Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-04-27T12:33:46Z No. of bitstreams: 1 fernandoantoniosimasvaz.pdf: 40063052 bytes, checksum: f272ddc4d930b7d243c50223436e02b2 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-05-13T13:00:49Z (GMT) No. of bitstreams: 1 fernandoantoniosimasvaz.pdf: 40063052 bytes, checksum: f272ddc4d930b7d243c50223436e02b2 (MD5) / Made available in DSpace on 2017-05-13T13:00:49Z (GMT). No. of bitstreams: 1 fernandoantoniosimasvaz.pdf: 40063052 bytes, checksum: f272ddc4d930b7d243c50223436e02b2 (MD5) Previous issue date: 2011-07-22 / FAPEMIG - Fundação de Amparo à Pesquisa do Estado de Minas Gerais / Nesta tese é descrita a preparação de novas fases estacionárias monolíticas (FEM) polimerizadas por fotoiniciação, através do método sol-gel, em capilares de sílica fundida revestidos com poliacrilato, para aplicação em eletrocromatografia capilar (ECC). Dentre as principais técnicas de separação em Química Analítica, a ECC tem despertado grande interesse no meio acadêmico, pelo fato desta combinar as vantagens tanto da cromatografia a líquido de alta eficiência quanto da eletroforese capilar. Grande parte do desenvolvimento da ECC se deve ao uso das FEM, as quais são semelhantemente aplicadas em outras técnicas cromatográficas. Ao contrário do revestimento de poliimida, amplamente empregado, o revestimento de poliacrilato, transparente acima de 370 nm e à luz visível, facilita a visualização da solução de sol no interior do capilar, o que permite controlar a injeção desta e de outras soluções, bem como observar a formação in situ da FEM. Além disso, é possível que seja feita a polimerização fotoiniciada sem a necessidade de remoção do revestimento polimérico que protege a coluna. O objetivo central deste trabalho foi entender e aprimorar o processo de fabricação das FEM para aplicações em ECC. Para isso, foram feitas modificações da câmara fotorreatora homemade utilizada para a polimerização das FEM, como uma correção na faixa espectral de trabalho de 350 a 700 nm para 350 a 400 nm; e instalação de dispositivos de segurança tanto para o operador quanto para o sistema elétrico. Para que fosse alcançado um melhor controle de injeção de fases líquidas no interior de tubos com dimensões capilares, a construção de um dispositivo de alta pressurização (DAP) que forneceu, além da pressão, grande precisão foi indispensável. O DAP, além de simples, teve ótima relação custo-benefício, comparado a modelos comerciais. O preparo das FEM foi otimizado mediante auxílio de planejamento fatorial fracionário 24-1, onde se buscou analisar propriedades eletrocromatográficas frente diferentes proporções dos reagentes empregados e tempo de incidência de luz ultravioleta (UV). Este último fator não apresentou significância e foi desconsiderado, de forma que o planejamento fosse devidamente reduzido para um planejamento fatorial completo 23, o que possibilitou uma análise mais apurada dos efeitos significativos. O fator mais influente foi a proporção de porogênio (tolueno), sendo que a melhor condição obtida foi utilizando 80,0 % (v/v) de solução porogênica; 3,5 % (m/m) de fotoiniciador óxido de bis(2,4,6-trimetilbenzoil)-fenilfosfino (Irgacure 819); razão molar água/ metacriloxipropiltrimetoxisilano (MPTMS) igual a 4 e tempo de incidência de luz UV de 10 minutos. As características morfológicas, espectroscópicas e porosidade foram avaliadas através de microscopia eletrônica de varredura, infravermelho e porosimetria por adsorção de nitrogênio, respectivamente. As FEM foram testadas em ECC pela separação de hidrocarbonetos policíclicos aromáticos (naftaleno, acenafteno, fluoreno, fenantreno e antraceno) e alquilbenzenos (etilbenzeno, propilbenzeno, butilbenzeno e hexilbenzeno), todos compostos eletricamente neutros, diluídos em metanol (1 mmol L-1 cada), utilizando tiouréia como marcador de fluxo. Como fase móvel foi utilizada a mistura de acetato de amônio 16,7 mmol L-1 pH 7,0 (60 %) e acetonitrila (40 %). A voltagem aplicada foi -20 kV; a temperatura de análise foi 20 ºC; a injeção dos analitos foi -25 mbar por 5 s; e a detecção no UV foram nos comprimentos de onda de 220 nm e 250 nm. Foi utilizado o modo ECC-rápida, que consiste na inversão do sentido de análise e injeção de