Comparison of gene coverage of mouse oligonucleotide microarray platforms

BACKGROUND: The increasing use of DNA microarrays for genetical genomics studies generates a need for platforms with complete coverage of the genome. We have compared the effective gene coverage in the mouse genome of different commercial and noncommercial oligonucleotide microarray platforms by performing an in-house gene annotation of probes. We only used information about probes that is available from vendors and followed a process that any researcher may take to find the gene targeted by a given probe. In order to make consistent comparisons between platforms, probes in each microarray were annotated with an Entrez Gene id and the chromosomal position for each gene was obtained from the UCSC Genome Browser Database. Gene coverage was estimated as the percentage of Entrez Genes with a unique position in the UCSC Genome database that is tested by a given microarray platform. RESULTS: A MySQL relational database was created to store the mapping information for 25,416 mouse genes and for the probes in five microarray platforms (gene coverage level in parenthesis): Affymetrix430 2.0 (75.6%), ABI Genome Survey (81.24%), Agilent (79.33%), Codelink (78.09%), Sentrix (90.47%); and four array-ready oligosets: Sigma (47.95%), Operon v.3 (69.89%), Operon v.4 (84.03%), and MEEBO (84.03%). The differences in coverage between platforms were highly conserved across chromosomes. Differences in the number of redundant and unspecific probes were also found among arrays. The database can be queried to compare specific genomic regions using a web interface. The software used to create, update and query the database is freely available as a toolbox named ArrayGene. CONCLUSION: The software developed here allows researchers to create updated custom databases by using public or proprietary information on genes for any organisms. ArrayGene allows easy comparisons of gene coverage between microarray platforms for any region of the genome. The comparison presented here reveals that the commercial microarray Sentrix, which is based on the MEEBO public oligoset, showed the best mouse genome coverage currently available. We also suggest the creation of guidelines to standardize the minimum set of information that vendors should provide to allow researchers to accurately evaluate the advantages and disadvantages of using a given platform

El silencio como manifestacion de voluntad de la administracion

70 p.El objeto de este trabajo es estudiar la figura jurídica del silencio como manifestación de voluntad de la Administración del Estado. Para cumplir este propósito, el estudio examina distintas líneas doctrinales nacionales e internacionales, jurisprudencia existente al respecto en nuestro país y aquellos documentos tomados en consideración por el Congreso para realizar la tramitación de la ley 19.880 que regula el silencio administrativo. Con este estudio se pretende descubrir las falencias que presenta dicho cuerpo legal en ésta materia y las consecuencias que acarrea la aplicación de esta ficción legal en los derechos de los administrados, relacionándose con la importancia del tiempo en la actividad administrativa, situaciones que se encuentran en estrecha conexión con los principios de legalidad, inexcusabilidad u oficialidad, contradictoriedad, no formalización, entre tantos otros, que se encuentran bajo el amparo de nuestro ordenamiento jurídico

Evaluacion de los canones neoclasicos faciales en adultos jovenes sanos estudiantes de Universidad de Talca

81 p.El propósito de este estudio fue evaluar los parámetros faciales de la población chilena para compararlos con los cánones neoclásicos y proporcionar información necesaria para la identificación médico legal, cirugía plástica y estética. Las reglas que definen la relación entre varias áreas de la cabeza y la cara fueron formuladas por estudiantes y artistas del renacimiento. Basados en los cánones griegos básicos. En la medicina el uso de las fórmulas neoclásicas fueron propagadas por artistasanatomistas del siglo diecisiete al diecinueve. La importancia de ver la cara en proporciones ha sido enfatizada por muchos cirujanos. Los cánones neoclásicos son conocidos por los cirujanos plásticos modernos, sin embargo su uso en la panificación quirúrgica han sido limitados al rol de guías de trabajo. El objetivo de este estudio es determinar cánones faciales característicos en adultos jóvenes sanos estudiantes de la Universidad de Talca. En este estudio participaron individuos Chilenos de ambos sexos, perteneciente a la Escuela de Odontología de la Universidad de Talca, con un total de 140 personas, 70 hombres y 70 mujeres, cuya edad fluctúa entre los 18 y los 30 años. Para determinar los 8 cánones neoclásicos se utilizó antropometría indirecta mediante 2 fotografías, frente y perfil, estas fueron captadas a través de una cámara digital Cyber Shot 7.2 y para asegurar la uniformidad y estandarización de las imágenes se utilizó una regla milimetrada. Obtenidas las imágenes estas se analizaron en el programa Antrophmeter que reproduce las imágenes en tamaño real. Los resultados se agruparon en tablas, en las cuales se describen las variables estudiadas y valores obtenidos en milímetros. Luego se analizó en el programa SPSS 15.0, con la finalidad de obtener la frecuencia de las proporciones y sus variaciones. El análisis estadísticamente descriptivo arrojó que existen cánones faciales característicos para los adultos jóvenes sanos estudiantes de la Universidad de Talca. Presentándose cánones faciales frecuentes tales como la distancias entre vertexendocanthion aumentada, nasión-subnasión disminuida, vertex-triquion y triquion-glabela disminuida, suprauricular-subauricular aumentado, alar-alar aumentado para quinto, séptimo y octavo parámetro. El parámetro con mayor equivalencia es el sexto donde la distancia endocanthion-endocanthion es muy similar a la distancia endocanthionexocanthion

