1,721,013 research outputs found
Linkage disequilibrium reveals different demographic history in egg laying chickens
Full text linkAbstract Background The availability of larger-scale SNP data sets in the chicken genome allows to achieve a higher resolution of the pattern of linkage disequilibrium (LD). In this study, 36 k and 57 k genotypes from two independent genotyping chips were used to systematically characterize genome-wide extent and structure of LD in the genome of four chicken populations. In total, we analyzed genotypes of 454 animals from two commercial and two experimental populations of white and brown layers which allows to some extent a generalization of the results. Results The number of usable SNPs in this study was 19 k to 37 k in brown layers and 8 k to 19 k in white layers. Our analyzes showed a large difference of LD between the lines of white and brown layers. A mean value of r2 = 0.73 ± 0.36 was observed in pair-wise distances of r2= 0.32 ± 0.33 was observed for SNPs less than 25 Kb apart from each other and dropped to 0.21 ± 0.26 at a distance of 100 kb in commercial brown layers. There was a remarkable similarity of the LD patterns among the two populations of white layers. The same was true for the two populations of brown layers, while the LD pattern between white and brown layers was clearly different. Inferring the population demographic history from LD data resulted in a larger effective population size in brown than white populations, reflecting less inbreeding among brown compared to white egg layers. Conclusions We report comprehensive LD map statistics for the genome of egg laying chickens with an up to 3 times higher resolution compared to the maps available so far. The results were found to be consistent between analyzes based on the parallel SNP chips and across different populations (commercial vs. experimental) within the brown and the white layers. It is concluded that the current density of usable markers in this study is sufficient for association mapping and the implementation of genomic selection in these populations to achieve a similar accuracy as in implementations of association mapping and genomic selection in mammalian farm animals.</p
Genetic resistance to natural helminth infections in two chicken layer lines
No full textGroups of Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) hens were reared under helminth-free conditions and kept afterwards together in a free range system. Mortality rate, body weight development, laying performance and faecal egg counts (FEC) were recorded during a 12 month laying period. At the end of the laying period, 246 LSL and 197 LB hens were necropsied and worms counted following the World Association for the Advancement of Veterinary Parasitology (W.A.A.V.P.) guidelines. In addition adult Heterakis gallinarum and Ascaridia galli were sexed and measured for length. Significant (P 0.05) different between the genotypes. There was no significant phenotypic correlation between body weight and worm burden in LSL, whereas it was the case in LB (r = 0.17, P < 0.05). Based on the estimated heritabilities it is possible to select for helminth resistance in both genotypes. (C) 2010 Elsevier B.V. All rights reserved
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Efficiency of genomic selection in an established commercial layer breeding program
Full text linkBackground: In breeding programs for layers, selection of hens and cocks is based on recording phenotypic data from hens in different housing systems. Genomic information can provide additional information for selection and/or allow for a strong reduction in the generation interval. In this study, a typical conventional layer breeding program using a four-line cross was modeled and the expected genetic progress was derived deterministically with the software ZPLAN+. This non-genomic reference scenario was compared to two genomic breeding programs to determine the best strategy for implementing genomic information in layer breeding programs. Results: In scenario I, genomic information was used in addition to all other information available in the conventional breeding program, so the generation interval was the same as in the reference scenario, i.e. 14.5 months. Here, we assumed that either only young cocks or young cocks and hens were genotyped as selection candidates. In scenario II, we assumed that breeders of both sexes were used at the biologically earliest possible age, so that at the time of selection only performance data of the parent generation and genomic information of the selection candidates were available. In this case, the generation interval was reduced to eight months. In both scenarios, the number of genotyped male selection candidates was varied between 800 and 4800 males and two sizes of the calibration set (500 or 2000 animals) were considered. All genomic scenarios increased the expected genetic gain and the economic profit of the breeding program. In scenario II, the increase was much more pronounced and even in the most conservative implementation led to a 60% improvement in genetic gain and economic profit. This increase was in all cases associated with higher breeding costs. Conclusions: While genomic selection is shown to have the potential to improve genetic gain in layer breeding programs, its implementation remains a business decision of the breeding company; the possible extra profit for the breeding company depends on whether the customers of breeding stock are willing to pay more for improved genetic quality
