Production of mutant biological molecules for understanding biological principles or as therapeutic agents has gained considerable interest recently. Synthetic genes are today being widely used for production of such molecules due to the substantial decrease in the costs associated with gene synthesis technology. Along one such line, we have engineered tRNA genes in order to dissect the effects of G:U base-pairs on the accuracy of the protein translation machinery. Our results provide greater detail into the thermodynamic interactions between tRNA molecules and an Elongation Factor protein (termed EF-Tu in bacteria and eEF1A in eukaryotes) and how these interactions influence the delivery of aminoacylated tRNAs to the ribosome. We anticipate that our studies not only shed light on the basic mechanisms of molecular machines but may also help us to develop therapeutic or novel proteins that contain unnatural amino acids. Further, the manipulation of the translation machinery holds promise for the development of new methods to understand the origins of life. Along another line, we have used the power of synthetic biology to experimentally validate an evolutionary model. We exploited the functional diversity contained within the EF-Tu/eEF1A gene family to experimentally validate the model of evolution termed ‘heterotachy’. Heterotachy refers to a switch in a site’s mutational rate class. For instance, a site in a protein sequence may be invariant across all bacterial homologs while that same site may be highly variable across eukaryotic homologs. Such patterns imply that the selective constraints acting on this site differs between bacteria and eukaryotes. Despite intense efforts and large interest in understanding these patterns, no studies have experimentally validated these concepts until now. In the present study, we analyzed EF-Tu/eEF1A gene family members between bacteria and eukaryotes to identify heterotachous patterns (also called Type-I functional divergence). We applied statistical tests to identify sites possibly responsible for biomolecular functional divergence between EF-Tu and eEF1A. We then synthesized protein variants in the laboratory to validate our computational predictions. The results demonstrate for the first time that the identification of heterotachous sites can be specifically implicated in functional divergence among homologous proteins. In total, this work supports an evolutionary synthetic biology paradigm that in one direction uses synthetic molecules to better understand the mechanisms and constraints governing biomolecular behavior while in another direction uses principles of molecular sequence evolution to generate novel biomolecules that have utility for industry and/or biomedicine.

The objective of the field of Synthetic Biology is to implement novel functionalities in a biological context or redesign existing biological systems. To achieve this, it employs tried and tested engineering principles, such as standardisation and the design-build-test cycle. A crucial part of this process is the convergence of modelling and experiment. The aim of this thesis is to improve the design principles employed by Synthetic Biology in the context of Gene Regulatory Networks (GRNs). Small Ribonucleic Acids (sRNAs), in particular, are focussed on as a mechanism for post-transcriptional expression regulation, as they present great potential as a tool to be harnessed in GRNs. Modelling sRNA regulation and its interaction with its associated chaperone Host-Factor of Bacteriophage Qβ (Hfq) is investigated. Inclusion of Hfq is found to be necessary in stochastic models, but not in deterministic models. Secondly, feedback is core to the thesis, as it presents a means to scale-up designed systems. A linear design framework for GRNs is then presented, focussing on Transcription Factor (TF) interactions. Such frameworks are powerful as they facilitate the design of feedback. The framework supplies a block diagram methodology for visualisation and analysis of the designed circuit. In this context, phase lead and lag controllers, well-known in the context of Control Engineering, are presented as genetic motifs. A design example, employing the genetic phase lag controller, is then presented, demonstrating how the developed framework can be used to design a genetic circuit. The framework is then extended to include sRNA regulation. Four GRNs, demonstrating the simplest forms of genetic feedback, are then modelled and implemented. The feedback occurs at three different levels: autoregulation, through an sRNA and through another TF. The models of these GRNs are inspired by the implemented biological topologies, focussing on steady state behaviour and various setups. Both deterministic and stochastic models are studied. Dynamic responses of the circuits are also briefly compared. Data is presented, showing good qualitative agreement between models and experiment. Both culture level data and cell population data is presented. The latter of these is particularly useful as the moments of the distributions can be calculated and compared to results from stochastic simulation. The fit of a deterministic model to data is attempted, which results in a suggested extension of the model. The conclusion summarises the thesis, stating that modelling and experiment are in good qualitative agreement. The required next step is to be able to predict behaviour quantitatively.

