Propuesta didáctica de enseñanza con simulaciones para estudiantes del profesorado en Ciencias Biológicas

The aim of this study was to develop a didactic proposal for teaching with simulations (DPTS) and analyze the conditions and didactic moments that accompany its implementation for students of the professorate in Biological Sciences. Thus, it is intended to facilitate the learning of disciplinary content and its didactics, and the acquisition of autonomy in the use of technological resources by future professors. The Forensic EA Lite simulation, a software designed for addressing contents of molecular evolution, was used. Molecular evolution is one of the program units of the subject “Molecular Genetics” in which this proposal was carried out. DPTS was designed, implemented, adjusted through practice and finally resulted in the following didactic moments: presentation, program exploration and appropriation of specific vocabulary, articulation between simulation and disciplinary content, correlation activities, time for metacognition and time for content transfer (enforcement activities). Difficulties and benefits of the proposal for learning the subject, acquisition of autonomy with the technological resource and contributions for teacher training were evaluated. The development and adjustment of the proposal were focused on both didactic decisions made by the teacher to design and put into practice a didactic sequence of the simulation used and on the learning demands of students, in a process of continuous feedback. The proposal facilitated learning of the molecular basis of evolution, made the students exercise autonomy when using technological resources, and provided a form of didactic intervention to teach with simulations in theoretical constructivist frameworks for the practice teachers in training in biology.El objetivo del presente trabajo consistió en desarrollar una propuesta didáctica para la enseñanza con simulaciones (PDES) y analizar las condiciones y momentos didácticos que acompañan su implementación con estudiantes del profesorado en Ciencias Biológicas. De esta forma, se pretende favorecer el aprendizaje del contenido disciplinar y de su didáctica, así como la adquisición de autonomía en el uso del recurso tecnológico de los futuros profesores. Se utilizó la simulación Forensic EA Lite, software diseñado para el abordaje de contenidos de evolución molecular, una de las unidades del programa de la asignatura Genética Molecular en la que se puso en práctica la PDES. La PDES se diseñó, se implementó, se fue ajustando desde la práctica y resultó, finalmente, en los siguientes momentos didácticos: presentación, exploración del programa y apropiación del vocabulario específico, articulación entre la simulación y el contenido disciplinar, actividades de correlación, momento de metacognición y momento de transferencia de contenido (actividades de aplicación). Se evaluaron las dificultades y los beneficios de la propuesta para el aprendizaje del tema, la adquisición de autonomía con el recurso tecnológico y los aportes para la formación docente. La elaboración y ajuste de la PDES se focalizó tanto en las decisiones didácticas tomadas por el docente para el diseño y puesta en el aula de una propuesta didáctica con la simulación utilizada, como en las demandas de los estudiantes, en un proceso de permanente retroalimentación. La PDES resultó facilitadora del aprendizaje de las bases moleculares de la evolución, logró generar autonomía en los estudiantes para la utilización del recurso tecnológico y aportó una forma de intervención didáctica de enseñanza con simulaciones en marcos teóricos constructivistas para la práctica de los docentes de biología en formación.Palabras clave: propuesta didáctica; simulaciones; evolución molecular; profesorado; TICDidactic proposal for teaching with simulations for students of professorate in Biological SciencesThe aim of this study was to develop a didactic proposal for teaching with simulations (DPTS) and analyze the conditions and didactic moments that accompany its implementation for students of the professorate in Biological Sciences. Thus, it is intended to facilitate the learning of disciplinary content and its didactics, and the acquisition of autonomy in the use of technological resources by future professors. The Forensic EA Lite simulation, a software designed for addressing contents of molecular evolution, was used. Molecular evolution is one of the program units of the subject “Molecular Genetics” in which this proposal was carried out. DPTS was designed, implemented, adjusted through practice and finally resulted in the following didactic moments: presentation, program exploration and appropriation of specific vocabulary, articulation between simulation and disciplinary content, correlation activities, time for metacognition and time for content transfer (enforcement activities). Difficulties and benefits of the proposal for learning the subject, acquisition of autonomy with the technological resource and contributions for teacher training were evaluated. The development and adjustment of the proposal were focused on both didactic decisions made by the teacher to design and put into practice a didactic sequence of the simulation used and on the learning demands of students, in a process of continuous feedback. The proposal facilitated learning of the molecular basis of evolution, made the students exercise autonomy when using technological resources, and provided a form of didactic intervention to teach with simulations in theoretical constructivist frameworks for the practice teachers in training in biology.Key words: didactic proposal; simulations; molecular evolution; professorate; IC

Didactic proposal for teaching with simulations for students of professorate in Biological Sciences

