Restriction modification (RM) systems play a crucial role in preventing the entry of foreign DNA into the bacterial cell. The best studied Type I RM system is EcoKI from Escherichia coli K12. Both bacteriophage and conjugative plasmids have developed a variety of strategies to circumvent the host RM system. One such strategy involves the production of antirestriction proteins that mimic a short segment of DNA and efficiently inhibit the RM system. The main aim of this project was to analyse the interaction of EcoKI and its cognate methylase (MTase) with the T7 antirestriction protein, known as overcome classical restriction (Ocr), and various ArdA antirestriction proteins. Currently, there is a paucity of structural data on the complex formed between the Type I system and the antirestriction proteins. The aim of this work was twofold; (i) compare the interaction of MTase with DNA and Ocr and (ii) quantify the strength of interaction between MTase and various ArdA proteins. The MTase was fused to the Green Fluorescent Protein (GFP) to facilitate determination of the orientation of interaction with DNA and Ocr. Time resolved fluorescence measurements were carried out using the GFP-MTase fusion to determine the fluorescence lifetime and anisotropy decay. These experiments were conducted using a time resolved fluorescence instrument fabricated in-house. The values determined in these experiments were then used to perform fluorescence resonance energy transfer (FRET) measurements with fluorescently labelled DNA or Ocr. These measurements gave information concerning the relative orientation of the MTase with either DNA or Ocr. The GFP-MTase fusion was also used to quantify the strength of interaction with various ArdA proteins. Previous attempts to determine the strength of interaction between MTase and ArdA proteins by employing conventional techniques have been unsuccessful. Therefore, a novel method was developed that exploits the interaction of MTase with a cation exchange medium, which can subsequently be displaced upon binding to ArdA. This method facilitated the determination, for the first time, of a set of binding affinities for the MTase and ArdA interaction.

Orientador: Marcel Otavio Cerri / Resumo: Avanços na biotecnologia proporcionaram possibilidades para o eficiente desempenho da produção em larga escala de diversas biomoléculas e consequentemente suas aplicações industriais. A Escherichia coli se destaca dentre a gama de microrganismos que agem como hospedeiros de genes, desempenhando a função de codificar a síntese proteica. Os vetores mais veiculados na produção de proteínas recombinantes em E. coli são baseados no operon lac, onde o isopropil β-D1-tio-galactopiranosídeo (IPTG), análogo a molécula de lactose, é utilizado para a indução da produção da proteína de interesse. Estudos descritos na literatura também observaram o bom desempenho da lactose como agente de indução da E. coli recombinante na expressão de proteína verde fluorescente melhorada (Enhanced Green Fluorescent Protein – EGFP), e suas vantagens quando comparada ao IPTG, como por exemplo menor custo e menor toxicidade. A EGFP se tornou promissora pelo fato de ser monomérica e não precisar de auxilio de quaisquer agentes adicionais para exibir atividade de fluorescência. Possui variadas utilidades no campo biológico como excelente biomarcador da expressão genica e biosensor. Em bioprocessos, operados em biorreatores convencionais é fundamental o estudo dos parâmetros interferentes nos cultivos para a otimização da expressão do produto desejado. A oxigenação em processos conduzidos de maneira aeróbica, também é uma tarefa desafiadora em biorreatores convencionais, sendo imprescindível o controle da con... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Advances in biotechnology have provided possibilities to the performance of large-scale of biomolecules and therefore of their industrial applications. Escherichia coli stands out among microorganisms that act as host genes, functioning as a synthetic protein. The most useful vectors for the production of recombinant proteins in E. coli are based on the operon lac, where isopropyl β-D1-thiogalactopyroside (IPTG), analogous to lactose, is used to induce the production of proteins of interest. Studies in the literature have also observed the good performance of lactose as an inducer of recombinant E. coli in the expression of Enhanced Green Fluorescent Protein (EGFP), and its advantages when compared to IPTG, such as lower cost and toxicity. EGFP becomes promising because it is monomeric and does not need to help the main agents for fluorescence activity. It has several uses in the biological field as an excellent biomarker of gene expression and biosensor. In bioprocesses, operated in conventional bioreactors, it is fundamental to study the interfering parameters in the cultures to optimize the expression of the desired product. Oxygenation in aerobically conducted processes is also a challenging task in conventional bioreactors, with control of the concentration of dissolved oxygen in the culture medium is essential, which may be limiting for growth and expression of the protein of interest. In processes of production of heterologous proteins, it is assumed that the productiv... (Complete abstract click electronic access below) / Mestre

