El aumento de la actividad minera en el Perú hace necesario el desarrollo de tecnologías rápidas y económicas de detección de contaminantes para su monitoreo y control. Implementando conocimientos de biología molecular y de la regulación génica podemos construir un circuito genético sintético que posibilite el monitoreo de sustancia toxicas que generen estrés oxidativo como son los compuestos cianurados. El objetivo de esta investigación es desarrollar un circuito genético sintético conformado por el promotor de la proteína del shock por fagos (psp) de Escherichia coli y las secuencia codificante del gen de la proteína verde fluorescente (GFP). La construcción de dicho circuito se logró usando estrategias de clonamiento por topoisomerasas y clonamiento clásico con enzimas de restricción, se usó la reacción en cadena de la polimerasa (PCR) para confirmar que todos los segmentos del circuito estén presentes en el vector. Los estudios preliminares de la actividad del nuevo circuito se realizaron transformando genéticamente células competentes de E. coli. La observación de dichas bacterias muestra una expresión de GFP continua, lo que indica que el circuito sintético está siendo activado sin estar en presencia de agentes de estrés oxidativo, lo que suponía una posible interacción con otros sistemas de regulación de estrés en la célula. Due to the increase of mining activity in Peru new technologies that can detect and monitor hazardous pollutants in a faster and cheaper way must be developed. Implementing molecular biology knowledge about genetic regulation we are able to construct a synthetic genetic circuit that can allow the monitoring of toxic substances that generate oxidative stress such us cyanide compounds. The objective of this research is to develop a synthetic genetic circuit from the promoter of the phage shock protein operon from E. coli and the complementary DNA of the green fluorescent gene (GFP). The construction of the circuit was achieved using classic cloning strategies with restriction enzymes and also more advanced strategies such us topoisomerase cloning, the polymerase chain reaction (PCR) was used to confirm the presence of all the desire segments in the vector. Preliminary studies of the circuit activity were carried out by genetically transforming competent E. coli cells. The observation of the bacteria shows a continuous expression of GFP without any inducer, this indicates that the synthetic circuit is being activated through a possible interaction with other stress response pathway.

Em 1978, o trabalho realizado por Stephenson e Zamecnik demonstrou a capacidade de um oligonucleotídeo de impedir a expressão de uma proteína específica. Atualmente, duas tecnologias são mais utilizadas para este propósito: os oligodeoxiribonucleotídeos antisense e o RNA de interferência (siRNA), que se aproveitam da capacidade de anelação entre as fitas complementares. A maior diferença entre as duas técnicas é a maquinaria proteica recrutada, isso é, o complexo RISC atua no funcionamento do siRNA, e a protease RNase H atua na clivagem da fita de RNA quando hibridizada com DNA. Apesar da grande aplicabilidade destas tecnologias, tanto para doenças metabólicas quanto para canceres, o veículo de entrega e proteção dessas sequências é de fundamental importância, visto que a aplicação desses oligonucleotídeos livres está sujeita à rápida degradação e ineficiência. A modificação das bases é uma das estratégias para conferir maior estabilidade às sequências, porém estas tem sido relacionadas a um aumento da toxicidade. Nessa dissertação, a quitosana, um polissacarídeo catiônico é utilizado para síntese de nanopartículas e encapsulamento dos oligodeoxiribonucleotídeos antisense (ASO). Para isso, foram realizadas modificações na quitosana comercial como despolimerização, trimetilação ou conjugação com PEG, seguida da síntese das nanopartículas com a adição de tripolifosfato de sódio (TPP) pelo método de gelatinização ionotrópica. A estabilidade das nanopartículas foi medida em função do tempo, da variação de temperatura e da diferença de pH. Além disso, a toxicidade dessas nanopartículas foi analisada através da viabilidade celular em diferentes linhagens, NB-4, HepaRG, HTC e BHK-570. A expressão da proteína verde fluorescente (GFP) na célula NB-4 foi utilizada para avaliar a entrega do ASO desenhado, sendo sua fluorescência monitorada por microscopia confocal. Os resultados demonstram que as nanopartículas se mantiveram estáveis durante o período de tempo analisado, assim como com a temperatura variando de 22 a 45°C e em pH ácido. Cada linhagem celular respondeu de forma diferente ao tratamento com as nanopartículas sem ASO, sendo a linhagem saudável BHK-570 com a maior resistência. Ademais, todas as células apresentaram viabilidade reduzida quando tratadas com concentrações na ordem de 1011 nanopartículas/mL a base de quitosana trimetilada. A fluorescência das células NB-4 quando tratada com as nanopartículas com ASO diminuiu consideravelmente nas 18 primeiras horas, seguida de um aumento após 42 horas. Dessa forma, pode-se concluir que as nanopartículas de quitosana propostas nessa dissertação apresentaram uma excelente alternativa para a entrega de material genético, principalmente para o trato gastro-intestinal, devido à sua estabilidade em pH ácido. / The property of an oligonucleotide to interfere in the expression of a protein was observed in 1978 by Stephenson and Zamecnik. To perform such interference, there are today, two main techniques being explored: antisense oligodeoxyribonucleotides and interference RNA. In both cases, the particularity of their chemical structure is taken into account as soon as they can bind in a complementary manner to the messenger RNA and inhibit its translation. The great difference between these techniques is related to the proteases involved in the process, while for interference RNA the RISC machinery acts, for antisense oligodeoxyribonucleotides RNase H cleaves the RNA in the duplex DNA-RNA. Although these tools to edit the translation process are relevant to the treatment and even cure of metabolic disorders and cancers, it is still not effective when employed without a coating to protect the sequences before it reaches the destiny in vivo. Efforts have been made in developing modified bases to be more stable, but they show some toxicity. In this dissertation, chitosan, a natural cationic polyssacharide, is used to produce nanoparticles to protect the antisense oligodeoxyribonucleotide (ASO). For this reason, the commercial chitosan was modified, depolymerized, trimetilated or PEGlated and the nanoparticles were synthesized with sodium tripolyphosphate (TPP) by ionotropic gelation method. The stability along time, in different pHs and temperatures was assessed. The toxicity of nanoparticles without ASO was quantified by MTT tests in NB-4, HepaRG, HTC and BHK-570 cell lines. A green fluorescent protein (GFP) expressed by NB-4 cells was the target to evaluate the delivery efficiency of the ASO, and its fluorescence was measured by confocal microscopy. Results showed that nanoparticles were stable over time as well as in temperatures ranging from 22 to 45°C and in acidic pH. Each cell line responded in a different manner to the treatment, with the health cell BHK-570 showing higher resistance. Furthermore, all of them presented lower viability when treated with trimetilated chitosan nanoparticles in the highest concentrations (ca 1011 nanoparticles/mL). NB-4 cells presented a decrease in fluorescence in 18 hours of treatment followed by an increase after 42 hours. We conclude that chitosan nanoparticles are a good alternative to the delivery of genetic material even more in the gastro intestinal tract due to its great stability in acid pH values.

