This thesis explores the genetic characterization of the mechanisms underlying complex traits in chicken through the use and development of bioinformatics tools. The characterization of quantitative trait loci controlling complex traits has proven to be very challenging. This thesis comprises the study of experimental designs, annotation procedures and functional analyses. These represent some of the main ‘bottlenecks’ involved in the integration of QTLs with the biological interpretation of high-throughput technologies. The thesis begins with an investigation of the bioinformatics tools and procedures available for genome research, briefly reviewing microarray technology and commonly applied experimental designs. A targeted experimental design based on the concept of genetical genomics is then presented and applied in order to study a known functional QTL responsible for chicken body weight. This approach contrasts the gene expression levels of two alternative QTL genotypes, hence narrowing the QTL-phenotype gap, and, giving a direct quantification of the link between the genotypes and the genetic responses. Potential candidate genes responsible for the chicken body weight QTL are identified by using the location of the genes, their expression and biological significance. In order to deal with the multiple sources of information and exploit the data effectively, a systematic approach and a relational database were developed to improve the annotation of the probes of the ARK-Genomics G. gallus 13K v4.0 cDNA array utilized on the experiment. To follow up the investigation of the targeted genetical genomics study, a detailed functional analysis is performed on the dataset. The aim is to identify the downstream effects through the identification of functional variation found in pathways, and secondly to achieve a further characterization of potential candidate genes by using comparative genomics and sequence analyses. Finally the investigation of the body weight QTL syntenic regions and their reported QTLs are presented.

A research project submitted in partial fulfilment of the requirements for the degree of Master of Arts in Social and Psychological Research by Coursework and Research Report in the Department of Psychology, Faculty of Humanities, at the University of the Witwatersrand, Johannesburg, March 2017 / Working memory (WM) is an executive function that may promote resilience by enabling individuals to generate novel solutions in adverse situations. Research regarding the relationship between these constructs is limited. It is particularly unclear whether, and how, WM may promote resilience in the South African context. This study thus used a mixed method concurrent triangulation design to quantitatively investigate whether WM is related to resilience; and to qualitatively investigate how WM processes feature in participants’ experiences of resilience, and how this is influenced by socio-cultural factors. Thirty-eight young Black South African adults from disadvantaged backgrounds (whose WM had been assessed in a pre-existing study) completed a demographic questionnaire and the Resilience Research Centre-Adult Resilience Measure in person or online. For the qualitative phase, 14 of these participants were interviewed using a semi-structured interview schedule. Quantitative findings were equivocal, but primarily non-significant. Qualitative findings indicated that WM processes featured in participants’ accounts of resilience-promoting resources, but that this was shaped by socio-cultural resources accessible to participants. Working memory also featured as one amongst many of the resilience-promoting resources accessible to participants. The disparity between the quantitative and qualitative findings may be due to the individualistic nature of the quantitative WM measure used. Findings are interpreted in relation to existing literature regarding cognitive functioning and resilience. Implications for understanding and promoting the resilience of Black South African young adults are discussed. / XL2018

Previous research supports the idea that individuals high in trait anger tend to experience more hostile attribution bias. According to the Integrative Cognitive Model, cognitive factors, such as rumination, may increase the risk of hostile attribution bias and any subsequent aggressive behaviors. Sex differences are apparent in rumination and anger expression. The present research explored the potential role trait rumination plays in hostile attribution bias as well as potential conditional effects of sex on this relationship. Participants were asked to complete a number of self-report measures and vignettes of ambiguously hostile situations adapted to improve reliability. Hypotheses were largely supported and trait anger rumination was significantly predictive of hostile attribution bias; however, conditional effects of sex were non-significant. The adapted hostile attribution bias measure had improved reliability and may have utility for a survey-based method to assessing hostile attribution bias. Findings may further our understanding of hostile interpretations and potential for subsequent aggressive behaviors in high trait ruminators in ambiguous situations as well as lead to potential areas of intervention to reduce anger and anger rumination.

