This Dissertation is broken into four chapters. In chapter 1 is an introduction into the thesis. In chapter 2, I review the Long Interspersed Element-1 (L1), which is a repetitive DNA retrotransposon capable of duplication by a "copy-and-paste" genetic mechanism. Scattered throughout mammalian genomes, L1 is typically quiescent in most somatic cell types. In developing neurons, however, L1 can express and retrotranspose at high frequency.

In chapter 3, I record my findings on using zinc-finger repressors to inhibit murine L1. The mouse has an estimated 3100 putatively active L1 elements, split into three families, TF, GF, and A. Each family is distinguished by their promoter-like 5'UTR. Using zinc-finger repressors, we inhibit the expression of mouse L1 TF family.

In chapter 4, I document my discoveries on ssDNA and L1 in three prime repair exonuclease 1 (TREX1)-deficient neural cells. Accumulation of deoxyribonucleic acid (DNA) species in the cytosol leads to a type I interferon response and inflammation. TREX1 removes single-stranded (ss) and double-stranded (ds) DNA from the cytosol, preventing accumulation and a subsequent inflammatory response. Several autoinflammatory diseases, such as Aicardi-Goutières syndrome syndrome (AGS) and systemic lupus erythematosus, arise when the function of TREX1 is compromised. AGS is a severe autoinflammatory disease most typically affecting the brain and the skin, resulting in severe psychomotor retardation. Research on the neurological aspects of AGS at a cellular and molecular level has proven difficult, due to the lack of relevant animal models. In particular, although demonstrating a lethal inflammatory state, the TREX1 knockout mouse does not exhibit a neurological phenotype, and is thus unsuitable to study AGS neuropathology. Here, we create pluripotent stem cell models devoid of TREX1 function, which we further differentiate into neural cells. We find an abundance of ssDNA in TREX1-deficient neural precursor cells, neurons, and astrocytes. Furthermore, we show the Long Interspersed Element-1 (LINE-1 or L1), a class of endogenous retrotransposons, is a major source of the ssDNA, and that inhibition of reverse transcription reduces ssDNA levels. TREX1-deficient neurons experience greater cytotoxicity, which can be rescued with reverse transcriptase inhibitors (RTi). Likewise, treating neurons with conditioned media from TREX1-deficient astrocytes increases neuronal toxicity, indicating the presence of toxic factors or a lack of neurotrophic factors. Our results demonstrate that TREX1 removes cytosolic ssDNA in neural cells created by L1 reverse transcription, thus preventing neurotoxicity.

Many materials are capable of organizing into multiple distinct solid phases, each exhibiting a unique set of material properties (e.g., mechanical, optical, electronic, catalytic, etc.). This material property diversity implies that a specific solid form or structure is typically preferred for a specific application. Thus, directing and controlling solid form during crystallization processes is a fundamental solid state engineering challenge. Here, for the first time, a general procedure is presented for designing continuous crystallizers that produce polymorphically pure crystal distributions of a preferred polymorph regardless of that polymorph's relative thermodynamic stability. The design rules were generated by developing and analyzing a multi-polymorph mixed suspension mixed product removal precipitator model, and they have been corroborated both by experimental data generated in our lab and by all of the applicable data in the published literature. These rules were developed to build understanding and aid in the process design of two sustainable energy technologies: carbon capture and utilization as structural materials (CCUSM) and methane pyrolysis (MP). Studying these processes also required the development of new models for calculating interphase mass transport in concentrated, electrolytic, reacting solutions and for describing the reactive transport that occurs in methane pyrolysis membrane reactors. The development and analysis of these models and a thermodynamic minimum energetic cost assessment of a wider set of sustainable energy technologies are also included in the dissertation.

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