A habilidade das células-tronco de se diferenciar em diferentes tipos celulares faz delas fortes candidatas para serem utilizadas em terapias celulares como tratamento de diversas doenças. No entanto, para explorar este potencial e necessário o estabelecimento de estratégias efetivas para modificações genéticas nessas células. Associado a outras tecnologias, o sistema de vetores lentivirais tem sido usado como um método atrativo para entrega de transgenes de interesse por possuírem uma alta eficiência de transdução. Além disso, eles permitem a transdução em células em proliferação ou quiescentes. A eficácia desses vetores para expressão de transgenes depende do uso de promotores corretos que possam garantir uma alta expressão genica e sustentável. Assim, o objetivo deste projeto foi comparar a eficiência dos promotores de citomegalovírus (CMV) e do fator de elongação-1<font face=\"Symbol\">a (EF1<font face=\"Symbol\">a) no sistema de entrega genica lentiviral em células-tronco mesenquimais de pele humana (HU). Para isso, foram construídos vetores lentivirais que possuem o promotor de CMV ou o promotor de EF1<font face=\"Symbol\">a, além do gene-repórter eGFP (\'\'enhanced green fluorescence protein\'\'). Para avaliar a eficiência de transfecção das construções, os vetores contendo os promotores e o gene-repórter (pLVCMVeGFP e pLVEF-1<font face=\"Symbol\">a-eGFP) foram utilizadas células 293T (produtora de partículas virais) e verificamos a presença da proteína fluorescente verde por microscopia de fluorescência, indicando a funcionalidade dos promotores. Visando analisar a eficiência das construções, células HU foram transduzidas e observamos a presença da proteína fluorescente nas transduções, demonstrando que os promotores encontram-se ativos em ambas as células. Após a verificação da eficácia das construções plasmidiais, foram feitas analises para avaliar a eficiência da transdução das construções em células HU. Para tal, as células foram transduzidas com lentivirus contendo um dos promotores analisados em diferentes multiplicidades de infecção (1, 5 e 10) e analisadas através da intensidade do sinal de fluorescencia e pela porcentagem de células eGFP positivas. Detectamos mais células eGFP positivas com a transdução do gene a partir do promotor PCMV do que com a do promotor PEF-1<font face=\"Symbol\">a. Assim, comparamos a eficiência destes promotores em MOI 1. Os resultados mostraram que a transdução com o promotor PEF-1<font face=\"Symbol\">a foi superior quando comparado ao promotor PCMV, portanto sendo a melhor escolha para esse sistema de entrega genica em células-tronco mesenquimais de pele humana. / The hability of stem cells to form a wide source spectrum of cell type makes them an interesting source for cell therapies. However, to exploit their remarkable potentials, the development of effective strategies for genetic modifications of MSCs is required. Lentiviral based vectors, with other techniques, offer an attractive system for efficient gene delivery in stem cells. These vectors efficiently transduce stem cells, and can infect dividing and nondividing cells. However, the efficiency of this vectors to genetic manipulation depends on the use of corrects cellular promoters for driving a high and stable expression of exogenous genes. In this study, we have chosen the cytomegalovirus (CMV) and the elongation factor 1-<font face=\"Symbol\">a promoters. We have compared the efficiency of this promoters in drive expression of the transgene in human dermal mesenchymal stem cells. The lentiviral vectors were constructed with the CMV promoter or the EF-1<font face=\"Symbol\">a promoter, together with the eGFP gene (enhanced green fluorescence protein). To evaluate the efficiency of the lentiviral vectors, 293T cells were transfected and analyzed for eGFP expression using fluorescence microscopy. We were able to observe the expression of eGFP, indicating that the vectors were working. Dermal mesenchymals stem cells were transduced with CMV- and EF-1<font face=\"Symbol\">a lentiviral vectors to evaluate the efficiency of the transductions. Efficiency of transductions was measured by flow cytometry (FACS) as percentage eGFP+ cells and signal intensity with different MOIs (multiplicity of infections).

