The field of molecular evolution has benefited greatly from the use of ancestral sequence reconstruction as a methodology to better understand the molecular mechanisms associated with functional divergence. The method of ancestral sequence reconstruction has never been experimentally validated despite the method being exploited to generate high profile publications and gaining wider use in many laboratories. The failure to validate such a method is a consequence of 1) our inability to travel back in time to document evolutionary transitions and 2) the slow pace of natural evolutionary processes that prevent biologists from ‘witnessing’ evolution in action (pace viruses). In this thesis research, we have generated an experimentally known phylogeny of fluorescent proteins in order to benchmark ancestral sequence reconstruction methods. The tips/leaves of the fluorescent protein experimental phylogeny are used to determine the performances of various ASR methods. This is the first example of combining experimental phylogenetics and ancestral sequence reconstruction.

No description available.

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°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.

Fluorescent proteins are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions result in improved photostabilities. Therefore, understanding oxygen diffusion pathways in FPs is important for both photostabilites and maturation of the chromophores. We used molecular dynamics calculations to investigate the protein barrel fluctuations in mCherry, which is one of the most useful monomeric mFruit variants, and its GFP homolog citrine. We employed implicit ligand sampling and locally enhanced sampling to determine oxygen pathways from the bulk solvent into the mCherry chromophore in the interior of the protein. The pathway contains several oxygen hosting pockets, which were identified by the amino acid residues that form the pocket. We calculated the free-energy of an oxygen molecule at points along the path. We also investigated an RFP variant known to be significantly less photostable than mCherry and find much easier oxygen access in this variant. We showed that oxygen pathways can be blocked or altered, and barrel fluctuations can be reduced by strategic amino acid substitutions. The results provide a better understanding of the mechanism of molecular oxygen access into the fully folded mCherry protein barrel and provide insight into the photobleaching process in these proteins.

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).

Introduction It is well known that resident adipose stem/stromal cells (ASCs) are a heterogeneous population of multipotent cells characterized by (a) their ability to adhere to plastic; (b) immunophenotypic expression of certain cell surface markers, while lacking others; and (c) the capacity to differentiate into cells of mesodermal origin including osteocytes, chondrocytes and adipocytes. Adipose derived stromal cells offer great therapeutic potential in multiple medical fields, including, orthopedics, cardiology, oncology and degenerative diseases, to name a few. Combining different disciplines of medicine and engineering, organ and tissue repair can be achieved through tissue engineering and regenerative medicine. Adipose derived stromal cells (ASCs) can be utilized as biological vehicles for vector-based gene delivery systems, since they home to sites of inflammation and infection in vivo. In order to reach the long-term aim of clinical translation of cell-based therapy, preclinical safety and efficacy need to be shown in animal models. This has motivated the development of standardized isolation, characterization and differentiation operating procedures as well as an in vivo tracking system for ASCs and lentiviral vector transduction for a vector-based gene delivery system. Methodology Human ASCs were isolated from lipoaspirate, expanded in culture, immunophenotyped using flow cytometery and induced to differentiate into adipogenic, osteogenic and chondrogenic lineages. Tri-lineage differentiation was confirmed by microscopy. The ASCs were then transduced with green fluorescent protein (GFP)-expressing lentiviral vectors in vitro. The effect of the GFP lentiviral vector on ASCs was investigated by studying ASC immunophenotypic expression of surface markers as well as their capacity to differentiate into osteocytes, chondrocytes and adipocytes. Results The isolated and expanded cell population, from harvested lipoaspirate adhered to recommended ASC identity criteria. The heterogeneity of ASCs was confirmed by the presence of sub-populations. Transduction efficiency in ASC cultures of approximately 80% was observed after introducing a total of 300 μl of concentrated lentiviral vector suspension per 4.8 x 104 cells. No immunophenotypic differences were observed between GFP positive and GFP negative cultures. Flow cytometric analysis revealed a progressive increase in GFP expression following in vitro expansion of transduced ASCs. Both non-transduced and transduced cultures successfully differentiated into osteocytes, chondrocytes and adipocytes. Conclusion The isolated and expanded cell population conformed to the recommended characterization criteria. Heterogeneity was demonstrated with the identification of immunophenotypic sub-populations and semi-quantification of adipogenesis was performed. ASCs were efficiently transduced using the GFP lentiviral vectors produced in our facility. In addition, transduced ASCs maintained adherence to plastic, ASC immunophenotype and were able to differentiate successfully into cells of the three lineages of mesodermal origin. This optimized GFP-ASC transduction technique offers a feasible tracking system as well as a vector-based gene delivery system for future preclinical studies. / Dissertation (MSc)--University of Pretoria, 2015. / tm2015 / Immunology / MSc / Unrestricted

The Master Thesis focuses on monitoring of intracellular ion concentrations in bacteria Escherichia coli and yeast Saccharomyces cerevisiae using genetically encoded fluorescent probes with green fluorescent protein (GFP). Aquired knowledge about this protein and its spectral characteristics is summarized in the introduction. For experimental study a pH-sensitive sensor which displays a ratio change of two excitation fluorescence peaks - pHluorin - was chosen. This probe was tested in bacteria and yeast cells. The experiments concentrated on the ability of the cell to maintain a constant cytosolic pH under various conditions like different pH values of the suspension, addition of glucose or KCl to the suspension. Another topic discussed in the thesis is the elimination of the cell autofluorescence from the GFP signal. For this purpose the synchronous fluorescence scan technique was succesfully used. I have found out that by using this method the measurements of cytosolic pH values are even more accurate thanks to the improved signal to noise ratio.

Fluorescent proteins (FPs) are the workhorses of biological molecular imaging. Important imaging modalities (such as polarization microscopy or FRET imaging) exploit anisotropic optical properties of fluorescent proteins. In this thesis, we present the results of our polarization microscopy and X-ray diffraction experiments on FP crystals, as well as mathematical interpretation of these results, yielding information on the directionality of one- and two-photon absorption within the investigated fluorescent protein molecules. For the anisotropy of one-photon absorption, we determine the transition dipole moment (TDM) orientations in three representative fluorescent proteins. Validation with available quantum mechanical predictions values and an experimentally determined TDM orientation of the GFP gives confidence to the results obtained. For the two-photon absorption, we first test our hypothesis that two-photon absorptivity tensors of representative FPs exhibit vector-like behaviour and then examine the applicability of this simplification as a basis for the interpretation of our two-photon polarization microscopy data.