The preservative challenge test is a regulatory requirement specified in various pharmacopoeias to determine the efficacy of preservatives. However, such testing is a labour-intensive repetitive task and often requires days before results can be generated. Microbial biosensors have the potential to provide a rapid and automated alternative to the traditional viable counting currently in use. However, the selection of appropriate promoters is essential. The bioluminescent reporter strains used in the current study comprise the Photorhabdus luminescence lux CDABE reporter genes under the control of five individual constitutive Escherichia coli promoters: outer lipoprotein (lpp); twin arginine translocase (tatA); lysine decarboxylase (ldc); lysyl t-RNA (lysS); and ribosomal protein (spc). The promoter plus lux CDABE constructs were cloned, ligated into the plasmid vector pBR322 and transformed into E. coli ATCC 8739. The bioluminescence intensity in the decreasing order of constitutive promoter was lpp > spc> tatA> ldc > lysS. The five biosensor strains tested successfully in PET assays and demonstrated accuracy with a minimum detection limit of 103 CFU/ml, a detection range of 6 orders magnitude, and yielded equivalent results to methods currently recommended by the pharmacopoeias. The bioluminescent biosensors were used to monitor the efficacy of preservatives; sorbic acid at concentrations of 0.031% to 0.2% at pH 5.0, and benzalkonium chloride at concentrations of 0.0062% to 0.00039% alone and in combination with 0.03% EDTA. The 99.9% percentage of bioluminescence reduction of tatA-lux, ldc-lux, lysS-lux, and spc-lux was statistically equivalent to the 3 log10 CFU/ml reduction as required by the Pharmacopeias’. Strong significant correlations between bioluminescence and the methods recommended by the pharmacopoeias were obtained when the biosensor strains were challenged with preservatives, for all except lpp-lux E. coli. The bioluminescence expressed by the lpp-lux biosensor was significantly lower during long-term stationary phase than it was for any of the other biosensors and was also significantly lower than for any of the other biosensors in the presence of preservatives. Since the plasmid copy number and viable counts for lpp-lux did not change under these conditions, it suggests that perhaps lpp-lux was down regulated under stress conditions. There were no statistically significant differences between the results of the bioluminescence assays and the results of the viable count and ATP chemiluminescence assay. Virtual foot printing (using Regulon DB database) demonstrated that two crp binding sites overlapping the -10 regions are located on the negative strand of the lysS promoter sequences and that one crp binding site is located in lpp. The biosensor strains ldc-lux exhibited levels of bioluminescence per cell significantly lower than spc in the presence of preservatives whilst there was a significant increase in bioluminescence per cell by tatA-lux under alkaline conditions (pH 8.9) during long-term stationary phase. Amongst the five biosensor strains tested in the current work, it was determined that the spc-lux strain would be the most attractive candidate for further work, since the bioluminescence expressed per cell was significantly greater, by 10-1000 times, than that expressed by the other four promoters when challenged with the preservatives tested with excellent significant correlations between bioluminescence expression and viable counts in the PET assays with the various preservatives in this study (R2: 8.79-1.00). The bioluminescent biosensor strains showed no statistical differences from the control strains (wildtype E.coli ATCC 8739 and E.coli carrying a promoterless [pBR322.lux] for adneylate energy charge (AEC), plasmid copy number (PCN) bioluminescence or viable counts over 28 days. The emission of bioluminescence by the four bioreporter strains across 28 days is reflected by the stability of PCN with correlations of 0.78-0.90, except for lpp-lux with R2: 0.59. The following promoter elements were found likely to assist greater expression of bioluminescence: an A+T level of approximately 50% between the -40 and -60 regions (the UP element); a G+C level of approximately 50% within the -10 and +1 regions; the extended -10 region and -10 region of consensus sequence RpoD (σ70/D).

The commensal fungus, Candida albicans, can cause life-threatening infections in at risk individuals. C. albicans colonizes mucosal surfaces of most people, adhering to and interacting with epithelial cells. At low concentrations, C. albicans is not pathogenic nor does it cause epithelial cell damage in vitro; at high concentrations, C. albicans causes mucosal infections and kills epithelial cells in vitro. Here we show that while there are quantitative dose-dependent differences in exposed epithelial cell populations, these reflect a fundamental qualitative difference in host cell response to C. albicans. Using transcriptional profiling experiments and real time PCR, we found that wild-type C. albicans induce dose-dependent responses from a FaDu epithelial cell line. However, real time PCR and Western blot analysis using a high dose of various C. albicans strains demonstrated that these dose-dependent responses are associated with ability to promote host cell damage. Our studies support the idea that epithelial cells play a key role in the immune system by monitoring the microbial community at mucosal surfaces and initiating defensive responses when this community is dysfunctional. This places epithelial cells at a pivotal position in the interaction with C. albicans as epithelial cells themselves promote C. albicans stimulated damage.