Calcium plays important roles in both eukaryotic and prokaryotic cells. Its actions help to stabilize cell synthesis, growth and development. In this thesis, studies have been completed to determine effects of calcium and pH on bacterial cell growth and protein expression using the bacterial cell strain E.coli BL21(DE3). Our studies demonstrated the addition of calcium addition in the media does not affect growth but increases protein expression, while reducing the pH from 7 to 4 through the addition of 10mM EGTA in LB media inhibits both. Additionally, we report studies on the design, expression, and purification of fluorescent mCherry variants and their differences in their optical properties, including: extinction coefficients , quantum yields and pKa values. Also, we report progress in the crystallization of two GFP calcium sensors: G1 and D1, using 13 and15% PEG 4000 and 3350 respectively in 50mM HEPES buffer (pH 6.8-7.0) in an effort to optimize crystallization.

Soft sensors have been suggested as potent tools for on-line estimations of critical bioprocess variables to be able to control the biological process in an as high extent as possible. The formation of inhibitory by-products in the form of organic acids, caused by an overflow of glucose, is a problem in most bioprocesses expressing recombinant proteins.    In this project a new method of controlling the glucose feeding in an Escherichia coli fed-batch cultivation expressing the green fluorescent protein (GFP) was investigated. The new controller system implemented in the software controlled the feed rate based on on-line HPLC measurements of the concentration of organic acids.      The results showed that the controller managed to down-regulate the inhibitory organic acids to a low level as it tried to keep the glucose uptake rate at an optimum for maximum cell growth. The results suggested that the controller could be a powerful tool to create a more secure reproducibility and to generate high product yields in recombinant protein productions.

No description available.

A new synthetic methodology for the combinatorial preparation of C-terminus-modified Green and Red Fluorescent Protein chromophores is described. This method involves the modification of the previously reported [2+3] cycloaddition reaction scheme to incorporate new R2 groups in the imidate used in the final step. This is achieved through two primary routes: (a) the imidation of nitriles using hydrochloric acid gas and (b) the O-alkylation of amides using a variant of Meerwein's Salt to provide conjugated imidates. The preparation of fluorescent microcrystals and nanofibers from Green Fluorescent Protein chromophore derivatives via the reprecipitation method is also demonstrated. The properties of these microcrystals and nanofibers, especially in relation to the powder obtained from organic solvents, are also explored. Additionally, it is demonstrated that the size and shape of the microcrystals and nanofibers can be modulated with varying experimental conditions for RP. A new class of AIE-active GFP chromophores is reported. These chromophores contain a benzoxazole group on the phenyl ring and varying lengths of alkyl chains on the imidazolidinone nitrogen. These benzoxazole-based chromophores exhibit unique properties in the solid state not previously observed for GFP chromophore derivatives, namely, a broadening of the excitation spectrum and red-shifting of the emission, likely caused by excimer formation. The crystal structure also reveals a unique "hot-dog" stacking motif. Additionally, some projects which require further work are discussed at the end of the thesis. These include a stress-responsive GFP-based polymer and DNA-binding fluorophores.