Entomopathogenic nematodes (EPNs) (genera Heterorhabditis and Steinernema) kill their invertebrate hosts with the aid of a mutualistic bacterium. The bacteria (Xenorhabdus spp. for steinernematids and Photorhabdus spp. for heterorhabditids) are primarily responsible for killing the host and providing the nematodes with nutrition and defense against secondary invaders. Photorhabdus is a Gram-negative bacterium in the Enterobacteriaceae family with high virulence towards their insect hosts. To achieve high mortality rates Photorhabdus produces a variety of virulence factors such as toxins, lipases, proteases, secretion systems, and fimbriae. EPNs are amenable to laboratory rearing and mass production for biocontrol applications against insects using in vivo or in vitro methods; however, in vitro liquid culture is considered to be the most efficient. In this method the symbiotic bacteria are cultured prior to the addition of their partner EPN. This can leave the bacteria susceptible to a number of problems such as genetic drift and inadvertent selection. Regardless of the culture method the symbiotic bacteria exhibit trait deterioration or changes due to laboratory rearing. This project had three primary aims: 1) investigate the role of nutrition in trait deterioration, 2) examine virulence evolution using a phylogenetic context, and 3) identify genes that are necessary for survival and virulence inside the insect host. Prior to studying these objectives we first determined the optimal conditions for growing and counting viable cells of Photorhabdus. We discovered that growth is enhanced by the addition of pyruvate to growth media. To determine the role of nutrition in trait deterioration we repeatedly sub-cultured Photorhabdus in three different media types. Throughout this study we found that, in contrast to previous studies, trait deterioration does not always happen and the environment influences trait deterioration. Furthermore, based on our phylogenetic studies we found that Photorhabdus spp. are evolving to an increase in insect virulence. Lastly, using Tn-seq we determined a list of 84 genes that are needed for efficient virulence inside the insect host and provide suggestions for ongoing research efforts.

Speciation – the process by which new species arise – is of fundamental importance in the biological sciences. The means by which new species arise, and the relationship among living species, has been a topic that has captivated both lay and scientific observers for centuries. In recent years, the study of speciation has enjoyed increased attention, resulting in significant advances in our understanding of how species form. Although our understanding of the processes that contribute to speciation has increased dramatically in recent years, our knowledge of how reproductive barriers accumulate as speciation proceeds is still limited. Thus, studies that evaluate trait divergence and its consequences at early verses late stages of divergence can provide valuable insight into the speciation process. Chapter 1 of my dissertation focuses on the role of animal personality in the speciation process. Animal personality – defined as consistent individual differences in behavioral tendencies – has been identified as a key player in several ecological and evolutionary processes, yet the role of personality in speciation remains unexplored. In this chapter I discuss the ways by which personality can contribute to a suite of reproductive barriers and drive the speciation process. Chapters 2 through 5 provide a case study evaluating how selection acts on traits at early and late stages of speciation, using the Neotropical Livebearing fish genus Brachyrhaphis as a model system. Brachyrhaphis is ideally suited for this research because several species pairs and population pairs within species occur in similarly divergent selective regimes. I first present results from a field demographic study that shows that the strength of divergent selection acting on life-history traits in populations from divergent predation environments diminishes as speciation proceeds. I then show that population pairs at different stages of divergence are evolving similar morphological patterns along parallel trajectories. At both early and late stages of divergence, populations from environments with dense predator populations have a body shape that appears to be optimized for burst-speed swimming, and important component of predator escape. In contrast, populations from environments lacking predators have a body shape optimized for endurance swimming ability, which is important in environments where competition for foods and mates is high. Next, I show that populations from divergent predation environments do indeed differ in their swimming abilities according to our predictions, reflecting a population level trade-off between burst and endurance swimming ability. Although population level trade-offs were strong, I found no evidence of within population level trade-offs, suggesting that populations have arrived at novel solutions to between population trade-offs that were not present within ancestral populations. Finally, I show that these specialized swimming modes are locally adaptive, and that divergent ecology selects against immigrants, effectively reducing gene flow between populations from divergent environments. Together, these studies provide a valuable glimpse into the repeatability and predictability of trait divergence at different stages of speciation.

