A major challenge in the post-genomic era is to understand how genome sequence variants (genotype) give rise to the enormous diversity observed in terms of morphology, physiology and behavior (phenotype) among living organisms. Domestic animals—with their tremendous phenotypic variation—are excellent model organisms for determining the relationships between genotype and phenotype. In this thesis, I describe the utilization of the chicken, in combination with modern genetic and genomic approaches, in developing our understanding of the genetic mechanisms underlying phenotypic variation. These studies provide novel information on the genetics behind variation in carotenoid- and melanin-based pigmentation—observed in many organisms—and also cast light on the genetic basis of chicken domestication. In paper I, we report that the yellow skin phenotype—observed in most commercial chickens—is caused by one or several tissue-specific mutations altering the expression of beta-carotene oxygenase 2 (BCO2 or BCDO2) in skin. In addition, we present the first conclusive evidence of a hybrid origin of the domestic chicken, since the allele causing yellow skin most likely originates from the grey jungle fowl (Gallus sonneratii) and not from the previously described sole ancestor, the red jungle fowl (Gallus gallus). In paper II, we detect a number of loci that were likely important during the domestication process of chicken and the later specialization into meat (broiler) and egg (layer) producing lines. One of the major findings was that worldwide, almost all domestic chickens carry a missense mutation in TSHR (thyroid stimulating hormone receptor) in a position that is completely conserved amongst vertebrates. We speculate that this “domestication-mutation” has played an important role in the transformation of the wild red jungle fowl ancestor into the modern domestic chicken. In paper III, we demonstrate that the dilution of red (pheomelanin) pigmentation—observed in the plumage of the Inhibitor of Gold chicken—is caused by a frame-shift mutation in the catechol-O-methyltransferase domain containing 1 (COMTD1) gene. The production and regulation of pheomelanin is poorly understood and this discovery advances our current knowledge of this pathway.

The purpose of this thesis is to gain knowledge about howthe public library in Skövde is being used as a public spaceand how different zones in the library are used according tothe theoretical perspective “the four spaces” byJochumsen, Hvenegaard Rasmussen and Skot-Hansen.The model consists of four abstract overlapping spaceswhich are inspiration space, learning space, meeting space,and performative space.The research method used in this study isthe observational method seating sweeps. The findingsfrom the observations were compiled in SPSS andfrom the diagrams that were developed we analysed theresults according to “the four spaces” model. The researchquestions used in this thesis are “How are the differentparts of the physical library room being used? and“How is the library used as a public place?”. Thefindings from Skövde public library were that usersused the different zones in different ways; using zone 1primarily as meeting place, inspiration place andperformative space; using zone 2 primarily as a learningplace; using zone 3 primarily as inspiration place andperformative place; and using zone 4 primarily asa learning place. Findings also showed that Skövde publiclibrary is mainly functioning as a low-intensivemeeting-place, but also has the opportunity to offer a highintensivemeeting-place for users.

No description available.

Expectations substantially influence perception, but the neural mechanisms underlying this influence are not fully understood. A prominent view is that sensory neurons encode prediction error with respect to expectations on upcoming sensory input. Although the encoding of prediction error has been previously demonstrated in the human auditory cortex (AC), previous studies often induced expectations using stimulus repetition, potentially confounding prediction error with neural habituation. These studies also measured AC as a single population, failing to consider possible predictive specializations of different AC fields. Moreover, the few studies that considered prediction error to stimuli other than pure tones yielded conflicting results. Here, we used functional magnetic resonance imaging (fMRI) to systematically investigate prediction error to subjective expectations in auditory cortical fields Te1.0, Te1.1, Te1.2, and Te3, and two types of stimuli: pure tones and frequency modulated (FM) sweeps. Our results show that prediction error is elicited with respect to the participants’ expectations independently of stimulus repetition and similarly expressed across auditory fields. Moreover, despite the radically different strategies underlying the decoding of pure tones and FM-sweeps, both stimulus modalities were encoded as prediction error in most fields of AC. Altogether, our results provide unequivocal evidence that predictive coding is the general encoding mechanism in AC.

