Next generation genomics tools for wheat improvement

In recent years the amount of genomic resources of wheat has increased to the point where manual analysis is unfeasible. The aim of this PhD was to develop bioinformatics tools that help answer biological questions relevant to research and breeding by addressing the complexities associated with the wheat genome. I took advantage of resources which became publicly available as the analyses were carried out and I developed new approaches, strategies and tools to help accelerate wheat research. Chapter 1 reviews the genomic resources used for the thesis, placing them in historic context with the work and analyses performed. Chapter 2 describes the development of PolyMarker, a bioinformatics pipeline to design genome-specific primers in a timely and effective manner. Examples of different applications of PolyMarker are also included. Chapter 3 describes the analysis of an F2 population to generate a genetic map for Yr15, a gene that provides resistance to yellow rust. The SNP calling was done from bulked segregating samples, sequenced with RNASeq as a method of reduced representation. Chapter 4 describes expVIP, a tool to integrate RNA-Seq experiments in a relational database. Data from different studies can be visualised simultaneously, enabling comparisons between them. Lastly, in Chapter 5 all the data types used for the analysis on each of the previous chapters is integrated into a relational database. The discussion further explores how genetic maps, SNP markers, novel SNPs, gene annotations, gene assemblies and gene expression can be used simultaneously in research and breeding programs. All the tools and pipelines described in this thesis are open source and are available on: https://github.com/homonecloco

Elementos del desarrollo local y recursos disponibles para el desarrollo del turismo alternativo en Ocuilan, México

La complejidad ambiental, enmarcada por la interrelación entre los procesos sociales y territoriales, constituye un argumento central para la delineación de estrategias que promuevan el desarrollo local acorde a las especificidades físicas y socioculturales. Para ello, la planificación territorial deberá avanzar en la adecuada integración de los diferentes recursos que conforman un espacio determinado, con la finalidad de impulsar el equilibrio entre la conservación, adecuado aprovechamiento de los recursos y el mejoramiento en las condiciones de vida de la población local, como una condición necesaria para alcanzar la justicia y el uso racional de los recursos presentes (Mantero, 2004). En este sentido, el aprovechamiento recreativo de los recursos naturales y culturales, puede ser considerado una alternativa económica y para la conservación ambiental, en espacios rurales que enfrentan profundas problemáticas ambientales, a partir del desplazamiento de corrientes de visitantes, atraídos por los elementos biofísicos, las manifestaciones de arte, técnica, folklore, hitos de la historia entre otros elementos culturales, tangibles e intangibles (Rivero, 2001).En México existen numerosas localidades rurales donde el turismo podría constituirse en un eje estratégico para el desarrollo local. Tal es el caso de Ocuilan en el Estado de México donde a partir del aprovechamiento recreativo de sus recursos, se podría estimular la dinamización económica y la conservación ambiental de la región. Para que este turismo alternativo se consolide y pueda contribuir al desarrollo local es preciso instrumentar procesos de planificación territorial que favorezcan el aprovechamiento recreativo del medio natural y los elementos culturales, satisfagan las expectativas de los usuarios y mejoren el nivel de vida los residentes. En este trabajo se identificaron los elementos que caracterizan al desarrollo local, los recursos disponibles y los agentes de desarrollo. Con la finalidad de obtener información sobre la percepción del entorno, los recursos naturales y culturales disponibles, y las posibilidades de participación en la oferta de servicios, se aplicó un cuestionario a 139 personas con estancia temporal y transitoria durante los meses de septiembre a diciembre de 2015. Los resultados mostraron una insuficiente infraestructura y equipamiento turístico para dar cobertura a las necesidades de la población, falta de servicios de transporte, y fallas constantes en los servicios de alcantarillado, recolección de residuos, energía eléctrica y telecomunicaciones. Los habitantes indicaron varias ventajas con respecto al turismo, como la mejora de ingresos, generación de empleos y mayor conocimiento de la cultura por parte de los visitantes. La principal conclusión sugiere que en el lugar de estudio existen recursos naturales y culturales con potencial turístico, interés de los actores locales y una afluencia turística considerable en la región, a partir de las cuales se pueden generar estrategias para el turismo alternativo como soporte del desarrollo local

Towards On-Chip Self-Referenced Frequency-Comb Sources Based on Semiconductor Mode-Locked Lasers.