padrões pela extremidade curta do capilar. Este modo se mostrou muito mais rápido, repetitivo e eficiente do que o modo normal, fornecendo em pouco mais de 12 minutos de análise, mais de 51400 pratos/m de coluna e desvios padrão relativos em tempo de migração/retenção entre 0,09 e 3,3 % e em área de pico relativa entre 0,14 e 1,6 %. Os perfis de separação em ECC corroboraram com os resultados de porosidade e morfologia obtidos. / This thesis describes the preparation of new monolithic stationary phases (MSP) polymerized by photoinitiation through sol-gel approach in polyacrylate-coated fused silica capillary, for application in capillary electrochromatography (CEC). CEC has been concentrated much attention among the major separation techniques in analytical chemistry because it combines the advantages of both high performance liquid chromatography and capillary electrophoresis. Much of the CEC development is due to the use of MSP, which are similarly applied to other chromatographic techniques. Unlike polyimide-coating, widely used, the polyacrylate-coating, which is transparent above 370 nm and visible, enables the visualization of the sol solution within the capillary, allowing one to control the injection of sol and other solutions, in addition to observe the in situ formation of the MSP. Furthermore, it is possible to perform the photoinitiated polymerization without removing this polymeric coating that protects the capillary. The main purpose of this work was to comprehend and improve the fabrication process of MSP, for CEC applications. For this, some changes were set in the homemade photo reactor chamber, used for the MSP polymerization, like correction in the work range from 350 – 700 nm to 350 – 400 nm; and installation of security devices for both operator and electric system safeties. For better control of liquid phases injection within tubes with capillary dimensions, the build of a high-pressure device (HPD) that provides a great precision, in addition to the high-pressure, was essential. HPD is simpler and relatively cheaper when compared to commercial models. The preparation of the MSP has been optimized through assistance of a 24-1 fractional factorial design, with the intention to investigate electrochromatographic properties with different amounts of employed reagents and ultraviolet (UV) light incidence time. The later factor did not show significance and was unconsidered, making the design possible to be reduced to a 23 complete factorial design, which allowed analyzing the significant effects accurately. The most influent factor was the porogen (toluene) proportion, and the best condition was obtained using 80.0 % (v/v) of porogenic solution; 3.5 % of photoinitiator bis(2,4,6 trimetylbenzoyl)-phenylphosphine oxide (Irgacure 819); water to metacryloxypropyltrimethoxysilane (MPTMS) molar ratio equal to 4 and 10 minutes of UV light incidence time. The MSP morphological, spectroscopic characteristics and porosity were evaluated through scanning electron microscopy, infrared spectroscopy and nitrogen adsorption porosimetry, respectively. The MSP has been tested in CEC through the separation of polycyclic aromatic hydrocarbons (naphthalene, acenaphthene, fluorene, phenanthrene and anthracene) and alkylbenzenes (ethylbenzene, propylbenzene, butylbenzene and hexylbenzene), which are electrically neutral compounds, after dilution in methanol (1 mmol L-1 each), using thiourea as the flow marker. As mobile phase a mixture of ammonium acetate 16.7 mmol L-1 at pH 7.0 (60.0 %) and acetonitrile (40.0 %) was used. The applied voltage was -20 kV, the temperature of analysis was 20 °C, the analyte injection was -25 mbar for 5 s, and UV detection was done at 220 and 250 nm. A fast-CEC mode, which consists to reverse the analysis direction and to introduce the analyte by capillary short-end injection, was performed. This mode was much more fast, repetitive and efficient than the normal one, providing in a little more than 12 minutes over than 51400 plates per meter of column and relative standard deviations ranging from 0.09 to 3.3 % for migration/retention time and from 0.14 to 1.6 % for relative peak area. The separation profiles in CEC corroborate with the porosity and morphology results.