Synthetic biology is a relatively new discipline within the field of biotechnologies. In essence it is the artificial creation of microorganisms. Though similar in principle, it differs from genetic engineering because it creates an organism from scratch, rather than cutting and pasting DNA (deoxyribonucleic acid) between existing organisms. This study investigates the ethical aspects (both rational and theological) concerned with synthetic biology through the use of a literature analysis. The study starts by investigating and describing the origins, pioneers, science and uses of synthetic biology. Secondly, it describes and ethically assesses the rational arguments for and against synthetic biology by comparing its benefits and risks. Lastly, the study describes and ethically assesses synthetic biology within the Reformed tradition, mainly by using the creational perspective of Christian ethical evaluations (including concepts such as creatio ex nihilio; creatio continua and imago Dei) and secondary the re-creational and eschatological perspectives. The final conclusion reached shows that synthetic biology is acceptable from a Reformed theological-ethical perspective, because humans as the image of God can create, just as God constantly creates new things and created a new universe from nothing. The rational arguments state that the potential benefits of synthetic biology surpass the risks it poses. Hence, it supports the idea that synthetic biology can be used to fulfil God’s commandment to love one’s neighbour, by improving his circumstances and activating hope. Nevertheless, Christians should always stay vigilant about motives and possible uses when dealing with new technologies. How and for what synthetic biology is used should in the future be constantly reviewed. In this way Christian scientists can still inquire about their work: Does it glorify God? / MA (Ethics), North-West University, Potchefstroom Campus, 2015

Synthetic biology is a relatively new discipline within the field of biotechnologies. In essence it is the artificial creation of microorganisms. Though similar in principle, it differs from genetic engineering because it creates an organism from scratch, rather than cutting and pasting DNA (deoxyribonucleic acid) between existing organisms. This study investigates the ethical aspects (both rational and theological) concerned with synthetic biology through the use of a literature analysis. The study starts by investigating and describing the origins, pioneers, science and uses of synthetic biology. Secondly, it describes and ethically assesses the rational arguments for and against synthetic biology by comparing its benefits and risks. Lastly, the study describes and ethically assesses synthetic biology within the Reformed tradition, mainly by using the creational perspective of Christian ethical evaluations (including concepts such as creatio ex nihilio; creatio continua and imago Dei) and secondary the re-creational and eschatological perspectives. The final conclusion reached shows that synthetic biology is acceptable from a Reformed theological-ethical perspective, because humans as the image of God can create, just as God constantly creates new things and created a new universe from nothing. The rational arguments state that the potential benefits of synthetic biology surpass the risks it poses. Hence, it supports the idea that synthetic biology can be used to fulfil God’s commandment to love one’s neighbour, by improving his circumstances and activating hope. Nevertheless, Christians should always stay vigilant about motives and possible uses when dealing with new technologies. How and for what synthetic biology is used should in the future be constantly reviewed. In this way Christian scientists can still inquire about their work: Does it glorify God? / MA (Ethics), North-West University, Potchefstroom Campus, 2015