We have synthesized dimethyl derivatives of the GFP chromophore (p-HOBDI) and several of its derivatives, and their photochemistry and photophysics were investigated using various steady-state and time-resolved techniques as follows. We first consider the effect of the £]-barrel on the optical properties of the GFP chromophore (p-HOBDI) experimentally by selective variation of the protonation state of chromophores and different solvents. Each of these forms shows a complex solvatochromic behavior and is governed by both polar and acid/base properties of the solvents. In contrast to their solution behavior, some O-alkyl GFP chromophore (alkoxy-BDI) derivatives exhibit large fluorescent enhancement in the solid state. The color of the crystalline BDI is tuned by substituent-mediated crystal packing, showing the potential applications in optoelectronic devices. Using femtosecond polarization-sensitive infrared (IR) spectrosceopy of the C=O stretching mode of the HOBDI, we have then discovered a near complete twisting around the ethylenic bridge between the phenolate and imidazolidinone groups upon electronic excitation. Cis/trans isomerization induced by the rotation around the bridge is thought to be responsible for the behavior of blinking in fluorescent protein; however, the mechanism of the thermal reverse isomerization is more problematic. Thus we synthesized BDI derivatives with decreasing para-donating ability, HO, CH3O, CH3, H, and Cl, and used a Hammett plot for the rate study. With a positive â value, we conceived, for the first time, a novel nucleophilic addition/elimination mechanism. Finally, the GFP chromophore falls into the general category of hydroxyarene photoacids, which exhibit high excited-state acidities but neutral ground states. A hydroxyl substituent at the meta position shows enhanced charge transfer and greater acidity in the excited state. As a result, we have demonstrated that the fast quenching of the excited state by internal conversion to the ground state is much slower in meta- than in para-HOBDI derivatives. This allows studies of this ultrafast intermolecular ESPT that competes with isomerization. The photoinduced dynamics of the meta isomer of GFP chromophore was further investigated using femtosecond transient absorption and fluorescence upconversion spectroscopies.

abstract: The energy required in a eukaryotic cell is provided by mitochondria. Mitochondrial electron transport chain (ETC) coupled with oxidative phosphorylation generates ATP. During electron transport, electron leakage from the ETC produces reactive oxygen species (ROS). In healthy cells, there are preventive and defense mechanisms in place to manage ROS. Maintaining a steady balance of ROS is very important because overproduction of ROS can lead to several pathological conditions. There are several strategies to prevent ROS production. Addition of external antioxidants is widely used among them. Discussed in the first part of Chapter 1 is the mitochondrial ETC, ROS production and antioxidant strategies. The second part of Chapter 1 is concerned with ribosomal protein synthesis in bacteria. Ribosome, the organelle that synthesizes proteins with exceptional fidelity, has a strong bias for α-L-amino acids. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome could enable the incorporation of both α-D-amino acids and β-amino acids into full length protein. Oxidative stress is a common cause of various neurological disorders such as Alzheimer’s disease and Parkinson’s disease. Antioxidative strategies are used widely for the treatment of these disorders. Although several antioxidants demonstrated positive results in vitro as well as in in vivo models, none of them have been effective in clinical settings. Hence, there is an ongoing search for effective neuroprotective drugs. Described in Chapter 2 is the synthesis and biological evaluation of several methylene blue analogues as potentially effective antioxidants for the treatment of pathologies related to oxidative stress. In Chapter 3, the synthesis and ribosomal incorporation of several rationally designed dipeptidomimetic analogues are discussed. The dipeptidomimetic analogues are structurally similar to the GFP chromophore and, therefore, highly fluorescent. In addition, the backbone of the dipeptidomimetic analogues resemble the peptide backbone of a dipeptide, due to which they can be incorporated into protein by modified ribosomes selected for the incorporation of dipeptides. Discussed in Chapter 4 is the synthesis of the pdCpA derivatives of several β-amino acids. The pdCpA derivatives were ligated to tRNA-COH and were used as probes for studying the regio- and stereoselectivity of modified ribosomes. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

