emergencia de los odonatos del cuerpo dulceacuícola lótico estudiado.


AbstractThe emergence patterns of tropical odonates (dragonflies and damselflies) are scarcely known. We studied the emergence patterns of odonates in a freshwater lotic system in Giro, Northern Santiago de Cuba, between January and December 2008. We visited the locality between 09:00 and 14:00, on a weekly basis, and collected exuviae from a fixed section (8 x 1 m2) offshore, along the riparian vegetation. We collected data on species composition and, for each species, abundance, relative biomass and emergence pattern. We collected 443 exuviae belonging to 22 species: seven Zygoptera and 15 Anisoptera. Half of the annual Odonata emergence took place in the dry season (December to March) with the highest value in February (25 %). For species for which we found seven or more exuviae per month, Enallagmacoecum and Macrothemis celeno tended to be a synchronal emergence. We also found temporal segregation of the emergence pattern between M. celeno and Protoneura capillaris, Neoneura maria, Progomphus integer and Scapanea frontalis. These differences were probably related to the highest annual fluctuations of temperature, relative humidity and number of rainy days per month. We concluded that there is an asynchrony and heterogeneity in Odonata emergence times in the studied freshwater lotic system.

20.
Mitochondrion ; 30: 51-8, 2016 09.
Article in English | MEDLINE | ID: mdl-27374853

ABSTRACT

We evaluated the coenzyme Q10 (CoQ) levels in patients who were diagnosed with mitochondrial oxidative phosphorylation (OXPHOS) and non-OXPHOS disorders (n=72). Data from the 72 cases in this study revealed that 44.4% of patients showed low CoQ concentrations in either their skeletal muscle or skin fibroblasts. Our findings suggest that secondary CoQ deficiency is a common finding in OXPHOS and non-OXPHOS disorders. We hypothesize that cases of CoQ deficiency associated with OXPHOS defects could be an adaptive mechanism to maintain a balanced OXPHOS, although the mechanisms explaining these deficiencies and the pathophysiological role of secondary CoQ deficiency deserves further investigation.


Subject(s)
Mitochondrial Diseases/pathology , Oxidative Phosphorylation , Ubiquinone/analogs & derivatives , Adolescent , Adult , Child , Child, Preschool , Cohort Studies , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Muscles/pathology , Prevalence , Skin/pathology , Ubiquinone/deficiency , Young Adult
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