Virulence characterization of avian Enterococcus faecalis field isolates and genetic approach to select more resistant laying hens
No full textEn los últimos 20 años ha habido un importante avance en la comprensión de la amiloidosis sistémica A-amiloide, también conocida en las aves como artropatía amiloide (AA). Sin embargo, algunas cuestiones relacionadas con esta enfermedad permanecen sin resolver, tales como la mayor susceptibilidad de las estirpes semipesadas (marrones) en comparación con las estirpes ligeras (rubias), el mecanismo bioquímico de la patogénesis y las vías de transmisión, así como un posible tratamiento eficaz para prevenir o curar la enfermedad. La AA es el único tipo de amiloidosis asociado con infecciones crónicas inducidas por cepas de Enterococus (E.) faecalis y por lo tanto el tratamiento de esta enfermedad se ha enfocado hasta la fecha en la prevención y/o tratamiento de dicha infección. Dada la resistencia intrínseca y adquirida de E. faecalis hacia los antimicrobianos y las nuevas regulaciones para la reducción del uso de antibióticos en la producción animal, su tratamiento es cada vez más limitado. Además, se desconoce el riesgo que suponen las cepas de campo y actualmente es difícil estimar el grado de virulencia de éstas. En consecuencia, las medidas de control de la infección por E. faecalis, tales como la bioseguridad, la higiene, el uso responsable de antibióticos, el desarrollo de vacunas efectivas o la selección genética para aumentar la resistencia a la infección por E. faecalis, son imprescindibles. Por lo tanto, en la presente tesis se caracterizaron diferentes cepas aviares de E. faecalis y se evaluó la posibilidad de seleccionar gallinas ponedoras más resistentes a la infección de E. faecalis mediante el Ensayo de Letalidad Embrionaria (ELA), el cual se propone como un modelo alternativo para reemplazar los ensayos de desafío con aves adultas. La prueba de desafío en aves adultas es el modelo animal más utilizado hasta la fecha para determinar el grado de virulencia de hongos y bacterias, así como para la selección genética de aves más resistentes a enfermedades. Sin embargo, este modelo está actualemente limitado por la exposición a gran escala de las aves a patógenos, su complejidad, los costes que supone y por razones éticas. Por lo tanto, el objetivo del Experimento 1 fue desarrollar una metodología genérica del ELA como modelo diagnóstico para caracterizar la virulencia de cepas de E. faecalis en embriones de gallinas ponedoras ligeras Leghorn. De particular interés fue determinar la virulencia de la cepa aviar de E. faecalis K923/96 y estimar su dosis letal media (LD50) para utilizarla como cepa de referencia en estudios posteriores. Se realizaron un total de cuatro ELAs. Se inocularon 0,2 ml de cinco dosis infecciosas (de 2,5 a 2500 unidades formadoras de colonias (CFU)/ml) de la citada cepa en la cavidad alantoidea (AC) de embriones de 10 días de edad. Durante siete días se registró diariamente la tasa de mortalidad embrionaria (EMR) mediante ovoscopía y, en base a esta información, se calculó la LD50. La dosis infecciosa mostró un efecto significativo sobre la EMR. La EMR con las dosis 2,5, 5, 25, 250 y 2500 CFU/ml fue 43%, 45%, 63%, 90% y 93% respectivamente. Se estimó una LD50 de 6,6 CFU/ml. La mayor EMR se produjo tres y cuatro días post-inoculación (p.i.) con todas las dosis. En resumen, la metodología propuesta en este estudio puede utilizarse como referencia en estudios futuros sobre la virulencia de cepas de E. faecalis, aunque se debe tener en cuenta que la EMR producida en un ELA depende de la dosis; cuanto mayor es la dosis de infección, mayor es la EMR y menor el tiempo de supervivencia de los embriones. Con el objetivo de caracterizar la virulencia de diferentes cepas aviares de campo de E. faecalis, y así poder corroborar la capacidad del ELA para distinguir diferentes cepas, en el Experimento 2 se caracterizaron 68 cepas aviares de E. faecalis mediante el ELA. De particular interés fue caracterizar la diversidad genética de estas cepas mediante la Amplificación de Secuencias Intergénicas de Consenso Repetitivas de Enterobacterias (ERIC-PCR) bajo la hipótesis de que las cepas con patrones de bandas de ADN similares pueden ser similares también en su capacidad de producir infección. Se llevaron a cabo un total de 10 ELAs con subgrupos de 7-8 cepas y dos grupos control (positivo y negativo). Se inocularon de 3 a 24 CFU en la AC de embriones de 10 días de edad de gallinas ponedoras ligeras Leghorn. Durante siete días se registró