Dissertation thesis is a 5-publications' collection concerning characterization and application potential of cyclodextrins, polysaccharides and macrocyclic antibiotics based chiral stationary phases. The effects of stationary phase and mobile phase are studied. This approach ensures the complex insight into separation systems studied. Systems with different nature of chiral selector were studied by HPLC. Namely, macrocyclic antibiotics and derivatized polysaccharides were used for experiments. Former ones provided better results for enantioseparation of non-coded amino acids than latter ones. Dynamic coating procedure was used for preparation of a new chiral stationary phase. Characterization of new cationic cyclodextrin based chiral stationary phase was performed. Linear free energy relationship method was used for characterization of two different separation systems, i.e. newly prepared stationary phase and commercially available stationary phase. Based on results obtained, newly prepared stationary phase showed better results for separation of different achiral groups of analysts. New stationary phase prepared by dynamic coating was compared with chromatographic system, in which the chiral selector was used as a mobile phase additive. The chiral selector used for the two different approaches was...

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Please find the referenced videos attached / The physical ends of eukaryotic chromosomes consist of repetitive DNA sequences, which are associated with specialized proteins forming a nucleoprotein structure essential for the integrity of the linear chromosomes, and are known as telomeres. Telomerase is an enzyme responsible for the maintenance of the telomeric repeats at the end of the chromosomes. Telomerase is a ribonucleoprotein, which contains a catalytic subunit that possesses reverse transcriptase activity, and a RNA subunit that acts as a template, since it possess the telomeric repeat sequences necessary to amplify telomere ends. Telomeres are transcribed in most eukaryotes into a non-coding RNA know as TERRA (Telomeric repeats-containing RNA). It has been proposed that TERRA may act as a regulator of telomere homeostasis, and as an inhibitor of telomerase, however, its specific function is still unknown. In Saccharomyces cerevisiae, TERRA is rapidly degraded by the 5’-3’ Rat1 exonuclease, which has hampered its study by classic biochemical experiments in yeast. In this thesis, we report the use of cytological approaches to study TERRA in budding yeast. Two different approaches were used for this purpose: the fluorescent in-situ hybridization (FISH) and the labeling of TERRA by the MS2-GFP system, which allow the visualization of TERRA transcripts form a single telomere in living cells. With these two approaches, we observed that TERRA is expressed from a single telomere and accumulates as a single perinuclear foci, in a small percentage of cells population. We also demonstrate that TERRA expression occurs due to telomere shortening. We demonstrate that TERRA interacts in vivo with the telomerase RNA (TLC1) in yeast. Telomere elongation depends on the action of several telomerase molecules that are visible as clusters, which associate with telomeres in late S phase in yeast, and mammalian cells. In adidition, we show that TERRA stimulates the nucleation of telomerase clusters. By performing time course experiments of TERRA and TLC1 RNA in live cells, we observed that TERRA acts as a scaffold for generating telomerase clusters, which are then recruited in late S phase to the telomere from which TERRA molecules originated. The recruitment of TERRA to its telomere of origin is dependent on factors that control telomerase recruitment at telomeres like: Mre11, Tel1 and the yKu complex. We propose that a short telomere expresses TERRA to assemble and organize telomerase molecules, which later on allows their recruitment at the short telomere, where elongation is needed. Finally we showed an up-regulation of TERRA, and telomerase RNA TLC1, accompanied by a predominant cytoplasmic localization as cell growth progresses from exponential growth to diauxic shift, and stationary phase. In these conditions, TERRA foci co-localize with TLC1 RNA foci, suggesting that the function of TERRA as a scaffold molecule to generate telomerase cluster is necessary for this yeast cell growth phases. / Les télomères à l’extrémité des chromosomes constituent une structure d’ADN et de protéines essentielle à l’intégrité de ces chromosomes. La télomérase est l’enzyme responsable du maintien des répétitions télomériques à l’extrémité des chromosomes. Cette enzyme est constituée d’une sous-unité catalytique, qui possède une activité de