Les bactéries symbiotiques facultatives, transmises verticalement de mère à descendants, sont connues pour avoir des effets importants sur la reproduction de leurs hôtes (incompatibilité cytoplasmique et biais de sex-ratio), sur l’adaptation à des situations de stress (spécialisation, résistance aux pathogènes et aux fortes températures) ainsi que sur l’évolution de l’ADN mitochondrial par l’induction de balayages sélectifs. Bemisia tabaci est un complexe d’espèces divisé en nombreux biotypes, principalement différenciés sur la base de marqueurs moléculaires (essentiellement mitochondrial). Cet insecte héberge 7 symbiotes, 1 symbiote nutritionnel obligatoire et 6 symbiotes facultatifs. Nos résultats ont montré une extrême diversité ainsi qu’une prévalence exceptionnelle des bactéries symbiotiques chez B. tabaci. Leur dynamique rapide a entraîné de nombreux balayages sélectifs sur l’ADN mitochondrial influençant nettement son évolution. La très forte fréquence des infections multiples chez cet insecte peut certainement être expliquée par la co-localisation de l’ensemble des bactéries au sein des mêmes cellules, avec le symbiote nutritionnelle. Enfin, la coexistence de différents cytotypes en sympatrie offre l’opportunité d’étudier les interactions qui se mettent en place entre différentes communautés symbiotiques et comment ces systèmes vont évoluer / Facultative endosymbiotic bacteria that are vertically transmitted from mother to offsprings, have important effects on their host reproduction (cytoplasmic incompatibilities and sex-ratio biais), on host adaptation to situation of stress (specialization, resistance against pathogens or high temperature) and also on the evolution of mtDNA, by inducing selective sweeps. Bemisia tabaci is a species complex divided into numerous, mainly differentiated based on molecular markers (essentially mtDNA markers). This insect is infected by 7 bacterial symbionts, one nutritionnal symbiont that is obligatory and 6 facultative symbionts. Our results show an extreme diversity of symbionts in this insect and a very high prevalence in B. tabaci populations. Moreover their rapid dynamic has strongly influenced mtDNA evolution by inducing recurrent selective sweeps. The colocalization of the whole symbiotic community in the same cells, with the nutritional symbiont, might certainly explain the very high frequency of multiple infections in B. tabaci. Finally, coexistence of very different cytotypes in sympatry allows to study the interactions that take place between different symbiotic communities and how these systems will evolve

