abstract: The portability of genetic tools from one organism to another is a cornerstone of synthetic biology. The shared biological language of DNA-to-RNA-to-protein allows for expression of polypeptide chains in phylogenetically distant organisms with little modification. The tools and contexts are diverse, ranging from catalytic RNAs in cell-free systems to bacterial proteins expressed in human cell lines, yet they exhibit an organizing principle: that genes and proteins may be treated as modular units that can be moved from their native organism to a novel one. However, protein behavior is always unpredictable; drop-in functionality is not guaranteed. My work characterizes how two different classes of tools behave in new contexts and explores methods to improve their functionality: 1. CRISPR/Cas9 in human cells and 2. quorum sensing networks in Escherichia coli. 1. The genome-editing tool CRISPR/Cas9 has facilitated easily targeted, effective, high throughput genome editing. However, Cas9 is a bacterially derived protein and its behavior in the complex microenvironment of the eukaryotic nucleus is not well understood. Using transgenic human cell lines, I found that gene-silencing heterochromatin impacts Cas9’s ability to bind and cut DNA in a site-specific manner and I investigated ways to improve CRISPR/Cas9 function in heterochromatin. 2. Bacteria use quorum sensing to monitor population density and regulate group behaviors such as virulence, motility, and biofilm formation. Homoserine lactone (HSL) quorum sensing networks are of particular interest to synthetic biologists because they can function as “wires” to connect multiple genetic circuits. However, only four of these networks have been widely implemented in engineered systems. I selected ten quorum sensing networks based on their HSL production profiles and confirmed their functionality in E. coli, significantly expanding the quorum sensing toolset available to synthetic biologists. / Dissertation/Thesis / Doctoral Dissertation Bioengineering 2017

Individual cells in a genetically identical population, exposed to the same environment, can show great variation in their protein expression levels. This is due to noise, which is inherent in many biological processes, due in part to the low molecule numbers and probabilistic interactions which lead to stochasticity. Much of the work in the field of noise and its propagation in gene expression networks, whether it is experimental, modelling or theoretical, has been conducted on networks/systems that occur within a single cell. However, cells do not exist solely in isolation and understanding how cells are able to coordinate their behaviour despite this noise is an interesting area of expansion for the field. In this study, a synthetic intercellular communication system was designed that allows the investigation of how noise is propagated in intercellular communication. The communication system consists of separate sender and receiver cells incorporating components of the Lux quorum sensing system of Vibrio fischeri. The sender cell was designed so that the production of the signalling molecule, 3-oxohexanoyl homoserine lactone, is able to be controlled by addition of isopropyl-β-D-thio-galactoside (IPTG) and monitored via a reporter gene. The receiver cell was designed with a dual reporter system to enable the response of the cell to the signalling molecule to be monitored and the intrinsic and extrinsic noise contributions to the total noise to be calculated. Sender and the receiver cells were engineered in Escherichia coli. The functionality of the receiver cells was tested in the presence of known concentrations of the signalling molecule. The population response and the noise characteristics of the receiver cells in the homogeneous environment were determined from single cell measurements. The functionality of the sender cells was tested in the presence of a range of IPTG concentrations and the induction of expression from the LacI-repressible promoter was monitored. Mathematical models of the system were developed. Stochastic simulations of the models were used to investigate any unexplained behaviour seen in the characterisation of the cells. The full functionality of the intercellular communication system was then tested by growing the receiver in the collected media of the induced sender cells. The response of the receiver cells to the signalling molecule in the media was again characterised using single cell measurements of the reporter expression levels. The analysis of mixed populations of the sender and receiver cells was hampered by the technical limitations of the instruments used for the single cell measurements. Difficulties were encountered in simultaneous and specific measurement of the three reporter genes. Two methods for overcoming this issue were proposed using microscopy, and one of these methods was shown to have potential in overcoming the issue.

The purpose of master’s thesis is to project virtualization solution together with replication of the servers. Thesis is divided into the three parts and that it theoretical, analytical and projection part. In analytical part there are basic information about virtualization technologies, in analytical part there is analysis of the present status of the company and mainly about status of the IT infrastructure and in the end projection part there is realization of the virtualization solution from choosing the right type of cluster to choosing hardware solution.