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.

Hepatitis delta virus (HDV) is the smallest known human RNA pathogen. It requires the human hepatitis B virus (HBV) for virion production and transmission, and is hence closely associated with HBV in natural infections. HDV RNA encodes only two viral proteins - the small and the large delta antigens. Due to its limited coding capacity, HDV needs to exploit host factors to ensure its propagation. However, few human proteins are known to interact with the HDV RNA genome. The current study has identified several host proteins interacting with an HDV-derived RNA promoter by multiple approaches: mass spectrometry of a UV-crosslinked ribonucleoprotein complex, RNA affinity chromatography, and screening of a library of purified RNA-binding proteins. Co-immunoprecipitation, both in vitro and ex vivo, confirmed the interactions of eEF1A1, p54nrb, PSF, hnRNP-L, GAPDH and ASF/SF2 with both polarities of the HDV RNA genome. In vitro transcription assays suggested a possible involvement of eEF1A1, GAPDH and PSF in HDV replication. At least three of these proteins, eEF1A1, GAPDH and ASF/SF2, have also been shown to associate with potato spindle tuber viroid (PSTVd) RNA. Because HDV’s structure and mechanism of replication share many similarities with viroids, subviral helper-independent plant pathogens, I transfected human hepatocytes with RNA derived from PSTVd. Here, I show that PSTVd RNA can replicate in human hepatocytes. I further demonstrate that a mutant of HDV, lacking the delta antigen coding region (miniHDV), can also replicate in human cells. However, both PSTVd and miniHDV require the function of the small delta antigen for successful replication. Our discovery that HDV and PSTVd RNAs associate with similar RNA-processing pathways and translation machineries during their replication provides new insight into HDV biology and its evolution.

Winter rye produces ice-modifying antifreeze proteins upon cold treatment. Two of these antifreeze proteins are members of the large, highly conserved, ??-1,3-endoglucanase family. This project was designed to identify glucanase genes that are expressed during cold acclimation, wounding, pathogen infection, drought or treatment with the phytohormones ethylene and MeJa. Additionally, a more detailed proteomic analysis was to be carried out to evaluate the glucanase content of the apoplast of cold-acclimated (CA) winter rye. Results of 2D SDS-PAGE analysis revealed that non-acclimated whole leaf protein extracts contain at least two ??-1,3-endoglucanses while CA whole leaf protein extracts contain at least three ??-1,3-endoglucanses. Subsequent 2D SDS-PAGE analysis was conducted on the apoplast extracts of NA and CA winter rye plants revealed the limitations of standard 1D SDS-PAGE. The 2-dimensional gel analysis revealed that there is a minimum of 25 proteins within the apoplast of CA winter rye, including at least 5 ??-1,3-endoglucanases. Genome walking was used to isolate cold-responsive glucanase genes. The five genes isolated were designated scGlu6, scGlu9, scGlu10, scGlu11 and scGlu12. The cis-element pattern within the promoter of each gene was evaluated using online databases of documented plant cis elements. As expected, all of the promoters contained elements associated with cold, biotic and abiotic stresses, light regulation, and development. The expression patterns predicted by the cis elements in each promoter were compared to the mRNA abundance produced by each gene as detected by semi-quantitative reverse transcriptase PCR. In most cases, the abundance of transcripts arising from each gene loosely corresponded to the expression pattern predicted by the cis elements the corresponding promoter. Transcripts of scGlu9, 10 and 11 were present in cold-treated tissues and are candidates for ??-1,3-endoglucanases with antifreeze activity. The results presented in this thesis provide additional insight into the apoplast proteome of CA winter rye plants as well as the complexity of the signals controlling the proteins that reside there. Although there are still a number of unresolved questions, this research opens new directions for future studies in the cold acclimation process in winter rye and specifically for the contribution of ?? -1,3-endoglucanses.