A cana-de-açúcar (Saccharum ssp.) é uma cultura valiosa na produção de alimento, fibra e energia para o Brasil e, especialmente, para o estado de São Paulo. Com o advento da biotecnologia, alternativas de melhoramento genético têm despertado a atenção da comunidade científica, sendo etapas cruciais para tais avanços o sequenciamento e a caracterização do genoma das espécies cultivadas. Dada sua natureza poliploide, com frequente aneuploidia, a cana-de-açúcar apresenta dificuldades às práticas convencionais em genômica, de maneira que é vantajoso fazer uso de recursos de sequenciamento de nova geração e de espécies próximas para elucidar de forma mais efetiva o genoma da gramínea. Uma contribuição interessante, nesse sentido, é a caracterização funcional de polimorfismos genéticos existentes entre genótipos do gênero Saccharum, auxiliando investigações relacionadas à genômica de poliploides complexos, desenvolvendo um recurso a ser utilizado futuramente por melhoristas. Esse trabalho realizou a caracterização da variabilidade genômica a partir de dados genotípicos de indivíduos do Painel Brasileiro de Genótipos de Cana-de-Açúcar, obtidos via genotipagem-por-sequenciamento, utilizando como referência o genoma já sequenciado do sorgo. Os sítios variantes (sobretudo polimorfismos de nucleotídeo único) foram detectados com o software FreeBayes e suas possíveis funções e posições foram anotadas com o programa SnpEff. Utilizaram-se estatísticas de genética de populações, como a frequência alélica para várias classes de polimorfimo, o Teste de McDonald & Kreitman (busca de evidêcias de evolução adaptativa) e a heterozigosidade combinada (busca de regiões genômicas com assinatura de seleção), de modo a identificar regiões genômicas potencialmente envolvidas em eventos evolutivos. Os resultados demonstraram a perda de variabilidade entre os genótipos melhorados em relação aos ancestrais, com evidências de assinaturas de seleção, envolvendo questões sensíveis ao funcionamento da maquinaria celular (como respiração e fotossíntese) e a características valoradas para a cultura (destacando-se a resistência a patógenos e a biossíntese da sacarose). Tais indícios fornecem subsídios à compreensão do genoma e ao melhoramento genético desse poliploide. / Sugarcane (Saccharum ssp.) is a valuable crop for food, fiber and energy production in Brazil, especially to the São Paulo State. With the advent of biotechnology, alternatives to breeding have enticed attention of the scientific community, with genome sequencing and characterization being crucial steps to these advances. Because sugarcane is polyploid, with frequent aneuploidy, it presents difficulties to the application of standard practices in genomics, such that it is advantageous to make use of next generation sequencing alternatives and resources from related species to more effectively elucidate the genome of this grass. Thus, an interesting contribution is the functional characterization of genetic polymorphisms from the Saccharum genus, aiding investigations related to genomics of complex polyploids, developing a resource to be used in the future by breeders. Our goal was to perform this characterization with genotypic data from individuals of the Brazilian Panel of Sugarcane Genotypes, obtained by genotyping-by-sequencing (GBS), using as reference the previously sequenced sorghum genome. We called the variants (mainly single nucleotide polymorphisms) with FreeBayes and annotated their functions and positions with SnpEff. We used population genetics statistics, such as the allele frequency, the McDonald & Kreitman Test and the pooled heterozygosity, to identify genomic regions potentially involved in evolutionary events. The results showed a loss of variability between bred genotypes in relation to the ancestors, with evidences of selective sweeps, involving regions related to the cellular machinery (such as respiration and photosynthesis) and specific crop traits (especially disease resistance and sucrose biosynthesis). These results support understanding of the genome and breeding efforts in this polyploid grass.

A central issue in auditory research is how the auditory brain encodes complex stimuli. However, the process by which the auditory cortex interprets complex sounds during development and the extent to which cortical organization can be manipulated by complex stimulation is still undetermined. We have addressed this gap in the following three studies. First, we characterized the responses of cortical neurons in adult chinchillas to frequency-modulated (FM) stimulation. Next, we asked whether FM coding at the cortical level is innate or if its development is influenced by normal postnatal environmental experience. Finally, we investigated the effect of sustained neonatal FM sweep exposure on the development of cortical responses to tonal and FM stimuli. In our adult study, results indicated that >90% of sampled neurons were responsive to FM sweeps. The population preference was for upward FM sweeps and for medium to fast speeds ( 0.3 kHz/ms). Three types of temporal response patterns were observed: a single peak at sweep onset/offset (‘onset’) and a single peak (‘late’) or multiple peaks (‘burst’) during the sweep. ‘Late’ units expressed the highest direction and speed selectivity; ‘onset’ units were selective only for direction and ‘burst’ units were selective for neither direction nor speed. In our developmental study, our results showed a significant developmental increase in FM direction selectivity. However, FM speed selectivity appeared to be established early in development. In our developmental plasticity study, we hypothesized that constant FM exposure would increase the proportion of auditory neurons that are selectively responsive to the conditioning FM sweep. However, our results showed that while tonal response latencies increased after the exposure period, the conditioning stimulus had minimal effect on the FM direction preferences of cortical neurons and decreased overall neuronal FM speed selectivity. In conclusion, we suggest that chinchilla auditory cortical neurons are not uniquely activated by FM sounds but that FM responses are largely predictable based on how changing frequency stimuli interact with the receptive fields of these neurons. We also propose that the development of FM direction sensitivity is experience-independent and that perhaps normal acoustic experience is required to maintain FM speed tuning.