A avaliação da estabilidade dos medicamentos e sua correta utilização em diferentes veículos de infusão são fundamentais para garantir a manutenção das características terapêuticas do fármaco e para promover minimização de eventos adversos. Incompatibilidades entre as estruturas dos fármacos, em diferentes veículos de administração, podem gerar possíveis associações antagônicas ou sinérgicas, resultando em alterações das propriedades físico-químicas e, consequentemente, dos efeitos farmacológicos e das respostas clínicas esperadas. A proteína verde fluorescente (GFP) por apresentar propriedades de sensibilidade e especificidade, mostra-se promissora como potencial biossensor da estabilidade de fármacos em soluções parenterais de grande volume (SPGV), por apresentar sensibilidade a alterações das propriedades físico-químicas do meio. GFP é uma proteína compacta, globular e ácida, composta de um monômero de 27kDa, que vem sendo extensivamente utilizada como indicador biológico em processos de esterilização e desinfecção devido a sua estabilidade a altas temperaturas. O surgimento de métodos analíticos modernos e de alta precisão como a espectrofotometria de UV e a cromatografia líquida de alta eficiência (HPLC), alinhados a potencial utilização das proteínas fluorescentes como forma de avaliar as alterações da estabilidade de fármacos nas SPGV, vêm contribuir para a correta e racional utilização dos medicamentos no ambiente hospitalar. Diante disso a avaliação da estabilidade do coquetel de fármacos composto por furosemida e aminofilina em solução parenteral de 20% manitol e 0,9% NaCl foi sugerida. Amostras foram preparadas nas seguintes soluções (v/v): 20% manitol ou 0,9% NaCl na seguintes proporções utilizadas frequentemente na prática clínica: (i) 80% solução parenteral adicionada de 16% furosemida e 4% água para injeção (excipiente do fármaco aminofilina), (ii) 80% solução parenteral adicionada de 4% aminofilina e 16% água para injeção + NaOH (excipiente do fármaco furosemida), (iii) 80% solução parenteral, adicionada de 16% furosemida e 4% aminofilina (coquetel). As amostras foram avaliadas em espectrofotômetro imediatamente após o preparo e após um período 20h, em y=228nm e y=275nm para os fármacos furosemida e aminofilina, respectivamente. Para os fármacos individualmente associados às SPGV na faixa de pH 10-11, as concentrações finais obtidas foram correspondente ás inicialmente adicionadas e para o fármaco aminofilina foi estável até o período de 20h. Para avaliar a estabilidade dos fármacos associados à solução de 20% manitol a utilização de HPLC mostrou manutenção da estabilidade dos fármacos durante o período de infusão de até 20h. A proteína GFP adicionada as soluções das amostras na concentração 8?g/mL e determinada em espectrofluorímetro (yex=394nm, yem=509nm), mostrou resultados promissores quanto ao sua potencial utilização como biossensor da estabilidade dos fármacos furosemida e aminofilina nas soluções parenterais, mostrando comportamento de concentração e intensidade de fluorescência característicos e proporcionais a perda da estabilidade das soluções. A utilização de proteínas fluorescentes como potencial biossensor da estabilidade de fármacos em soluções parenterais é importante por fornecer parâmetros que garantam a eficácia dos medicamentos veiculados em soluções parenterais, racionalizando a sua utilização no ambiente hospitalar. / Parenteral solutions (PS) are used as vehicles in drugs administration to the organism. The development of analytical techniques that enables the detection of incompatibilities between drugs and PS is mandatory to guarantee their correct association with minimum adverse events. Incompatibilities of drugs in different infusion vehicles change according to physical-chemical properties of solutions, because of the molecular structure, chemical compounds used for preservation and stability of PS components. This fact can promote antagonic or synergic effects with loss of clinical response. The green fluorescent protein (GFP) is compact, globular, and acidic, with 27KDa and has been used as a biologic indicator of sterilization and disinfection process because it is easily detected using UV light, spectrofluorometry, with high thermal stability. GFP specificity and