diariamente la EMR mediante ovoscopía. El ELA fue capaz de diferenciar las cepas de E. faecalis con respecto a la EMR que produjeron. Se clasificaron 26 cepas de E. faecalis como avirulentas con una EMR inferior al 40%. Cinco cepas fueron altamente virulentas con una EMR por encima del 80%, y las 37 cepas restantes presentaron moderada virulencia con una EMR entre 40% y 80%. La mayor EMR se registró tres y cuatro días p.i. A partir del cuarto día apenas se obsevó mortalidad embrionaria, por lo que el ELA podría ser optimizado reduciendo el tiempo de observación a cuatro días. La ERIC-PCR no agrupó las cepas de acuerdo a su virulencia, aunque los patrones de bandas revelaron una considerable diversidad genética. En base a los resultados obtenidos, se puede concluir que el ELA es una herramienta fiable y útil para predecir la virulencia de cepas aviares de E. faecalis. Los resultados obtenidos en este experimento pueden utilizarse como base para futuras investigaciones sobre la virulencia de E. faecalis, y las cepas de alta patogenicidad halladas podrían ser buenas candidatas para la producción de vacunas. El objetivo del Experimento 3 fue investigar la posibilidad de seleccionar aves más resistentes a la infección por E. faecalis mediante el ELA, el cual se propone como un modelo alternativo para reemplazar el ensayo con aves adultas. Se llevó a cabo un estudio preliminar bajo la hipótesis de que los embriones de gallinas ponedoras semipesadas podrían ser más susceptibles que los embriones de gallinas ponedoras ligeras cuando se infectan con la misma cepa de E. faecalis y la misma dosis, ya que las gallinas ponedoras ligeras son menos susceptibles a la AA que las gallinas ponedoras semipesadas. Durante el estudio preliminar se llevaron a cabo seis ELAs. Se inocularon 0,2 ml de dos dosis infecciosas (2,5 y 5 CFU/ml) de la cepa de E. faecalis K923/96 en la AC de embriones de 10 días de edad de gallinas ponedoras semipesadas. Durante cuatro días se registró diariamente la EMR mediante ovoscopía. La dosis infecciosa mostró un efecto significativo sobre la EMR. La EMR media con las dosis de 2,5 UCF/ml y 5 CFU/ml fue 69% y 83% respectivamente, y fueron significativamente diferentes. En base a estos resultados, se infectaron 7563 embriones de 10 días de edad de 500 familias de gallinas ponedoras semipesadas (de uno a ocho embriones por familia) con una única dosis infecciosa de 2,5 CFU/ml de la cepa de E. faecalis K923/96 en tres ELAs adicionales. Durante cuatro días se registró diariamente la EMR mediante ovoscopía. Se estimaron los parámetros genéticos de la supervivencia embrionaria a la infección por E. faecalis para juzgar el valor de la selección genética, y se investigó la relación entre la supervivencia embrionaria y algunos parámetros de interés económico tales como el rendimiento de producción, el peso del huevo (EW), el peso corporal (BW), la resistencia a la rotura (BS) y la rigidez dinámica (Kdyn). La EMR media de estos tres ELAs fue 50% y la mayor mortalidad se produjo los días tres y cuatro p.i., como era de esperar. La heredabilidad estimada para la supervivencia embrionaria a la infección por E. faecalis fue h2= 0,17 – 0,20 indicando que la selección de gallinas ponedoras más resistentes a la infección por E. faecalis es factible. Sin embargo, se estimó una alta correlación genética entre la supervivencia embrionaria y el rendimiento de producción en el pico de puesta (rg= -0,69) y al final de la producción (rg= -0,55), así como con BS (de rg= -0,48 a -0,30), lo cual es indeseable desde el punto de vista de la selección genética. Se encontró una correlación positiva entre EW y la supervivencia embrionaria (rg= +0,16) y no se observó correlación genética con BW y Kdyn. Por lo tanto, aunque se ha demostrado que es posible seleccionar aves más resistentes a la infección por E. faecalis, esto podría penalizar la mejora de otros parámetros importantes. En base a los resultados obtenidos en la presente tesis se puede concluir que el ELA es una herramienta útil y fiable para la caracterización de la virulencia de cepas aviares de E. faecalis así como para la selección de gallinas ponedoras más resistentes a la infección por E. faecalis, el cual puede utilizarse como modelo alternativo para sustituir los ensayos de desafío con aves adultas. La caracterización de la virulencia de las cepas aviares de E. faecalis aisladas en brotes de campo nos permite conocer el riesgo que éstas suponen y proporciona información valiosa para futuras investigaciones epidemiológicas. Además, esta información puede ser importante en la selección de aislados para la producción de vacunas. En cuanto a la posibilidad de seleccionar gallinas ponedoras más resistentes a la infección por E. faecalis, la heredabilidad estimada para la supervivencia embrionaria a la infección por E. faecalis indica que es factible. No obstante, las correlaciones indeseables entre la capacidad de supervivencia embrionaria y algunos de los parámetros analizados muestran la necesidad de tener en cuenta todos los parámetros y sus correlaciones genétias para lograr un progreso genético equilibrado. La presente tesis ofrece una nueva perspectiva para la implementación de la selección genética para la susceptibilidad de E. faecalis en gallinas ponedoras. La implementación práctica de la selección contra la susceptibilidad a la infección por E. faecalis requerirá que la empresa de genética se convenza de que la AA tiene una importancia económica significativa, la cual depende de la incidencia de la enfermedad, los costes de producción y las pérdidas asociadas a los animales enfermos además de las preocupaciones sobre el bienestar de los animales y la seguridad alimentaria de los consumidores. ----------ABSTRACT----------