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

Der Typ I Plasminogenmangel ist eine seltene Multisystemerkrankung mit einer gestörten extravaskulären Fibrinolyse, die zur Ausbildung fibrinreicher Pseudomembranen auf Schleimhäuten führt. Kausale Therapien existieren bisher nicht, Fallberichte beschreiben jedoch eine Besserung der Symptomatik bei Patientinnen bei Einnahme oraler Kontrazeptiva. Östrogen wirkt im Körper über Rezeptoren durch Beeinflussung der Genexpression an bestimmten regulatorischen Elementen im Bereich der Promotoren (Estrogen responsive Elements (EREs)). Dies führte zu der Fragestellung, ob und durch welche Promotorelemente der Plasminogen Promotor durch Östrogen regulierbar und die Genexpression hierdurch modulierbar ist. Hierfür wurden verschiedene Promotorkonstrukte mit und ohne regulatorische Elemente kloniert und mittels Dual Luciferase Reporter Assay analysiert. In silico wurden 2 EREs (-11,5 kb und +4,2 kb relativ zur Transkriptionsstartstelle) identifiziert und anschließend ebenfalls in den Konstrukten getestet. Der kleinste „Plasminogenminimalpromotor“ war nicht durch Östrogen beeinflussbar. Proximale Promotorelemente wie die DNAse hypersensitive Region II mit einer beschriebenen Estrogen Responsive Unit sowie ein -2,4kb umfassendes Promotorkonstrukt wirkten unter Östrogenstimulation hemmend auf die Promotoraktivität. Ursächlich dafür sind wahrscheinlich weitere Interaktionen des Östrogen Rezeptors mit transkriptionsmodulierenden Proteinen, z.B. sind Interaktionen vermittelt über eine AP-3 Bindungsstelle denkbar. Die hemmenden Effekte konnten als Plasminogen-Gen-spezifisch und Leberzell-spezifisch demonstriert werden. Im Gegensatz dazu lösten beide vor die Minimalpromotoren klonierten EREs eine starke Stimulation aus, die sich auch in nichthepatischen Zelllinien - dort jedoch in geringerem Ausmaß ¬- zeigte. Somit sind diese EREs starke Enhancer, die eine Leberspezifität aufweisen. Die in der Summe komplexe Regulation der Östrogen-vermittelten Plasminogen Transkriptionskontrolle lässt auf eine Mitwirkung zusätzlicher Faktoren schließen. Um den in vitro Effekt der scheinbar widersprüchlichen Ergebnisse zu untersuchen, wurden humane Leberzellen einer Primärzellkultur mit Östrogen stimuliert und anschließend hinsichtlich der Plasminogen Expression untersucht. Diese Methode ließ sich jedoch aufgrund der Limitierung des Probenmaterials auf Leberbiopsien von Patienten mit gastrointestinalen Karzinomen mit Lebermetastasierung, damit einhergehend fehlender Östrogenrezeptorexpression, sowie fehlender Plasminogenexpression nicht etablieren, sodass hier der Nachweis des wirklichen Effektes des Östrogeneinflusses nicht gelang. In dieser Arbeit konnte gezeigt werden, dass sich der Plasminogen Promotor durch Östrogen regulieren lässt. Der genaue Mechanismus und der in vitro Effekt ließ sich jedoch nicht abschließend klären und bedarf weiterer Forschung. Eine vielversprechende Fortführung der Arbeit, besonders im Hinblick auf adäquate Therapieoptionen des Typ I-Plasminogenmangels, wäre die Etablierung eines geeigneten Zellmodells und die Erprobung weiterer Plasminogen modifizierender Substanzen.