sensibility to physical-chemical changes in the media favors its use as a biosensor for drugs stability in parenteral solutions. The development of analytical methods such as spectrophotometry and high performance liquid chromatography (HPLC) in association with the fluorescent properties of some proteins enable the detection of potential incompatibilities between drugs and parenteral solutions, promoting a rational utilization of drugs in hospital. The evaluation of a diuretic cocktail with furosemide and aminophylline administrated in parenteral solutions of 20% mannitol and 0.9% NaCl was studied. Samples were prepared either in 20% mannitol or 0.9 % NaCl (PS), as follows: (i) 80% parenteral solution added with 16% furosemide and 4% WFI (solvent for aminophylline), (ii) 80% parenteral solution 4% aminophylline and 16% WFI+NaOH (pH 9-10, solvent for furosemide), (iii) 80% parenteral solution, added with 16% furosemide and 4% aminophylline (cocktail). Samples were diluted and prepared in a pH range of 6.5-7.5 and pH 10-11 for aminophylline and furosemide, individually and associated. The samples were prepared with PS including the excipients used in the drugs formulations. The absorbance was determined immediately after preparation and after 20 hours at 25°C and y= 228 nm, 275 nm, respectively for furosemide and aminophylline. GFP stability was determined in a spectrofluorometer (yex=394nm, yem=509nm) by adding 8 µg/mL of the purified protein in a 3.0mL sample (25°C) and the fluorescence intensity was evaluated after 20 hours. For both drugs in parenteral solutions (pH 10-11) the final concentrations observed were similar to the expected, aminophylline was also stable after 20h. When both drugs were associated in parenteral solutions of 20% mannitol, the use of HPLC showed stability for both drugs in the first 20h. The fluorescence intensity of GFP added to the samples was determined in spectrofluorometer (yex=394nm, yem=509nm), showing that fluorescence intensity was proportional to the drugs stability loss. Therefore, the utilization of fluorescence proteins is important to assure the drugs effectiveness and rational utilization in hospital places.

BCG é uma das vacinas mais usadas no mundo. Avanços na manipulação genética têm permitido o seu uso como carreador de antígenos heterólogos, porém o aprimoramento dos sistemas de expressão se faz necessário, sendo o promotor um importante elemento, uma vez que regula o nível de produção do antígeno, induzindo uma resposta imunológica adequada. Avaliamos a atividade de diferentes promotores de micobactérias, como o PAg, PAN, PBlaF*, Phsp60 e um promotor ainda não caracterizado do micobacteriófago L5, usando o gene gfp como repórter da expressão, todos clonados no vetor extracromossomal, pLA71. Foi possível avaliar as cepas de M. smegmatis e BCG fluorescentes para quase todas as construções e alguns plasmídeos pLA71-p mostraram características diferentes dependentes da micobactéria transformada. Numa escala de força de expressão, os diferentes promotores se apresentaram como fraco (pLA71-PAN-gfp), médio (pLA71-PBlaf*-gfp) e forte (pLA71-Phsp60-gfp). Os rBCG foram usados para infecção de macrófagos e a atividade dos promotores não foi afetada após a internalização. Para ensaio de localização, camundongos foram inoculados com BCG e foi possível confirmar a presença de colônias (recombinantes ou não) nos pulmões após 1 e 3 dias de inoculação, por plaqueamento em meio sólido e por microscopia confocal. / BCG is one of the most widely used vaccines in the world. Advances in genetic manipulation have allowed their use as a carrier for heterologous antigens, however the improvement of systems of expression is necessary, the promoter being an important element, since it regulates the expression level of the antigen, inducing an adequate immune response. We evaluated the activity of different promoters of mycobacteria, such as PAg, PAN, PBlaF* and Phsp60, and the not yet characterized promoter of the micobacteriophage L5, using GFP as a reporter gene expression activity, all cloned in the extrachromosomal vector, pLA71. It was possible to evaluate promoters in the M. smegmatis and BCG strains, fluorescent for almost all constructions and some pLA71-p plasmids showed different characteristics dependent on the transformed mycobacterium. The different promoters showed expression levels as weak (pLA71-PAN-gfp), medium (pLA71-PBlaf*-gfp) and strong (pLA71-Phsp60-gfp). The rBCG were used for infection of macrophages and the activity of the promoters wasnt affected after internalization. For BCG location test, mice were inoculated and it was possible to confirm the presence of colonies (recombinant or not) in the lungs after 1 and 3 days after inoculation by plating on solid medium and by confocal microscopy.

