Diseño y Desarrollo de un Sistema de Información para la Gestión de Información sobre Cáncer de Mama

Diagnosis, treatment and research about such complex diseases as breast cancer is an increasingly complex task due to the big quantity and diversity of involved data and the need of relating them properly to obtain relevant conclusions. Clinical data generation has to be followed by an efficient data management. So, the use of advanced information system technologies is essential to ensure a correct storage, management and exploitation of data. Following a deep study of domain and technologies used to store and manage clinical and biological data about the disease, the main goal of this thesis is to provide a methodological basis to design and implement software systems to manage breast cancer data in a trustable and efficient way. Using Conceptual Modelling techniques in an environment where their use is not as common as it should be, allows to create information systems perfectly adapted to the studied domain. Under this approach, in this thesis some tasks have been carried out among which are conceptual modelling of diagnosis, treatment and research of breast cancer's domain; archetypes' designing under ISO13606 standard to allow systems interoperability; breast cancer data integration from different data sources in a unified database; and designing a prototype of tool for managing and analysing clinical and genic expression data. In order to validate the proposal, a validation process in a real environment as Research Foundation INCLIVA in Valencia has been carried out. During this process, medical and biological researchers have use and assess the efficiency of solution proposed in this doctoral thesis.El diagnóstico, tratamiento e investigación sobre enfermedades tan complejas como el cáncer de mama es una tarea cada vez más complicada por la gran cantidad y diversidad de datos implicados y por la necesidad de relacionarlos adecuadamente para obtener conclusiones relevantes. La generación de los datos clínicos tiene que estar acompañada de una gestión eficiente de los mismos. Ello hace imprescindible la utilización de tecnologías avanzadas de Sistemas de Información que aseguren un correcto almacenamiento, gestión y explotación de los datos. Tras un profundo estudio del dominio y de las tecnologías utilizadas para el almacenamiento y gestión de datos clínicos y biológicos sobre la enfermedad, el objetivo principal de esta tesis es ofrecer una base metodológica que permita diseñar y desarrollar sistemas software para la manipulación eficiente y fiable de la información sobre el cáncer de mama. La utilización de técnicas de Modelado Conceptual en un entorno donde su uso no es tan habitual como debiera ser, permitirá disponer de un sistema de información perfectamente adaptado al dominio de aplicación. Bajo este planteamiento, en esta tesis se ha llevado a cabo el modelado conceptual del dominio del diagnóstico, tratamiento e investigación del cáncer de mama, el diseño de arquetipos bajo el estándar ISO13606 para ofrecer interoperabilidad entre sistemas, la integración de datos de distintos orígenes relacionados con el cáncer de mama en una base de datos unificadora y el diseño de un prototipo de herramienta de gestión y análisis de datos clínicos y de expresión génica. Para validar la idoneidad de esta propuesta, se ha llevado a cabo un proceso de validación en un entorno real como es la Fundación de Investigación INCLIVA de Valencia, donde investigadores clínicos y biólogos han probado y valorado la eficiencia de la solución planteada en esta tesis doctoral.El diagnòstic, tractament i investigació sobre malalties tan complexes com ara el càncer de mama és una tasca cada vegada més complexa per la gran quantitat i diversitat de dades implicades i per la necessitat de relacionar-les adequadament per a obtenir conclusions rellevants. La generació de dades clíniques ha d'estar acompanyada d'una gestió eficient de les mateixes. Açò fa imprescindible la utilització de tecnologies avançades de Sistemes d'Informació que asseguren un correcte emmagatzematge, gestió i explotació de les dades. Després d'un profund estudi del domini i de les tecnologies utilitzades per l'emmagatzematge i gestió de dades clíniques i biològiques sobre la malaltia, el principal objectiu d'aquesta tesi és oferir una base metodològica que permeta dissenyar i desenvolupar sistemes programaris per a la manipulació eficient i fiable de la informació sobre el càncer de mama. La utilització de tècniques de Modelat Conceptual en un entorn on el seu ús no és tan habitual com deuria ser, permetrà disposar d'un sistema d'informació perfectament adaptat al domini d'aplicació. Baix aquest plantejament, en aquesta tesi s'ha dut a terme el modelat conceptual del domini del diagnòstic, tractament i investigació del càncer de mama, el disseny d'arquetips baix l'estàndard ISO13606 per oferir interoperabilitat entre sistemes, la integració de dades de distints orígens sobre el càncer de mama en una base de dades unificadora i el disseny d'un prototip d'eina de gestió i anàlisi de dades clíniques i d'expressió gènica. Per a validar la idoneïtat d'aquesta proposta, s'ha dut a terme un procés de validació en un entorn real com és la Fundació d'Investigació INCLIVA de València, on investigadors clínics i biòlegs han provat i valorat l'eficiència de la solució plantejada en aquesta tesi doctoral.Burriel Coll, V. (2017). Diseño y Desarrollo de un Sistema de Información para la Gestión de Información sobre Cáncer de Mama [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/86158TESI