Serious limitations of the QTL/Microarray approach for QTL gene discovery

<p>Abstract</p> <p>Background</p> <p>It has been proposed that the use of gene expression microarrays in nonrecombinant parental or congenic strains can accelerate the process of isolating individual genes underlying quantitative trait loci (QTL). However, the effectiveness of this approach has not been assessed.</p> <p>Results</p> <p>Thirty-seven studies that have implemented the QTL/microarray approach in rodents were reviewed. About 30% of studies showed enrichment for QTL candidates, mostly in comparisons<b/> between congenic and background strains. Three studies led to the identification of an underlying <it>QTL </it>gene. To complement the literature results, a microarray experiment was performed using three mouse congenic strains isolating the effects of at least 25 biometric QTL. Results show that genes in the congenic donor regions were preferentially selected. However, within donor regions, the distribution of differentially expressed genes was homogeneous once gene density was accounted for. Genes within identical-by-descent (IBD) regions were less likely to be differentially expressed in chromosome 2, but not in chromosomes 11 and 17. Furthermore, expression of <it>QTL </it>regulated in <it>cis </it>(<it>cis </it>eQTL) showed higher expression in the background genotype, which was partially explained by the presence of single nucleotide polymorphisms (SNP).</p> <p>Conclusions</p> <p>The literature shows limited successes from the QTL/microarray approach to identify <it>QTL </it>genes. Our own results from microarray profiling of three congenic strains revealed a strong tendency to select <it>cis-</it>eQTL over <it>trans-</it>eQTL. IBD regions had little effect on rate of differential expression, and we provide several reasons why IBD should not be used to discard eQTL candidates. In addition, mismatch probes produced false <it>cis-</it>eQTL that could not be completely removed with the current strains genotypes and low probe density microarrays. The reviewed studies did not account for lack of coverage from the platforms used and therefore removed genes that were not tested. Together, our results explain the tendency to report QTL candidates as differentially expressed and indicate that the utility of the QTL/microarray as currently implemented is limited. Alternatives are proposed that make use of microarray data from multiple experiments to overcome the outlined limitations.</p

Realidad nacional del implante coclear : los primeros 17 años en Chile

Tesis (Magíster en Audiología)Entre los beneficios que entrega el implante coclear a las personas que sufren hipoacusia sensorioneural bilateral severa-profunda, están la habilitación de la vía auditiva y las mejoras en la calidad de vida. El objetivo de esta tesis es caracterizar a la población que ha sido receptora de un dispositivo en Chile, durante los primeros 17 años de su entrada al país. Para recolectar la información se confeccionó un instrumento que se aplicó en entrevistas a profesionales que atienden a los receptores de implante coclear así como también a través de la revisión de los registros escritos. Se incluyó la información de 382 sujetos, implantados hasta julio de 2011, distribuidos principalmente en los cinco centros de implante en Chile. Los resultados muestran que en Chile los receptores han sido principalmente niños. La mayor cantidad de sujetos ha accedido al dispositivo de forma particular, pero también existe acceso mediante el uso de recursos públicos. Por otro lado, una baja cantidad de sujetos ha accedido a la implementación coclear bilateral. Mayoritariamente, las personas se encuentran en ambientes educativos normoyentes e insertos en un sistema laboral remunerado