In the last twenty years, major progress in the understanding of systemic amyloid-A amyloidosis, also known as amyloid arthropathy (AA) in chickens, has been gained. However, several topics related to this disease remain unclear, such as the higher susceptibility of brown layers compared to white layers, the biochemical mechanism of the pathogenesis and the transmission route as well as a possible effective treatment to prevent or cure the disease. AA is the only type of amyloidosis that has been associated with chronic infections induced by Enterococcus (E.) faecalis strains and, therefore, the treatment of this disease has focused to date on the prevention and/or treatment of this infection. Given the intrinsic and acquired resistance of E. faecalis to several antimicrobials and the new regulations to reduce the antibiotic use in animal production, its treatment becomes more complicated. Additionally, little is known about the risk from field avian E. faecalis strains and it is currently difficult to estimate its virulence degree. Consequently, control measures against E. faecalis infection such as biosecurity, hygiene, responsible use of antibiotics, development of effective vaccines or the breeding and genetic selection are essential. Therefore, in the present dissertation different avian E. faecalis field strains were characterized and the possibility to select more resistant laying hens against E. faecalis infection through the Embryo Lethality Assay (ELA) was investigated. The ELA is proposed as an alternative model to replace the adult avian challenge assays. To date, adult avian challenge assay is the most used animal model in order to determine the degree of virulence of isolated fungi and bacteria, as well as in the selection for disease resistance. However, this model is currently limited by the exposure to pathogens on a large scale, its technical complexity, the cost associated and for ethical reasons. Therefore, the aim of the Experiment 1 was to develop a generic methodology of the ELA as a diagnostic model to establish the pathogenicity of E. faecalis strains in embryos of White Leghorn layers. Of particular interest was to determine the virulence of the avian E. faecalis strain K923/96 and assess its median lethality dose (LD50) in order to use it as reference strain in further analyses. The ELA was repeated four times. 0.2 ml of different infectious doses of the cited strain (from 2.5 to 2500 colony-forming units (CFU) per ml) were inoculated into the allantoic cavity (AC) of 10-day-old embryos. The embryo mortality rate (EMR) was determined by daily candling of the eggs over a period of seven days and based on this information the LD50 was calculated. The infectious dose showed a significant effect on the EMR. The EMR with the doses of 2.5, 5, 25, 250 and 2500 CFU/ml was 43%, 45%, 63%, 90% and 93%, respectively. The estimated dose at LD50 was 6.6 CFU/ml. The highest EMR was recorded after three and four days post-inoculation (p.i.) in all doses. In summary, the methodology proposed in this experiment can be used as reference in further researches on E. faecalis virulence taking into account that the EMR produced in the ELA depends on the dose; the higher the infectious dose, the greater the EMR and the lower the embryo survival time. In order to characterize the virulence of different avian E. faecalis field strains and thus corroborate the ELA capacity for distinguishing E. faecalis strains, 68 avian E. faecalis strains through the ELA were characterized in the Experiment 2. Of particular interest was to characterize the genetic diversity of these strains by Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) under the hypothesis that strains with similar DNA banding patterns might be similar also in its infective ability. The ELA was performed ten times with subsets of 7-8 E. faecalis strains on a sample of 9987 eggs, including two control groups (positive and negative). An estimated 3-24 CFU were inoculated into the AC of 10-day-old embryos of White Leghorn layer hens. The EMR was determined by means of candling the eggs over a period of seven days. The ELA was able to distinguish the virulence of the E. faecalis strains. Twenty-six strains were considered as avirulent strains with an EMR of below 40%. Five strains were highly virulent with an EMR above 80%, and the remaining 37 