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Mosquitoes belonging to the genera Anopheles transmit malaria parasites, attributing the highest mortality of any vector-borne disease worldwide. Mosquitoes belonging to the genera Aedes transmit arboviruses including dengue, which has become the most important vector-borne virus due to a drastic surge in disease incidence. The scope of the studies in this dissertation is broad, with investigations bringing together elements of classical genetics, recent advances in sequencing and genome-editing technologies, and the use of modern forward genetics approaches. Chapter 2 of this dissertation explores the use of the Oxford Nanopore Sequencing Technology for the first time in mosquitoes. This new technology provides long reads that were used to piece together the AabS3 chromosomal assembly for Anopheles albimanus. The utility of this genomic resource is demonstrated by the discovery of novel telomeric repeats at the ends of the chromosomes that could have important implications in mosquito biology and control. Chapter 3 describes a forward genetics strategy called 'Marker-Assisted Mapping' (MAM) that enables high-resolution mapping of the causal gene locus of a mutant phenotype. The principle and effectiveness of MAM is first demonstrated by mapping a known transgene insertion. MAM is then used to identify cardinal as a candidate causal gene for the spontaneous red-eye (re) mutation. Genetic crosses between the re mutant and cardinal knocking out individuals generated using CRISPR/Cas9 confirmed that cardinal indeed is the causal gene for re mutation. Chapter 4 explores three innovative strategies for mosquito sex separation by exploiting several sex-linked marker lines. We show that by linking a transgenic marker to the male-determining locus (M locus), or by linking the male-determining Nix gene to a marker, males can be precisely separated from females. We also produce a two-marker transgenic line that allows for both non-transgenic male separation and for efficient line maintenance. Finally, we discuss further applications of the resources generated and future directions stemming from these findings. Altogether, the studies described in this dissertation contribute to the overall goal of understanding mosquito biology and of controlling mosquito-borne infectious diseases. / Doctor of Philosophy / Female mosquitoes bite and transmit deadly pathogens including the malaria parasite, and viruses such as dengue, Zika, and West Nile. Control programs that attempt to limit the spread of these deadly diseases rely on the control of mosquitoes themselves. These mosquito control methods have relied heavily on indoor and outdoor insecticidal spraying. However, the efficacy of these methods has been jeopardized by the increasing prevalence of insecticide resistance. Thus, it is necessary to implement other methods for effective mosquito control. Genetic control strategies such as the Sterile Insect Technique (SIT) and Wolbachia-based Incompatible Insect Technique (IIT) are excellent solutions to overcome the limitations of current control strategies. As female mosquitoes bite and transmit disease-causing pathogens, only males are released, which necessitate the separation of the non-biting males from females before release. The aim of this work was to use recent technological advancements to better understand the genome and basic genetics of vector mosquito species, and to identify possible approaches to improve current sex separation practices. To develop a deep understanding of mosquito biology and genetics, it is crucial that a high-quality and accurate genome assembly is available. However, many mosquito genome assemblies remain fragmented. To address this limitation, we used recent advances in sequencing technologies to produce a high-quality genome assembly for the New World malaria mosquito, Anopheles albimanus. These sequencing and assembly efforts led to the discovery of novel telomere sequences at the ends of chromosomes, which could have implications for mosquito control. Forward genetics, which identifies the gene(s) responsible for a given phenotype, has been hindered by the low recombination rate in the yellow and dengue fever mosquito, Aedes aegypti. We develop a Marker-Assisted Mapping (MAM) strategy to address this problem. We first demonstrate this method by mapping the known insertion of a transgene. MAM is then used to identify cardinal as a candidate causal gene for the spontaneous red-eye (re) mutation. MAM identification of the Cardinal gene was then verified by knocking out Cardinal, which represents the first successful gene mapping in Aedes aegypti using forward genetics. The MAM strategy has broad implications as it could enable the discovery of genes involved in important traits such as insecticide resistance. To improve sex separation methods, we took advantage of several sex-linked transgenic lines to develop three novel strategies. First, we demonstrate that screening for a genetic marker that is tightly linked to the male-determining locus (M locus) is an effective approach to reduce female contamination. Second, we demonstrate that instead of linking a marker to the M locus, we can link the male-determining factor, Nix, to a genetic marker. When a Nix transgene is located adjacent to the red-eye locus with extremely tight linkage, the red-eye phenotype becomes a faithful marker for separation of males and females. Finally, we developed a two-marker genetic sexing strain that produces non-transgenic males that could be used for release, and transgenic marked males and females for efficient line maintenance.

