Transposable elements (Transposons; TEs) constitute the majority of DNA in genomes and are a major source of genetic polymorphisms. TEs act as potential regulators of gene expression and lead to phenotypic plasticity in plants and animals. In crops, several TEs were identified to influence alleles associated with important agronomic traits, such as apical dominance in maize and seed number in rice. Crops may harbor more TE-mediated genetic regulations than expected in view of multifunctional TEs in genomes. However, tools that accurately annotate TEs and clarify their associations with agronomic traits are still lacking, which largely limits applications of TEs in crop breeding. Here we 1) evaluate performances of popular tools and strategies to identify TEs in genomes, 2) develop a tool 'DeepTE' to annotate TEs based on deep learning models, and 3) develop a tool 'TE-marker' to identify potential TE-regulated alleles associated with agronomic traits. As a result, we propose a series of recommendations and a guideline to develop a comprehensive library to precisely identify TEs in genomes. Secondly, 'DeepTE' classifies TEs into 15-24 super families according to sequences from plants, metazoans, and fungi. For unknown sequences, this tool can distinguish non-TEs and TEs in plant species. Finally, the 'TE-marker' tool builds a TE-based marker system that is able to cluster rice populations similar to a classical SNP marker approach. This system can also detect association peaks that are equivalent to the ones produced by SNP markers. 'TE-marker' is a novel complementary approach to the classical SNP markers that it assists in revealing population structures and in identifying alleles associated with agronomic traits. / Doctor of Philosophy / Transposable elements (Transposons; TEs) are DNA fragments that can jump and integrate into new positions in the genome. TEs potentially act as regulators of gene expression and alter traits of plants and animals. In crops, several TEs were identified to influence functions of genes that control important agronomic traits, such as branching in maize and seed number in rice. However, tools that identify these associations in the crops are still lacking, which largely limits applications of TEs in crop breeding. Here we evaluated performance of popular tools and strategies that identify TEs, and provide a series of recommendations to efficiently apply these tools to the TE identification. In view of structural and sequence differences, TEs are classified into multiple families. We developed a 'DeepTE' tool to precisely cluster TEs into different families using a deep learning method. Finally, a 'TE-marker' tool was developed to build TE-based genetic markers to identify nearby alleles associated with agronomic traits. Overall, this work could promote the use of TEs as markers in improving quality and yielding crops.

Two concerns dominate speculation about the lack of progress in motivational disposition research. First, truly unique dispositional constructs have not been identified since wide acceptance of the approach / avoidance distinction. Second, research has largely neglected to account for context in models of motivated behavior. Effective avoidance has systematically been unassessed in motivation research. Social cognitive theory was used to define an effective avoidance motivational trait, vigilance, as an antecedent to effective regulatory behaviors that are avoidant in nature and/or strategy. Two studies were conducted: First, development and psychometric evaluation of a scale measuring vigilance within the existing motivational trait framework (Heggestad and Kanfer, 2000). Exploratory and confirmatory analyses provided initial validity evidence for the vigilance construct; composed of diligence and error-detection facets. Convergent – discriminant analysis revealed that vigilance is significantly related to approach and avoidance motivational constructs identifying two possible sources of contamination in self-report measures of motivational traits. Measurement items may be contaminated with implied outcomes and measurement items may be contaminated with generalized self-efficacy. In the second study, a within-subjects experiment tested the predictive validity of the vigilance measurement scale for task-specific self-efficacy and performance on a task that rewards avoidance-oriented strategies. Vigilance predicted prevention task-specific self-efficacy ( = .29) in one of two experimental conditions. The validation study also offered construct validity evidence for the vigilance construct. Implications and future directions are discussed. / Ph. D.

