Desarrollo de una plataforma bioinformática para la gestión de datos fenotípicos y moleculares

Este proyecto está orientado a ayudar a un grupo de investigadores del Departamento de Ciencia Animal y de los Alimentos (UAB), que se dedican a recopilar datos genómicos obtenidos en experimentos. La aplicación constará de dos partes. La primera es la parte de los usuarios, donde se podrá crear proyectos, insertar, modificar o eliminar datos y consultar la información ya existente en la aplicación. La segunda parte es la del administrador, que como tal podrá dar de alta a nuevos usuarios, restaurar versiones anteriores de la base de datos, eliminar usuarios y consultar las acciones realizadas por los usuarios.

The non-LTR retrotransposons in Ciona intestinalis: new insights into the evolution of chordate genomes

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

Molecular evidence to suggest the origin of a colonization: Drosophila subobscura in America

Abstract The recent colonization of America by Drosophila subobscura represents a great opportunity for evolutionary biology studies. Knowledge of the populations from which the colonization started would provide an understanding of how genetic composition changed during adaptation to the new environment. Thus, a 793 nucleotide fragment of the Odh (Octanol dehydrogenase) gene was sequenced in 66 chromosomal lines from Barcelona (western Mediterranean) and in 66 from Mt. Parnes (Greece, eastern Mediterranean). No sequence of Odh fragment in Barcelona or Mt. Parnes was identical to any of those previously detected in America. However, an Odh sequence from Barcelona differed in only one nucleotide from another found in American populations. In both cases, the chromosomal lines presented the same inversion: O7, and the Odh gene was located within this inversion. This evidence suggests a possible western Mediterranean origin for the colonization. Finally, the molecular and inversion data indicate that the colonization was not characterized by multiple reintroductions.

Estimativa de la edad y peso a la primera monta de novillas en el Pantanal brasileño

Esto trabajo tuvo como objetivo estimar la edad y peso a la primera monta de novillas de las razas Nelore (N), Pantaneira (P) y Mestizas Pantaneira x Nelore (PxN). Se utilizó un total de 98 hembras, siendo 51, 24 y 23 pertenecientes a las razas N, P y PxN, respectivamente. El análisis estadístico de los datos no reveló diferencia significativa (P = 0,3595) para el peso a la primera monta entre las razas estudiadas. El análisis de varianza no reveló diferencia significativa (P = 0,307) entre las edades a la primera monta entre razas, mostrando 3,5, 3,4 y 3,2 años para las novillas P, N y ½PxN, respectivamente.

Copy number variation in the porcine genome inferred from a 60 k SNP BeadChip

Background: Recent studies in pigs have detected copy number variants (CNVs) using the Comparative Genomic Hybridization technique in arrays designed to cover specific porcine chromosomes. The goal of this study was to identify CNV regions (CNVRs) in swine species based on whole genome SNP genotyping chips. Results: We used predictions from three different programs (cnvPartition, PennCNV and GADA) to analyze data from the Porcine SNP60 BeadChip. A total of 49 CNVRs were identified in 55 animals from an Iberian x Landrace cross (IBMAP) according to three criteria: detected in at least two animals, contained three or more consecutive SNPs and recalled by at least two programs. Mendelian inheritance of CNVRs was confirmed in animals belonging to several generations of the IBMAP cross. Subsequently, a segregation analysis of these CNVRs was performed in 372 additional animals from the IBMAP cross and its distribution was studied in 133 unrelated pig samples from different geographical origins. Five out of seven analyzed CNVRs were validated by real time quantitative PCR, some of which coincide with well known examples of CNVs conserved across mammalian species. Conclusions: Our results illustrate the usefulness of Porcine SNP60 BeadChip to detect CNVRs and show that structural variants can not be neglected when studying the genetic variability in this species.

RNA interference is ineffective as a routine method for gene silencing in chick embryos as monitored by fgf8 silencing.

