Throughout this thesis, I have endeavored to apply an engineer’s mindset in my pursuit to better understand the marvelously convoluted immune system. In doing so, my colleagues and I have generated... Show moreThroughout this thesis, I have endeavored to apply an engineer’s mindset in my pursuit to better understand the marvelously convoluted immune system. In doing so, my colleagues and I have generated a number of new ‘hardware’(i.e., genetically engineered) tools and ‘software’ modules (i.e., custom analyses and models) that enable the investigation of several otherwise difficult-to- study concepts. Although we have used these modules here to study immune responses, I hope they may be utilized as tools and approaches to crack outstanding questions in other fields of research. Show less
This thesis pioneers diatom molecular identification and quantification through genome-scale methods, with four key aims: (i) reviewing DNA/RNA sequencing methods in aquatic biomonitoring to... Show moreThis thesis pioneers diatom molecular identification and quantification through genome-scale methods, with four key aims: (i) reviewing DNA/RNA sequencing methods in aquatic biomonitoring to highlight their strengths and limitations; (ii) unraveling the evolutionary history of Nitzschia palea and investigating species delimitation within the species complex; (iii) identifying silica genes in N. palea for insights into ecology and evolution; and (iv) assessing a genome-scale quantification method for diatom biomonitoring to improve accuracy and scalability in estimating abundances. The review (Chapter 2) emphasizes disparities between molecular and morphology-based approaches and introduces the challenges in accurately estimating species abundances. Chapter 3 explores N. palea's evolutionary history using transcriptome data and reveals reticulate evolutionary patterns resulting in a putative hybrid between populations with different morphological characteristics. Chapter 4 pinpoints silica genes in N. palea and reveals variations among different populations that may lead to differences in silica metabolism. Chapter 5 introduces a genome-scale quantification approach that provides a promising alternative for molecular diatom biomonitoring due to its improved taxonomic resolution and quantification accuracy. In summary, this thesis underscores that genome-scale methods' have a critical role in diatom identification and quantification, and in advancing our understanding of microalgal taxonomy, ecology, and evolution. Show less
The human ovary is responsible for producing eggs and steroid hormones necessary for reproduction. Ovarian factors, such as anovulation, polycystic ovarian syndrome, and decreased egg quality, can... Show moreThe human ovary is responsible for producing eggs and steroid hormones necessary for reproduction. Ovarian factors, such as anovulation, polycystic ovarian syndrome, and decreased egg quality, can lead to female infertility. Although advances have been made in assisted reproductive technologies (ART) and fertility preservation approaches, there is still a demand for new treatments and approaches for ovarian diseases and female infertility. The main obstacle to developing effective approaches is the lack of knowledge about the human ovary, especially the cellular development and molecular basis of oogenesis and folliculogenesis processes. The advances in single-cell RNA sequencing (scRNA-seq) techniques have opened up opportunities for studying the transcriptomes of human ovarian cells, decoding cell types and sub-populations, and identifying signature genes during oogenesis and folliculogenesis. In my research, we utilized the scRNA-seq technique to provide valuable transcriptomic datasets of human ovarian cells, contributing to the establishment of the molecular landscape of human oogenesis and folliculogenesis. Show less
The study of orchid flowers, fruits, and inflorescences is crucial due to the remarkable diversity of orchid species and their unique adaptations to pollinators and seed dispersers. However, our... Show moreThe study of orchid flowers, fruits, and inflorescences is crucial due to the remarkable diversity of orchid species and their unique adaptations to pollinators and seed dispersers. However, our understanding of the evolution and development of these organs within the orchid family remains limited. This research aims to fill this knowledge gap by investigating the genetic mechanisms underlying the evolution and development of floral structures, fruits and resupination in orchids, and the relationship between inflorescence stalk lignification and orientation. The research also includes a methodological chapter on the application of transcriptomics for plant species identification. Using advanced techniques such as microscopy imaging, 3D CT scanning, and anatomical analysis, the study provides detailed insights into the processes of root and fruit resupination and shows that inflorescence lignification is a heritable trait, with closely related orchid species displaying similar levels of lignification compared to distantly related species. The findings significantly advance our understanding of orchid biology by filling gaps in our knowledge of the evolutionary and developmental processes involved in flower and fruit development, resupination, and inflorescence lignification. By identifying specific genes and pathways associated with these traits, the study offers valuable insights into the genetic mechanisms that drive orchid diversity and adaptation. From a practical perspective, these findings hold great promise for the development of new orchid varieties with more robust and visually appealing varieties. The research also highlights the importance of conservation efforts to protect orchid diversity and their ecological relationships with pollinators and seed dispersal vectors. Show less