Sickle cell trait (SCT), sickle cell disease’s carrier status, is a common genetic variant found in many people of African, South Asian, Middle Eastern and Mediterranean descent. While overall considered a benign carrier status, it has been associated with an increased risk of several diseases, including exertional rhabdomyolysis (ER), and chronic kidney disease. While epidemiological evidence links SCT with ER, the actual pathophysiological mechanism less understood. Additionally, while there is an increased prevalence of atrial fibrillation (AF) documented in people with sickle cell disease, studies in individuals with SCT are lacking. The objectives of this thesis are twofold: The first chapter is a literature review of studies to examine the physiological mechanisms linking SCT and exertional rhabdomyolysis. The second chapter is original research into the associations of SCT with AF. The first chapter reviews studies that identify aggravating factors that may promote ER. It then reviews observed pathophysiological changes in people with SCT that may increase the risk of ER. It summarizes studies that assess mitigating factors that decrease the risk of ER. It then presents a postulated pathway of mechanisms that associate SCT with ER. The second chapter uses data from African-American participants in the REasons for Geographic and Racial Differences in Stroke (REGARDS) study to assess the association of SCT with prevalent AF (by electrocardiogram or medical history) using logistic regression models adjusting for age, sex, income, education, history of stroke, myocardial infarction, diabetes, hypertension, and chronic kidney disease. In 10,409 participants with baseline ECG data and genotyping, 778 (7.5%) had SCT and 811 (7.8%) had prevalent AF. After adjusting for age, sex, education and income, SCT was associated with AF, OR 1.32 (95% CI 1.03-1.70). SCT remained associated with prevalent AF after adjusting for potential factors on the causal pathway such as hypertension and chronic kidney disease suggesting alternate mechanisms for the increased risk. SCT was associated with a higher prevalence of AF and a non-significantly higher incident AF over a 9.2 year period independent of AF risk factors.

Project success is a measure of both project manager efficacy and stakeholder satisfaction. One of the primary measures of success for construction projects is meeting cost targets and yet recent data indicates up to 9 out of 10 construction projects fail to meet this target. Unsuccessful construction projects can have ramifications that affect project teams, internal stakeholders, customers and the local community. The purpose of this correlational study was to examine the relationship between project managers' well-being, self-control, emotionality, and sociability and project success using Petrides and Furnham's theoretical framework of trait emotional intelligence. Using the Trait Emotional Intelligence Questionnaire short form self-assessment instrument, data were collected from a sample of 104 construction project managers in the United States who had executed a project in the last 5 years. Data analysis revealed both the combination of the four predictor variables, and the self-control variable taken individually, resulted in a statistically significant relationship to project success at the p < .05 level with each having a p value of .001. Hiring managers and organizational leadership can use this information to guide hiring processes and training programs to help improve success rates in the construction industry. Improved project success could result in positive social change through the stabilization of the job market and improved partnerships between construction organizations, local governments, and the community.

Mindfulness engagement has become increasingly popular in therapeutic settings and is promising in terms of possibly reducing physical and mental health symptoms among a wide variety of clients (including college students) presenting diverse diagnoses. While a number of studies suggest that mindfulness interventions increase mindfulness ability, this assertion has not been validated because many researchers utilizing a mindfulness intervention fail to include measures assessing change in trait mindfulness ability. The present study examined mindfulness engagement and trait mindfulness, as well as physical and mental health correlates of trait mindfulness, in 300 college students (74% female) via an online survey. Mindfulness ability in this general college population was similar to the overall mindfulness ability in the general population. Seventy-nine percent of respondents reported mindfulness engagement. Fifty-nine percent of the sample reported previous mindfulness engagement and only 32% of these individuals stated continued engagement. While no overall differences in trait mindfulness were found between respondents who had reported previous mindfulness and those who had not, individuals who spent more time in their mindfulness practice, also reported higher amounts of trait mindfulness ability. These data suggest that in order for these specific mindfulness engagements to impact trait mindfulness ability, a time engagement threshold must be met. A number of trait mindfulness variables were significantly related to a number of mental and physical health variables. However, relationships between trait mindfulness and health variables were not uniform. Multiple subscales from the Five Factor Mindfulness Scale (FFMQ) were significantly correlated with mental and physical health variables. There were few physical and mental health variables that were significantly correlated or suggested trends with the Mindful Attention Awareness Scale (MAAS). Increased cognitive symptoms of depression, yet nonclinically significant levels as measured by the Beck Depression Inventory (BDI), were significantly positively related to increased levels of trait mindfulness ability. More efforts are needed, including, measurement of mindfulness throughout intervention, increased focus regarding the construct of mindfulness ability and novel forms for measurement, and the relationship between mindfulness ability measurement of mindfulness ability and specific mental and physical health variables.

