Shaping RNA Structures with Metal Ions and Metal Ion Complexes

The research in our laboratory focuses on the role of metal ions and their complexes in structure formation and folding of nucleic acids. Large catalytic RNAs, like group II introns and some riboswitches, as well as shorter RNAs and DNAs containing modified nucleotides for the assembly of nanodevices are examined. Abundant metal ions like Mg2+ or natural metabolites like coenzyme B12 are in the center of interest, but also other metal ions, complexes thereof and B12 derivatives are applied with the aim to understand the largely unknown and manifold non-covalent interactions with nucleic acids. We apply a multitude of techniques, including potentiometric pH titrations, NMR spectroscopy, X-ray crystallography, gel electrophoresis and single molecule FRET experiments. Here we briefly summarize each of our research topics emphasizing the interaction of coenzyme B12 and its derivatives with the btuB riboswitch of E. coli. This highly conserved sequence, found in the 5'-untranslated region (5'-UTR) of the btuB mRNA, is involved in the regulation of the btuB protein expression. After a summary on the historical discovery of such riboswitches and their mechanism of action, we shortly focus on our own contributions to understand the structural equilibrium, high affinity and selectivity of the interaction between this specific RNA sequence and the largest and most complex cellular metabolite, coenzyme B12

Exposure to polychlorinated biphenyls and hexachlorobenzene, semen quality and testicular cancer risk

PURPOSE: We carried out a case-control study to investigate the possible role of occupational and environmental exposure to endocrine disruptors in the onset of testicular cancer (TC). METHODS: We evaluated 125 TC patients and 103 controls. Seminal fluid examination and organochlorine analysis were performed in all subjects. Cases and controls were also interviewed using a structured questionnaire to collect demographic information, residence, andrological medical history and dietary information. RESULTS: We found that a higher level of reproductive tract birth defects was associated with a higher risk of TC. With regard to diet, cases reported a higher consumption of milk and dairy products than controls. Overall, there was a statistically significant increase in TC risk in cases with detectable values of total polychlorinated organic compounds against controls (14.4 vs. 1.0 %; p < 0.001). TC patients with detectable levels of organochlorines had lower mean semen parameters than those with undetectable levels, although this difference was not statistically significant. CONCLUSION: The International Agency for Research on Cancer recently included dioxin-like polychlorinated biphenyls (PCBs) in Group 1 of known human carcinogens. Our study confirmed and identified various risk factors for testicular cancer: cryptorchidism, consumption of milk and dairy products, parents' occupation and serum concentration of hexachlorobenzene and PCBs and, for the first time, we showed the correlation between semen quality and the serum concentration of these pollutants

Tb3+-Cleavage Assays Reveal Specific Mg2+ Binding Sites Necessary to Pre-fold the btuB Riboswitch for AdoCbl Binding

Riboswitches are RNA elements that bind specific metabolites in order to regulate the gene expression involved in controlling the cellular concentration of the respective molecule or ion. Ligand recognition is mostly facilitated by Mg2+ mediated pre-organization of the riboswitch to an active tertiary fold. To predict these specific Mg2+ induced tertiary interactions of the btuB riboswitch from E. coli, we here report Mg2+ binding pockets in its aptameric part in both, the ligand-free and the ligand-bound form. An ensemble of weak and strong metal ion binding sites distributed over the entire aptamer was detected by terbium(III) cleavage assays, Tb3+ being an established Mg2+ mimic. Interestingly many of the Mn+ (n = 2 or 3) binding sites involve conserved bases within the class of coenzyme B12-binding riboswitches. Comparison with the published crystal structure of the coenzyme B12 riboswitch of S. thermophilum aided in identifying a common set of Mn+ binding sites that might be crucial for tertiary interactions involved in the organization of the aptamer. Our results suggest that Mn+ binding at strategic locations of the btuB riboswitch indeed facilitates the assembly of the binding pocket needed for ligand recognition. Binding of the specific ligand, coenzyme B12 (AdoCbl), to the btuB aptamer does however not lead to drastic alterations of these Mn+ binding cores, indicating the lack of a major rearrangement within the three-dimensional structure of the RNA. This finding is strengthened by Tb3+ mediated footprints of the riboswitch's structure in its ligand-free and ligand-bound state indicating that AdoCbl indeed induces local changes rather than a global structural rearrangement