transcriptase réverse, et d’une sous-unité d’ARN, qui fourni la matrice nécessaire à la synthèse des répétitions télomériques. Les ARN contenant des répétions télomériques (ou Telomeric repeats-containing RNA; TERRA) constitue une nouvelle classe d’ARN non-codants transcrits à partir des télomères et conservée chez la plupart des eucaryotes. TERRA a été proposé d’agir comme un régulateur de l‘homéostasie des télomères et comme inhibiteur de la télomérase, mais sa fonction spécifique reste inconnue. De plus, chez la levure Saccharomyces cerevisiae, TERRA est rapidement dégradé par l’exonucléase 5’-3’ Rat1, ce qui complique l’étude de cet ARN par les méthodes biochimiques classiques. Dans cette thèse, nous rapportons l‘utilisation d’une approche cytologique pour étudier TERRA dans les cellules de levures. Deux approches sont utilisées : l’hybridation in situ en fluorescence (FISH) et l’étiquetage de TERRA à l’aide du système MS2-GFP, qui nous permet de visualiser l’expression de TERRA transcrit d’un seul télomère dans des cellules vivantes. Avec ces deux approches, nous observons que TERRA exprimé à partir d’un seul télomère s’accumule dans un faible nombre de cellules, sous la forme d’un focus périnucléaire. De plus, nous montrons que TERRA est exprimé lorsque son télomère raccourcit. Par immunoprécipitation, nous montrons que TERRA interagit in vivo avec l’ARN de la télomérase de levure, TLC1. L’élongation des télomères dépend de l‘action de multiples molécules de télomérase, qui sont visibles sous la forme de clusters de télomérases, qui s‘associent en phase S avec les télomères chez la levure et les cellules de mammifère. Nous démontrons que TERRA stimule la nucléation de ces clusters de télomérase. Par imagerie en temps réel de TERRA et de l’ARN TLC1, nous observons que TERRA agit comme molécule d’échafaudage pour générer des clusters de télomérases, qui sont par la suite recrutés, en phase S, au télomère duquel TERRA a été exprimé. Le recrutement d’un focus de TERRA à son télomère d’origine dépend des facteurs contrôlant le recrutement de la télomérase aux télomères : Mre11, Tel1 et le complexe yKu. Nous proposons qu’un télomère court exprime TERRA pour assembler et organiser les molécules de télomérase, afin que celles-ci soit puissent être recrutées au télomère court pour permettre son élongation. Enfin, nous observons une surexpression de l’ARN de la télomérase TLC1 et de TERRA, ainsi qu’une accumulation cytoplasmique de ceux-ci sous la forme de foci, lorsque la cellule passe de la phase de croissance exponentiel à la phase diauxique, puis à la phase stationnaire. Dans ces conditions, les foci d’ARN TLC1 colocalisent avec les foci de TERRA, suggérant que la fonction de TERRA comme molécule d’échafaudage pour générer des foci de télomérase est aussi nécessaire durant ces phases du cycle de croissance des levures.

<p>In this thesis, porous graphitic carbon (PGC) has been used as packing material in packed capillary liquid chromatography. The unique chromatographic properties of PGC has been studied in some detail and applied to different analytical challenges using both electrospray ionization-mass spectrometry (ESI-MS) and ultra violet (UV) absorbance detection. </p><p>The crucial importance of disengaging the conductive PGC chromatographic separation media from the high voltage mass spectrometric interface has been shown. In the absence of a grounded point between the column and ESI emitter, a current through the column was present, and changed retention behaviors for 3-O-methyl-DOPA and tyrosine were observed. An alteration of the chromatographic properties was also seen when PGC was chemically oxidized with permanganate, possibly due to an oxidation of the few surface groups present on the PGC material. </p><p>The dynamic adsorption of the chiral selector lasalocid onto the PGC support resulted in a useful and stable chiral stationary phase. Extraordinary enantioselectivity was observed for 1-(1-naphthyl)ethylamine, and enantioseparation was also achieved for other amines, amino acids, acids and alcohols. </p><p>Finally, a new strategy for separation of small biologically active compounds in plasma and brain tissue has been developed. With PGC as stationary phase it was possible to utilize a mobile phase of high content of organic modifier, without the addition of ion-pairing agents, and still selectively separate the analytes. </p>

