Final publication is available at http://www.sciencedirect.com/science/article/pii/S0002939414000488 / 京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19586号 / 医博第4093号 / 新制||医||1014(附属図書館) / 32622 / 京都大学大学院医学研究科医学専攻 / (主査)教授 大森 孝一, 教授 宮本 享, 教授 横出 正之 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20975号 / 医博第4321号 / 新制||医||1026(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 川上 浩司, 教授 鈴木 茂彦, 教授 開 祐司 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第20994号 / 医博第4340号 / 新制||医||1027(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 鈴木 茂彦, 教授 伊佐 正, 教授 大森 孝一 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21651号 / 医博第4457号 / 新制||医||1034(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 髙橋 良輔, 教授 伊達 洋至, 教授 松原 和夫 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

No description available.

No description available.

Inherited Retinal Degenerations (IRDs) are a heterogenous group of diseases which lead to vision impairment and can be found both in humans and in dogs. About 1 in 1,380 humans is estimated to suffer from an autosomal recessive IRD, which would be 5.5 million people worldwide, and many more are estimated to be unaffected carriers. This makes autosomal recessive IRDs likely the most common group of Mendelian diseases in humans. Today, about 300 genetic mutations have been connected to cause retinal diseases in humans. Whilst in dogs only 32 genes have been identified, numerous eye conditions have been described where the genetic cause has not yet been identified. This suggests that there are much more genetic causes to discover in the dog genome. Additionally, the dog serves well as a model organism to investigate IRDs as it is sharing morphological and genetic similarities with humans. For these reasons, proper software, a canine reference genome of high quality, and smart implementation of bioinformatic tools and methods are a big advantage to increase chances of finding new causative genetic variants and subsequently enable faster detection of possible preventions of the disease or at least alleviating its symptoms via early diagnosis. In this project, a pre-existing pipeline consisting of Bash scripts was stepwise improved with the goal to increase its efficiency. After controlling whether previous data could still be reproduced with the old pipeline in a first step, the software was exchanged to more updated versions in a second step. A main change was the replacement of the mapping tool Burrows-Wheeler Aligner (BWA) from bwa mem to bwa-mem2 mem, and the update of deprecated Genome Analysis Toolkit (GATK) 3.7 to version 4.3 or 4.4. Thirdly, the scripts were adapted from using the older canine reference genome CanFam3.1 to CanFam4. In a fourth step, for automatization and fastening the running time, the pipeline steps were implemented into the workflow management system Nextflow. Additionally, this step was partly aiming to make the pipeline in concordance with the FAIR-principles. All steps were tested on the same test data set, a Labrador retriever family trio, in which one genetic cause for a canine form of the IRD Stargardt disease in a previous study had been detected, namely an insertion in the ABCA4 gene. Lastly, the workflow was also tested on a second data set of a novel IRD of unknown genetic origin on two sibling pairs of Chinese Crested Dogs (CCR). The adjustment of the pipeline shows similar results regarding the change of mapping tool. Introducing the new reference genome revealed a drop of average coverage by one read average for when using CanFam4, while other results were similar. Using the new reference genome increased the number of unknown variants compared to findings with CanFam3.1. However, the known causative variant for the canine form of Stargardt disease, an insertion in ABCA4 gene, could be found in all cases. The run with Nextflow produced identical results to when the respective steps were run with Bash scripts, but it reduced the running time. Running the workflow on the new data set (CCR) and subsequent annotation and filtering indicate new candidates which could be further investigated as a potential cause for this currently unknown cause for an IRD.

No description available.

No description available.

Despite being the most prevalent presentation of Age-Related Macular Degeneration (AMD), dry AMD (dAMD) lacks a therapeutic treatment. Retinal pigment epithelium (RPE) dysfunction preceding the onset of dAMD has inspired interest in regenerative medicine approaches seeking to replenish the RPE and preserve visual acuity. Cell delivery to the subretinal space however has been met with challenges surrounding ease of access and invasive surgical implantation. Two-dimensional scaffolds have made use of natural and polymeric materials to act as carriers for RPE cells and various progenitor lines. These substrates mitigate issues surrounding the handling of delicate cell sheets harvested for transplant. As well, they are often successful in preserving RPE phenotype, supporting growth, and can be fine tuned to possess morphologies comparable to native extracellular matrix (ECM). Despite aiming to act as replacement Bruch’s membrane on which RPE resides, two-dimensional substrates are often notably bulky and require traumatic surgery for implantation. As a result, the use of injectable methods of cell delivery has gained appeal. Bolus injections, despite improved methods of administration, are correlated with issues of inadequate cell localization. In response, three-dimensional hydrogel carriers for retinal applications aim to encapsulate cells, allowing for better cell distribution as these materials spread throughout the subretinal space. Increased viscosity of hydrogels as compared to saline injections, is hypothesized to improve cell loss and reduce aggregation. Of particular interest are in situ gelling systems, which undergo physical changes upon injection. Gelation upon delivery works to further assist in maintaining the cells within their target site. Purity and reproducibility concerns associated with the use of natural materials in the development of hydrogel cell carriers, have inspired the use of synthetic thermoresponsive poly-N-isopropylacrylamide (pNIPAAm). pNIPAAm undergoes a liquid to gel transition at a lower critical solution temperature (LCST) of 32°C. Copolymerization with various hydrophobic and hydrophilic groups can be used to adjust gel properties such as increasing or decreasing LCST, allowing for degradation, and improving water retention. In the work described herein, two NIPAAm-based thermoresponsive hydrogels intended for use as subretinal cell carriers are proposed. / Thesis / Master of Applied Science (MASc)