Natural history of Sanfilippo syndrome in Spain

BACKGROUND: Mucopolysaccharidosis type III (MPS III), or Sanfilippo syndrome, is caused by a deficiency in one of the four enzymes involved in the lysosomal degradation of heparan sulphate. Four MPS III types have been recognized, characterized by a large phenotypic heterogeneity. This is the first Spanish study describing the natural history of Sanfilippo patients (MPSIIIA, MPSIIIB and MPSIIIC), representing an essential step for understanding patient prognosis and for the establishment and application of future therapies. METHODS: This retrospective study aimed to establish the natural history of MPS III in Spain based on an extensive chronological data survey involving physicians and parents of 55 Spanish MPSIII patients. In addition to clinical description we report biochemical and molecular analysis already performed in the majority of cases. RESULTS: The most frequent subtype was MPS IIIA (62%). Symptoms before diagnosis were speech delay in 85%, followed by coarse facial features in 78%, and hyperactivity in 65% of cases at a mean age of 3 years old. The median age at clinical and biochemical diagnosis for each MPS III subtype were as follows: IIIA 4.4 years (1.2 – 16 years), IIIB 3.1 years (1–29 years), and IIIC 6.3 years (3.4-22 years). 45% of patients developed epilepsy at a median age of 8.7 (2.5 – 37) years old. Age of death for MPS IIIA patients was 15 years (11.5 – 26 years). Molecular analysis of our cohort reveals, as alluded to above, a great allelic heterogeneity in the three subtypes without clear genotype-phenotype correlations in most cases. CONCLUSION: MPS IIIA is the most frequent subtype in Spanish Sanfilippo patients. Diagnosing physicians should consider Sanfilippo syndrome in children with non-specific speech delay, behavioural abnormalities, and/or mild dysmorphic features. We stress the importance of establishing early diagnosis procedures as soon as possible so as to be able to determine future short-term enzymatic or gene therapy treatments that can change the prognosis of the disease

In Silico Functional Networks Identified in Fish Nucleated Red Blood Cells by Means of Transcriptomic and Proteomic Profiling

Nucleated red blood cells (RBCs) of fish have, in the last decade, been implicated in several immune-related functions, such as antiviral response, phagocytosis or cytokine-mediated signaling. RNA-sequencing (RNA-seq) and label-free shotgun proteomic analyses were carried out for in silico functional pathway profiling of rainbow trout RBCs. For RNA-seq, a de novo assembly was conducted, in order to create a transcriptome database for RBCs. For proteome profiling, we developed a proteomic method that combined: (a) fractionation into cytosolic and membrane fractions, (b) hemoglobin removal of the cytosolic fraction, (c) protein digestion, and (d) a novel step with pH reversed-phase peptide fractionation and final Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC ESI-MS/MS) analysis of each fraction. Combined transcriptome- and proteome- sequencing data identified, in silico, novel and striking immune functional networks for rainbow trout nucleated RBCs, which are mainly linked to innate and adaptive immunity. Functional pathways related to regulation of hematopoietic cell differentiation, antigen presentation via major histocompatibility complex class II (MHCII), leukocyte differentiation and regulation of leukocyte activation were identified. These preliminary findings further implicate nucleated RBCs in immune function, such as antigen presentation and leukocyte activationThis work was supported by the European Research Council (ERC Starting Grant GA639249The proteomic analyses were performed in the Proteomics Facility of The Spanish National Center for Biotechnology (CNB-CSIC) that belongs to ProteoRed, PRB2-ISCIII, supported by Grant PT13/000

Selection of Trichoderma Strain to Enhanced Cellulase-Poor Xylanase Production Using Sugarcane Bagasse as Sole Carbon Source under Light