In this thesis, porous graphitic carbon (PGC) has been used as packing material in packed capillary liquid chromatography. The unique chromatographic properties of PGC has been studied in some detail and applied to different analytical challenges using both electrospray ionization-mass spectrometry (ESI-MS) and ultra violet (UV) absorbance detection. The crucial importance of disengaging the conductive PGC chromatographic separation media from the high voltage mass spectrometric interface has been shown. In the absence of a grounded point between the column and ESI emitter, a current through the column was present, and changed retention behaviors for 3-O-methyl-DOPA and tyrosine were observed. An alteration of the chromatographic properties was also seen when PGC was chemically oxidized with permanganate, possibly due to an oxidation of the few surface groups present on the PGC material. The dynamic adsorption of the chiral selector lasalocid onto the PGC support resulted in a useful and stable chiral stationary phase. Extraordinary enantioselectivity was observed for 1-(1-naphthyl)ethylamine, and enantioseparation was also achieved for other amines, amino acids, acids and alcohols. Finally, a new strategy for separation of small biologically active compounds in plasma and brain tissue has been developed. With PGC as stationary phase it was possible to utilize a mobile phase of high content of organic modifier, without the addition of ion-pairing agents, and still selectively separate the analytes.

A unique mechanism of protein oligomerization is domain swapping. It is a feature found in some proteins wherein a dimer or a higher oligomer is formed by the exchange of identical structural segments between protomers. Domain swapping is thought to have played a key role in the evolution of stable oligomeric proteins and in oligomerization of amyloid proteins. This thesis deals with studies to understand the significance of hinges involved in domain swapping for protein oligomerization and function. The stationary phase survival protein SurE from Salmonella typhimurium (StSurE) and Sesbania mosaic virus (SeMV) coat protein have been used as models for studies on domain swapping. This thesis has been divided into eight chapters. Chapter 1 provides a brief introduction to domain swapping, while Chapters 2 to 6 describes the studies carried out on StSurE protein, Chapter 7 deals with studies on SeMV coat protein. The final Chapter 8 provides brief descriptions of various experimental techniques employed during these investigations. Chapter 1 deals with a brief introduction to domain swapping in proteins. Examples where different domains are exchanged are cited. Then it describes physiological relevance of domain swapping in proteins and probable factors which promote swapping. Finally it also discusses the uncertainties that are inevitable in protein structure prediction and design. Chapter 2 describes the structure of Salmonella typhimurium SurE (StSurE; Pappachan et al., 2008) determined at a higher resolution. The chapter also deals with the sequence and structure based comparison of StSurE with other known SurE homolog structures. A comparative analysis of the relative conservation of N- and C-terminal halves of SurE protomer and variations observed in the quaternary structures of SurE homologs are presented. Then a brief introduction is provided on function of StSurE. The conserved active site of StSurE that might be important for its phosphatase activity is described. A plausible mechanism for the phosphatase activity as proposed by Pappachan et al. (2008) is presented. Crystal structures of StSurE bound with AMP, pNPP and pNP that was determined with the view of better understanding the mechanism of enzyme function is presented. These structures provide structural evidence for the mechanism proposed by Pappachan et al. (2008). Finally a substrate entry channel inferred from these structures is discussed. SurE from Salmonella typhimurium (StSurE) was selected for studies on domain swapping as there is at least one homologous structure (Pyrobaculum aerophilum - PaSurE) in which swapping of the C-terminal helices appears to have been avoided without leading to the loss of oligomeric structure or function. It was of interest to examine if an unswapped dimer of StSurE resembling PaSurE dimer could be constructed by mutagenesis. To achieve this objective, a crucial hydrogen bond in the hinge involved in C-terminal helix swapping was abolished by mutagenesis. These mutants were constructed with the intention of increasing the flexibility of the hinge which might bring the C-terminal helices closer to the respective protomer as in PaSurE. Chapter 3 presents a comparative analysis of the hinges involved in C-terminal helix swapping in PaSurE and StSurE. Based on the comparison of structure and sequence, crucial residues important for C-terminal helix swapping in StSurE were identified as D230 and H234. The chapter describes the construction of mutants obtained by substituting D230 and H234 by