GENOMIC VARIATION IN LIVESTOCK USING DENSE SNP CHIP DATA

Part I describes two possible approaches to investigate Mexican chicken genetic variation, using selective sweeps and Copy Number Variants (CNV). CNVs are genomic polymorphisms that influence phenotypic expression and are an important source of genetic variation in populations. The aim of the first study here presented was to characterize the genetic variability of the Mexican chicken\u2019s population and to disclose any underlying population structure. A total of 213 chickens were sampled in different rural production units located in 25 states of M\ue9xico. Genotypes were obtained using the Affymetrix Axiom\uae 600K Chicken Genotyping Array. The Identity by Descent (IBD) and the Principal Components Analysis (PCA) were performed by SVS software on pruned SNPs. Analyses done with ADMIXTURE identified three ancestors and determined, for each individual, the proportion of the genetic contribution from each of the three ancestors. The results of the Neighbor-Joining (NJ) analysis were consistent with those obtained by the PCA. All methods used in this study did not allow a classification of Mexican chicken in distinct genetic groups. A total of 3,059 Run of homozygosity (ROH) were identified and, being mainly short in length (< 4 Mb), these regions are indicative of a low inbreeding level in the population. Finally, findings from the ROH analysis indicated the presence of natural selective pressure in the population of Mexican chicken. In the second study we used CNVs to investigate genetic variability in the Mexican Creole chicken and to relate this variation to the available gene annotation. The Hidden Markov Model of the PennCNV software detected a total of 1,924 CNVs in the chicken genome of 256 individuals. Input data were LOGR Ratio and B allele frequency obtained with the Axiom\uae Genome-Wide Chicken Genotyping Array (Affymetrix). The mapped CNVs comprised 1,538 gains and 386 losses resulting, at population level, in 1,216 CNV regions (CNVRs), of which 959 gains, 226 losses and 31 complexes (i.e. containing both losses and gains). The CNVRs covered a total of 47 Mb of the whole genome sequence length, corresponding to 5.12 % of the chicken galGal4 autosome assembly. This study allowed a deep insight into the structural variation in the genome of unselected Mexican chicken population, which up to now has not been genetically characterized. The genomic study disclosed that the population, even if presenting extreme morphological variation, couldn\u2019t be organized in differentiated genetic subpopulations. Finally, this study provided a chicken CNV map based on the 600K SNP chip array, jointly with a genome-wide gene copy number estimates in a native, unselected for more than 500 years, chicken population. Genetic variation can be caused by adaptive evolutionary changes and by artificial selection. The genetic makeup of populations is the result of a long-term process of selection and adaptation to specific environments and ecosystems. The two studies here presented indicate that the Mexican chicken clearly appear to be a unique Creole chicken population that was not subjected to a specific directional selection. Results provide a genetic knowledge that can be used as a basis for the genetic management of a unique genetic resource. Industry is likely envisaging to use the female native populations mating them with selected males to increase the productivity and the economic revenue of family farming agriculture, which is a large reality of United States of M\ue9xico. \u2022 Part II describes a CNV scan and a population analysis of turkey populations coming from different countries. The domesticated turkey was brought to Europe in late 1500 by Spanish conquerors from Central America, likely from Mexico. The evolution of the Mexican turkey population occurred as such independently for more than 500 years from the European ones and the commercial hybrids. This study investigates the genomic diversity of several turkey populations using CNVs as source of variation. A total of 116 individuals from 6 Italian breeds (Colle Euganei, Bronzato Comune Italiano, Parma e Piacenza, Brianzolo, Nero d\u2019Italia and Ermellinato di Rovigo), 7 Narragansett, 38 commercial hybrids and 31 Mexican turkeys, were processed with the Affymetrix 600K SNP turkey array. The CNV calling was performed with the HMM of PennCNV software. CNV were summarized into CNV regions (CNVRs) at population level using BEDTools. Variability among populations has been addressed by hierarchical clustering (pvclust R package) and by principal component analysis (PCA). A total of 2,987 CNV were identified covering 4.65% of the autosomes of the Turkey_5.0/melGal5 assembly. The CNVRs including at least 2 individuals were 362, 189 gains, 116 losses and 57 complexes. Among these regions the 51% contain genes. This study is the first CNV mapping of turkey population using 600K SNP chip. CNVs clustered the individuals according to population and their geographical origin. CNVs are also known to be indicators of adaptation, as some researches are suggesting investigating different species. The outcomes of this are likely reflecting the human action on domestication of domesticated turkey after its introduction into Europe and the directional selection occurring in the last 40 years to produce a fast-growing heavy bird. \u2022 Part III describes the CNV mapping in the Valdostana Red Pied (VRP) cattle breed, an autochthonous Italian dual-purpose cattle population reared in the Alps, and the comparison with the CNV maps detected in previous studies in the Italian Brown Swiss (IBS) and in the Mexican Holstein (HOL). Many studies have focused on identifying CNVs within and between human and livestock populations alike, but only few have explored population-genetic properties in cattle based on CNVs derived from a high-density SNP array. In this study in cattle we report a high-resolution CNV scan, using the Illumina 777k BovineHD Beadchip, for VRP, a population that did not undergo strong selection for production traits. After stringent quality control and filtering, CNVs were called across 108 bulls using the PennCNV software. A total of 6,784 CNVs were identified, summarized to 1,723 CNV regions (CNVRs) on 29 autosomes covering a total of ~59 Mb of the UMD3.1 assembly. Among the mapped CNVRs, there were 812 losses, 832 gains and 79 complexes. A total of 171 CNVRs were common to VRP, IBS and HOL. Between VRP and IBS, 474 regions overlapped, while only 313 were in common between VRP and HOL, indicating a more similar genetic structure among populations with common origins, i.e. the Alps. The clustering and admixture analyses showed a clear separation of the three breeds into three distinct clusters. In order to describe the distribution of CNVs within and among breeds we used the pair VST statistic. We considered only the CNVRs shared by more than 5 individuals within breed. We identified unique and highly differentiated CNVs (n=33), some of which could be due to specific breed selection and adaptation. Genes and QTL within these regions were also characterized adding evidence to the relationship between CNV and adaptation