Species from fungal genus Trichoderma were found to produce culture broths rich in xylanase activity, an enzyme which plays an essential role for efficient and complete hydrolysis of lignocellulosic biomass. This research aimed to enhance cellulase-poor xylanase production using a low-cost medium. Firstly, several native Trichoderma strains isolated from subtropical environments of Misiones (Argentina) were evaluated based on its xylanase producing potential. Among these, T. atroviride LBM 117 produced the highest cellulase-poor xylanase enzymes, 29 U mL-1 and 28 U mL1 in experiment with and without light, respectively, using sugarcane bagasse as a sole carbon source. Besides, when experiments were carried out with light, the highest xylanase production occurred in shorter incubation period than experiments without it. Xylanase activity was characterized in both supernatants showing the maximum xylanase activity at 50 °C and pH 4.8. Results of electrophoresis on polyacrylamide gels showed two isoenzymes of 105 and 150 KDa in supernatants from experiment with light and only one isoenzyme of 105 KDa from experiment in darkness.Fil: Barchuk, Mónica Lucrecia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas Químicas y Naturales. Departamento de Bioquímica Clínica. Laboratorio de Biotecnología Molecular; ArgentinaFil: Díaz, Gabriela Verónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas Químicas y Naturales. Departamento de Bioquímica Clínica. Laboratorio de Biotecnología Molecular; ArgentinaFil: Coll, Pedro Agustín Francisco. Universidad Nacional de Misiones. Facultad de Ciencias Exactas Químicas y Naturales. Departamento de Bioquímica Clínica. Laboratorio de Biotecnología Molecular; ArgentinaFil: Velázquez, Juan Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas Químicas y Naturales. Departamento de Bioquímica Clínica. Laboratorio de Biotecnología Molecular; ArgentinaFil: Fonseca, Maria Isabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas Químicas y Naturales. Departamento de Bioquímica Clínica. Laboratorio de Biotecnología Molecular; ArgentinaFil: Villalba, Laura. Universidad Nacional de Misiones. Facultad de Ciencias Exactas Químicas y Naturales. Departamento de Bioquímica Clínica. Laboratorio de Biotecnología Molecular; ArgentinaFil: Zapata, Pedro Dario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste; Argentina. Universidad Nacional de Misiones. Facultad de Ciencias Exactas Químicas y Naturales. Departamento de Bioquímica Clínica. Laboratorio de Biotecnología Molecular; Argentin

Rainbow Trout Erythrocytes ex vivo Transfection With a DNA Vaccine Encoding VHSV Glycoprotein G Induces an Antiviral Immune Response

Fish red blood cells (RBCs), are integral in several biologic processes relevant to immunity, such as pathogen recognition, pathogen binding and clearance, and production of effector molecules and cytokines. So far, one of the best strategies to control and prevent viral diseases in aquaculture is DNA immunization. DNA vaccines (based on the rhabdoviral glycoprotein G [gpG] gene) have been shown to be effective against fish rhabdoviruses. However, more knowledge about the immune response triggered by DNA immunization is necessary to develop novel and more effective strategies. In this study, we investigated the role of fish RBCs in immune responses induced by DNA vaccines. We show for the first time that rainbow trout RBCs express gpG of viral hemorrhagic septicaemia virus (VHSV) (GVHSV) when transfected with the DNA vaccine ex vivo and modulate the expression of immune genes and proteins. Functional network analysis of transcriptome profiling of RBCs expressing GVHSV revealed changes in gene expression related to G-protein coupled receptor (GPCR)-downstream signaling, complement activation, and RAR related orphan receptor a (RORA). Proteomic profile functional network analysis of GVHSV-transfected RBCs revealed proteins involved in the detoxification of reactive oxygen species, interferon-stimulated gene 15 (ISG15) antiviral mechanisms, antigen presentation of exogenous peptides, and the proteasome. Conditioned medium of GVHSV-transfected RBCs conferred antiviral protection and induced ifn1 and mx gene expression in RTG-2 cells infected with VHSV. In summary, rainbow trout nucleated RBCs could be actively participating in the regulation of the fish immune response to GVHSV DNA vaccine, and thus may represent a possible carrier cells for the development of new vaccine approaches.This work was supported by the European Research Council (ERC Starting Grant GA639249)The proteomic analysis was performed in the Proteomics Facility of The Spanish National Center for Biotechnology (CNB-CSIC) belonging to ProteoRed, PRB3-ISCIII, supported by grant PT17/0019This work was supported by the European Research Council (ERC Starting Grant GA639249).The proteomic analysis was performed in the Proteomics Facility of The Spanish National Center for Biotechnology (CNB-CSIC) of ProteoRed, PRB3- ISCIII, supported by grant PT17/001