Diplomado de profundización cisco Prueba de habilidades prácticas CCNP

Este documento contiene la prueba habilidades del curso, DIPLOMADO DE PROFUNDIZACION CISCO CCNP, el cual consta de 6 partes las cuales se dividen en dos escenarios y se realizan en dos entregas. El primer escenario propone, la configuración de una red en la cual se realiza un enrutamiento, con el objetivo de comunicar un extremo con el otro, que los protocolos implementados sean operativos dentro de la red de la compañía, por medio de dispositivos CISCO especializados en la conmutación y enrutamiento de paquetes. El segundo escenario comprende la parte de autenticación, listas de control de acceso (ACL), HSRP versión 2 para brindar redundancia a los hosts, configuración de mecanismos de seguridad para las redes y sus dispositivos, configuración de horario en los hosts, etc.This document contains the skills test of the course, CISCO CCNP DEEPENING DIPLOMA, which consists of 6 parts which are divided into two scenarios and are carried out in two deliveries. The first scenario proposes, the configuration of a network in which a routing is carried out, in order to communicate one end with the other, that the implemented protocols are operative within the company network, by means of CISCO devices specialized in packet switching and routing. The second scenario comprises the authentication part, access control lists (ACLs), HSRP version 2 to provide redundancy to the hosts, configuration of security mechanisms for the networks and their devices, configuration of the schedule in the hosts, etc

The structural features of the ligand-free moaA riboswitch and its ion-dependent folding

Riboswitches are structural elements of mRNA involved in the regulation of gene expression by responding to specific cellular metabolites. To fulfil their regulatory function, riboswitches prefold into an active state, the so-called binding competent form, that guarantees metabolite binding and allows a consecutive refolding of the RNA. Here, we describe the folding pathway to the binding competent form as well as the ligand free structure of the moaA riboswitch of E. coli. This RNA proposedly responds to the molybdenum cofactor (Moco), a highly oxygen-sensitive metabolite, essential in the carbon and sulfur cycles of eukaryotes. K+- and Mg2+-dependent footprinting assays and spectroscopic investigations show a high degree of structure formation of this RNA already at very low ion-concentrations. Mg2+ facilitates additionally a general compaction of the riboswitch towards its proposed active structure. We show that this fold agrees with the earlier suggested secondary structure which included also a long-range tetraloop/tetraloop-receptor like interaction. Metal ion cleavage assays revealed specific Mg2+-binding pockets within the moaA riboswitch. These Mg2+ binding pockets are good indicators for the potential Moco binding site, since in riboswitches, Mg2+ was shown to be necessary to bind phosphate-carrying metabolites. The importance of the phosphate and of other functional groups of Moco is highlighted by binding assays with tetrahydrobiopterin, the reduced and oxygen-sensitive core moiety of Moco. We demonstrate that the general molecular shape of pterin by its own is insufficient for the recognition by the riboswitch

Inter- and intracontinental migrations and local differentiation have shaped the contemporary epidemiological landscape of canine parvovirus in South America