Contact fatigue limits of gears, railway wheels and rails determined by means of multiaxial fatigue criteria

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Radical Generic Initial Ideals

In this paper, we survey the theory of Cartwright\u2013Sturmfels ideals. These are \u2124n-graded ideals, whose multigraded generic initial ideal is radical. Cartwright\u2013Sturmfels ideals have surprising properties, mostly stemming from the fact that their Hilbert scheme only contains one Borel-fixed point. This has consequences, e.g., on their universal Gr\uf6bner bases and on the family of their initial ideals. In this paper, we discuss several known classes of Cartwright\u2013Sturmfels ideals and we find a new one. Among determinantal ideals of same-size minors of a matrix of variables and Schubert determinantal ideals, we are able to characterize those that are Cartwright\u2013Sturmfels

The sensitivity of the ordinary runs test for evaluating the spatial pattern of infected plants

The influence of disease incidence, clumping of infected plants, and size of the sampling unit on the sensitivity of the ordinary runs test was simulated in order to identify the optimum sampling profile for investigating the spatial pattern of plant diseases. A simulation programme was written to generate plant populations with random and clustered spatial patterns displayed in quadrats of 50 by 200 plants. 600 and 1200 independent populations were generated for random and clustered patterns, respectively. 12 levels of disease incidence were simulated within the range 0.01-0.95. For every population, the simulation performed a sampling procedure with 9 sizes of the sampling unit (20, 30, 40, 50, 60, 80, 100, 120 and 150 plants). In each case the simulation was based on 1000 samples of continuous series of plants. In order to evaluate the sensitivity of ordinary runs test to the degree of aggregation, plant populations were simulated with two additional values of clumping power, for two levels of disease incidence. When a random pattern was simulated, the probability of rejecting the null hypothesis was almost unaffected by the size of the sampling unit and slightly decreased with disease incidence. When clustered patterns were generated, the probability of error clearly decreased both with disease incidence and size of the sampling unit. The probability of error was also affected by the degree of aggregation. As expected, the higher the clumping power the higher the probability of rejecting the null hypothesis. The implications of the sensitivity of the runs test on the design of sampling schemes are discussed

Experimental evaluation of insecticidal paints against Triatoma infestans (Hemiptera: Reduviidae), under natural climatic conditions