The in vivo accessibility of the chick embryo makes it a favoured model system for experimental developmental biology. Although the range of available techniques now extends to miss-expression of genes through in ovo electroporation, it remains difficult to knock out individual gene expression. Recently, the possibility of silencing gene expression by RNAi in chick embryos has been reported. However, published studies show only discrete quantitative differences in the expression of the endogenous targeted genes and unclear morphological alterations. To elucidate whether the tools currently available are adequate to silence gene expression sufficiently to produce a clear and specific null-like mutant phenotype, we have performed several experiments with different molecules that trigger RNAi: dsRNA, siRNA, and shRNA produced from a plasmid coexpressing green fluorescent protein as an internal marker. Focussing on fgf8 expression in the developing isthmus, we show that no morphological defects are observed, and that fgf8 expression is neither silenced in embryos microinjected with dsRNA nor in embryos microinjected and electroporated with a pool of siRNAs. Moreover, fgf8 expression was not significantly silenced in most isthmic cells transformed with a plasmid producing engineered shRNAs to fgf8. We also show that siRNA molecules do not spread significantly from cell to cell as reported for invertebrates, suggesting the existence of molecular differences between different model systems that may explain the different responses to RNAi. Although our results are basically in agreement with previously reported studies, we suggest, in contrast to them, that with currently available tools and techniques the number of cells in which fgf8 gene expression is decreased, if any, is not sufficient to generate a detectable mutant phenotype, thus making RNAi useless as a routine method for functional gene analysis in chick embryos.

Comparing multiple criteria for species identification in two recently diverged seabirds

Correct species identification is a crucial issue in systematics with key implications for prioritising conservation effort. However, it can be particularly challenging in recently diverged species due to their strong similarity and relatedness. In such cases, species identification requires multiple and integrative approaches. In this study we used multiple criteria, namely plumage colouration, biometric measurements, geometric morphometrics, stable isotopes analysis (SIA) and genetics (mtDNA), to identify the species of 107 bycatch birds from two closely related seabird species, the Balearic (Puffinus mauretanicus) and Yelkouan (P. yelkouan) shearwaters. Biometric measurements, stable isotopes and genetic data produced two stable clusters of bycatch birds matching the two study species, as indicated by reference birds of known origin. Geometric morphometrics was excluded as a species identification criterion since the two clusters were not stable. The combination of plumage colouration, linear biometrics, stable isotope and genetic criteria was crucial to infer the species of 103 of the bycatch specimens. In the present study, particularly SIA emerged as a powerful criterion for species identification, but temporal stability of the isotopic values is critical for this purpose. Indeed, we found some variability in stable isotope values over the years within each species, but species differences explained most of the variance in the isotopic data. Yet this result pinpoints the importance of examining sources of variability in the isotopic data in a case-by-case basis prior to the cross-application of the SIA approach to other species. Our findings illustrate how the integration of several methodological approaches can help to correctly identify individuals from recently diverged species, as each criterion measures different biological phenomena and species divergence is not expressed simultaneously in all biological traits.

Prototypical Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.

Estudio citogenético en células espermatogénicas de ratón (C57BLx CD1)F1 tratado con etilmetanosulfonato

Tesis (Maestría en Ciencias con Especialidad en Morfología) UANL

Determinación del número de variantes y frecuencias génicas de 8microsatélites del ADN en las razas de bovinos Beefmaster y ganado suizo de registro en México

Tesis (Maestría en Ciencias Veterinarias, con Especialidad en Génetica Animal) UANL

Estimativa de la edad y peso a la primera monta de novillas en el Pantanal brasileño

Esto trabajo tuvo como objetivo estimar la edad y peso a la primera monta de novillas de las razas Nelore (N), Pantaneira (P) y Mestizas Pantaneira x Nelore (PxN). Se utilizó un total de 98 hembras, siendo 51, 24 y 23 pertenecientes a las razas N, P y PxN, respectivamente. El análisis estadístico de los datos no reveló diferencia significativa (P = 0,3595) para el peso a la primera monta entre las razas estudiadas. El análisis de varianza no reveló diferencia significativa (P = 0,307) entre las edades a la primera monta entre razas, mostrando 3,5, 3,4 y 3,2 años para las novillas P, N y ½PxN, respectivamente.

Evaluation of nine microsatellite loci and misidentification paternity frequency in a population of Gyr breed bovines