In the growing landscape of innovative non-viral delivery vehicles, polymeric and lipid nanoparticles remain at the forefront for their versatility in encapsulating a variety of therapeutic payloads. This thesis investigates their potential for facilitating the transport of nucleic acid components into cells, with a focus on targeted delivery to the liver and brain. To achieve this, we address key considerations including the composition of the delivery vector, the nature of the therapeutic cargo, and the chosen delivery route. The challenge of targeted delivery to specific organs or cell types, i.e. hepatocytes or neurons, is addressed through rational design and development of libraries of nanoparticulate systems tailored for nucleic acid therapeutics. Although liver gene editing using non-viral systems has been extensively studied, oral delivery for liver targeting remains challenging due to the mucosal barrier. To that end, we explore intraduodenal delivery as a strategy to bypass the mucosal barrier and target the liver. Furthermore, insights from collaborative research with the Mao lab at Johns Hopkins University reveal that tuning the composition of lipid nanoparticles (LNPs) can influence their preferential targeting of specific cell types. Leveraging this, we employed an in vitro library screening and machine learning approach to identify populations of LNPs capable of preferentially transfecting hepatocytes. The efficacy of these LNPs in liver gene editing is then evaluated through “cluster-mode” screening in vivo, and therapeutic efficacy was demonstrated using a proof-of-concept in vivo model for PCSK9 and ANGPTL3 knockdown, resulting in 27% serum cholesterol knockdown. In addition to liver-targeted gene delivery, this thesis also investigates the potential of polymeric and lipid nanoparticles for delivering nucleic acid therapeutics to the brain. However, overcoming the blood-brain barrier (BBB) is crucial for systemic delivery to the brain. To circumvent the BBB, we explored two methods: intracranial injection and theranostic ultrasound (THUS)-mediated temporary opening of the BBB. While intracranial injection achieves localized gene editing, THUS offers a non-invasive approach for transient and widespread BBB opening. Utilizing the previously validated in vitro screening and machine learning approaches for chitosan-grafted bPEI (CS-PEI) and lipid nanoparticle (LNP) carriers with tunable compositions, we assessed their efficacy in systemic gene delivery to the brain, and specifically their capability in preferentially transfecting neuronal cells over hepatocytes. Subsequently, we validated their efficiency via intracranial administration using the Ai14 reporter mouse model and observed up to 20% gene editing of the targeted cross-sectional area of the brain hemisphere using the top-performing cluster. Through comprehensive investigations into both brain and liver gene delivery, this thesis aims to contribute to the advancement of non-viral nanoparticle-based gene therapy strategies for treating a range of cholestatic liver diseases and hereditary neurodegenerative diseases.

In vitro systems like those used for in vitro embryo production are invaluable for our understanding of embryogenesis and the processes that regulate it. However, extensive research has also highlighted that in vitro produced embryos negatively differ from their in vivo counterparts in various ways. Not surprisingly, there is ~20% decrease in pregnancy success from pregnancies established using in vitro produced embryos. Therefore, much research has relied on attempting to produce a better in vitro embryo that more closely resembles their in vivo counterparts. Our laboratory has investigated this by supplementing a cytokine, interleukin-6 (IL6), during in vitro embryo culture. My dissertation work expands upon those initial efforts by answering more detailed questions related to the biological role of IL6 during cattle embryogenesis. In the work presented herein, IL6 supplementation during in vitro culture was able to transform the transcriptome of resulting conceptuses post embryo transfer. The transcriptome of these conceptuses included an abundance of genes associated with survival. Indeed, we witnessed IL6-treated conceptuses resulted in a 20% increased survival rate and were longer than their non-treated counterparts. In the second research project, we employed CRISPR-Cas9 genome editing technology to understand the embryo phenotype after part of the IL6 receptor responsible for signal transduction, interleukin-6 signal transducer (IL6ST), is disrupted. We discovered that IL6ST is required for development before the blastocyst stage. In addition, IL6ST disrupted blastocysts, presumed to contain wildtype, presented with severe, abnormal morphology. Not only did this group of embryos have decreased ICM and TE cell numbers, but they also had an increased occurrence of cells within the TE region that were negative for its traditional marker, CDX2. This suggests IL6ST is likely involved in a pathway responsible for determining cell fate identity at the blastocyst stage. Collectively, IL6 in cooperation with IL6ST, is a key controller of embryogenesis in cattle. / Doctor of Philosophy / There are major events that an embryo must successfully advance from to continue development to form into an organism capable of survival after birth. Over 30% of pregnancies in cattle and humans will fail within the first 30 days of gestation. This time period coincides with several key developmental events that ultimately modify the morphology of the growing embryo. Our laboratory primarily focuses on embryo development around the blastocyst stage. If an embryo advances to this stage, it has a greater likelihood of maintaining viability. Therefore, my dissertation research has focused on early embryonic development from the time of first cleavage (~day 2 of gestation) through embryo elongation (~day 15 of gestation), which encompasses the blastocyst stage. Within this time frame, I have been investigating embryonic effects after supplementation of a protein, interleukin-6 (IL6). Previously, our laboratory has identified IL6 to cause favorable impacts on the developing embryo, but its mode of action was unknown. Therefore, my dissertation research has investigated the mechanistic actions of IL6, and its beta receptor subunit, interleukin-6 signal transducer (IL6ST). In my first research project, we discovered that supplementing IL6 during in vitro embryo culture resulted in increased embryo elongation and survival. In my second research project, we found IL6ST is an absolute requirement for embryo survival to the blastocyst stage. Together, these results indicate IL6 is a very important protein needed for sustained pregnancy viability.