A avaliação da estabilidade dos medicamentos e sua correta utilização em diferentes veículos de infusão são fundamentais para garantir a manutenção das características terapêuticas do fármaco e para promover minimização de eventos adversos. Incompatibilidades entre as estruturas dos fármacos, em diferentes veículos de administração, podem gerar possíveis associações antagônicas ou sinérgicas, resultando em alterações das propriedades físico-químicas e, consequentemente, dos efeitos farmacológicos e das respostas clínicas esperadas. A proteína verde fluorescente (GFP) por apresentar propriedades de sensibilidade e especificidade, mostra-se promissora como potencial biossensor da estabilidade de fármacos em soluções parenterais de grande volume (SPGV), por apresentar sensibilidade a alterações das propriedades físico-químicas do meio. GFP é uma proteína compacta, globular e ácida, composta de um monômero de 27kDa, que vem sendo extensivamente utilizada como indicador biológico em processos de esterilização e desinfecção devido a sua estabilidade a altas temperaturas. O surgimento de métodos analíticos modernos e de alta precisão como a espectrofotometria de UV e a cromatografia líquida de alta eficiência (HPLC), alinhados a potencial utilização das proteínas fluorescentes como forma de avaliar as alterações da estabilidade de fármacos nas SPGV, vêm contribuir para a correta e racional utilização dos medicamentos no ambiente hospitalar. Diante disso a avaliação da estabilidade do coquetel de fármacos composto por furosemida e aminofilina em solução parenteral de 20% manitol e 0,9% NaCl foi sugerida. Amostras foram preparadas nas seguintes soluções (v/v): 20% manitol ou 0,9% NaCl na seguintes proporções utilizadas frequentemente na prática clínica: (i) 80% solução parenteral adicionada de 16% furosemida e 4% água para injeção (excipiente do fármaco aminofilina), (ii) 80% solução parenteral adicionada de 4% aminofilina e 16% água para injeção + NaOH (excipiente do fármaco furosemida), (iii) 80% solução parenteral, adicionada de 16% furosemida e 4% aminofilina (coquetel). As amostras foram avaliadas em espectrofotômetro imediatamente após o preparo e após um período 20h, em y=228nm e y=275nm para os fármacos furosemida e aminofilina, respectivamente. Para os fármacos individualmente associados às SPGV na faixa de pH 10-11, as concentrações finais obtidas foram correspondente ás inicialmente adicionadas e para o fármaco aminofilina foi estável até o período de 20h. Para avaliar a estabilidade dos fármacos associados à solução de 20% manitol a utilização de HPLC mostrou manutenção da estabilidade dos fármacos durante o período de infusão de até 20h. A proteína GFP adicionada as soluções das amostras na concentração 8?g/mL e determinada em espectrofluorímetro (yex=394nm, yem=509nm), mostrou resultados promissores quanto ao sua potencial utilização como biossensor da estabilidade dos fármacos furosemida e aminofilina nas soluções parenterais, mostrando comportamento de concentração e intensidade de fluorescência característicos e proporcionais a perda da estabilidade das soluções. A utilização de proteínas fluorescentes como potencial biossensor da estabilidade de fármacos em soluções parenterais é importante por fornecer parâmetros que garantam a eficácia dos medicamentos veiculados em soluções parenterais, racionalizando a sua utilização no ambiente hospitalar. / Parenteral solutions (PS) are used as vehicles in drugs administration to the organism. The development of analytical techniques that enables the detection of incompatibilities between drugs and PS is mandatory to guarantee their correct association with minimum adverse events. Incompatibilities of drugs in different infusion vehicles change according to physical-chemical properties of solutions, because of the molecular structure, chemical compounds used for preservation and stability of PS components. This fact can promote antagonic or synergic effects with loss of clinical response. The green fluorescent protein (GFP) is compact, globular, and acidic, with 27KDa and has been used as a biologic indicator of sterilization and disinfection process because it is easily detected using UV light, spectrofluorometry, with high thermal stability. GFP specificity and sensibility to physical-chemical changes in the media favors its use as a biosensor for drugs stability in parenteral solutions. The development of analytical methods such as spectrophotometry and high performance liquid chromatography (HPLC) in