Triatoma infestans is the main vector of Chagas disease in the Gran Chaco region of South America. The traditional spraying technique used for the application of pyrethroid insecticides has shown low efficiency in the elimination of the vector species populations occupying peridomestic structures of rural houses in the endemic area of Argentina. As part of studies looking for better alternatives, we evaluated the residual effect of insecticidal paints on the mortality of fourth instar nymphs of T. infestans. Results. The study was based on an experimental design that included two groups treated with an organophosphate (Inesfly 5A IGR) and a pyrethroid (Inesfly 5A IGR NG) formulations of the paint, that were applied on wood, cement blocks and adobe bricks under natural climatic conditions. A third group was an untreated control. Both paint formulations showed very long residual activity, producing mortality of 84% and 98% (pyrethroid and organophosphate formulations, respectively) after 12 months of the paint application. After eight months, nymphs exposed during 6 hours to the painted surfaces with the pyrethroid and organophosphate formulations showed 81.33% and 100% mortality, respectively. Conclusion. The organophosphate- and pyrethroid-based insecticidal paints showed a very long residual activity on the mortality of fourth instar nymphs of T infestans, compared with the traditional spraying technique used for the application of pyrethroid insecticides in peridomestic structures of rural houses in the endemic region for Chagas disease in the Gran Chaco of Argentina. The application of the paints by trained personnel of the vector control programmes could be considered as an alternative control tool in areas where the traditional methods have failed or showed low efficacy.Fil: Amelotti, Ivana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Universidad Nacional de La Rioja. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Universidad Nacional de Catamarca. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Secretaría de Industria y Minería. Servicio Geológico Minero Argentino. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Provincia de La Rioja. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja; ArgentinaFil: Catala, Silvia Susana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Universidad Nacional de La Rioja. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Universidad Nacional de Catamarca. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Secretaría de Industria y Minería. Servicio Geológico Minero Argentino. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Provincia de La Rioja. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja; ArgentinaFil: Gorla, David Eladio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Universidad Nacional de La Rioja. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Universidad Nacional de Catamarca. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Secretaría de Industria y Minería. Servicio Geológico Minero Argentino. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja. - Provincia de La Rioja. Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja; Argentin

Effect of food competition on Culex pipiens quinquefasciatus under laboratory conditions

Se estudió experimentalmente el efecto de la competencia por alimento era la fase larval de Culex pipiens quinquefasciatus y su efecto sobre el estado adulto, bajo condiciones de laboratorio. Cohortes con diferente densidad inicial de larvas de primer estadio (desde 50 a 4000 individuos por gramo de comida) fueron estudiadas hasta la emergencia de adultos, incluyendo la postura de huevos. El número de individuos en las cohortes fue contado cada dos días, hasta que todos los adultos emergieron. Las hembras adultas fueron alimentadas cada cuatro días. Los adultos sobrevivientes y los huevos puestos fueron contados diariamente. La proporción de hembras adultas, el peso de adultos y la fertilidad de hembras disminuyeron a medida que la densidad larval aumentó. La longevidad de adultos y la fecundidad de hembras no mostró un cambio densodependiente. El tiempo generacional se incrementó y la tasa intrínseca de crecimiento natural y la tasa neta de incremento mostraron una relación negativa con la densidad larval.Food competition in the larval phase of Culex pipiens quinquefasciatus and its effect on the adult stage was experimentally studied under laboratory conditions. Cohorts with different densities of initial first instar larvae (from 50 to 4000 individuals per g of food) were followed until adult emergence, including egg laying. The number of individuals in the cohorts were counted every two days, until all adults emerged. Adult females were fed every four days. Surviving adults and eggs laid were counted daily. The proportion of adult females, adult weight, and female fertility decreased as larval density increased. Adult longevity and female fecundity did not show a density dependent change. The generation time increased and the realized rate of natural increase and net rate of increase showed a negative relationship with larval density

The spatial pattern of “Mal de Río Cuarto del Maíz” (Rio Cuarto Corn disease) in corn fields

Se estudió el patrón de disposición espacial del “Mal de Rio Cuarto del maíz “ durante tres campañas agrícolas en la Provincia de Córdoba, Argentina. El trabajo combinó estimaciones por la prueba de ELISA en un campo experimental durante la primera campaña, con datos de .síntomas microscópicos tomados en la misma situación y en campos comerciales durante dos campañas posteriores. Las muestras analizadas por medio de ELISA mostraron un patrón espacial de la enfermedad indistinguible del esperado por izar. Los datos de síntomas, analizados mediante el “test común de runs “, mostraron que solo 13 de las 120 muestras estudiadas en la primera campaña en el campo experimental tenían disposición espacial agregada y que sólo 3 de lis 23 muestras analizadas en los campos comerciales durante dos campañas posteriores mostraron agregación. No se identificó ningún gradiente de incidencia de Mal de Rio Cuarto desde el perímetro al centro del cultivo, observación que sugiere que el vector no se dispersa a lotes de maíz desde fuentes cercanas.The spatial pattern of Mal de Río Cuarto del maíz (Rio Cuarto Corn Disease) was studied during three growing seasons in Córdoba Province, Argentina. The study combined ELISA determinations in experimental plots outside the endemic area during the first growing season with symptom assessments in that situation and in commercial plots in or near the endemic area during the two subsequent growing seasons. For the experimental plots studied during the first growing season, ELISA data indicated i random spatial pattern of the disease, whereas symptoms data, analyzed by ordinary runs test, showed only 13 out of 120 simples with clumped pattern. Symptom analysis during the next two seasons revealed only 3 of 23 samples with significant aggregation. No edge-to-center disease gradients were identified, suggesting that the vector does not disperse from nearby sources. Our results agree with the hypothesis of a random spatial pattern of this disease, consistent with i monocyclic nature