Ensino superior e pandemia: um estudo piloto do questionário de experiência educacional durante pandemia

Introduction. The COVID-19 pandemic led most countries to suspend face-to-face educational activities. In Mexico, it was determined to continue the school year through distance learning. Due to the atypical nature of the situation, there are no tools to evaluate the student’s experience with this measure. Objective. Design and evaluate the psychometric properties of the Pandemic Educational Experience Questionnaire (CEEP). Method. The CEEP consists of 89 items on a Likert scale, it was applied to a non-probabilistic sample of 1,441 Mexican students of higher education. Results. An Exploratory Factor Analysis was carried out, items with a factor load lower than 0.40 were eliminated, the remaining items were grouped into 9 factors (50.836% of the total variance). The factors and the questionnaire in general yielded acceptable internal consistency values (0.670 &gt; a &gt; 0.991). Discussion. The CEEP is considered an adequate tool to evaluate the student experience during the pandemic. Results showed that students valued positively their aptitudes for distance learning (EaD), as well as the quality and behavior of their teachers; despite this, they report less satisfaction with the dynamics of the EaD and a negative emotional experience.Introducción. La pandemia de la COVID-19 llevó a que la mayoría de los países suspendieran las actividades educativas de forma presencial. En México se optó por continuar el ciclo escolar a distancia. Debido a lo atípico de la situación, no se cuentan con herramientas para evaluar la experiencia del estudiantado ante esta medida. Objetivo. Diseñar y evaluar las propiedades psicométricas del Cuestionario de Experiencia Educativa durante Pandemia (CEEP). Método. El CEEP consta de 89 ítems en escala Likert, se aplicó a una muestra no probabilística de 1,441 estudiantes mexicanos de educación superior. Resultados. Se realizó un Análisis Factorial Exploratorio, se eliminaron ítems con carga factorial inferior a 0.40, ítems restantes se agruparon en 9 factores (50.836% de la varianza total). Los factores y el cuestionario en general arrojaron valores aceptables de consistencia interna (0.670 &gt; a &gt; 0.991). Discusión. Se considera que el CEEP es una herramienta adecuada para evaluar la experiencia estudiantil durante la pandemia. El estudiantado valora positivamente sus aptitudes para la educación a distancia (EaD), así como la calidad y proceder de sus docentes; pese a ello reportan menor satisfacción con la dinámica de la EaD y una experiencia emocional negativa.Introdução. A pandemia COVID-19 levou a maioria dos países a suspender as atividades educacionais presenciais. No México, foi decidido continuar o ano letivo remotamente. Devido à natureza atípica da situação, não existem ferramentas para avaliar a experiência do aluno com esta medida. Objetivo. Projetar e avaliar as propriedades psicométricas do Questionário de Experiência Educacional Pandêmica (CEEP). Método. O CEEP é composto por 89 itens em escala Likert e foi aplicado a uma amostra não probabilística de 1.441 estudantes mexicanos do ensino superior. Resultados. Foi realizada uma Análise Fatorial Exploratória, os itens com carga fatorial inferior a 0,40 foram eliminados, os demais itens foram agrupados em 9 fatores (50,836% da variância total). Os fatores e o questionário em geral produziram valores de consistência interna aceitáveis (0,670&gt; a&gt; 0,991). Discussão. O CEEP é considerado uma ferramenta adequada para avaliar a experiência do aluno durante a pandemia. O corpo discente valoriza positivamente suas aptidões para a educação a distância (EaD), bem como a qualidade e o comportamento de seus professores; apesar disso, relatam menos satisfação com a dinâmica da EaD e experiência emocional negativa

Pd-Catalyzed (3 + 2) Heterocycloadditions between Alkylidenecyclopropanes and Carbonyls: Straightforward Assembly of Highly Substituted Tetrahydrofurans