The scope of this project was to implement a quorum sensing model capable of synchronised oscillations from the article ”A synchronized quorum of genetic clocks” [1] in the software framework URDME [2]. The model consists of a system of partial differential equations describing time delayed and coupled biochemical reactions. In URDME, the time delay system was formed using a cascade of reactions in which the rate of each reaction was set so that the expected total time for all reactions in the cascade corresponds to a certain delay time. One reason for this cascade delay model is that it might better capture the inherently stochastic nature of the delay mechanism in the quorum sensing network, as opposed to a model using explicit delays.Another reason is simplicity of implementation, as delays are not explicitly supported in URDME. After initial tests suggested that the cascade delay model gave satisfying results, it was incorporated into the quorum sensing model from the article, which was implemented by rewriting the differential equations as a system of biochemical reactions. Simulations in one and two dimensions were then done, with both stochastic and deterministic solution methods. The one dimensional and two dimensional simulations yielded distinct synchronised oscillations with a cascade delay containing five sub-reactions. Several results from the simulations of the original article could be reproduced. From the results, it was concluded that the proposed cascade delay model was successful in modelling the delayed reactions in the quorum sensing network. In future studies, it is suggested that the individual cells, in which most of the reactions in the quorum sensing network happen, are modelled with greater resolution.

A charismatically created organization works to tear down the routine and the norm of everyday society, replacing them with new institutions. Max Weber has stated that a charismatic organization can only exist in the creation stage, after which it will either collapse under the weight of the changes it has made, or begin a move towards the routine, making it as well-established and routinized as the society it sought to replace. The changes to the seniority of the Quorum of the Twelve Apostles of The Church of Jesus Christ of Latter-day Saints demonstrate the movement of the church from charismatic to routinized leadership. They also show how the charismatic attributes of the first leader of the church were institutionalized in the office of President of the Church. The first change occurred in 1861, reversing the seniority of John Taylor and Wilford Woodruff. The second change occurred in 1875, making Taylor and Woodruff senior to two original members of the Quorum of the Twelve, Orson Hyde and Orson Pratt. The final change occurred in 1900, making Joseph F. Smith senior to Brigham Young, Jr. The few scholars who have addressed these changes tend to focus on either the official explanations or personal relationships and motives of those involved. This thesis moves beyond these to explore the broader institutional motives. It also discusses the effects of changing the rules determining who would succeed to the presidency of the church. The 1861 and 1900 changes have not been examined in any substantial way before. All three changes affected who became president of the church, thus changing the direction of the church. More than satisfying personal vendettas or righting obvious problems in the rules of seniority, the three changes highlight difficult choices church leaders made that moved The Church of Jesus Christ of Latter-day Saints from a charismatically led organization to a highly routinized bureaucracy.

No description available.

Polymicrobial communities of bacterial and fungal species are present on the skin and mucosal surfaces of the body. Invasive infections caused by Candida species are commonly seen in immunocompromised individuals (HIV, transplants, cancer) and ranks as the third leading cause of infection in hospitalized patients. C. albicans is a polymorphic opportunistic fungus that infects critically ill patients and has the ability to change its morphology from yeast to hyphal form.The morphogenesis of C. albicans is a major aspect of its virulence and is regulated by quorum sensing (QS) molecules they produce, as well as the presence of neighboring microbes.In this study, we examined two transporter mutants, cdr4 and ssu1, for their ability to form biofilms in the presence of cyclic-di-GMP and 3-oxo-12-homoserine lactone. To quantify biomass, wild type and mutant cells were grown overnight at 30˚C in YPD. The cells were washed, counted and diluted to a desired density of 106 cells/ml in medium 199, pH7.5. Cells were added to 96-well plates pre-incubated with 5% fetal bovine serum at densities of 105, 104, and 103 cells/well and allowed to adhere at 37˚C for one hour. The wells were then covered with fresh M199 media containing the QS molecule and monitored for 48 hours at 37˚C. After this time, the media and planktonic cells were removed. The biofilms were fixed with methanol, dried, then stained with 0.05% crystal violet. Bulk biomass was assessed by spectrophotometry. We did observe a difference in biofilm density when incubated in the presence of cyclic-diGMP. We noted that for the wild type and ssu1 strain their biofilms biomass increased by as much as 10% at 104 and 103 cell densities when compared with the control. While the cdr4 strain had a slight reduction in biofilm density when cyclic-diGMP was present. This result also indicates a potentially positive role in which cyclic-diGMP can help C. albicans develop denser biofilms, potentially in the presence of bacteria like P. aeruginsa, which secrete cyclic di-GMP, but kill hyphal forms of C. albicans. Additionally, it has been shown that C. albicans mutants lacking the hybrid histidine kinase, Chk1p, are refractory to the effects of farnesol, a QS molecule that inhibits morphogenesis.Given that mutations in CDR4 and SSU1 impact the QS response in C. albicans, we investigated whether these genes were regulated through two-component signaling by Chk1. To assess CDR4 and SSU1 expression, wild type and mutant strains were grown overnight in YPD media at 30˚C. Cells were then harvested and RNA was obtained by acid phenol extraction. Using RT-PCR, we determined both CDR4 and SSU1 expression is reduced or highly repressed in the chk1, ypd1, and skn7 null strains. These results suggest the two genes are downstream targets in a pathway regulated by Chk1p. The finding that QS proceeds through a two-component pathway can be exploited in antifungal drug development. Given that two-component signaling is absent in mammalian cells, development of novel compounds that interfere with this pathway may be a useful alternative for treating patients with candidiasis.

