The field of synthetic biology seeks to use design principles of life to create new genes, organisms and populations to both better understand biology as well as generate species with useful properties. Budding yeast has been a workhorse for synthetic biology, as well as an important model organism in the broader fields of molecular biology and genetics. This thesis aimed to create genome engineering tools for the manipulation of genomes, with direct applications in yeast. I focused developing high-throughput and highly efficient methods for making genomic modifications in yeast to allow for the generation of large libraries of precisely modified yeast genomes. By manipulation of endogenous DNA recombinases and mismatch repair enzymes in yeast, we were able to develop an oligonucleotide only method for genome engineering to generate libraries as large as 10^5 individuals with a frequency of modification as high as 1%. Additionally, we validated the use of RNA-guided CRISPR/Cas9 endonucleases to make changes in yeast genomes, resulting in frequencies of genome modification >90% in transformed populations. We further optimized this method to generate larger libraries as high as 10^5 individuals and explored a proof of concept epistasis experiment involving thermotolerance. Lastly, the propagation of changes to successive generations is useful when engineering organisms on the population level. To this end we explored the use of RNA-guided gene drives to bias inheritance in S. cerevisiae. We show that inheritance of these selfish elements can be biased to over 99% and is reversible.

Mosquitoes are vectors for many diseases that cause significant mortality and morbidity across the globe such as malaria, dengue fever and Zika. As mosquito populations expand their range into new areas, they may undergo mate-finding Allee effects such that their ability to successfully reproduce becomes difficult at low population densities. With new technology, creating target specific gene modification may now be a viable method for mosquito population control. We develop a mathematical model to investigate the effects of releasing transgenic mosquitoes into newly established low-density mosquito populations. Our model consists of two life stages (aquatic and adult), which are further divided into three genetically distinct groups: heterogeneous and homogeneous transgenic alleles that cause female infertility and a homogeneous wild type. We perform analytical and numerical analyses on the equilibria to determine the level of saturation needed to eliminate mosquitoes in a given area. This model demonstrates the potential for a gene drive system to reduce the spread of invading mosquito populations. / Master of Science

This thesis is concerned with presenting analyses regarding key ethical issues regarding and arising from the development and potential use of gene drive modified mosquitoes for the purpose of malaria elimination. Each of the chapters constituting this thesis offers a rigorously researched analysis which attempts to answer questions thus far unanswered in the academic literature. Chapter one explores whether the development and use of this technology can be fairly considered unethical in principle; concluding it cannot be. Chapter two explores the appropriate relationship between this technology and the precautionary principle, a prominent regulatory and governance principle which has been invoked as ostensible support for an indefinite global moratorium on all gene drive technology. The chapter concludes that the precautionary principle, at least as articulated by UNESCO, does not provide justification for a global moratorium on gene drive technology. In fact, the precautionary principle is likely unfit as a regulatory norm for some kinds of gene drive products and purposes. Chapter three was co-authored with Delphine Thizy, Global Stakeholder Engagement Manager for Target Malaria, one of the leading consortiums working on research and development of gene drive biotechnology for malaria control. Together we articulate the ethical principles selected to guide Target Malaria’s stakeholder engagement, as well as provide the rationale for their selection and expound upon some early lessons from their implementation. Chapter four offers an analysis with the goal of locating the ethically appropriate locus of political organization from which to seek permission for a gene drive modified organism release into the shared environment. The chapter considers the appropriateness of each of the following levels of political organization: consent of individuals, local communities, nation states, and international governance institutions. The conclusion arrived at, with some caveats, is that such a decision is most appropriately issued by a nation state. / Thesis / Doctor of Philosophy (PhD) / This thesis is concerned with presenting analyses regarding key ethical issues regarding and arising from the development and potential use of gene drive modified mosquitoes for the purpose of malaria elimination. Chapter one explores whether the development and use of this technology can be fairly considered unethical in principle; concluding it cannot be. Chapter two explores the appropriate relationship between this technology and the precautionary principle, a prominent regulatory and governance principle which has been invoked as ostensible support for an indefinite global moratorium on all gene drive technology. Chapter three articulates, expounds, and provides rationale for the ethical principles selected to guide stakeholder engagement by Target Malaria, one of the leading consortiums working on research and development of gene drive biotechnology for malaria control. Chapter four attempts to locate the ethically appropriate locus of political organization from which to seek permission for a gene drive modified organism release.

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Genetic control strategies are a novel method for reducing populations of pest insects such as the yellow fever mosquito Aedes aegypti, a major vector of several important arboviral diseases. This thesis describes efforts to develop new tools to engineer the Ae. aegypti genome and to better understand existing tools, and furthermore to use these to engineer a gene drive system in Ae. aegypti. The piggyBac transposon was found to be extremely stable in the germline of Ae. aegypti, and transposons engineered into the germline could not be remobilized with either an endogenous or exogenous source of piggyBac transposase. Conversely, somatic remobilization of piggyBac transposons was found to be readily detectable in the presence of a source of active transposase, the first report of such remobilization in Ae. aegypti. Toward new tools for genome engineering, the site-specific integrase from the phage φC31 was successfully used to promote exchange between a transgene cassette inserted into the genome of Ae. aegypti and a cassette in a plasmid vector, in the first demonstration of recombinase mediated cassette exchange technology in a pest insect species. The integrases from phages φRV1 and Bxb1 were not found to be active in the germline of the mosquito. Finally, development of a gene drive system in Ae. aegypti using an RNAi-mediated killer-rescue mechanism was attempted. Tissue-specific expression of tTAV-regulated-toxic effectors genes, using the promoter regions of the blood meal induced genes Carboxypeptidase A-1, 30Kb and Vitellogenin A, was possible, but sex-specificity was not achieved. A blood meal inducible lethal phenotype was not possible using the chosen promoters, with expression of the effectors either leading to death in early development or to a sublethal phenotype. RNAi against tTAV fused to the Mnp fragment of the dengue virus’ genome was tissue specific, but was found to be highly effective in the fat body suggesting that the Vitellogenin A was the best candidate for the engineering of killer-rescue systems in the mosquito.

Derived from and inspired by the adaptive immune system of bacteria, CRISPR has gone from basic biology knowledge to a revolutionizing biotechnological tool, applicable in many research areas such as medicine, industry and agriculture. The full mechanism of CRISPR-Cas9 was first published in 2012 and various CRISPR-Cas systems have already passed the first stages of clinical trials as new gene therapies. The immense research has resulted in continuously growing knowledge of CRISPR systems and the technique seems to have the potential to greatly impact all life on our planet. Therefore, this literature study aims to thoroughly describe the CRISPR-Cas system, and further suggest an undergraduate laboratory exercise involving gene editing with the CRISPR-Cas9 tool. In this paper, we describe the fundamental technical background of the CRISPR-Cas system, especially emphasizing the most studied CRISPR-Cas9 system, its development and applications areas, as well as highlighting its current limitations and ethical concerns. The history of genetic engineering and the discovery of the CRISPR system is also described, along with a comparison with other established gene editing techniques.  This study concludes that a deeper knowledge about CRISPR is important and required since the technique is applicable in many research areas. A laboratory exercise will not only inspire but also provide extended theoretical and practical knowledge for undergraduate students.