Canine parvovirus (CPV) is a fast-evolving single-stranded DNA virus that causes one of the most significant infectious diseasesof dogs. Although the virus dispersed over long distances in the past, current populations are considered to be spatiallyconfined and with only a few instances of migration between specific localities. It is unclear whether these dynamicsoccur in South America where global studies have not been performed. The aim of this study is to analyze the patterns ofgenetic variability in South American CPV populations and explore their evolutionary relationships with global strains.Genomic sequences of sixty-three strains from South America and Europe were generated and analyzed using a phylodynamicapproach. All the obtained strains belong to the CPV-2a lineage and associate with global strains in four monophyleticgroups or clades. European and South American strains from all the countries here analyzed are representative of awidely distributed clade (Eur-I) that emerged in Southern Europe during 1990?98 to later spread to South America in theearly 2000s. The emergence and spread of the Eur-I clade were correlated with a significant rise in the CPV effective populationsize in Europe and South America. The Asia-I clade includes strains from Asia and Uruguay. This clade originated in Asia during the late 1980s and evolved locally before spreading to South America during 2009?10. The third clade (Eur-II)comprises strains from Italy, Brazil, and Ecuador. This clade appears in South America as a consequence of an early introductionfrom Italy to Ecuador in the middle 1980s and has experienced extensive local genetic differentiation. Some strainsfrom Argentina, Uruguay, and Brazil constitute an exclusive South American clade (SA-I) that emerged in Argentina in the1990s. These results indicate that the current epidemiological scenario is a consequence of inter- and intracontinentalmigrations of strains with different geographic and temporal origins that set the conditions for competition and local differentiationof CPV populations. The coexistence and interaction of highly divergent strains are the main responsible for thedrastic epidemiological changes observed in South America in the last two decades. This highlights the threat of invasionfrom external sources and the importance of whole-genome resolution to robustly infer the origin and spread of new CPVvariants. From a taxonomic standpoint, the findings herein show that the classification system that uses a single aminoacid to identify variants (2a, 2b, and 2c) within the CPV-2a lineage does not reflect phylogenetic relationships and is not suitableto analyze CPV evolution. In this regard, the identification of clades or sublineages within circulating CPV strains is thefirst step towards a genetic and evolutionary classification of the virus.Fil: Grecco, Sofia. Universidad de la República; UruguayFil: Iraola, Gregorio. Universidad de la República; UruguayFil: Decaro, Nicola. Università degli Studi di Bari; ItaliaFil: Alfieri, Alice. Universidade Estadual de Londrina; BrasilFil: Alfieri, Amauri. Universidade Estadual de Londrina; BrasilFil: Gallo Calderon, Marina Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ciencia y Tecnología "Dr. César Milstein". Fundación Pablo Cassará. Instituto de Ciencia y Tecnología "Dr. César Milstein"; ArgentinaFil: da Silva, Ana Paula. Universidade Estadual de Londrina; BrasilFil: Name, Daniela. Universidad de la República. Facultad de Ciencias; UruguayFil: Aldaz, Jaime. Universidad Estatal de Bolivar; EcuadorFil: Calleros, Lucia. Universidad de la República. Facultad de Ciencias; UruguayFil: Marandino, Ana. Universidad de la República. Facultad de Ciencias; UruguayFil: Gonzalo, Tomas. Universidad de la República. Facultad de Ciencias; Urugua

Como afecta las relaciones familiares la llegada de un Niño(a) con discapacidad

En esta investigación titulada “Cómo Afecta la Relaciones Familiares la Llegada de un Niño con Discapacidad” se observa, analiza e interpreta como es el desenvolvimiento, la interacción y en general las relaciones dentro de la familia que convive con un niño que presenta alguna discapacidad. Se observa y analiza cómo la familia afronta la nueva circunstancia desde el nacimiento de un niño con estas característica, o de la aparición intempestiva, cuando se trata de algún accidente y la manera progresiva de como lo va asimilando. La investigación se adelanta teniendo en cuenta los parámetros del construccionismo y la psicología social con una metodología eminentemente cualitativa. Por lo tanto aparte de los factores psicológicos o subjetivos propiamente dichos que se tienen en cuenta como elementos de primer orden, también se toman otras variables como el factor étnico, socioeconómico, cultural; biopsicológico (costumbres y hábitos) que permiten una visión integral y elementos de juicio más contundentes, para el análisis y enriquecimiento de la investigación. Se observa y analiza cómo las familias reestructuran sus estilos de vida, sus valores, sus prioridades, su desempeño laboral. También se identifican los comportamientos más comunes, las actitudes y la afectación psicológica de la familia frente a la situación del niño con discapacidad. A partir del trabajo de campo de entrevistas semiestructuradas y fragmentos de historias de vida, se construyen todos los elementos de juicio, que permiten un análisis y una interpretación lo más objetiva posible. Se pretende en este análisis y desde la psicología social generar alternativas de comportamiento, adaptación y asimilación de la problemática que conlleve una mejor calidad de vida, tanto para la familia como para el niño discapacitado. Se procuró que los protagonistas pertenecieran a estratos diferentes y con variadas clases de discapacidades en sus familiares, con el propósito de evaluar más ampliamente el objeto de investigación y evitar sesgos por estrato social o tipos particulares de discapacidad.In this titled investigation “How it Affects the Family Relationships the Arrival of a boy with Discapacidad” it i observed, it analyzes and he/she interprets like it i the development, the interaction and in general the relationships inside the family that he/she cohabits with to boy that presents some discapacidad. It is observed and it analyzes how the family confronts the new circumstance from the birth of a boy with these characteristic, or of the inopportune appearance, when it is some accident and the progressive way of as he/she goes him assimilating. The investigation is ahead keeping in mind the parameters of the construccionismo and the social psychology with an eminently qualitative methodology. Therefore apart from the properly this psychological or subjective factors that are kept in mind as elements of first order, they take also other variables as the ethnic, socioeconomic, cultural factor; biopsicológico (customs and habits) that allow an integral vision and more overwhelming trial elements, for the analysis and enrichment of the investigation. It is observed and it analyzes how the families restructure their lifestyles, their securities, their priorities, their labor acting. The behaviors more comunes, the attitudes and the psychological affectation of the family are also identified in front of the boy's situation with discapacidad. Starting from the work of field of interviews semiestructuradas and fragments of histories of life, all the trial elements are built that allow an analysis and an interpretation the most objective thing possible. It is sought in this analysis and from the social psychology to generate alternative of behavior, adaptation and assimilation of the problem that bears a better quality of life, as much for the family as for the boy discapacitado. It was tried the main character to belong to different strata and with varied discapacidades classes in her relatives, with the purpose of to evaluate the investigation object more thoroughly and to avoid biases for social stratum or types peculiar of discapacidad

