Thesis (Ph. D.)--Georgia State University, 2006. / Title from title screen. Dabne White Dixon, committee chair; Kathryn Betty Grant, Markus W. Germann, committee members. Electronic text (252 p. : ill., charts (some col.)) : digital, PDF file. Description based on contents viewed June 18, 2007. Includes bibliographical references.

No description available.

No description available.

No description available.

Made available in DSpace on 2014-06-11T19:32:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-07-19Bitstream added on 2014-06-13T20:24:23Z : No. of bitstreams: 1 lovaglio_rb_dr_rcla.pdf: 1731223 bytes, checksum: 43dfc85c18edb74e4fc520e7b8f963ac (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Os biossurfactantes são metabólitos secundários que apresentam atividade de superfície, podendo ser aplicados em diferentes processos industriais, como produção de fármacos, compostos químicos, cosméticos, biorremediação de ambientes poluídos por petróleo e derivados e recuperação terciária do petróleo. A maior vantagem destes compostos quando comparado aos surfactantes sintéticos reside na sua diversidade estrutural, baixa toxicidade e alta biodegradabilidade. Apesar das inúmeras vantagens apresentadas pelos biotensoativos, eles não são comercialmente utilizados devido ao alto custo de produção. O objetivo deste trabalho foi estudar a produção de ramnolipídios por mutantes de P. aeruginosa a partir de resíduos industriais e óleos vegetais, bem como caracterizar as propriedades de solução desses biossurfactante, além de verificar a influência da fonte de carbono na produção de homólogos de ramnolipídios por P. aeruginosa. Na primeira etapa as fermentações foram conduzidas em tubos de ensaio, após a seleção dos micro-organismos com potencial para alta produção, os mesmos foram testados em frascos Erlenmeyer. O mutante com potencial para elevada produção foi avaliado, junto com a linhagem selvagem, em fermentadores. A linhagem selecionada e a utilização do meio de cultura livre de cálcio contendo óleo de girassol como fonte de carbono acarretou em um aumento de 70% na produção de ramnolipídios. A adição de etanol às soluções de ramnolipídios comprovou o potencial desse tensoativo para serem aplicados na indústria de cosméticos, já que as propriedades de tensão superficial, agregação e emulsificação foram mantidas nas três concentrações de álcool adicionadas. Além disso, verificou-se que a mudança da fonte de carbono acarreta alteração nos tipos ácidos graxos e proporções de homólogos de ramnolipídios produzidos por P. aeruginosa LBI 2A1 / The biosurfactants are secondary metabolites that exhibit surface activity and can be applied in different industrial processes such as production of pharmaceuticals, chemicals, cosmetics, bioremediation of environments polluted by oil and derivatives and tertiary recovery of oil. The greatest advantage of these compounds compared to synthetic surfactants lies in their structural diversity, low toxicity and high biodegradability. Despite the numerous advantages provided by biosurfactants, they are not commercially used due to the high cost of production. The present study aimed to evaluate the production of rhamnolipids by mutants of P. aeruginosa using industrial waste and vegetable oils as carbon source, as well as to characterize the properties of these biosurfactant solutions and investigate the influence of carbon source in the production of homologous rhamnolipds by P. aeruginosa. In the first stage fermentations were conducted in test tubes, after selection of microorganisms with potential for high production they were tested in Erlenmeyer flasks. The mutant with the potential for increased production was assessed, along with the wild strain in bioreactors. The selected strain and the calcium free medium used with sunflower oil as carbon source resulted in an 70% increase in the production of rhamnolipids. The addition of ethanol to the rhamnolipids solutions proved the potential of this biosurfactant to be applied in the cosmetic industry, since the properties of surface tension, emulsification and aggregation were held in all three concentrations of ethanol added. Moreover, it was found that changing the carbon source caused alteration in the types of fatty acids and rhamnolipids counterparts proportions produced by P. aeruginosa LBI 2A1