Natural cellular networks are very good at processing diverse inputs, generating complicated responses, and confounding researchers with their complexities. As an alternative to traditional cellular engineering approaches, the field of synthetic biology attempts to avoid the complexities of natural systems by focusing on the bottom-up construction of artificial cellular circuits. By rationally building up circuit complexity, synthetic biologists hope to both create novel systems capable of programming unique cellular responses, and gain insights into the design principles of natural systems. Circuits that allow for the programming of intercellular responses are of particular interest, and researchers have focused on the use of bacterial communication mechanisms (quorum sensing) to construct such circuits. At their most basic, quorum-sensing systems are composed of three main components, making them amenable to genetic manipulation. These components, however, have properties that have been finely tuned through evolution to function in very specific ways, and repurposing them for our own uses requires methods to overcome their naturally evolved properties. This thesis details our work in the construction and engineering of synthetic circuits based on components of the LuxI-LuxR quorum-sensing system. Using these components, we demonstrate methods for altering both the sensitivity and the form of the quorum-sensing response through the creation of three unique systems: an ultrasensitive positive feedback loop, a logical AND gate, and a coupled feedback loop oscillator. Construction and tuning of each circuit's properties were achieved through a mixture of rational and evolutionary approaches, with particular emphasis on the directed evolution of the LuxR transcriptional activator. Mathematical modeling was also used during the construction of the more complex circuits to predict the properties that were essential to their functionalities. With the construction and characterization of these circuits, we have provided both well-defined modules that can be used in the construction of more complex systems, and developed methods that will allow for the creation and engineering of additional synthetic circuits.

No description available.

Work over the past two decades has revealed that non-coding RNAs (ncRNAs) are prevalent in all kingdoms of life. Using RNA-seq we discovered hundreds of ncRNAs in the antibiotic-producing genus of bacteria, Streptomyces. These included trans-encoded small RNAS (sRNAs), cis-antisense RNAs, and a new type of antisense RNA we termed cutoRNAs (convergent untranslated overlapping RNAs) that arise when transcription termination does not occur in the intergenic region between two convergently arranged genes. Many of these ncRNAs feature prominently in the specialized metabolite biosynthetic clusters (e.g. antibiotics, anticancer agents, immunosuppressants). Hence, it is likely that understanding the functions of these RNAs will be important for new molecule discovery. We found that one highly expressed antisense RNA (ScbN) was expressed opposite the -butyrolactone synthase scbA in the model streptomycete Streptomyces coelicolor. However, ScbN had no detectible impact on the expression of scbA. Instead, the transcription terminator of scbN, which also forms a hairpin within the coding sequence of scbA, was found to reduce expression of scbA more than 10-fold. This led us to bioinformatically search for similar coding-sequence hairpins throughout all bacteria, leading to the discovery of many stable RNA structures with conserved locations throughout very divergent bacteria (e.g. Streptomyces, Escherichia coli, Bacillus subtilis). / Thesis / Doctor of Philosophy (PhD) / The flow of genetic information, from DNA to RNA to proteins, often portrays RNA as a mere intermediary molecule. An alternative, and perhaps more accurate, way to view RNA is that it is central to all cellular processes. Many RNAs are not translated into proteins and instead act as regulatory molecules, impacting the expression of other genes. In this work we found many examples of these regulatory RNAs in a group of bacteria known to produce many of the world’s antibiotics. Understanding the roles these regulatory RNAs play in impacting gene expression will be important for the discovery of new molecules, such as antibiotics. In addition to distinct regulatory RNAs mentioned above, we found that RNA structures within the coding sequences of mRNAs that are translated into proteins have dramatic regulatory consequences. We describe the characterization of one such RNA structure in a gene involved in bacterial communication, and develop a bioinformatic tool to hunt for other such structures conserved throughout bacteria.