Anxiety is a common problem for patients with cancer. Anxiety may have a negative impact on decision making and overall emotional well being of patients and may be related to the uncertainties faced by people with cancer. This study examined the relationship between uncertainty in illness and anxiety in patients with cancer. The sample consisted of 30 patients, predominantly males (n=23), being treated as outpatients in the Clinical Research Unit at a National Cancer Institute designated cancer center in Florida. After agreeing to participate, patients completed the State-Trait Anxiety Inventory as well as Mishel's Uncertainty in Illness Scale. Participants' ages ranged from 21 to 86, with a mean age of 64 years. Forty percent of the patients completed high school, 30% had some college education and almost 30% had a bachelor's degree or higher. Almost 47% of the sample had melanoma, other patients had renal cancer (n=3), or pancreatic cancer (n=2), acute myeloid leukemia (n=2), sarcoma (n=2), lung cancer (n=2), myeloma (n=2), chronic myeloid leukemia (n=1), glioblastoma (n=1), and rectal cancer (n=1). Seventy percent of the patients had stage IV disease. The results of the study showed a significant positive relationship between uncertainty and both state anxiety (r=0.52, p=0.00.) and trait anxiety (r=0.61, p=0.000). A significant positive relationship was also found between the uncertainty subscale of ambiguity and both, state anxiety (r=0.538, p=0.002) and trait anxiety (r=0.56, p=0.001). Both state anxiety (r=0.39, p=0.034) and trait anxiety (r=0.64, p=0.000) were positively related to the uncertainty subset of inconsistency. Although the sample size was small and not demographically diverse, the findings of this study are supportive of previous studies. The implications of this study in nursing are significant because they examine two emotional aspects that evidently exist among cancer patients, and that very likely cause distress to this population. The findings of this study suggest that additional focus in uncertainty and anxiety should take place in the clinical outpatient setting.

<p>Preferential processing favouring threatening information has received increased attention because cognitive formulations have placed increased emphasis on its role as a key cognitive factor underlying vulnerability to and maintenance of anxiety disorders. The present dissertation comprises four empirical studies within the area of preferential processing. Two different outcome measures were used to index preferential processing of threat-related information: Skin conductance responses (SCRs) were used in Studies I, II, and III. The emotional Stroop task was used in Study IV. The main focus has been on preferential processing of threat-related information that occurs outside awareness, thus <i>preferential preattentive processing</i>. Study I investigated the role of traumatic combat experience with regard to preferential processing among UN soldiers following a presentation of threat-related pictures. Results indicated that soldiers with combat experience consistently reacted with lower SCRs compared to soldiers without combat experience. One issue addressed in the individual studies was the association between preferential preattentive processing and trait anxiety. Studies II, III, and IV showed that elevated levels of trait anxiety promote preferential preattentive processing of negatively valenced information, whereas elevated levels of social desirability generally prevent preferential preattentive processing of negatively valenced information. Study II highlighted the importance of including the social desirability factor when studying effects of trait anxiety on preferential processing. In addition, Studies III and IV explored the relationship between preferential processing and emotional vulnerability. The main findings support the notion of preferential preattentive processing of threat representing an underlying predisposition to heightened emotional vulnerability in response to stressful events.</p>