Bacteria use Two Component Systems (TCS) to sense and respond to changes in their external environment. TCS are used to navigate to nutrients or away from toxins (chemotaxis) and to adapt to changes in osmolarity (osomosensing). TCS are composed of a histidine protein kinase (HPK) which trans-autophosphorylates in response to environmental change, transferring the phosphoryl group to a cognate response regulator (RR). Phosphorylated RRs modulate an output response such as protein-protein interaction for chemotaxis, and transcription for osmosensing. RRs are composed of a conserved amino terminal REC domain, and where present a variable effector domain. CheY, the chemotaxis RR, contains only a REC domain, whilst OmpR, the osmosensing RR, also contains a DNA binding effector domain. Recently, TCS have been used in synthetic biology applications due to their modularity and conserved signalling mechanism. This thesis aimed to investigate whether it was possible to design a synthetic TCS composed of fused chemotaxis and osmosensing components. Synthetic RRs were designed, fusing the highly conserved REC domains of CheY and OmpR upstream of the OmpR effector domain. REC domains were fused across the α₄-β₅-α₅ region, a region which transmits REC domain phosphorylation into effector domain activation. Synthetic RRs were designed to undergo phosphotransfer to their fused REC domains from the chemotaxis HPK, CheA, activate the attached OmpR effector domain and bind promoter DNA. Four chimeric RRs were created, although only three were structurally viable; F2, F3 and F4. Each fusion bound CheA, and F3 and F4 bound CheA with a significantly higher affinity than CheY. The chimeric RRs could all be phosphorylated byCheA-P; F4 and F3 were phosphorylated to wild-type levels. DNA binding affinitywas investigated with fluorescence anisotropy, hosphorylated and unphosphorylated F3 could not bind promoter DNA. F2 bound promoter DNA regardless of phosphorylation state. These data indicate that phosphorylation of the F2 REC domain does not lead to activation of the effector domain. F2 is likely to be constitutively active suggesting a previously unknown role for OmpR α₅ as a mediator of effector domain activation. Furthermore, using a simple fusion approach to design RRs is not a viable method to create a synthetic TCS with a controllable output.

Synthetic biology views a complex biological system as an ensemble in the hierarchy of parts, devices, systems, and networks. The practice of using engineering rules such as decoupling and standardization to understand, predict, and re-build novel biological functions from model-driven designed genetic circuits is emphasized. It is one of the top ten technologies that could help solving the current and potential risks in human society. Cyanobacteria have been considered as a promising biological system in conducting oxygenic photosynthesis to convert solar energy into reducing power, which drives biochemical reactions to assimilate and generate chemicals for a specific purpose such as CO2 fixation, N2 fixation, bioremediation, or fuels production. The promoter is a key biological part to construct feedback loops in genetic circuits for a desired biological function. In this thesis, promoters that don't work in the cyanobacterium Synechocystis PCC 6803 in terms of promoter strength, and dynamic range of gene regulation are identified. Biological parts, such as ribosome binding sites, and reporter genes with and without protease tags were also characterized with the home-built broad-host-range BioBrick shuttle vector pPMQAK1. The strong L03 promoter, which can be tightly regulated in a wide dynamic range by the foreign Tet repressor, was created through an iterative promoter engineering cycle. The iteration cycle of DNA breathing dynamic simulations and quantification of a reporting signal at a single-cell level should guide through the engineering process of making promoters with intended regulatory properties. This thesis is an essential step in creating functional promoters and it could be applied to create more diverse promoters to realize the emphasized practices of synthetic biology to build synthetic cyanobacteria for direct fuel production and CO2 assimilation.

Systems biology is a rapidly growing field which seeks a refined quantitative understanding of organisms, particularly studying how molecular species such as metabolites, proteins and genes interact in cells to form the complex emerging behaviour exhibited by living systems. Synthetic biology is a related and emerging field which seeks to engineer new organisms for practical purposes. Both fields can benefit from formal languages for modelling, simulation and analysis. In systems biology there is however a trade-off in the landscape of existing formal languages: some are modular but may be difficult for some biologists to understand (e.g. process calculi) while others are more intuitive but monolithic (e.g. rule-based languages). The first major contribution of this thesis is to bridge this gap with a Language for Biochemical Systems (LBS). LBS is based on the modular Calculus of Biochemical Systems and adds e.g. parameterised modules with subtyping and a notion of nondeterminism for handling combinatorial explosion. LBS can also incorporate other rule-based languages such as Kappa, hence adding modularity to these. Modularity is important for a rational structuring of models but can also be exploited in analysis as is shown for the specific case of Petri net flows. On the synthetic biology side, none of the few existing dedicated languages allow for a high-level description of designs that can be automatically translated into DNA sequences for implementation in living cells. The second major contribution of this thesis is exactly such a language for Genetic Engineering of Cells (GEC). GEC exploits the recent advent of standard genetic parts (“biobricks”) and allows for the composition of such parts into genes in a modular and abstract manner using logical constraints. GEC programs can then be translated to DNA sequences using a constraint satisfaction engine based on a given database of genetic parts.