Erros de identificação de paternidade são prejudiciais por reduzir o ganho genético anual e comprometer um programa eficiente de melhoramento genético. O objetivo principal deste trabalho foi avaliar o potencial de uso de nove microssatélites em testes de paternidade e investigar a freqüência de erro de identificação de famílias de um rebanho de animais da raça Gir. No experimento foram utilizadas amostras de sangue de quarenta famílias (touro/ vaca/ bezerro) de animais da raça Gir, Puros de Origem e registrados na Associação Brasileira dos Criadores de Zebu (ABCZ). A maior parte dos microssatélites avaliados neste trabalho são recomendados, para Testes de Paternidade em bovinos, pela Sociedade Internacional de Genética Animal (ISAG). As regiões microssatélites TGLA122, TGLA126, BM1824, BMS2533, SPS115, ETH3, ETH10, ETH225 e POTCHA foram amplificadas por meio da técnica de PCR. Os produtos da amplificação foram separados por eletroforese em gel de poliacrilamida desnaturante. A partir dos dados obtidos foram calculadas as freqüências alélicas, diversidade gênica, conteúdo de polimorfismo informativo e probabilidade de exclusão para cada microssatélite. Também foram calculadas as freqüências genotípicas, heterozigosidade, probabilidade de exclusão combinada e probabilidade de Paternidade nas famílias consideradas. A probabilidade de exclusão combinada para todos os microssatélites estudados foi de 0,9789. Os resultados dos testes de paternidade acusaram erro de identificação em onze das 40 famílias estudadas, ou seja, 27,5% da amostra. A probabilidade de paternidade variou entre 0,8691 e 0,9999, com valor médio de 0,9512.

Desenvolvimento e implementação de modelos para simulação de dados SNPs

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic variability and efficiency of DNA microsatellite markers for paternity testing in horse breeds from the Brazilian Marajó archipelago

In this study, 15 microsatellite DNA loci used in comparative tests by the International Society for Animal Genetics were applied to the evaluation of genetic diversity and management, and the efficiency of paternity testing in Marajoara horses and Puruca ponies from the Marajó Archipelago. Based on the genotyping of 93 animals, mean allelic diversity was estimated as 9.14 and 7.00 for the Marajoara and Puruca breeds, respectively. While these values are similar to those recorded in most European breeds, mean levels of heterozygosity were much lower (Marajoara 49%, Puruca 40%), probably as a result of high levels of inbreeding in the Marajó populations. The mean informative polymorphic content of this 15-marker system was over 50% in both breeds, and was slightly higher in the Marajoara horses. The discriminative power and exclusion probabilities derived from this system were over 99% for both populations, emphasizing the efficacy of these markers for paternity testing and genetic management in the two breeds.

Estimativas de parâmetros genéticos para a produção de leite e idade ao primeiro parto em vacas da raça pardo-suiça utilizando amostrador de Gibbs

Registros de 2.981 lactações de vacas da raça Pardo-Suiça, distribuídas em 62 rebanhos, com parições nos anos de 1980 a 2002, foram utilizados para verificar a influência de fatores genéticos e não genéticos, sobre a produção de leite e idade ao primeiro parto. O modelo empregado incluiu os efeitos fixos de rebanho, ano e estação de parto, além dos efeitos aleatórios de animal e ambiente temporário. Para a produção de leite, além dos efeitos fixos descritos anteriormente, incluíram-se também os efeitos linear da duração da lactação e linear e quadrático da idade da vaca ao parto, como co-variáveis. Na estimação dos componentes de (co) variâncias foi utilizada a inferência Bayesiana por meio de amostrador de Gibbs, com tamanho de cadeia de 1.500.000 rounds e período de queima 500.000 rounds. A frequência de amostragem foi de 500 rounds. As médias estimadas para produção de leite e idade ao primeiro parto foram iguais a 5347,47 1849,13 kg e 29,65 4,51 meses, respectivamente. Os efeitos de rebanho, ano de parto e duração da lactação, influenciaram significativamente a produção de leite (P< 0,01). A idade ao primeiro parto foi influenciada pelos efeitos de rebanho, ano de parto (P<0,01), além do efeito de estação de parto (P<0,05). As estimativas de herdabilidade obtidas para a produção de leite e idade ao primeiro parto foram iguais a 0,23 e 0,18, respectivamente. A correlação genética entre as duas foi igual a -0,31. A tendência genética e fenotípica, em função do reprodutor, para produção de leite foi de 1,09 kg e 115,34 kg de leite, respectivamente, para cada ano de produção. Para idade ao primeiro parto, os valores genéticos dos reprodutores tornaram-se negativos a partir de 1988, com redução aproximada de 0,05 meses a cada ano e fenotipicamente verificou-se uma redução de 32 para 28 meses de idade ao primeiro. Filhas de touros com alto valor genético para produção de leite tendem a apresentar crescimento mais acelerado ou maturidade fisiológica a uma idade mais precoce, diminuindo a idade ao primeiro parto.