El objetivo del presente trabajo consistió en desarrollar una propuesta didáctica para la enseñanza con simulaciones (PDES) y analizar las condiciones y momentos didácticos que acompañan su implementación con estudiantes del profesorado en Ciencias Biológicas. De esta forma, se pretende favorecer el aprendizaje del contenido disciplinar y de su didáctica, así como la adquisición de autonomía en el uso del recurso tecnológico de los futuros profesores. Se utilizó la simulación Forensic EA Lite, software diseñado para el abordaje de contenidos de evolución molecular, una de las unidades del programa de la asignatura Genética Molecular en la que se puso en práctica la PDES. La PDES se diseñó, se implementó, se fue ajustando desde la práctica y resultó, finalmente, en los siguientes momentos didácticos: presentación, exploración del programa y apropiación del vocabulario específico, articulación entre la simulación y el contenido disciplinar, actividades de correlación, momento de metacognición y momento de transferencia de contenido (actividades de aplicación). Se evaluaron las dificultades y los beneficios de la propuesta para el aprendizaje del tema, la adquisición de autonomía con el recurso tecnológico y los aportes para la formación docente. La elaboración y ajuste de la PDES se focalizó tanto en las decisiones didácticas tomadas por el docente para el diseño y puesta en el aula de una propuesta didáctica con la simulación utilizada, como en las demandas de los estudiantes, en un proceso de permanente retroalimentación. La PDES resultó facilitadora del aprendizaje de las bases moleculares de la evolución, logró generar autonomía en los estudiantes para la utilización del recurso tecnológico y aportó una forma de intervención didáctica de enseñanza con simulaciones en marcos teóricos constructivistas para la práctica de los docentes de biología en formación.The aim of this study was to develop a didactic proposal for teaching with simulations (DPTS) and analyze the conditions and didactic moments that accompany its implementation for students of the professorate in Biological Sciences. Thus, it is intended to facilitate the learning of disciplinary content and its didactics, and the acquisition of autonomy in the use of technological resources by future professors. The Forensic EA Lite simulation, a software designed for addressing contents of molecular evolution, was used. Molecular evolution is one of the program units of the subject “Molecular Genetics” in which this proposal was carried out. DPTS was designed, implemented, adjusted through practice and finally resulted in the following didactic moments: presentation, program exploration and appropriation of specific vocabulary, articulation between simulation and disciplinary content, correlation activities, time for metacognition and time for content transfer (enforcement activities). Difficulties and benefits of the proposal for learning the subject, acquisition of autonomy with the technological resource and contributions for teacher training were evaluated. The development and adjustment of the proposal were focused on both didactic decisions made by the teacher to design and put into practice a didactic sequence of the simulation used and on the learning demands of students, in a process of continuous feedback. The proposal facilitated learning of the molecular basis of evolution, made the students exercise autonomy when using technological resources, and provided a form of didactic intervention to teach with simulations in theoretical constructivist frameworks for the practice teachers in training in biology

A disordered region retains the full protease inhibitor activity and the capacity to induce CD8+ T cells in vivo of the oral vaccine adjuvant U-Omp19

U-Omp19 is a bacterial protease inhibitor from Brucella abortus that inhibits gastrointestinal and lysosomal proteases, enhancing the half-life and immunogenicity of co-delivered antigens. U-Omp19 is a novel adjuvant that is in preclinical development with various vaccine candidates. However, the molecular mechanisms by which it exerts these functions and the structural elements responsible for these activities remain unknown. In this work, a structural, biochemical, and functional characterization of U-Omp19 is presented. Dynamic features of U-Omp19 in solution by NMR and the crystal structure of its C-terminal domain are described. The protein consists of a compact C-terminal beta-barrel domain and a flexible N-terminal domain. The latter domain behaves as an intrinsically disordered protein and retains the full protease inhibitor activity against pancreatic elastase, papain and pepsin. This domain also retains the capacity to induce CD8+ T cells in vivo of U-Omp19. This information may lead to future rationale vaccine designs using U-Omp19 as an adjuvant to deliver other proteins or peptides in oral formulations against infectious diseases, as well as to design strategies to incorporate modifications in its structure that may improve its adjuvanticity.Fil: Darriba, María Laura. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Pueblas Castro, Celeste. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Coria, Lorena M. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Bruno, Laura. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Cerutti, María Laura. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Chemes, Lucía B. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Cassataro, Juliana. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Pasquevich, Karina A. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Darriba, María Laura. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Pueblas Castro, Celeste. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Coria, Lorena M. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Bruno, Laura. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Cerutti, María Laura. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Chemes, Lucía B. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Cassataro, Juliana. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Pasquevich, Karina A. Universidad Nacional de San Martín. Escuela de Bio y Nanotecnologías (EByN); Argentina.Fil: Otero, Lisandro H. Fundación Instituto Leloir. Plataforma Argentina de Biología Estructural y Metabolómica. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Klinke, Sebastián. Fundación Instituto Leloir. Plataforma Argentina de Biología Estructural y Metabolómica. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Rasia, Rodolfo M. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario. Plataforma Argentina de Biología Estructural y Metabolómica; Argentina