The ability to control expression of a gene of interest is an important tool of molecular biologists and genetic engineers. This allows the phenotype associated with the regulated gene or genetic pathway to be partially de-coupled from the genotype and expressed only under condition that lend to induction of the genetic control system employed. Such control is typically implemented through a repressor protein (Eg. TetR, LacI) which will repress transcription when bound to a promoter containing a binding site (operator) recognized specifically by that repressor. Many such repressors and their cognate promoters are well-defined and characterized in model genetic systems, such as Escherichia coli, and may function poorly in other bacterial species. A lack of genetic components that allow the controlled expression of heterologous genes in less well studied bacterial species may limit their bio-industrial potential and the sophistication of engineered phenotypes. The work presented here uses random mutagenesis and selection to isolate mutants of TetR that are inducible by increased culture temperature. Induction of protein expression by temperature change can have benefits over repressors that require small-molecule inducers in bio-industrial applications as reversal of induction and reuse of growth medium are possible. The host range of these, or any, repressor protein is limited by the host range in which its cognate promoter will function. To bypass this limitation and allow use of TetR in Francisella novicida, a method was developed by which TetR-responsive promoters that function in this host could be selected from random DNA sequence flanking the TetR binding site, tetO. Many unique TetR-repressible promoters that function in Francisella were recovered and tightly-regulated expression of both exogenous reporter genes and host virulence genes were demonstrated. This promoter selection technique was also applied to E. coli, which allowed comparison between Francisella-selected promoters and those selected in an E. coli host. Adaption of this process for production of promoters responsive to transcription factors other than TetR would simply require the use of a different operator sequence, suggesting diverse applications for this technique. This success in promoter engineering should enable advances in synthetic biology and genetic engineering in non-model bacterial species. / Graduate

Thesis advisor: Welkin E. Johnson / Thesis advisor: Peter G. Clote / Synthetic biology currently is a rapidly emerging discipline, where innovative and interdisciplinary work has led to promising results. Synthetic design of RNA requires novel methods to study and analyze known functional molecules, as well as to generate design candidates that have a high likelihood of being functional. This thesis is primarily focused on the development of novel algorithms for the design of synthetic RNAs. Previous strategies, such as RNAinverse, NUPACK-DESIGN, etc. use heuristic methods, such as adaptive walk, ensemble defect optimization (a form of simulated annealing), genetic algorithms, etc. to generate sequences that minimize specific measures (probability of the target structure, ensemble defect). In contrast, our approach is to generate a large number of sequences whose minimum free energy structure is identical to the target design structure, and subsequently filter with respect to different criteria in order to select the most promising candidates for biochemical validation. In addition, our software must be made accessible and user-friendly, thus allowing researchers from different backgrounds to use our software in their work. Therefore, the work presented in this thesis concerns three areas: Create a potent, versatile and user friendly RNA inverse folding algorithm suitable for the specific requirements of each project, implement tools to analyze the properties that differentiate known functional RNA structures, and use these methods for synthetic design of de-novo functional RNA molecules. / Thesis (PhD) — Boston College, 2016. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.

