California yellowtail are revered in Southern California as the “premiere” game fish of the region. As members of the jack family (Carangidae), these fish are renowned by recreational fishermen (anglers) for both their fight and their flavor. While the total catch was dominated by the commercial fishery in the first half of the 20^th century, currently there exists only small local commercial operations that mostly serve the Southern California region. The majority of yellowtail being landed today is through the recreational fishery.

Despite the importance of the California yellowtail to Southern California’s recreational fishing industry, management of the species remains relatively static. Regulations regarding recreational take of the species have seen only minor updates to size limits since the 1960s. Furthermore, no formal stock assessment has been conducted on the Southern California yellowtail stock, and there are not currently plans to do so. Due to climate change, population growth, and a boom in interest in recreational fishing since the mid-2010s, the risk facing the health of the yellowtail fishery is quickly increasing.

This project draws attention to the California yellowtail through exploring the fish’s impact in Southern California’s economy, culture, and history. Communicated through a website dedicated to telling the story of the California yellowtail, it draws attention to the fish’s important role in the region and encourages a push for proactive management of the species. The hope is to ensure that the California yellowtail fishery will remain thriving and healthy long-term, with big and powerful fish for locals to enjoy in the future.

The website can be found here: https://kehuang2.wixsite.com/website-5

The regulatory capacities of epigenetic mechanisms including DNA methylation, histone modifications, and non-coding RNAs, have seen a rising interest in recent years. These epigenetic marks are pervasive and non-randomly distributed across the genome, raising intriguing questions on how epigenetics contributes to genomic features that define cellular identity and function. Unlike fixed genetic information that is shared between all cell types, epigenetics involve multiple layers of regulation and can vary dramatically across different cell types and genomic contexts. Thus, much more effort is required to procure a complete perspective of the manifold epigenetic landscape. The body of work in this dissertation focuses on epigenetic studies in the mammalian pluripotent stem cell model system. We utilize high-throughput technologies such as microarrays and next-generation sequencing (NGS) as well as leverage existing epigenetic maps to address a wide range of molecular questions on a comprehensive global scale. This dissertation is organized into three overarching themes:

First, we employed genome-wide gene expression and DNA methylation profiling tools to determine whether different cell types display unique biomarkers that can be used to distinguish them from other cell types (Chapters 2-5). We found that human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) carry distinct features in both gene expression and DNA methylation patterns, arguing in favor of the idea that these two pluripotent cell types are different. Furthermore, we compared pluripotent stem cell derived retinal pigmented epithelium (hESC-RPE and hiPSC-RPE) with fetal and adult RPE and found that all RPE cells share a core set of signature genes that distinguishes them from all other cell types. We propose these signature genes will be useful for evaluating the quality of stem-cell derived RPE. Finally, novel corneal endothelial cells (CECs) biomarkers were identified through comparing 12 other tissue types, paving the way for future studies to evaluate properties of stem-cell derived CECs.

We next examined how molecular features of pluripotent stem cells are altered during the differentiation process of stem cells (Chapters 6-8). Using the RPE differentiation paradigm, we profiled both microRNA and DNA methylation patterns in intermediate stages between pluripotent stem cells and mature RPE. These two separate studies identified subsets of dynamically regulated epigenetic marks, some of which are associated with RPE signature gene expression. Furthermore, we used a highly innovative and powerful single-cell RNA-sequencing approach to profile transcriptional changes in the early embryo beginning from mature oocyte to morula stages. This study identified a conserved genetic program describing a highly dynamic transcriptional architecture during early embryogenesis.

Finally, we took a focused analysis on how DNA methyltransferases contribute to shaping the pluripotent stem cell epigenome (Chapters 9-10). Using mouse ESCs null of DNA methylation, we determined DNA methylation regulates a large set of genes through action with H3K27me3. Furthermore, we determined shared and unique genomic targets of each DNA methyltransferase, including novel de novo methylation activity for Dnmt1 in vivo. In the human model system, we generated iPSCs from ICF Syndrome patient fibroblasts which carry double heterozygous mutations in DNMT3B. We found DNMT3B is involved in a wave of de novo methylation during the reprogramming process and has unique genomic targets.

In recent history, humans have discovered and constructed many different mechanisms of flight. As far as technologies have advanced, flying birds and insects still outperform the agility, maneuverability, and stability of human-made air crafts. The research of flapping-wing micro-air-vehicles (FWMAV) studies the phenomenon behind the flapping wing and examines ways to design a similarly efficient flight mechanism. FWMAV utilizes biomimetic oscillatory vibrations for propulsion and control. Engineers create these mechanisms to be used as tools for scientific discovery, as there is much to learn from how biological creatures fly. Nature utilizes phenomena such as vibrational stabilization and the clapping effects of the wings to generate their flying capabilities. Engineers at UCI have found a clever way to increase the understanding of the complex wing aerodynamics and utilize the information to create a unique drone that can be seen nowhere else in the world. With the knowledge of the clapping effect, there should exist an optimal design and selection of materials where the capacity of the FWMAV to generate thrust and lift is maximized. Using a familiar flapping mechanism, iterating the maximum wing closure to adjust the clapping effect, and gathering the thrust and lift data to find the change in the force generation capacity. With this information, any appropriate wing configuration should be able to be adjusted in such a way that the clapping effect is optimized. A deeper understanding of wing aerodynamics provides a good basis for designing more efficient FWMAV drones.