Research has shown that children displaying conduct problems (CP) early in life are at greater risk for severe CP and other negative outcomes later in life. However, not all children with early-onset CP will develop severe CP over the life-course. Thus, it is important to identify those at greater risk, preferably as early as possible, in order to adequately prevent a negative development. Psychopathic traits have received much attention in research on risk for severe CP, involving attempts to extend these traits, and their association to CP to childhood. However, research has thus far mainly focused on one dimension of psychopathic traits, that is callousunemotional (CU) traits, to some extent neglecting two other dimensions of traits commonly included in a psychopathic personality: an interpersonal, and a behavioural dimension. Hence, we still do not know if a full psychopathic personality is identifiable in early childhood, and if and how it is related to the development of severe and persistent CP. The aim of this dissertation was to examine if a psychopathic personality could be identified in early childhood, if psychopathic traits are stable over time, and if and how the psychopathic personality is related to childhood CP. Overall, the results show that psychopathic traits, as well as the display of a psychopathic personality, could be identified in early childhood. These traits were stable over time, and they were clearly and strongly related to childhood CP. Additionally, the combination of early-onset CP and a full psychopathic personality seems to be the most precarious for severe and persistent CP, even more so than the combination of CP and CU traits. With careful consideration to ethical aspects, these results are discussed both in relation to a developmental psychopathology perspective on CP, as well as in relation to diagnostic practice as it is framed today.

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Made available in DSpace on 2014-06-11T19:22:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-12-17Bitstream added on 2014-06-13T18:48:43Z : No. of bitstreams: 1 pincelli_rp_me_botfca.pdf: 933139 bytes, checksum: dc525360fa3fad2d769f79bc71a084be (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / A seca é um dos principais fatores limitantes à produtividade agrícola ao redor do mundo. Com a expansão da área de plantio da cana-de-açúcar para regiões brasileiras caracterizadas por apresentarem deficiência hídrica por longos períodos durante o ano, torna-se essencial a obtenção de germoplasma de cana-de-açúcar tolerante a esse estresse. Identificar ferramentas adequadas de seleção e características quantificáveis podem facilitar o processo de melhoramento da cultura para tolerância à seca, visto que há dificuldade em identificar características únicas que possam ser utilizadas para a seleção. O objetivo do presente trabalho foi verificar a habilidade de algumas variáveis morfofisiológicas para distinguir entre tolerantes e susceptíveis quatro cultivares comerciais de cana-de-açúcar sob dois regimes hídricos. O experimento foi conduzido em vasos contendo 22 litros de substrato, em casa de vegetação localizada na Unidade de Pesquisa e Desenvolvimento da APTA Polo Centro-Oeste, Jaú,SP. O delineamento experimental foi inteiramente casualizado, em esquema fatorial 4x2x3 (cultivares x regimes hídricos x épocas de avaliação), com três repetições. Aos 84 dias após a emergência, as cultivares RB72454, RB855453, SP81-3250 e SP83-2847 foram submetidas aos tratamentos de teor de umidade (%): sem deficiência (-D) e com deficiência (+D) promovida por 50% do teor de umidade ideal e avaliadas durante três épocas: 0, 28 e 56 dias após o início dos tratamentos. As variáveis avaliadas foram: altura do colmo, número de folhas verdes, comprimento e largura da folha +3, área foliar, densidade estomática, massa foliar específica, estimativa do conteúdo de clorofila (via SPAD e via espectrofotômetro), máxima eficiência fotoquímica do fotossistema II (Fv/Fm), condutância estomática, conteúdo relativo de água, potencial hídrico foliar e massa... / Drought is one of major limiting factors to agricultural productivity around the world. With the expansion of planting area of sugarcane for Brazilian regions characterized by water stress for long periods during the year, it becomes essential to obtain germplasm of tolerant sugarcane. Identify appropriate tools for selection and quantifiable characteristics can facilitate the process of crop breeding for drought tolerance, since there is difficulty in identifying unique characteristics that can be used for selection. This study aimed to verify the ability of some morphological and physiological variables to distinguish between tolerant and susceptible four sugarcane commercial cultivars under two water regimes. The experiment was carried out in pots containing 22 liters of substrate, in a greenhouse located in the Unit of Research and Development of APTA, Jaú, SP. The experimental design was randomized in factorial 4x2x3 (genotypes x water regimes x evaluation times) with three replicates. At 84 days after emergence, cultivars RB72454, RB855453, SP81-3250 and SP83-2847 were exposed to humidity treatments: no stress (-D) and stress (+ D) promoted by 50% of the ideal humidity and evaluated for three times: 0, 28 and 56 days after the initiation of the treatments (DAT). The variables evaluated were: stalk height, green leaf number, length and width of leaf +3, leaf area, stomatal density, specific leaf mass, estimated chlorophyll content (via SPAD and via spectrophotometer), maximum photochemical efficiency of photosystem II (Fv/Fm), stomatal conductance, relative water content, leaf water potential and dry weight of shoots and roots. We found a higher height of stalk, number of green leaves, leaf area, stomatal density at adaxial and abaxial surfaces, higher maximal photochemical efficiency of photosystem II (Fv/Fm), estimation of chlorophyll content (SPAD index) and leaf water potential... (Complete abstract click electronic access below)