alanine and their biophysical characterization. Finally it describes structural studies carried out on these mutants. The mutation H234A and D230A/H234A resulted in highly distorted dimers, although helix swapping was not avoided. Comparative analysis of the X-ray crystal structures of native StSurE and mutants H234A and D230A/H234A reveal large structural changes in the mutants relative to the native structure. However the crystal structures do not provide information on the changes in dynamics of the protein resulting from these mutations. To gain better insights into the dynamics involved in the native and mutants H234A and D230A/H234A, MD simulations were carried on using GROMACS 4.0.7. Chapter 4 deals with a brief description of the theory of molecular dynamics, followed by results of simulation studies carried out on monomeric and dimeric forms of StSurE and dimeric forms of its mutants H234A and D230A/H234A. The conformational changes and dynamics of different swapped segments are discussed. Crystal structures of H234A and D230A/H234A mutants reveal that they form highly distorted dimers with altered dimeric interfaces. Chapter 5 focuses on comparison of dimeric interfaces of the native StSurE and hinge mutants H234A and D230A/H234A. Based on the analysis, three sets of interactions were selected to investigate the importance of the interface formed by swapped segments in StSurE mutants H234A and D230A/H234A. One of the selected sites corresponds to a novel interaction involving tetramerization loop in the hinge mutants H234A and D230A/H234A resulting in a salt bridge between E112 – R179’ and E112’ – H180 (prime denotes residue from the other chain of the dimeric protein). This salt bridge seems to stabilize the distorted dimer. It is shown by structural studies that the loss of this salt bridge due to targeted mutation restores symmetry and dimeric organization of the mutants. Loss of a crucial hydrogen bond in the hinge region involved in C-terminal helix swapping in SurE not only leads to large structural changes but also alters the conformation of a loop near the active site. It is of interest to understand functional consequences of these structural changes. StSurE is a phosphatase, and its activity could be conveniently monitored using the synthetic substrate para nitrophenyl phosphate (pNPP) at pH 7 and 25 ºC. Chapter 6 deals with the functional studies carried out with various StSurE mutants. The studies suggest that there is a drastic loss in phosphatase activity in hinge mutants D230A, H234A and D230A/H234A, while in the salt bridge mutants the function seems to have been restored. Few of these mutants also exhibit positive cooperativity, which could probably be due to altered dynamics of domains. Sesbania mosaic virus (SeMV) is a plant virus, belonging to genus sobemovirus. SeMV is a T=3 icosahedral virus (532 symmetry) made up of 180 coat protein (CP) subunits enclosing a positive-sense RNA genome. The asymmetric unit of the icosahedral capsid is composed of chemically identical A, B and C subunits occupying quasi-equivalent environments. Residues 48 – 59 of the N-terminal arms of the C subunits interact at the nearby icosahedral three-fold axes through a network of hydrogen bonds to form a structure called the “β-annulus”. Residues 60 – 73 form the “βA-arm” that connects the N-terminal β-annulus to the rest of the protomer. Various studies on SeMV-CP suggest that different lengths of the N-terminal segments affect the assembly of virus. It might be possible to exploit this flexibility of the N-terminus in SeMV-CP to introduce swapping of this segment between two 2-fold related C subunits as is found in Rice yellow mottle virus (RYMV), another sobemovirus, with which SeMV shares significant sequence similarity. Chapter 7 focuses on attempts made to examine the mutational effects planned to introduce domain swapping. The strategy used for introducing swapping in SeMV-CP was based on the sequence of the βA-arm or the hinge involved in swapping of β-annulus in RYMV. TEM images of the mutant virus like particles obtained suggest that they are heterogeneous. These mutants could not be crystallized, probably due to the heterogeneity. However, the assembly of the expressed proteins to virus like particles was profoundly influenced by the mutations. Chapter 8 discusses various crystallographic, biophysical and biochemical techniques used during these investigations. Finally the thesis concludes with Conclusions and Future perspectives of the various studies reported in the thesis. In summary, I have addressed the importance of amino acid residues and interactions of hinges involved in domain swapping for the quaternary structure and function of proteins.