In modern society, cameras on intelligent devices can generate a huge amount of natural images, including images of the human body and face. Therefore, there is a huge social demand for more efficient editing of images to meet human production and life needs, including entertainment, such as image beauty. In recent years, Generative Models with Deep Learning techniques have attracted lots of attention in the Artificial Intelligence field, and some powerful methods, such as Variational Autoencoder and Generative Adversarial Networks, can generate very high-resolution and realistic images, especially for facial images, human body image. In this thesis, we follow the powerful generative model to achieve image generation and editing tasks, and we focus on human image generation and editing tasks, including local eye and face generation and editing, global human body generation, and editing. We introduce different methods to improve previous baselines based on different human regions. 1) Eye region of human image: Gaze correction and redirection aim to manipulate the eye gaze to a desired direction. Previous common gaze correction methods require annotating training data with precise gaze and head pose information. To address this issue, we proposed the new datasets as training data and formulated the gaze correction task as a generative inpainting problem, addressed using two new modules. 2) Face region of human image: Based on a powerful generative model for face region, many papers have learned to control the latent space to manipulate face attributes. However, they need more precise controls on 3d factors such as camera pose because they tend to ignore the underlying 3D scene rendering process. Thus, we take the pre-trained 3D-Aware generative model as the backbone and learn to manipulate the latent space using the attribute labels as conditional information to achieve the 3D-Aware face generation and editing task. 3) Human Body region of human image: 3D-Aware generative models have been shown to produce realistic images representing rigid/semi-rigid objects, such as facial regions. However, they usually struggle to generate high-quality images representing non-rigid objects, such as the human body, which greatly interests many computer graphics applications. Thus, we introduce semantic segmentation into the model. We split the entire generation pipeline into two stages and use intermediate segmentation masks to bridge these two stages. Furthermore, our model can control pose, semantic, and appearance codes by using multiple latent codes to achieve human image editing.

Fusobacterium nucleatum is an anaerobic, Gram-negative, oral bacterium that disseminates from the mouth, and contributes to preterm birth, tissue infections, and acceleration of multiple cancers including colorectal and pancreatic. It is well-established that most Fusobacterium species exhibit genetic recalcitrance, which has led to hindrance in the understanding of their biology and molecular pathogenesis. Though the association of Fusobacterium in diseases is well-established, the majority of our experimental work stems from the strain F. nucleatum ATCC 23726 because it is genetically tractable. Here, in this dissertation, we show that we are able to enhance our existing molecular tools for genome editing to introduce the first mutants in a clinically relevant strain, F. nucleatum ATCC 25586, a feat that was never accomplished in decades of trying. Furthermore, we created a deletion library of genes predicted to be involved in host cellular invasion and survival. In this work, we identified a novel small adhesin, FadA2, that played a significant role in the invasive ability of F. nucleatum ATCC 25586 to colorectal cancer cells. This dissertation also sheds the first insight into the roles of the type 5a autotransporters. Using a deletion library of genes encoding for the type 5a autotransporter proteins in F. nucleatum ATCC 23726, we systemically characterized altogether 12 type 5a proteins with a focus on the invasion of colorectal cancer cells. Most notably, we found that a wide assortment of type 5a proteins contributing to binding and invasion of F. nucleatum to HCT116 cancer cells. Furthermore, we identified that RadD was not directly involved in inducing secretions of the cytokines IL-8 and CXCL1 while confirmed the specific association of Fap2 in bacterial-induced cytokine secretion. Thus, our findings provided the first comparative and functional analysis of Fusobacterium type 5a autotransporter proteins in colorectal cancer cells which will be crucial to the understanding of Fusobacterium involvement in cancer progression. Finally, this dissertation reported on the first ever observation on the survival strategy of Fusobacterium inside the host cells. We uncovered a novel protein that contributed to enhanced survival of Fusobacterium residing in colorectal cancer cells. This work undoubtedly helps expand the current Fusobacterium genetic toolkit to study proteins and mechanisms relevant to Fusobacterium-accelerated diseases. By identifying and characterizing novel virulence strategies that Fusobacterium can take advantage of, we can increase our comprehension on this opportunistic microbe while devising innovative therapeutic treatments. / Doctor of Philosophy / Fusobacterium, a member of