A central issue in auditory research is how the auditory brain encodes complex stimuli. However, the process by which the auditory cortex interprets complex sounds during development and the extent to which cortical organization can be manipulated by complex stimulation is still undetermined. We have addressed this gap in the following three studies. First, we characterized the responses of cortical neurons in adult chinchillas to frequency-modulated (FM) stimulation. Next, we asked whether FM coding at the cortical level is innate or if its development is influenced by normal postnatal environmental experience. Finally, we investigated the effect of sustained neonatal FM sweep exposure on the development of cortical responses to tonal and FM stimuli. In our adult study, results indicated that >90% of sampled neurons were responsive to FM sweeps. The population preference was for upward FM sweeps and for medium to fast speeds ( 0.3 kHz/ms). Three types of temporal response patterns were observed: a single peak at sweep onset/offset (‘onset’) and a single peak (‘late’) or multiple peaks (‘burst’) during the sweep. ‘Late’ units expressed the highest direction and speed selectivity; ‘onset’ units were selective only for direction and ‘burst’ units were selective for neither direction nor speed. In our developmental study, our results showed a significant developmental increase in FM direction selectivity. However, FM speed selectivity appeared to be established early in development. In our developmental plasticity study, we hypothesized that constant FM exposure would increase the proportion of auditory neurons that are selectively responsive to the conditioning FM sweep. However, our results showed that while tonal response latencies increased after the exposure period, the conditioning stimulus had minimal effect on the FM direction preferences of cortical neurons and decreased overall neuronal FM speed selectivity. In conclusion, we suggest that chinchilla auditory cortical neurons are not uniquely activated by FM sounds but that FM responses are largely predictable based on how changing frequency stimuli interact with the receptive fields of these neurons. We also propose that the development of FM direction sensitivity is experience-independent and that perhaps normal acoustic experience is required to maintain FM speed tuning.

This study examined portrayals of African-American women shown in professional careers on prime-time network television during the May 2005 sweeps month. Specifically, the study compares these portrayals to actual U.S. Department of Labor workforce statistics to observe a possible similarity. Additionally, the study identifies any behavioral and conversational stereotyped attributes ascribed to African-American female characters shown in the workplace. A quantitative content analysis of four broadcast networks (FOX, ABC, UPN, and WB) ranked by Nielsen Media as having the highest rated prime-time television programming among minority households for 2003-2004 revealed that African-American female characters on network television are over-represented in terms of professional careers in comparison to their actual presence in U.S. workforce statistics. However, their actual presence in these careers is higher than that of African-American male characters on network television, which closely resembles the distribution of professional African-American males and females in the U.S. working population. The results also revealed that out of the four networks, UPN had a substantially greater number of African-American female characters in professional careers, but their representations include subtle messages of racial/ethnic stereotypical behaviors commonly associated with African-Americans.

The purpose of this thesis is to strengthen the state of knowledge and understanding of visitors use of the library area at Skellefteå city library based on the development of guidelines for how to work with the future library area based on Jochumsen, Hvenegaard Rasmussen, Skot-Hansen’s (2012) model of the four-spaces. The model contains four important spaces for libraries; the learning, the inspiration, the meeting and the performative space and all of them interact in an ideal library. The research question in this study is: How does the library in Skellefteå work as an inspiring, learning, meeting and performative space? And according to these questions, what kind of model should a new library have according to the four-spaces? The research method that is used in this study is Given and Leckie´s observational method the seating sweeps and complementing interviews with both visitors and one of the managing librarians. The result illustrated that the most common activity was the physical search for books among children, young adults and adults. For elderly people and especially men the most popular activity was reading the newspaper. These findings showed that the library is used primarily as learning and meeting space for adults but as an inspiring and performative space only for the younger children.