Recent transcriptome data from yeast, worm, plants, and humans has shown that alternative polyadenylation (APA), a mechanism that enables expression of multiple 3′UTR isoforms for the same gene, is widespread in eukaryotic organisms. It is still poorly understood why metazoans require multiple 3′UTRs for the same gene, but accumulating evidence suggests that APA is largely regulated at a tissue-specific level. APA may direct combinatorial variation between cis-elements and microRNAs, perhaps to regulate gene expression in a tissue-specific manner. Apart from a few single gene anecdotes, this idea has not been systematically explored.
This dissertation research employs a systems biology approach to study the somatic tissue dynamics of APA and its impact on microRNA targeting networks in the small nematode C. elegans. In the first aim, tools were developed and applied to isolate and sequence mRNA from worm intestine and muscle tissues, which revealed pervasive tissue-specific APA correlated with microRNA regulation. The second aim provides genetic evidence that two worm genes use APA to escape repression by microRNAs in the body muscle. Finally, in aim three, mRNA from five additional somatic worm tissues was sequenced and their 3′ends mapped, allowing for an integrative study of APA and microRNA targeting dynamics in worms. Together, this work provides evidence that APA is a pervasive mechanism operating in somatic tissues of C. elegans with the potential to significantly rearrange their microRNA regulatory networks and precisely dose their gene expression.
This project utilized computational tools to analyze large data sets and interpreted the results from historical and philosophical perspectives. Tools deployed were derived from scientometrics, corpus linguistics, text-based analysis, network analysis, and GIS analysis to analyze more than 9000 articles (metadata and text) on systems biology. The application of these tools to a HPS project represents a novel approach.
The dissertation shows that systems biology has transitioned from a more mathematical, computational, and engineering-oriented discipline focusing on modeling to a more biology-oriented discipline that uses modeling as a means to address real biological problems. Also, the results show that bioengineering and medical research has increased within systems biology. This is reflected in the increase of the centrality of biology-related concepts such as cancer, over time. The dissertation also compares the development of systems biology in China with some other parts of the world, and reveals regional differences, such as a unique trajectory of systems biology in China related to a focus on traditional Chinese medicine.
This dissertation adds to the historiography of modern biology where few studies have focused on systems biology compared with the history of molecular biology and evolutionary biology.
The first chapter revisits some of the key experiments that contributed to the development of the repression model of genetic regulation in the lac operon and concludes that the early research on gene expression and genetic regulation depict an iterative and integrative process, which was neither reductionist nor holist. In doing so, it challenges a common application of a conceptual framework in the history of biology and offers an alternative framework. The second chapter argues that the concept of emergence in the history and philosophy of biology is too ambiguous to account for the current research in post-genomic molecular biology and it is often erroneously used to argue against some reductionist theses. The third chapter investigates the use of network representations of gene expression in developmental evolution research and takes up some of the conceptual and methodological problems it has generated. The concluding comments present potential avenues for future research arising from each substantial chapter.
In sum, this dissertation argues that the epistemic practices of gene expression research are an iterative and integrative process, which produces theoretical representations of the complex interactions in gene expression as networks. Moreover, conceptualizing these interactions as networks constrains empirical research strategies by the limited number of ways in which gene expression can be controlled through general rules of network interactions. Making these strategies explicit helps to clarify how they can explain the dynamic and adaptive features of genomes.
The purpose of this study was to identify the different contributors and predictors related to athlete burnout. Athlete burnout consists of emotional and physical exhaustion, reduced sense of accomplishments and sport devaluation. Moreover, motivation type, athletic identity, and being a student athlete can affect athlete burnout. Participants of this study were female, Division I soccer student-athletes located in Tempe, Arizona [n=22]. Athlete burnout was assessed with the Athlete Burnout Questionnaire (ABQ). Motivation type was assessed with the Behavioral Regulation in Sport Questionnaire (BRSQ). Athletic identity was assessed with the Athletic Identity Measurement Scale (AIMS). Student burnout was assessed with the Maslach Burnout Inventory - Student Survey (MBI-SS). All of the questionnaires were answered based on a Likert scale. Pearson correlations were used to find relationships between the different variables and athlete burnout. The results showed that 50% of the participants were burnt out at the end of their competitive season. Correlations were shown between the ABQ and its subscales: reduced accomplishment (r=0.6101, p<0.05), physical and mental exhaustion (r=0.8170, p<0.05), and devaluation (r=0.8697, p<0.05). Furthermore, the ABQ was also negatively correlated with general intrinsic motivation (r=-0.4943, p<0.05) and intrinsic motivation to know (r=-0.4865, p<0.05). The results from this study should be used for further research that focuses on education and prevention of athlete burnout in female soccer players.
The purpose of this study was to identify the different contributors and predictors related to athlete burnout. Athlete burnout consists of emotional and physical exhaustion, reduced sense of accomplishments and sport devaluation. Moreover, motivation type, athletic identity, and being a student athlete can affect athlete burnout. Participants of this study were female, Division I soccer student-athletes located in Tempe, Arizona [n=22]. Athlete burnout was assessed with the Athlete Burnout Questionnaire (ABQ). Motivation type was assessed with the Behavioral Regulation in Sport Questionnaire (BRSQ). Athletic identity was assessed with the Athletic Identity Measurement Scale (AIMS). Student burnout was assessed with the Maslach Burnout Inventory - Student Survey (MBI-SS). All of the questionnaires were answered based on a Likert scale. Pearson correlations were used to find relationships between the different variables and athlete burnout. The results showed that 50% of the participants were burnt out at the end of their competitive season. Correlations were shown between the ABQ and its subscales: reduced accomplishment (r=0.6101, p<0.05), physical and mental exhaustion (r=0.8170, p<0.05), and devaluation (r=0.8697, p<0.05). Furthermore, the ABQ was also negatively correlated with general intrinsic motivation (r=-0.4943, p<0.05) and intrinsic motivation to know (r=-0.4865, p<0.05). The results from this study should be used for further research that focuses on education and prevention of athlete burnout in female soccer players.
Analyzed the primary resources such as the Qur'an along with several Muslim scholarly pieces of literature written by Muslim Feminists regarding Women in Islam. Interpretations of the Qur'an have been passed from generation to another, and therefore there is a strict reliance on such established interpretation that is mainly conducted by men. There is a lack of participation in women reading and interpreting the Qur'an. This is a disadvantage to the Muslim community, as it encourages interpretive cultural practices that constitute politics and power, rather than a true and authentic translation of the Qur'an as cohesive guidance for gender justice. Feminism in Islam does exist as it aligns with the Quranic principles of gender justice. Feminism was showcased in many historical movements in the following Middle Eastern countries such as Egypt, Morocco, Yemen, and Iran. These events are important to analyze and consider to further understand the framework of Muslim feminism and how it aligns with the Qur'an. My focus was analyzing Muslim Feminist scholars, who have blueprinted a path for Muslim women to understand their role in Islam and provide an accurate interpretation of the Qur'an versus socio-cultural practices which have impacted how women in Islam are perceived and treated.