The G-quadruplex DNA is a four-stranded DNA structure that is highly susceptible to oxidation due to its G-rich sequence and its structure. Oxidative DNA base damages can be mutagenic or lethal to cells if they are left unrepaired. The base excision repair (BER) pathway is the predominant pathway for repair of oxidized DNA bases. DNA glycosylases are the first enzymes in BER and are responsible for removing base lesions from DNA. How DNA glycosylases remove base lesions from duplex and single-stranded DNA has been intensively studied, while how they act on G-quadruplex DNA remains to be explored. In Chapter II of this dissertation, we studied the glycosylase activity of the five mammalian DNA glycosylases (OGG1, NTH1, NEIL1, NEIL2 and mouse Neil3) on G-quadruplex DNA formed by telomere sequences that contain a single base lesion. We found that telomeric sequences that contain thymine glycol (Tg), 8-oxo-7,8-dihydroguanine (8-oxoG), guanidinohydantoin (Gh) or spiroiminodihydantoin (Sp) all formed the basket form of an antiparallel G-quadruplex DNA structure in Na+ solution. We also showed that no glycosylase was able to remove 8-oxoG from quadruplex DNA, while its further oxidation products, Sp and Gh, were good substrates for mNeil3 and NEIL1 in quadruplex DNA. In addition, mNeil3 is the only enzyme that removes Tg from quadruplex DNA and the glycosylase strongly prefers Tg in the telomere sequence context in both single-stranded and double-stranded DNA. In Chapter III, we extended our study to telomeric G-quadruplex DNA in K+ solution and we also studied quadruplex DNA formed by promoter sequences. We found that 8-oxoG, Gh and Sp reduce the thermostability and alter the folding of telomeric quadruplex DNA in a location-dependent manner. Also, the NEIL1 and NEIL3 DNA glycosylases are able to remove hydantoin lesions but none of the glycosylases, including OGG1, are able to remove 8-oxoG from telomeric quadruplex DNA in K+ solution. Interestingly, NEIL1 or NEIL3 do not efficiently remove hydantoin lesions at the site that is most prone to oxidation in quadruplex DNA. However, hydantoin lesions at the same site in quadruplex DNA are removed much more rapidly by NEIL1, NEIL2 and NEIL3, when an extra telomere TTAGGG repeat is added to the commonly studied four-repeat quadruplex DNA to make it a five-repeat telomere quadruplex DNA. We also show that APE1 cleaves furan in selected positions in Na+-coordinated telomeric quadruplex DNA structures. We use promoter sequences of the VEGF and c-MYC genes as models to study promoter G-quadruplex DNA structures, and show that the NEIL glycosylases primarily remove Gh from Na+-coordinated antiparallel quadruplex DNA but not from K+-coordinated parallel quadruplex DNA containing VEGF or c-MYC promoter sequences. Taken together, our data show that the NEIL DNA glycosylases may be involved in both telomere maintenance and gene regulation.

Alternative splicing is an important cellular mechanism. It allows to produce multiple protein isoforms from a limited number of genes. Regulation of alternative splicing involves cis-acting elements on pre-mRNA and trans-acting splicing factors (SR and hnRNP proteins). Because splicing occurs co-transcriptionaly, chromatin structure appears to have a role in the regulation of alternative splicing. We have studied the effect of histone acetylation on alternative splicing. We have prepared splicing reporter for alternative EDB exon, which is part of the fibronectin gene. We have shown, that the inhibition of histone deacetylases affects splicing pattern of EDB exon from the reporter in the same way as the splicing of the endogenous EDB exon. Furthermore, we have shown, that the structure of the promoter affects splicing of alternative EDB exon from splicing reporter. Currently we have found out, that the structure of the promoter influences the degree of histone H4 acetylation. Inclusion of alternative EDB exon in mRNA was inversely proportional to histon acetylation on the reporter. This work might explain why various promoters have different splicing patterns of alternative exons.

It was shown that 95 % of human multi-exon genes are alternatively spliced and the regulation of alternative splicing is extremely complex. Most pre-mRNA splicing events occur co- transcriptionally and there is increasing body of evidence, that chromatin modifications play an important role in the regulation of alternative splicing. Here we showed that inhibition of histone deacetylases (HDACs) modulates alternative splicing of ~700 genes via induction of histone H4 acetylation and increase of Pol II elongation rate along alternative region. We identified HDAC1 the catalytic activity of which is responsible for changes in alternative splicing. Then, we analyzed whether acetylhistone binding protein Brd2 regulates alternative splicing and showed that Brd2 occupies promoter regions of targeted genes and controls alternative splicing of ~300 genes. Later we showed that knockdown of histone acetyltransferase p300 promotes inclusion of the alternative fibronectin (FN1) EDB exon. p300 associates with CRE sites in the promoter via the CREB transcription factor. We created mini-gene reporters driven by an artificial promoter containing CRE sites. Both deletion and mutation of the CRE site affected EDB alternative splicing in the same manner as the p300 knockdown. Next we showed that p300 controls histone...