DisProt: intrinsic protein disorder annotation in 2020

The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the ‘dark’ proteome

Critical assessment of protein intrinsic disorder prediction

Abstract: Intrinsically disordered proteins, defying the traditional protein structure–function paradigm, are a challenge to study experimentally. Because a large part of our knowledge rests on computational predictions, it is crucial that their accuracy is high. The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was established as a community-based blind test to determine the state of the art in prediction of intrinsically disordered regions and the subset of residues involved in binding. A total of 43 methods were evaluated on a dataset of 646 proteins from DisProt. The best methods use deep learning techniques and notably outperform physicochemical methods. The top disorder predictor has Fmax = 0.483 on the full dataset and Fmax = 0.792 following filtering out of bona fide structured regions. Disordered binding regions remain hard to predict, with Fmax = 0.231. Interestingly, computing times among methods can vary by up to four orders of magnitude

A Thermodynamic Analysis of the Binding Specificity between Four Human PDZ Domains and Eight Host, Viral and Designed Ligands

PDZ domains are binding modules mostly involved in cell signaling and cell–cell junctions. These domains are able to recognize a wide variety of natural targets and, among the PDZ partners, viruses have been discovered to interact with their host via a PDZ domain. With such an array of relevant and diverse interactions, PDZ binding specificity has been thoroughly studied and a traditional classification has grouped PDZ domains in three major specificity classes. In this work, we have selected four human PDZ domains covering the three canonical specificity-class binding mode and a set of their corresponding binders, including host/natural, viral and designed PDZ motifs. Through calorimetric techniques, we have covered the entire cross interactions between the selected PDZ domains and partners. The results indicate a rather basic specificity in each PDZ domain, with two of the domains that bind their cognate and some non-cognate ligands and the two other domains that basically bind their cognate partners. On the other hand, the host partners mostly bind their corresponding PDZ domain and, interestingly, the viral ligands are able to bind most of the studied PDZ domains, even those not previously described. Some viruses may have evolved to use of the ability of the PDZ fold to bind multiple targets, with resulting affinities for the virus–host interactions that are, in some cases, higher than for host–host interactions.Andalusian Regional Government, grant number CVI-5915ANPCyT, grant numbers PICT 2012-2550 and PICT 2015-1213CONICE

Intrinsically Disordered Linkers Impart Processivity on Enzymes by Spatial Confinement of Binding Domains

(1) Background: Processivity is common among enzymes and mechanochemical motors that synthesize, degrade, modify or move along polymeric substrates, such as DNA, RNA, polysaccharides or proteins. Processive enzymes can make multiple rounds of modification without releasing the substrate/partner, making their operation extremely effective and economical. The molecular mechanism of processivity is rather well understood in cases when the enzyme structurally confines the substrate, such as the DNA replication factor PCNA, and also when ATP energy is used to confine the succession of molecular events, such as with mechanochemical motors. Processivity may also result from the kinetic bias of binding imposed by spatial confinement of two binding elements connected by an intrinsically disordered (ID) linker. (2) Method: By statistical physical modeling, we show that this arrangement results in processive systems, in which the linker ensures an optimized effective concentration around novel binding site(s), favoring rebinding over full release of the polymeric partner. (3) Results: By analyzing 12 such proteins, such as cellulase, and RNAse-H, we illustrate that in these proteins linker length and flexibility, and the kinetic parameters of binding elements, are fine-tuned for optimizing processivity. We also report a conservation of structural disorder, special amino acid composition of linkers, and the correlation of their length with step size. (4) Conclusion: These observations suggest a unique type of entropic chain function of ID proteins, that may impart functional advantages on diverse enzymes in a variety of biological contexts

Sequence Evolution of the Intrinsically Disordered and Globular Domains of a Model Viral Oncoprotein

<div><p>In the present work, we have used the papillomavirus E7 oncoprotein to pursue structure-function and evolutionary studies that take into account intrinsic disorder and the conformational diversity of globular domains. The intrinsically disordered (E7N) and globular (E7C) domains of E7 show similar degrees of conservation and co-evolution. We found that E7N can be described in terms of conserved and coevolving linear motifs separated by variable linkers, while sequence evolution of E7C is compatible with the known homodimeric structure yet suggests other activities for the domain. Within E7N, inter-residue relationships such as residue co-evolution and restricted intermotif distances map functional coupling and co-occurrence of linear motifs that evolve in a coordinate manner. Within E7C, additional cysteine residues proximal to the zinc-binding site may allow redox regulation of E7 function. Moreover, we describe a conserved binding site for disordered domains on the surface of E7C and suggest a putative target linear motif. Both homodimerization and peptide binding activities of E7C are also present in the distantly related host PHD domains, showing that these two proteins share not only structural homology but also functional similarities, and strengthening the view that they evolved from a common ancestor. Finally, we integrate the multiple activities and conformations of E7 into a hierarchy of structure-function relationships.</p> </div