the microbial community in our mouth, has been a captivating study target due to its association with human health and diseases. By nature, Fusobacterium lives in oxygen-free pockets between our teeth and gumline in which this organism has been correlated with a multitude of complications and diseases including periodontitis, inflammatory bowel disease, preterm birth, and most importantly colorectal cancer. Though the connection to human health is established, we still have to learn more about the mechanisms utilized by Fusobacterium to exacerbate diseases. This challenge is mainly hindered by the lack of efficient tools and resources to systematically investigate the relationship between the bacterium and its human host. Therefore, the work in this dissertation focuses on expanding the existing molecular toolkit to study clinically relevant Fusobacterium strain, which provides the power and convenience to discover novel mechanisms that Fusobacterium can take advantage of to be a successful pathogen. Accordingly, we first enhanced our ability to work with a wider range of Fusobacterium species. We successfully introduced exogenous genetic materials into a clinical strain of Fusobacterium, Fusobacterium nucleatum ATCC 25586. This breakthrough was built on the success of our current toolkit to make genetic modifications to a sister strain, Fusobacterium nucleatum ATCC 23726. With this newfound capacity to modify F. nucleatum ATCC 25586, we have described the importance of a novel protein aiding in the invasion of Fusobacterium to colorectal cancer. Furthermore, we have determined that certain proteins within the fusobacterial type 5a protein family can play a key role in governing binding and invasion of colorectal cancer cells in this study. Concurrently, for the first time, we provided the snapshot of a small protein and its role in fusobacterial long-term survival inside its targeted host cells. Altogether, the findings in this dissertation will bring forth an innovative framework to better the comprehension of current Fusobacterium-induced disease implications, while exploring alternative treatments for enhanced patient health.

Cloud-based collaborative editors enable real-time document processing via remote connections. Their common application is to allow Internet users to collaboratively work on their documents stored in the cloud, even if these users are physically a world apart. However, this convenience comes at a cost in terms of user privacy. Hence, the growth of popularity of cloud computing application stipulates the growth in importance of cloud security. A major concern with the cloud is who has access to user data. In order to address this issue, various third-party services offer encryption mechanisms for protection of the user data in the case of insider attacks or data leakage. However, these services often only encrypt data-at-rest, leaving the data which is being processed potentially vulnerable. The purpose of this study is to propose a prototype software system that encrypts collaboratively edited data in real-time, preserving the user experience similar to that of, e.g., Google Docs.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第25316号 / 農博第2582号 / 新制||農||1104(附属図書館) / 学位論文||R6||N5488 / DGAM / 京都大学大学院農学研究科農学専攻 / (主査)教授 田尾 龍太郎, 教授 田中 義行, 准教授 中野 龍平 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Please note: this work is permanently embargoed in OpenBU. No public access is forecasted for these. To request private access, please click on the lock icon and filled out the appropriate web form. / The meeting of poets Friederike Mayröcker and Ernst Jandl in 1954 changed the course of their own lives as well as post-war German-language poetry in Vienna, in Austria, and in Europe. This selected critical edition charts their creative processes from April 1954 through April 1957, which spans Mayröcker’s composition and editing of the core of her first poetry collection, and Jandl’s decisive turn away from a narrative into a visual and aural poetic structure. The poems included were critical to the foundational work of their seminal collections of 1966, and to the growth of the distinctive writing styles that would later bring each international renown. This dissertation presents the first known genetic editorial work on these poems, written as they were negotiating the development of their relationship and recommitting themselves to their lives and practices as artists. Illustrating their experimentation, their linguistic inventiveness, and their revision processes, as well as evidencing each poet’s evolution in style, this edition shows each poet’s synthesis and stylistic development surrounded by patterns and mysteries. Both Jandl and Mayröcker demonstrate specific types of manuscript or typescript variants that distinguish their composition and revision styles. In addition to the catalogues of these variants, correspondence and other paratextual material by both poets place their revisions in historical, anecdotal, and creative research contexts. Presenting their typescripts, manuscripts, and letters shows the relevance of extant archival material, and of Jandl and Mayröcker’s revision processes, to their poetry. Each poem is accompanied by my English-language translation, and by a catalogue of variants when available. / 2999-01-01T00:00:00Z