Chicken is a major protein source and intensively selected for economically important traits by humans. As such, this generated a huge range of phenotypes that representing a diverse spectrum of genetic variation. Understanding the functional basis of the genetic variants that underlie these traits, however, remains a formidable endeavour particularly for complex traits. Nonetheless, molecular phenotyping of an organism from sequenced data is doable with the advances in bioinformatics analysis and unparalleled surveys of genome wide genetic variants. This provides the opportunity to gain insights into the genome architecture and assists in identifying chromosomal regions underlying selection through a “sequences to consequences” approach. Combining a whole genome re-sequencing (WGS) approach with the knowledge of selection history, this thesis aimed to study the chromosomal regions and genetic variants underlying traits of interest in various selected chicken populations. To achieve this, genetic (quantitative and population genetics), genomic and bioinformatics approaches were employed and integrated to investigate the genome wide selection signatures in a number of different lines of chicken selected for different complex traits. This includes analysing: (i) divergently selected broilers for fatness traits (Chapter 2), (ii) a closed population of layer chickens (Chapter 3), (iii) selection signatures unique to broiler or layer chickens (Chapter 4) and (iv) selection signatures in colony stimulating factor 1 (CSF1) associated with gene expression differences in broiler and layer populations (Chapter 5). Candidate genes and nucleotides underlying potential selection regions were identified, and attempts were made to further elucidate the potential interplay between genes and the biological pathways involved in regulating traits in these selected chicken lines. Incorporating integrative approaches, variants within selection signatures were annotated to provide further evidence of their functional consequences. Overall, non-coding regions were enriched in selection signatures implied that causative variants may have regulatory roles. Capitalising on the millions of genetic variants discovered from WGS, chromosomal regions subject to selection were detected using a number of population genetics statistics. In broiler chicken lines divergently selected for very low-density plasma lipoprotein (VLDL) (Chapter 2), incorporating signatures of selection helped to improve the resolution of previously mapped quantitative traits loci (QTL) intervals. This research demonstrated that the integration of the analysis of selection signatures with functional annotation of genetic variants enabled refinement and characterisation of the QTL for fatness traits. In a closed population of brown leghorn layers (Chapter 3), evidence of selection signatures was found through Tajima’s D analysis. The analysis unravelled selection signatures encoding genes involved in numerous pathways and genes having key roles such as in behaviour, including feather pecking. Combining population differentiation statistic (FST) and Tajima’s D, a number of regions subject to divergent selection between broilers and white egg layers were identified (Chapter 4). Selection signatures were found to harbour mutations involved in cellular and tissue development, including genes having important roles in growth, fatness, egg shell strength and muscle development. These regions and the overlapping genes thereby may be potentially contributing to the different phenotypic variations observed between broilers and layers. In Chapter 5, a revised gene model for colony stimulating factor 1 (CSF1) showing complex pattern of alternate transcripts was predicted from transcriptome analysis of RNA isolated from 21 different tissues. In parallel, selection signatures analysis with the FST statistic, identified selection signatures that differentiate broilers to white egg layers (3 regions) or brown egg layers to white egg layers (4 regions). All these selection signatures were located within non-coding regions, indicating potential divergent selection of CSF1 within regulatory regions. Overall, the results presented in this thesis using the “sequences to consequences” approach, link several genomic regions and genes to phenotypic variation in domesticated chicken lines. The work reported here serves as a foundation for further study to decipher the relationship between “genotype and phenotype” and its functional consequences due to selection.