Semi-regular sequences and other random systems of equations

The security of multivariate cryptosystems and digital signature schemes relies on the hardness of solving a system of polynomial equations over a finite field. Polynomial system solving is also currently a bottleneck of index-calculus algorithms to solve the elliptic and hyperelliptic curve discrete logarithm problem. The complexity of solving a system of polynomial equations is closely related to the cost of computing Groebner bases, since computing the solutions of a polynomial system can be reduced to finding a lexicographic Groebner basis for the ideal generated by the equations. Several algorithms for computing such bases exist: We consider those based on repeated Gaussian elimination of Macaulay matrices. In this paper, we analyze the case of random systems, where random systems means either semi-regular systems, or quadratic systems in n variables which contain a regular sequence of n polynomials. We provide explicit formulae for bounds on the solving degree of semi-regular systems with m > n equations in n variables, for equations of arbitrary degrees for m = n+1, and for any m for systems of quadratic or cubic polynomials. In the appendix, we provide a table of bounds for the solving degree of semi-regular systems of m = n + k quadratic equations in n variables for 2 <= k; n <= 100 and online we provide the values of the bounds for 2 <= k; n <= 500. For quadratic systems which contain a regular sequence of n polynomials, we argue that the Eisenbud-Green-Harris Conjecture, if true, provides a sharp bound for their solving degree, which we compute explicitly.Comment: 27 pages, 4 table

Úlcera bilateral por Acanthamoeba em usuária de lentes de contato gelatinosas descartáveis: um incidente trágico ou uma conseqüência da política agressiva de venda de lentes de contato gelatinosas?

This is the report of a case of bilateral Acanthamoeba keratitis in a 19-year-old woman who bought a pair of disposable soft contact lenses in a boutique. She wore this same pair of lenses for 3 months daily without the appropriate care. This led to bilateral corneal transplantation with cataract extraction and also trabeculectomy in the right eye. When last seen, both grafts were crystal clear but the visual acuities were far from satisfactory. She also had bilateral secondary glaucoma, barely controlled by topical medication. Actually, the physical features and the wearing time characteristics of the disposable soft contact lenses created unprecedented difficulties to the medical surveillance of their wearers. Without the right assistance they tend to become careless regarding routine cleaning. They also feel free to buy less expensive lenses, to use saline instead of lens solutions, to violate the limits of wearing time and to extend the use over the sleeping period. Additionally, the aggressive marketing and the wide distribution of these lenses increase the chances that economically or educationally unprepared people will acquire them. The question that remains is: Is the present case an accidental event or an example of what is likely to happen in the future if the indiscriminate selling of disposable soft contact lenses continues to evolve?Este é o relato de uma paciente do sexo feminino, de 19 anos, com ceratite bilateral por Acanthamoeba, devido ao uso de lentes de contato descartáveis, adquiridas em uma butique. Fez uso do mesmo par de lentes durante três meses, sem os cuidados adequados. Foi submetida a transplante penetrante de córnea e facectomia bilateral, além de trabeculectomia no olho direito. Quando vista pela última vez, os enxertos estavam transparentes, mas a visão de ambos os olhos não era satisfatória. Ela também apresentava glaucoma secundário bilateral, controlado precariamente com medicação tópica. Ocorre que, as características físicas e o regime de uso das lentes de contato gelatinosas descartáveis criam dificuldades adicionais para a vigilância médica dos seus usuários. Sem a assistência correta, eles relaxam com a rotina de limpeza, compram lentes mais baratas, usam soro fisiológico ao invés das soluções adequadas, violam os limites de uso e dormem com as mesmas. Além disso, o "marketing" agressivo e a ampla distribuição dessas lentes aumentam as chances de que pessoas, não preparadas econômica e educacionalmente, venham ter acesso às mesmas. A pergunta que fica é: Seria o presente caso um evento acidental ou um exemplo do que pode acontecer no futuro caso as lentes de contato descartáveis continuem sendo vendidas indiscriminadamente