This document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Catalysis, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acscatal.0c01827A Pd catalyst made from a Pd(0) source and a bulky biaryl phosphine ligand promotes highly efficient intramolecular (3 + 2) heterocycloadditions between alkylidenecyclopropanes (ACPs) and carbonyls. The annulations provide a straightforward access to fused polycyclic systems featuring β-methylene tetrahydrofuran moieties. DFT data support a pallada–ene process and shed light on the critical role of hemilabile interactions between the Pd center and the bulky biaryl phosphine. Significantly, these Pd(0) catalysts are also effective for promoting intermolecular formal cycloadditions between ACPs and trifluoromethyl ketones, thus providing for a direct entry to chiral tetrahydrofuran moieties (THFs) bearing trifluoromethyl–substituted carbonsThis work received financial support from the Spanish MINECO (SAF2016-76689-R, CTQ2017-84767-P), the Xunta de Galicia (ED431C 2017/19, 2015-CP082, Centro Singular de Investigación de Galicia accreditation 2019-2022, ED431G 2019/03, and a predoctoral Fellowship to E.d.C. and M.C.), CONICYT (grant to F.V.), and the ERDF, ERC (Adv. Grant 340055). The Orfeo–Cinqa network (CTQ2016-81797-REDC) is also acknowledgedS

Overexpression of Scg5 increases enzymatic activity of PCSK2 and is inversely correlated with body weight in congenic mice

<p>Abstract</p> <p>Background</p> <p>The identification of novel genes is critical to understanding the molecular basis of body weight. Towards this goal, we have identified secretogranin V (<it>Scg5</it>; also referred to as <it>Sgne1</it>), as a candidate gene for growth traits.</p> <p>Results</p> <p>Through a combination of DNA microarray analysis and quantitative PCR we identified a strong expression quantitative trait locus (eQTL) regulating <it>Scg5 </it>expression in two mouse chromosome 2 congenic strains and three additional F2 intercrosses. More importantly, the eQTL was coincident with a body weight QTL in congenic mice and <it>Scg5 </it>expression was negatively correlated with body weight in two of the F2 intercrosses. Analysis of haplotype blocks and genomic sequencing of <it>Scg5 </it>in high (C3H/HeJ, DBA/2J, BALB/cByJ, CAST/EiJ) and low (C57BL/6J) expressing strains revealed mutations unique to C57BL/6J and possibly responsible for the difference in mRNA abundance. To evaluate the functional consequence of <it>Scg5 </it>overexpression we measured the pituitary levels of 7B2 protein and PCSK2 activity and found both to be increased. In spite of this increase, the level of pituitary α-MSH, a PCSK2 processing product, was unaltered.</p> <p>Conclusion</p> <p>Together, these data support a role for <it>Scg5 </it>in the modulation of body weight.</p

Importance of randomization in microarray experimental designs with Illumina platforms

Measurements of gene expression from microarray experiments are highly dependent on experimental design. Systematic noise can be introduced into the data at numerous steps. On Illumina BeadChips, multiple samples are assayed in an ordered series of arrays. Two experiments were performed using the same samples but different hybridization designs. An experiment confounding genotype with BeadChip and treatment with array position was compared to another experiment in which these factors were randomized to BeadChip and array position. An ordinal effect of array position on intensity values was observed in both experiments. We demonstrate that there is increased rate of false-positive results in the confounded design and that attempts to correct for confounded effects by statistical modeling reduce power of detection for true differential expression. Simple analysis models without post hoc corrections provide the best results possible for a given experimental design. Normalization improved differential expression testing in both experiments but randomization was the most important factor for establishing accurate results. We conclude that lack of randomization cannot be corrected by normalization or by analytical methods. Proper randomization is essential for successful microarray experiments

Análisis Estructural del conocimiento didáctico del contenido científico escolar en futuros maestros de primaria

Pedagogical Content Knowledge (PCK) in science is the specific professional knowledge of a teacher, which characterizes and differentiates this type of professional from other science-based professionals. Recent research at an international level shows certain diversity in its definition by experts and also in their suggested composition. This diversity has generated a multiplicity of instruments for assessing PCK. It seems convenient to explore whether or not this variety of proposals hides a convergent underlying and steady structure. If this conceptual structure existed, it could be revealed in empirical studies, confirming or rejecting experts' criteria. As the construct of PCK is so complex, simplified situations should be considered first. Therefore, the present study analyses the possible underlying structure of PCK in elementary science shown by primary school teachers prior to acquiring professional expertise. Two independent studies were conducted in different years with pre-service primary school teachers. PCK in elementary science was assessed with CoRe, an instrument used in many international studies. Results show a steady bi-factorial structure grouping 'instructional analysis' (factor 1) and 'instructional action' (factor 2) components. Between-component relationships were conceptually analogous to those observed in previous empirical studies