association with the fluorescent properties of some proteins enable the detection of potential incompatibilities between drugs and parenteral solutions, promoting a rational utilization of drugs in hospital. The evaluation of a diuretic cocktail with furosemide and aminophylline administrated in parenteral solutions of 20% mannitol and 0.9% NaCl was studied. Samples were prepared either in 20% mannitol or 0.9 % NaCl (PS), as follows: (i) 80% parenteral solution added with 16% furosemide and 4% WFI (solvent for aminophylline), (ii) 80% parenteral solution 4% aminophylline and 16% WFI+NaOH (pH 9-10, solvent for furosemide), (iii) 80% parenteral solution, added with 16% furosemide and 4% aminophylline (cocktail). Samples were diluted and prepared in a pH range of 6.5-7.5 and pH 10-11 for aminophylline and furosemide, individually and associated. The samples were prepared with PS including the excipients used in the drugs formulations. The absorbance was determined immediately after preparation and after 20 hours at 25°C and y= 228 nm, 275 nm, respectively for furosemide and aminophylline. GFP stability was determined in a spectrofluorometer (yex=394nm, yem=509nm) by adding 8 µg/mL of the purified protein in a 3.0mL sample (25°C) and the fluorescence intensity was evaluated after 20 hours. For both drugs in parenteral solutions (pH 10-11) the final concentrations observed were similar to the expected, aminophylline was also stable after 20h. When both drugs were associated in parenteral solutions of 20% mannitol, the use of HPLC showed stability for both drugs in the first 20h. The fluorescence intensity of GFP added to the samples was determined in spectrofluorometer (yex=394nm, yem=509nm), showing that fluorescence intensity was proportional to the drugs stability loss. Therefore, the utilization of fluorescence proteins is important to assure the drugs effectiveness and rational utilization in hospital places.

Lubricin, or proteoglycan 4 (PRG4), is a secreted, glycosylated protein that binds to cartilage surfaces, which functions as a boundary lubricant. The loss of lubricin from cartilage is identified as a major pathogenic factor in post-traumatic osteoarthritis (PTOA) that has now been the aim of therapeutic intervention. Intra-articular injection of PRG4 protein provides short-term benefits that might be extended using sustained delivery methods such as in gene therapy. Here we describe the development and testing of such therapy using adeno-associated virus (AAV) as a vector for the transfer of PRG4-green fluorescent protein (GFP) fusion gene. Our recombinant PRG4 gene produces a PRG4-GFP fusion protein to facilitate tracking of its expression and distribution on joint surfaces. We hypothesized that PRG4-GFP is fully functional as a cartilage lubricant and that PRG4-GFP produced in vivo is expressed by synoviocytes and other joint cells, and cartilage surfaces remained coated for several weeks up to months after intra-articular injection of the virus. PRG4-GFP showed lubricin-like cartilage binding in vitro, and lubrication immunoblot analysis confirmed that purified PRG4-GFP from cultured media conditioned by PRG4-GFP-transduced synoviocytes was heavily glycosylated, while confocal microscopy revealed binding of the fluorescent fusion protein to cartilage surfaces. Metal-on-cartilage friction tests showed that PRG4-GFP reduced friction coefficients to a degree comparable to that of synovial fluid and had strong chondro-protective effects in explanted cartilage exposed to shear loading. The chondrocyte viability after shear loading showed that PRG4-GFP had a strong chondro-protective effect on par with that of the synovial fluid. Confocal microscopy and immunohistology confirmed that cartilage surfaces in the stifle joints of mice injected with viruses were coated with PRG4-GFP for up to 2 or 4 weeks after the treatment. The overexpression of PRG4-GFP and coating of cartilage surfaces in the stifle joints of mice injected with Adeno-Associated Virus for the transfer of PRG4-GFP fusion gene (AAV-PRG4-GFP) was confirmed by confocal microscopy and immunohistology for up to 2 or 4 weeks post-injection. The μCT imaging and immunohistology in AAV-PRG4-GFP injected rabbit knees showed stronger inhibition in degeneration of damaged tissues than in AAV-GFP injected control group. Collectively these findings indicate that AAV-PRG4-GFP transduction is a valuable new tool for evaluating the effects of long-term lubricant supplementation on PTOA in animal models.