Potential Role of Rainbow Trout Erythrocytes as Mediators in the Immune Response Induced by a DNA Vaccine in Fish

In recent years, fish nucleated red blood cells (RBCs) have been implicated in the response against viral infections. We have demonstrated that rainbow trout RBCs can express the antigen encoded by a DNA vaccine against viral hemorrhagic septicemia virus (VHSV) and mount an immune response to the antigen in vitro. In this manuscript, we show, for the first time, the role of RBCs in the immune response triggered by DNA immunization of rainbow trout with glycoprotein G of VHSV (GVHSV). Transcriptomic and proteomic profiles of RBCs revealed genes and proteins involved in antigen processing and presentation of exogenous peptide antigen via MHC class I, the Fc receptor signaling pathway, the autophagy pathway, and the activation of the innate immune response, among others. On the other hand, GVHSV-transfected RBCs induce specific antibodies against VHSV in the serum of rainbow trout which shows that RBCs expressing a DNA vaccine are able to elicit a humoral response. These results open a new direction in the research of vaccination strategies for fish since rainbow trout RBCs actively participate in the innate and adaptive immune response in DNA vaccination. Based on our findings, we suggest the use of RBCs as target cells or carriers for the future design of novel vaccine strategiesThis research was funded by the European Research Council, grant number GA639249 (ERC Starting Grant)We would like to thank The Spanish National Center for Biotechnology (CNB-CSIC) of ProteoRed, PRB3-ISCIII for the proteomic analysis supported by grant PT17/001

Infectious pancreatic necrosis virus triggers antiviral immune response in rainbow trout red blood cells, despite not being infective [version 2; referees: 2 approved]

Background: Some fish viruses, such as piscine orthoreovirus and infectious salmon anemia virus, target red blood cells (RBCs), replicate inside them and induce an immune response. However, the roles of RBCs in the context of infectious pancreatic necrosis virus (IPNV) infection have not been studied yet. Methods: Ex vivo rainbow trout RBCs were obtained from peripheral blood, Ficoll purified and exposed to IPNV in order to analyze infectivity and immune response using RT-qPCR, immune fluorescence imaging, flow cytometry and western-blotting techniques. Results: IPNV could not infect RBCs; however, IPNV increased the expression of the INF1-related genes ifn-1, pkr and mx genes. Moreover, conditioned media from IPNV-exposed RBCs conferred protection against IPNV infection in CHSE-214 fish cell line. Conclusions: Despite not being infected, rainbow trout RBCs could respond to IPNV with increased expression of antiviral genes. Fish RBCs could be considered as mediators of the antiviral response and therefore targets of new strategies against fish viral infections. Further research is ongoing to completely understand the molecular mechanism that triggers this antiviral response in rainbow trout RBCs.This work was supported by the European Research Council (ERC starting grant 2014 GA639249

CD200 is up-regulated in R6/1 transgenic mouse model of Huntington's disease

In Huntington's disease (HD), striatal medium spiny neurons (MSNs) are particularly sensitive to the presence of a CAG repeat in the huntingtin (HTT) gene. However, there are many evidences that cells from the peripheral immune system and central nervous system (CNS) immune cells, namely microglia, play an important role in the etiology and the progression of HD. However, it remains unclear whether MSNs neurodegeneration is mediated by a non-cell autonomous mechanism. The homeostasis in the healthy CNS is maintained by several mechanisms of interaction between all brain cells. Neurons can control microglia activation through several inhibitory mechanisms, such as the CD200-CD200R1 interaction. Due to the complete lack of knowledge about the CD200-CD200R1 system in HD, we determined the temporal patterns of CD200 and CD200R1 expression in the neocortex, hippocampus and striatum in the HD mouse models R6/1 and HdhQ111/7 from pre-symptomatic to manifest stages. In order to explore any alteration in the peripheral immune system, we also studied the levels of expression of CD200 and CD200R1 in whole blood. Although CD200R1 expression was not altered, we observed and increase in CD200 gene expression and protein levels in the brain parenchyma of all the regions we examined, along with HD pathogenesis in R6/1 mice. Interestingly, the expression of CD200 mRNA was also up-regulated in blood following a similar temporal pattern. These results suggest that canonical neuronal-microglial communication through CD200-CD200R1 interaction is not compromised, and CD200 up-regulation in R6/1 brain parenchyma could represent a neurotrophic signal to sustain or extend neuronal function in the latest stages of HD as pro-survival mechanism