Miniaturization of frequency-comb sources could open a host of potential applications in spectroscopy, biomedical monitoring, astronomy, microwave signal generation, and distribution of precise time or frequency across networks. This review article places emphasis on an architecture with a semiconductor mode-locked laser at the heart of the system and subsequent supercontinuum generation and carrier-envelope offset detection and stabilization in nonlinear integrated optics

Neonatal hearing screening in high-risk patients with otoacoustic emissions: evaluation of results

Resumen Objetivo: evaluar la efectividad del programa de tamizaje auditivo del Homic en pacientes de alto riesgo de hipoacusia neurosensorial, el cual está basado en la realización de otoemisiones acústicas Diseño: estudio de cohorte retrospectiva, en el que se incluirán a los pacientes mayores de 12 meses de edad nacidos en el Hospital Militar central (HMC) entre enero de 2009 y diciembre de 2012; a quienes por condiciones de alto riesgo de hipoacusia neurosensorial se les realizó antes de los 6 meses de edad otoemisiones acústicas como prueba de tamizaje auditivo. A esta población, se le realizara diagnostico auditivo por medio del método diagnostico Gold Standart el cual es el “cross cheking”. Resultados: Se estudiaron los factores de riesgo para hipoacusia neurosensorial encontrando que el peso al nacer ≤1500 gr. Se relacionó con hipoacusia en un 16%. El 5.6% tiene antecedente familiar de hipoacusia neurosensorial en primer y segundo grado de consanguinidad. La infección congénita (TORCHS: toxoplasmosis, sífilis, rubéola, citomegalovirus, o herpes) como factor de riesgo se presentó en el 2.4% únicamente con la presencia de Toxoplasmosis, de los cuales 2 oídos presentaron cofosis. Conclusiones: La sensibilidad de las Otoemisiones acusticas para sospechar hipoacusia neurosensorial fue del 82.5%. La especificidad estimada en nuestro estudio fue de 90.9%Hospital Militar CentralObjective: To evaluate the effectiveness of auditory screening program Central Military Hospital in patients at high risk of sensorineural hearing loss, which is based on the realization of otoacoustic emissions. Design: Retrospective cohort study, in which over 12 months of age born patients in the Central Military Hospital (HOMIC) between January 2009 and December 2012 were included; who by conditions of high risk of sensorineural hearing loss was performed before 6 months of age otoacoustic emissions and hearing screening test. Total population was 125 patients. We evaluated each ear separately for a total of 250 measurements, this population was conducted auditory diagnosis through cross cheking diagnosis method were analyzed. Results: Risk factors for sensorineural hearing loss were studied. We found that birth weight ≤1500 g. It was associated with hearing loss by 16%. 5.6% have a family history of sensorineural hearing loss in first and second degree of consanguinity. Congenital infection (TORCHS: toxoplasmosis, syphilis, rubella, cytomegalovirus, or herpes) as a risk factor occurred in 2.4% only in the presence of Toxoplasmosis, of which 2 ears presented deafness. Conclusions: The otoacoustic emissions are effective as hearing screening test in Military Central Hospital in patients at high risk of Sensorineural hearing loss. The sensitivity of otoacoustic emissions to suspect sensorineural hearing loss was 82.5%. The estimated specificity in our study was 90.9

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data.

The use of next generation sequencing (NGS) to identify novel viral sequences from eukaryotic tissue samples is challenging. Issues can include the low proportion and copy number of viral reads and the high number of contigs (post-assembly), making subsequent viral analysis difficult. Comparison of assembly algorithms with pre-assembly host-mapping subtraction using a short-read mapping tool, a k-mer frequency based filter and a low complexity filter, has been validated for viral discovery with Illumina data derived from naturally infected liver tissue and simulated data. Assembled contig numbers were significantly reduced (up to 99.97%) by the application of these pre-assembly filtering methods. This approach provides a validated method for maximizing viral contig size as well as reducing the total number of assembled contigs that require down-stream analysis as putative viral nucleic acids.This work was supported by Wellcome Trust WT091501MAThis is the author accepted manuscript. It is currently under an indefinite embargo pending publication by PLOS

Magmatic arc evolution during the tectonic closure of the Rocas Verdes basin: insights from Cretaceous–earliest Paleocene intrusive rocks of Navarino Island (55°S), Fuegian Andes