The costs associated with cellular product recovery commonly account for as much as 80% of the total production expense. As a specific example, significant recovery costs limit commercial use of polyhydroxyalkanoates (PHA), which comprise a class of microbially-accumulated polyesters. PHAs are biodegradable compounds that are of interest as a sustainable alternative to petrochemically-derived plastics. Secretion-based recovery of PHAs was studied to decrease PHA production costs. Type I and II secretory pathways are commonly used for the translocation of recombinant proteins out of the cytoplasm of E. coli. Proteins were targeted for translocation using four signal peptides (HlyA, TorA, GeneIII, and PelB) that operate via type I and II secretory machinery. GFP translocation was investigated in parallel due to its relative ease of monitoring to gather information about the functionality of signal peptide sequences. The translocation of phasin was investigated because of its physical binding interaction with the PHA granule surface. Genetic fusion of phasin with targeting signal peptides creates a PHA-phasin-signal peptide complex that can then be potentially used for cellular export. An important design aspect of this investigation is that synthetic biological engineering principles and standardized technical formats BBF RFC 10 and BBF RFC 23 were applied for more efficient construction of genetic devices. As an additional part of this study, an 1H NMR-based PHA quantification method was developed to facilitate analysis of intracellular PHAs. Overall, this study demonstrated that the BioBrick model can be used to construct functional devices that promote secretion of cellular compounds. The information gathered from this work can be further optimized and applied to more complex cellular manufacturing systems.

This research studied recombinant DNA-derived protein expression utilising expression vectors containing IRES sequences to link the gene of interest with the gene encoding selectable marker in mammalian cell cultures. Polycistronic expression constructs utilising internal ribosome entry site (IRES) can link unrelated genes under control of a single promoter. Transient study on the IRESlinked gene expression was performed. It was possible to standardise the level of protein expression to plasmid number by determining the number of free plasmids in the cytoplasm. The expression of a selectable marker when downstream of IRES was reduced in comparison to the monocistronic construct. Importantly when IRES was used, there were no negative effects on recombinant gene expression upstream of IRES. Down-regulating the selectable marker gene expression has been shown to enhance the probability of obtaining highly expressing clones. To investigate the effects of down-regulating fusion metallothionein green fluorescent protein (MTGFP), new constructs were created to combine metal inducible M2.6 promoter to drive the expression of human growth hormone linked to MTGFP by an attenuated IRES. This resulted in less MTGFP expression, reduced survivability and mean fluorescence in the presence of heavy metal. The increased metal sensitivity lengthened the initial selection period using reduced metal concentration in comparison to cells transfected with wildtype MTGFP. FACS can be used to select for resistance conferred by MTGFP despite reduced expression. FACS enrichment and sorting increased the hGH expression, which was correlated with mean fluorescence of the population; therefore fluorescence can be used as an indication of the final recombinant protein expression. Different approaches to isolate suitable clones were also investigated. It is preferable to select the transfected pool in low metal concentration for two weeks, sort for cells of high-fluorescence, and allow for recovery and proliferation. It is then possible to amplify gene expression by culturing the clones in increasing metal, resulting in further improvement of recombinant protein expression.