Differential Uptake of Endosulfan in the South American Toad Under Sublethal Exposure

Agroecosystems are usually polluted with a wide variety of contaminants with pesticides being very frequently detected. Endosulfan, an organochlorine pesticide, has been shown to cause both lethal and sublethal effects on aquatic organisms such as amphibians and especially on its early developmental stages. In this context, the aim of this study was to evaluate the uptake of environmentally relevant concentrations of endosulfan and its correlation with differential sensitivity in the early development stages of the common South American toad, Rhinella arenarum. Embryos and larvae were exposed to sublethal concentrations of endosulfan for several periods of exposures. According to the developmental stage at which they were exposed, the uptake rate was different. Bioconcentration factors (BCFs) for embryos significantly decreased with exposure time and concentration (p < 0.05) reaching a BCF of ≤1679 for embryos at 96 h of exposure to 0.001 mg endosulfan L⁻¹. BCFs for larvae significantly increased with exposure time (p < 0.05) obtaining a maximum of 40 at 504 h. In our previous study, we reported that embryos were less sensitive to the effects of endosulfan than larvae, which is in line with the main tendency of embryos to bioconcentrate endosulfan as observed in this study.Facultad de Ciencias ExactasCentro de Investigaciones del Medioambient

La identidad cultural y el ecoturismo bajo un enfoque de género:: la comunidad nativa Ese’ Eja de Infierno, Madre de Dios, Perú

La comunidad nativa Ese’ Eja de Infierno y su alianza con la empresa privada ha significado una intervención de un turismo sostenible en comunidad. A lo largo de veinte años se ha tejido una relación entre esta comunidad y Rainforest, que ha permitido el desarrollo del ecoturismo en la zona. A partir del covid-19 y el confinamiento, nuevas amenazas tomaron la comunidad y debilitaron su gestión en el proyecto de ecoturismo Posada Amazonas. El presente artículo propone un avance sobre el proyecto de investigación que aborda identidad cultural, género y ecoturismo en la comunidad nativa de Infierno bajo un enfoque de género. El artículo que presentamos es un primer resultado de una investigación interdisciplinaria situada en los estudios de culturales, la psicología y biología con entrevistas a líderes mujeres de la comunidad nativa Infierno y líderes de la comunidad Palma Real, utilizando el método participativo en talleres a jóvenes adolescentes y niñas y niños. El estudio evidencia la participación de la comunidad en el desarrollo del ecoturismo, la participación de mujeres líderes en el desarrollo de la comunidad, así como una preocupación por la pérdida de la lengua ese’ eja por parte de jóvenes y adolescentes. Al mismo tiempo, plantea cómo el acercamiento de la comunidad Palma Real a Infierno podría ser clave para el desarrollo del ecoturismo y el rescate de la lengua ese’ eja.The Ese’ Eja Infierno Native community and the alliance with the private company has meant a sustainable tourism intervention in their community. Over the course of twenty years, a relationship has been woven between the Ese’ Eja Native community and the private Rainforest company that has allowed the development of ecotourism in the area. Since COVID 19 and the confinement, new threats have taken over the community and weakened its management of the «Posada Amazonas» ecotourism project. The following article proposes an advance on the research project that addresses cultural identity, gender and ecotourism in the native community of Infierno from a gender perspective. This article is the first result of an interdisciplinary research project based on cultural studies, psychology and biology, with interviews with women leaders of the native community of Infierno and leaders of the community of Palma Real, using the participatory method in workshops with young adolescents and children. The study shows the participation of the community in the development of ecotourism, the participation of women leaders in the development of the community, as well as a concern about the loss of cultural identity on the part of young people and adolescents. At the same time, it suggests how bringing the Palma Real community closer to Infierno could be key to the development of ecotourism and the rescue of the Ese’ Eja language