Navarino Island is located in the southernmost part of the Fuegian Andes, south of the Beagle Channel. Its geological record documents the complex tectonic history of Tierra del Fuego that includes the opening and closure of the Rocas Verdes basin, Cordillera arc collision and subsequent subduction processes. The geology of the island is mostly comprised of the Cretaceous Yahgan Formation, a marine meta-sedimentary sequence, which is intruded by diverse plutons that are mostly exposed on the northwestern tip of the island. We herein present a new dataset that shows the presence of three Cretaceous-earliest Paleocene magmatic suites of active margin magmatism emplaced during the early stage of the Fuegian Andes, which are referred to as (i) the Dientes de Navarino Microdioritic Sills, a suite of pre-tectonic microdioritic sills that formed during ~101-97 Ma; (ii) the Castores Plutonic Complex, a series of pre- to syn-tectonic gabbroic to tonalitic plutons emplaced during ~90-87 Ma and (iii) the Samantha Monzonites, a suite of isolated monzonitic to monzodioritic post-tectonic plutons that formed at ~66-65 Ma. These distinct magmatic episodes are recognised by field observations, geological mapping, petrography and whole-rock geochemistry integrated with amphibole and biotite 40Ar/39Ar and U-Pb zircon LA-ICP-MS geochronology. The geochemical compositions of these rocks are consistent with a continental arc setting that formed during the interval ~101-65 Ma. While the three pulses spatially overlap in Navarino Island, the arc magmatism shows a migration (or expansion) throughout the Late Cretaceous. The locus of the arc then migrated at ~68-66 Ma towards the southwest. We suggest that this trench-ward migration at ~68-66 Ma may be associated with a change in the subduction angle. The three Cretaceous- earliest Paleocene plutonic pulses recorded in Navarino Island formed during the early stages of development of the Fuegian Andes, and are pre-, syn-and post-tectonic with respect to a major compressional event caused by the collision and obduction of the back-arc Rocas Verdes oceanic floor.Fil: Velásquez, Ricardo. Servicio Nacional de Geología y Minería;Fil: Bastías, Joaquín. Universidad Andrés Bello; Chile. Trinity College; IrlandaFil: Salazar, Esteban. Servicio Nacional de Geología y Minería;Fil: Poblete, Fernando. Universidad de Chile; Chile. Universidad de O Higgins;Fil: Gonzalez Guillot, Mauricio Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; Argentina. Universidad Nacional de Tierra del Fuego, Antártida e Islas del Atlántico Sur. Instituto de Ciencias Polares, Ambientales y Recursos Naturales; ArgentinaFil: Chew, David. Trinity College; IrlandaFil: Peña, Matías. Universidad Mayor.; ChileFil: Tapia Silva, Felipe Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; ArgentinaFil: Ramirez, Adán. Servicio Nacional de Geología y Minería;Fil: Drakou, Foteini. Trinity College; Irland

Critical analysis of physical therapy groups promoting scientific research in Colombia. A cross sectional study

Objective. To analyze of physical therapy groups promoting scientific research in Colombia. Material and methods. Were individually analyzed all curricula vitae from researchers in the available field in the COLCIENCIAS database of CvLac-database. We also analyzed the statistical reports on scientific production available on the Scienti-website (http://www.colciencias.gov.co/scienti/). Scientific production and level of training was evaluated of 43 curricula during the months of April and May 2012 for the collection of information and this information was analyzed in June 2012. Results. We identified 768 usable records (Biomedical and Health Science). Of the articles included, 942 were original research reports. The number of publications in Colombia grew ten-fold between 1990 and 2010. Between 1990 and 2003, the growth rate was 9% per year, whereas from 2005 and 2008 the rate dropped to about 10% per year. The average number of included articles published per year was 45 with a range from 12 to 187. A nonlinear, bimodal distribution of articles published per year was observed (R2=0.85), with peak publications in 1992 and 2011. There was a significant difference in publication productivity over the 10 years across (P<0.001). Pair-wise comparisons revealed that groups with Master´s degree produced significantly more publications (median=19) than any other category, with the exception of Doctoral degree (median=13). Conclusion. This study provides ample direction for future inquiry regarding the status of curriculum and of scholars in physical therapy. However, this production is still lower than that of other Latin American countries having similar socioeconomic and demographic condition

Cancer stem cells from human glioblastoma resemble but do not mimic original tumors after in vitro passaging in serum-free media

Human gliomas harbour cancer stem cells (CSCs) that evolve along the course of the disease, forming highly heterogeneous subpopulations within the tumour mass. These cells possess self-renewal properties and appear to contribute to tumour initiation, metastasis and resistance to therapy. CSC cultures isolated from surgical samples are considered the best preclinical in vitro model for primary human gliomas. However, it is not yet well characterized to which extent their biological and functional properties change during in vitro passaging in the serum-free culture conditions. Here, we demonstrate that our CSC-enriched cultures harboured from one to several CSC clones from the human glioma sample. When xenotransplanted into mouse brain, these cells generated tumours that reproduced at least three different dissemination patterns found in original tumours. Along the passages in culture, CSCs displayed increased expression of stem cell markers, different ratios of chromosomal instability events, and a varied response to drug treatment. Our findings highlight the need for better characterization of CSC-enriched cultures in the context of their evolution in vitro, in order to uncover their full potential as preclinical models in the studies aimed at identifying molecular biomarkers and developing new therapeutic approaches of human gliomas.Peer reviewe