Em 1978, o trabalho realizado por Stephenson e Zamecnik demonstrou a capacidade de um oligonucleotídeo de impedir a expressão de uma proteína específica. Atualmente, duas tecnologias são mais utilizadas para este propósito: os oligodeoxiribonucleotídeos antisense e o RNA de interferência (siRNA), que se aproveitam da capacidade de anelação entre as fitas complementares. A maior diferença entre as duas técnicas é a maquinaria proteica recrutada, isso é, o complexo RISC atua no funcionamento do siRNA, e a protease RNase H atua na clivagem da fita de RNA quando hibridizada com DNA. Apesar da grande aplicabilidade destas tecnologias, tanto para doenças metabólicas quanto para canceres, o veículo de entrega e proteção dessas sequências é de fundamental importância, visto que a aplicação desses oligonucleotídeos livres está sujeita à rápida degradação e ineficiência. A modificação das bases é uma das estratégias para conferir maior estabilidade às sequências, porém estas tem sido relacionadas a um aumento da toxicidade. Nessa dissertação, a quitosana, um polissacarídeo catiônico é utilizado para síntese de nanopartículas e encapsulamento dos oligodeoxiribonucleotídeos antisense (ASO). Para isso, foram realizadas modificações na quitosana comercial como despolimerização, trimetilação ou conjugação com PEG, seguida da síntese das nanopartículas com a adição de tripolifosfato de sódio (TPP) pelo método de gelatinização ionotrópica. A estabilidade das nanopartículas foi medida em função do tempo, da variação de temperatura e da diferença de pH. Além disso, a toxicidade dessas nanopartículas foi analisada através da viabilidade celular em diferentes linhagens, NB-4, HepaRG, HTC e BHK-570. A expressão da proteína verde fluorescente (GFP) na célula NB-4 foi utilizada para avaliar a entrega do ASO desenhado, sendo sua fluorescência monitorada por microscopia confocal. Os resultados demonstram que as nanopartículas se mantiveram estáveis durante o período de tempo analisado, assim como com a temperatura variando de 22 a 45&deg;C e em pH ácido. Cada linhagem celular respondeu de forma diferente ao tratamento com as nanopartículas sem ASO, sendo a linhagem saudável BHK-570 com a maior resistência. Ademais, todas as células apresentaram viabilidade reduzida quando tratadas com concentrações na ordem de 1011 nanopartículas/mL a base de quitosana trimetilada. A fluorescência das células NB-4 quando tratada com as nanopartículas com ASO diminuiu consideravelmente nas 18 primeiras horas, seguida de um aumento após 42 horas. Dessa forma, pode-se concluir que as nanopartículas de quitosana propostas nessa dissertação apresentaram uma excelente alternativa para a entrega de material genético, principalmente para o trato gastro-intestinal, devido à sua estabilidade em pH ácido. / The property of an oligonucleotide to interfere in the expression of a protein was observed in 1978 by Stephenson and Zamecnik. To perform such interference, there are today, two main techniques being explored: antisense oligodeoxyribonucleotides and interference RNA. In both cases, the particularity of their chemical structure is taken into account as soon as they can bind in a complementary manner to the messenger RNA and inhibit its translation. The great difference between these techniques is related to the proteases involved in the process, while for interference RNA the RISC machinery acts, for antisense oligodeoxyribonucleotides RNase H cleaves the RNA in the duplex DNA-RNA. Although these tools to edit the translation process are relevant to the treatment and even cure of metabolic disorders and cancers, it is still not effective when employed without a coating to protect the sequences before it reaches the destiny in vivo. Efforts have been made in developing modified bases to be more stable, but they show some toxicity. In this dissertation, chitosan, a natural cationic polyssacharide, is used to produce nanoparticles to protect the antisense oligodeoxyribonucleotide (ASO). For this reason, the commercial chitosan was modified, depolymerized, trimetilated or PEGlated and the nanoparticles were synthesized with sodium tripolyphosphate (TPP) by ionotropic gelation method. The stability along time, in different pHs and temperatures was assessed. The toxicity of nanoparticles without ASO was quantified by MTT tests in NB-4, HepaRG, HTC and BHK-570 cell lines. A green fluorescent protein (GFP) expressed by NB-4 cells was the target to evaluate the delivery efficiency of the ASO, and its fluorescence was measured by confocal microscopy. Results showed that nanoparticles were stable over time as well as in temperatures ranging from 22 to 45&deg;C and in acidic pH. Each cell line responded in a different manner to the treatment, with the health cell BHK-570 showing higher resistance. Furthermore, all of them presented lower viability when treated with trimetilated chitosan nanoparticles in the highest concentrations (ca 1011 nanoparticles/mL). NB-4 cells presented a decrease in fluorescence in 18 hours of treatment followed by an increase after 42 hours. We conclude that chitosan nanoparticles are a good alternative to the delivery of genetic material even more in the gastro intestinal tract due to its great stability in acid pH values.