The present study focuses on the relationship between personality and Life Satisfaction. I analyzed the Big Five traits, six Narrow personality traits, and levels of Life Satisfaction in a sample of 5,932 individuals. A review of existing literature on other variables that contribute to Life Satisfaction was also conducted and used to measure against personality traits. The narrow traits added variance above and beyond the Big Five personality traits. All the Big Five traits and Optimism, Assertiveness, Intrinsic Motivation, and Tough-Mindedness were significantly and positively correlated with Life Satisfaction. Image Management was significantly and negatively correlated with Life Satisfaction. Results were discussed in terms of the relation of personality traits to Life Satisfaction and the amount narrow personality traits related to Life Satisfaction after controlling for the Big Five. Explanations were offered as to how these traits might have value in relation to Life Satisfaction.

¡@¡@The related researches on voluntary services in Taiwan, instead of focusing on psychological extent, such as personality traits, have mainly been centered on its external fields, including volunteer recruitment, training and management. In terms of the research on personality traits, people usually take the paid staff, such as police officers, medical staff, teachers and leaders as the subject. However, unpaid volunteer is not often to be seen in such study based on the big five personality traits or five factor model (FFM). By questionnaires, the basic statuses of volunteers in Kaohsiung Hakka Cultural Museum have been analyzed in this research, as well as the impact of FFM on the motivations of volunteers. The findings are: ¡@¡@A. Most of the volunteers in Hakka Cultural Museum are usually retired with the average age around 50 years old. The status of them is usually married, having 2 or 3 children. The education level is either college, senior high or vocational high school. Their years of services are more than 5 years, and they would provide voluntary services continuously. ¡@¡@B. In the perspective of personality traits, the volunteers in Hakka Cultural Museum are often full of energy (extraversion), with the preference for adventure and discussing popular issues (openness to experience), with the tendency to be cooperative rather then antagonistic (agreeableness), responsible (conscientiousness) and seldom to experience helplessness (emotional stability). ¡@¡@C. The volunteers who provide services with the motivations for self-fulfillment, willingness of learning and interest have the tendencies of extraversion, agreeableness and conscientiousness. As for the volunteers who provide service due to the introduction of family or friend, or with the motivation for killing time, they have the characteristics of openness to experience. Finally, the volunteers with the motivations for material things have the tendency of neuroticism.

Individual differences, particularly callous and unemotional (C&U) traits, and parenting practices are some of the strongest predictors of externalizing behavior in adolescents. However, findings on the associations between C&U traits, parenting, and externalizing behaviors have been mixed, with studies often utilizing single scores to represent these multidimensional constructs. The current study used a developmental-contextual framework to examine how dimensions of C&U traits predict aggressive and non-aggressive rule-breaking behaviors through positive and negative parenting practices. The study used archival data from 174 pairs of adolescent males, ages 11-16 years old, and their mothers. Results showed that C&U traits influenced externalizing behaviors through parenting practices. Findings also showed specificities among these relationships. Particularly, the associations between Uncaring and aggressive, as well as non-aggressive rule-breaking, behaviors was mediated by negative parenting, whereas the association between Unemotional and rule-breaking behaviors was mediated by positive parenting practices. Research and clinical implications are discussed.

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