strains were classified as strains of moderate virulence, causing an EMR between 40% and 80%. The highest EMR occurred three and four days p.i. From the fourth day p.i., almost no embryonic mortality was observed. Therefore, the ELA could be optimized by reducing experiment duration to four days p.i. ERIC-PCR did not cluster the strains according to its virulence, although ERIC banding patterns revealed a considerable genetic diversity. In conclusion, the ELA can be considered a reliable and useful tool to predict the virulence of avian E. faecalis strains. The results obtained in this experiment can be used as a basis for future researches on the E. faecalis virulence, and high pathogenic isolates tested might be good candidates for the production of vaccines. The aim of the Experiment 3 was to investigate the possibility to select more resistant laying hens against E. faecalis infection through the ELA, which is proposed as an alternative model to replace the adult avian challenge assays. A preliminary study was first carried out under the hypothesis that chicken embryos of brown layers would be more susceptible compared with embryos of white layers when they are infected with the same E. faecalis strain and infectious dose since white layers are less susceptible to AA than brown layers. To this end, the ELA was performed six times in the preliminary study. 0.2 ml of two infectious doses of the avian E. faecalis strain K923/96 (2.5 and 5 CFU/per ml) were inoculated into the AC of 10-day-old embryos of brown layers. The EMR was determined by daily candling of the eggs over a period of four days. The infectious dose showed a significant effect on the EMR. The average EMR estimated for the doses of 2.5 and 5 CFU/ml was 69% and 83%, respectively. They differed significantly from each other. On the basis of these results, 7563 embryos of 10-day-old from 500 families of brown layers (from one to eight embryos per family) were inoculated into the AC with only one infectious dose of 2.5 CFU/ml of the avian E. faecalis strain K923/96 in three more ELAs. The EMR was determined by daily candling of the eggs over a period of four days. Genetic parameters of embryonic survivability to E. faecalis infection were estimated to judge the possibility to apply the value of genetic selection. Furthermore, the genetic correlation between embryonic survivability and some traits of economic interest such as laying performance, egg weight (EW), body weight (BW), breaking strength (BS) and dynamic stiffness (Kdyn) was calculated. The average EMR estimated of these three ELAs was 50% and the highest EMR occurred three and four days p.i. as expected. The estimated heritability for embryonic survivability to the infection by E. faecalis was h2 = 0.17 – 0.20 indicating that the selection of more resistant laying hens to E. faecalis infection is feasible. However, a high genetic negative correlation was estimated between embryonic survivability and laying performance at the peak of lay (rg= -0.69) and at the end of the production (rg= -0.55), as well as with BS (rg = -0.48 to -0.30), which is undesirable from a breeding point of view. A positive correlation was found between EW and the embryonic survivability (rg= +0.16) and no genetic correlation with BW and Kdyn was found. Therefore, although it was demonstrated that it is possible to breed for E. faecalis resistance, the improvement of other important traits will be penalized. On the basis of the results obtained in the present dissertation it can be concluded that the ELA is a reliable and useful tool to characterize the virulence of avian E. faecalis strains as well as to select more resistant laying hens against E. faecalis infection, which can be use as alternative model to replace the adult avian challenge assays. Virulence characterization of avian E. faecalis field isolates allows us to know the risk that the strains represent and provide valuable information, which can be important for the selection of isolates for the production of vaccines. Regarding to the possibility to select more resistant laying hens against E. faecalis infection, the estimated heritability for embryonic survivability to the infection of E. faecalis indicates that it is feasible. However, the undesirable correlations between the embryonic survivability and some analysed traits show the need to take into account all traits and their genetic correlations to achieve a balanced genetic progress. A new perspective for the implementation of genetic selection for E. faecalis susceptibility in laying hens is offered in the present dissertation. Practical implementation of selection against susceptibility to E. faecalis infection will require that breeding company is convinced that AA is of significant economic importance, which depends on disease incidence, production costs and losses associated with sick and/or dead birds, in addition to welfare and food safety concerns of consumers
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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