Anemia de diamond-blackfan

Diamond-Blackfan anemia is a rare, congenital, autosomal dominant disease in which the main defect is a mutation in a ribosomal protein. It is characterized by erythroid aplasia that results in normochromic macrocytic anemia, this disease begins in childhood and associates congenital malformations and susceptibility to malignancies. The diagnosis is based on clinical and molecular features. The initial treatment is blood transfusions and corticosteroids; but currently the only known curative treatment is allogeneic hematopoietic stem cell transplantation from a compatible donor.La anemia de Diamond-Blackfan es una enfermedad infrecuente, congénita, autosómica dominante, en la que el defecto principal es la mutación en una proteína ribosomal. Se caracteriza por una aplasia eritroide que da como resultado una anemia macrocítica normocrómica de inicio en la infancia y asocia malformaciones congénitas y susceptibilidad a padecer malignidades. El diagnóstico está basado en factores clínicos y moleculares. El tratamiento inicial son transfusiones sanguíneas y corticoesteriodes; pero en la actualidad el único tratamiento curativo conocido es el trasplante alogénico de células madre hematopoyéticas de un donador compatible

Viabilidad de la implementación de energía undimotriz en la costa Pacífica Colombiana

Colombia, in recent years has had an increase in the production of fossil fuels and each time it increases to a greater extent, the above is supported by data from the World Bank with an average of 76.7% of total energy consumption under conventional sources . Despite this high consumption, we can evidence the growing social problems that some coastal areas of the country are facing in terms of the lack of access to electricity for different communities in the Colombian Pacific Region, comprised between the entire department of Chocó, and the coastal areas of the departments of Valle del Cauca, Cauca and Nariño. Therefore, it is necessary to determine the viability of the implementation of wave energy in the Colombian Pacific, reaching the conclusion that its applicability is possible thanks to its characteristics and conditions.Colombia en los últimos años ha tenido un aumento en la producción de combustibles fósiles y cada vez se incrementa en mayor medida, lo anterior se sustenta bajo datos del Banco Mundial con un promedio de 76,7 % del consumo total de energía bajo fuentes convencionales. A pesar de este alto consumo, podemos evidenciar la creciente problemática social que atraviesan algunas zonas costeras del país en cuanto a la falta de acceso de energía eléctrica para diferentes comunidades de la Región Pacífica Colombiana, comprendida entre la totalidad del departamento del Chocó, y las zonas costeras de los departamentos del Valle del Cauca, Cauca y Nariño. Por ello se ve la necesidad de determinar la viabilidad de la implementación de energía undimotriz en el Pacifico Colombiano, llegando a la conclusión que si es posible su aplicabilidad gracias a sus características y condiciones