A terapia gênica consiste em introduzir uma sequência de nucleotídeos, codificante ou não-codificante, que tenha a capacidade de interferir na progressão de uma doença por ativação, inativação ou modulação da expressão de um gene alvo. Uma das rotas de transferência gênica é a ex vivo. Essa rota consiste em realizar a modificação gênica ex vivo de um tipo celular do organismo afetado, seguida do transplante celular no indivíduo para a correção do fenótipo. Dentre os vários vetores virais utilizados para transferência gênica, o sistema lentiviral é considerado um dos mais eficazes, visto que é capaz de manter altos níveis de expressão a longo prazo. Além disso, dentre os vetores virais que se integram no genoma, esse é considerado o mais seguro, tendo apresentado apenas um caso com relatado de efeito colateral sem reação adversa. Uma nova tecnologia utilizada para padronizar sistemas biológicos é a biologia sintética. Essa tecnologia pode ser utilizada como ferramenta para produzir e/ou otimizar sistemas de expressão para produção de proteínas de interesse terapêutico. O objetivo desse trabalho é gerar um vetor lentiviral sintético, para terapia gênica ex vivo, para reposição enzimática. Foram geradas quatro linhagens celulares humanas com produção transiente das proteínas terapêuticas Prot_Ctr e Prot_Mut sob controle dos promotores CMV e HeF1a. Para padronização do ensaio de transfecção, foram geradas duas linhagens celulares humanas que expressão da proteína fluorescente verde (GFP) sob controle dos mesmos promotores citados acima. Como controle negativo das linhagens produtoras da proteína terapêutica, foi gerada uma linhagem como vetor plasmidial vazio pLV_GTW_Mock. O nível de expressão do mRNA relativo às proteínas terapêuticas variou de 3.581,95 ± 1.322 a 10.377,18 ± 2.562 URE, não havendo diferenças significativas entre as linhagens produzidas (p > 0,05). O nível de produção da proteínas terapêuticas variou de 30,98 UI/mL a 241,1 UI/mL. A linhagem com maior produção dessa proteína foi a 293T/HeF1a_Prot_Mut, e essa diferença é significativa (p < 0,05). A partir da transfecção dos plasmídeos auxiliares e plasmídeo portador do cDNA que codifica a Prot-Mut na linhagem celular 293-T foi obtido o vetor lentiviral com título de 1,68x107 pLV/mL. Em conclusão, é possível gerar um vetor lentiviral funcional portador da Prot_Mut para utilização em terapia gênica ex vivo. Espera-se que o produto desse projeto de pesquisa gere uma patente. Para evitar a quebra de novidade, atividade inventiva e suficiência descritiva, requisitos mínimos de patenteabilidade, os resultados foram apresentados sem mencionar a doença e o gene em estudo / Gene therapy involves introducing a nucleotide sequence, coding or non-coding that can to interfere with the progression of a disease by activating, inactivating or modulating the expression of a target gene. One of the gene transfer routes is the ex vivo. This route consists in producing a ex vivo gene modification of a cellular kind of the affected organismo, following the transplant of those cells to correct the fenotype. Among the various viral vectors used for gene transfer, the lentiviral system is considered one of the most effective, since it is able to maintain high levels of long-term expression. Between the viral vectors that integrate into the genome, the lentiviral system is considered the safest, and It has only filed a case with reported side effect without adverse reaction. A new technology used to standardize biological systems is the synthetic biology. This technology can be used as a tool to produce and/or optimize expression systems for production of proteins of therapeutic interest. The aim of this study is to generate a synthetic lentiviral vector for ex vivo gene therapy, for enzyme replacement therapy. It were generated four human cell lines with transient production of therapeutic proteins Prot_Ctr and Prot_Mut under the control of CMV and HeF1a promoters. To standardize the transfection assay were generated two human cell lines expressing green fluorescent protein (GFP) under control of the same promoters cited above. As a negative control of the producing cell lines, It was generated a human cell line with an empty plasmid vector pLV_GTW_Mock. The level of mRNA expression relative to the therapeutic proteins ranged from 3581,95 ± 1322 to 10377,18 ± 2562 REU, there were no significant differences among the produced cell lines ( p > 0.05 ). The production level of therapeutic proteins ranged from 30.98 IU/mL to 241.1 IU/mL. The cell line with the highest production of the therapeutic protein was 93T/HeF1a_Prot_Mut+, and this difference is significant (p < 0.05 ). From the transfection of the plasmid containing the cDNA encoding the Prot_Mut and packing plasmid It was obtained lentiviral vector with the titer 1,68x107 pLV/mL. In conclusion, it is possible to generate a functional lentiviral vector carrying the Prot_Mut for use in ex vivo gene therapy. It is expected that the product of this research project generates a patent. To avoid breaking novelty, inventive activity and descriptive sufficiency, minimum requirements for patentability, the results were presented without mentioning the disease and the gene under study