Nuclear receptors are ligand activated transcription factors, where upon binding with small molecule ligands, these proteins are involved in the regulation of gene expression. To date there are approximately 48 human nuclear receptors known, involved in multiple biological and cellular processes, ranging from differentiation to maintenance of homeostasis. Due to their critical role in transcriptional regulation, these receptors are implicated in several diseases. Currently, 13% of prescribed drugs in the market are NR ligands for diseases such as cancer, diabetes and osteoporosis. In addition to drug discovery, the mechanism of function, mobility and trafficking of these receptors is poorly understood. Gaining insight into the relationship between the function and /or dysfunction of these receptors and their mobility will aid in a better understanding of the role of these receptors. The green fluorescent protein (GFP) has revolutionized molecular biology by providing the ability to monitor protein function and structure via fluorescence. The fluorescence contribution from this biological marker is the chromophore, formed from the polypeptide backbone of three amino acid residues, buried inside 11-stranded â-barrel protein. Synthesis of GFP derivatives of is based on the structure of the arylmethyleneimidazolidinone (AMI), creating a molecule that is only weakly fluorescent. Characterizing these AMI derivatives for other proteins can provide a powerful visualization tool for analysis of protein function and structure. This development could provide a very powerful method for protein analysis in vitro and in vivo. Development of such fluorescent ligands will prove beneficial for the nuclear receptors. In this work, libraries of AMIs derviatives were synthesized by manipulating various R groups around the core structure, and tested for their ability to serve as nuclear receptor ligands with the ability to fluoresce upon binding. The fluorogens are developed for steroidal and non-steroidal receptors, two general classes of nuclear receptors. Specific AMIs were designed and developed for steroid receptor estrogen receptor á (ERá). These ligands are showed to activate the receptor with an EC50 of value 3 ìM and the 10-fold activation with AMI 1 and AMI 2 in comparison to the 21-fold activation observed with natural ERá ligand, 17â-estradiol. These novel ligands were not able to display the fluorescence upon binding the receptor. However, fluorescence localized in nucleus was observed in case of another AMI derivative, AMI 10, which does not activate the receptor. Such ligands open new avenues for developing fluorescent probes for ERá that do not involve fluorescent conjugates attached to a known ERá ligand core. AMIs were also characterized for non-steroidal receptors,specifically the pregnane x receptor (PXR) and retinoic acid receptor á (RARá). To date, fluorogens which turn fluorescence upon binding and activate the receptor have not been developed for these receptors. With respect to PXR, several AMI derivatives were discovered to bind and activate this receptor with a fold-activation better than the known agonist, rifampicin. The best characterized AMI derivative, AMI 4, activates the receptor with an EC50 of value 6.3 ìM and the 154-fold activation in comparison to the 90-fold activation and an EC50 value of 1.3 ìM seen with rifamipicin. This ligand is not only able to activate PXR but also displays fluorescence upon binding to the receptor. The fluroscence pattern was observed around the nucleus. Besides AMI 4, 16 other AMI derivatives are identified that activate PXR with different activation profiles. Thus, a novel class of PXR ligands with fluorescence ability has been developed. The AMI derivatives able to bind and activate RAR, also displayed activation profiles that were comparable to the wild-type ligand, all trans retinoic acid. These ligands activated the receptor with an EC50 value of 220 nM with AMI 109 in comparison to an EC50 value of 0.8 nM with the natural ligand for RARá. When these ligands were tested for fluorescence in yeast, the yeast were able to fluoresce only in the presence of the receptor and the AMI derivative, indicating that these agonists also have the ability to fluoresce.

Cold acclimation is a complex process where plants acquire increased freezing tolerance following exposure to low, non-freezing temperatures. Microtubules are dynamic components of the cytoskeleton that are essential for plant growth and development, and there are multiple lines of evidence indicating microtubules are involved in the acquisition of freezing tolerance. <p>The organization of microtubules (MTs) was tracked over the course of a cold acclimation period using GFP:TUB6 and fluorescent imaging tools. Experiments found that MTs undergo incomplete, transient disassembly following exposure to acclimating temperatures, which is accompanied by intranuclear tubulin accumulation and followed by MT reassembly. The importance of the observed changes to MT organization was examined with MT disrupting chemicals that caused reduced MT dynamics or induced transient MT disassembly similar to that of cold acclimation. Results of these experiments suggest that MT reorganization is important for cold acclimation, but the disassembly and reassembly do not directly control cold acclimation.<p>MT binding proteins are likely to play a key role in the low temperature response because they control MT activity and organization, participate in low temperature signal transduction pathways, and mediate interactions between various elements of this pathway. By employing a number of proteomics techniques we were able to identify 96 tubulin-binding proteins from untreated and short term cold acclimated Arabidopsis plants. Proteins both known to and predicted to bind to MTs and unexpected MT binding proteins were identified. The identified tubulin binding proteins have a range of cellular functions, including RNA transport and protein translation, stress responses, and functions related to various metabolic pathways, and cell growth and organization. <p>Exposure to low temperatures affected the binding of some of these proteins to MTs with the identified tubulin binding proteins potentially involved in the cold acclimation process and stress response through a number of possible pathways.<p>This study represents the first live cell imaging of MT reorganization in response to low temperatures and the first time microtubule binding proteins from whole plant protein extracts were identified using 1D gel LC-MS/MS analysis.