Made available in DSpace on 2015-03-03T11:52:47Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-09-05Bitstream added on 2015-03-03T12:07:02Z : No. of bitstreams: 1 000794866_20160904.pdf: 841244 bytes, checksum: 15789344d00520491ff203ff9f7b6fa2 (MD5) Bitstreams deleted on 2016-09-09T14:06:02Z: 000794866_20160904.pdf,. Added 1 bitstream(s) on 2016-09-09T14:06:35Z : No. of bitstreams: 1 000794866.pdf: 3309197 bytes, checksum: 719601c6e873cea248933afaaa2f8cf8 (MD5) Bitstreams deleted on 2016-09-12T15:36:45Z: 000794866.pdf,. Added 1 bitstream(s) on 2016-09-12T15:37:23Z : No. of bitstreams: 1 000794866.pdf: 3309197 bytes, checksum: 719601c6e873cea248933afaaa2f8cf8 (MD5) / Caesalpinia ferrea Mart. pertence à familia Fabaceae ( Caesalpinioideae ) , cresce em todo o terr itório brasileiro, sendo largamente distribuída nas regiões norte e nordeste, conhecida vulgarmente como pau - ferro ou jucá. N este trabalho , foi realizado o estudo fitoquímico, a determinação quantitativa de metabólitos secundários, a avaliação das atividad es mutagênica e an tirradicalar e a determinação dos teores de fenóis totais do extrato etanólico das cascas do caule de C . ferrea . Análises por HPLC - ESI - IT - MS ( High Performance Liquid Chromatography - Electrospray Ionization - Ion Trap – Mass Spectrometry ) e FIA - ESI - IT - MS n ( Flow Injection Analysis - Electrospray Ionization - Ion Trap – Mass Spectrometry ), modo negativo , permitiram identificar vinte substâncias pela análise dos padrões de fragmentações e comparação com dados da literatura ( ácido gálico e der ivad o s , ácido elágico e derivados , galotaninos, elagitaninos, catequina e uma procianidina ) . No estudo fitoquímico, foram utilizadas técnicas cromatográficas usuais, como Cromatografia em Coluna Clássica (sílica gel e s ephadex LH - 20 ), MPLC ( Medium Pressure Liquid Chromatrography ) e HPLC , que forneceram um éster de ftalato, um açúcar, ácido gálico, dois derivados do ácido quínico e um derivado glicosilado do ácido elágico, que foram identificados por métodos espectroscópicos ( Ultra vi oleta e Ressonância Magné tica Nuclear) e espectrométricos ( Espectrometria de Massas ). Um método analítico foi desenvolvido utilizando a técnica de HPLC - PDA ( High Performance Liquid Chromatography - Photodiode Array Detector ) que permitiu a quantificação d e seis substâncias ( ácido gálico, ácido galoil quínico, galato de etila, dilactona do ácido valoneico, ácido elágico e ácido 3 - O - metilelágico - 4 ' - O - ? - D - arabinopiranosídeo ) no extrato. Nesta... / Caesalpinia ferrea Mart. belongs to the family Fabaceae (Caesalpin ioideae) grows throughout the Brazilian territory, being widely distributed in the northern and northeastern regions, known commonly as pau - ferro or jucá . In t his research describes the phytochemical study, and the determination of the quantitative seconda ry metabolites, the mutagenic evaluation and antiradical activities and the total phenol levels determination of the ethanolic extract from the C . ferrea Martius stem bark. The analyses by the HPLC - ESI - IT - MS (High Performance Liquid Chromatography – Electr ospray Ionization – Ion trap – Mass Spectometry) and FIA – ESI - IT - MS n (Flow Injection Analysis – Electrospray Ionization – Ion Trap – Mass Spectometry), negative mode, it allowed to identify twenty substances by the standard analyses of the fragmentation a nd comparison with the data that are in the literature (gallic acid and derived, ellagic acid and derivatives, gallotannins, ellagitannis, cathechin and proantocyanidin). In the phytochemical study, it was used common chromatographic technical, like the Cl assical Column Chromatography (silica gel and sephadex LH - 20), MPLC (Medium Pressure Liquid Chromatrography) and HPLC , that provided a phthalate ester, a sugar, a gallic acid, two quinic acid derived and a glycosylated ellagic acid derivative , that were id entified by spectroscopic (Ultraviolet and Nuclear Magnetic Ressonance) and spectrometric (Mass s pectrometry ). An analytical method was developed using th e HPLC - PDA (High Performance Liquid Chromatography - Photodiode Array Detector) , which permitted quant ification of six substances (gallic acid, gal l o y l quinic acid, ethyl gallate, valoneic acid dilactone, ellagic acid and 3 - O - metilel la gic acid - 4 ' - O - ? - D - arabinopyranoside) in the extract. In this quantification, ellagic acid (57.64 ± 1.22 ?g.mL - 1 ) and...

Orientador: Maysa Furlan / Co-orientador: Lidiane Gaspareto Felippe / Banca: Rafael Victorio Carvalho Guido / Banca: Adriana Aparecida Lopes / Resumo: A clonagem de oxidoesqualeno ciclase das folhas de M. ilicifolia já foi estudada por nosso grupo, bem como os estudos de expressão em S. cerevisiae geneticamente modificada para melhor produção da friedelina. Para o desenvolvimento do trabalho, optou-se por realizar a expressão do gene de friedelina sintase de Kalanchoe daigremontiana obtido comercialmente, cuja sequência foi otimizada de acordo com o codon usage de S. cerevisiae. A partir das mutações sítio-dirigidas, duas mutações no gene sintético foram confirmadas. A primeira mutação do resíduo de leucina para valina na posição 483 do gene sintético levou à produção da friedelina e dos triterpenos -amirina e taraxerol enquanto a segunda mutação do resíduo de leucina para treonina na mesma posição deste gene produziu unicamente a -amirina. Após a padronização e análises das mutações no gene sintético, as mesmas mutações foram realizadas no gene da friedelina sintase de Maytenus ilicifolia. A mutação por valina levou à produção de -amirina e friedelina e, igualmente ao gene sintético, a mutação por treonina levou à formação apenas da -amirina. De acordo com a mutação gerada, os compostos produzidos pela levedura foram analisados por cromatografia gasosa acoplada a detector de massas e observou-se que algumas mutações levavam a uma alteração da especificidade do produto formado pela enzima. Esses estudos sugerem que a relação da estrutura proteica-função da enzima produtora da friedelina possa estar associada ao ajuste da cavidade ativa da enzima e, quando um resíduo de aminoácido do sítio ativo é substituído por resíduos menores, a ampliação da cavidade proporciona a estabilização prévia do carbocátion em um triterpeno com menor número de rearranjos, como a -amirina. Desta forma, estes dados contribuem com o entendimento da especificidade desta enzima, são os primeiros a... / Abstract: The cloning of oxidosqualene cyclase from Maytenus ilicifolia leaves and expression in Saccharomyces cerevisiae has been studied by our group to generate friedelin. The main objective of this project was to carry out the expression of friedelin synthase gene using commercially Kalanchoe daigremontiana, whose sequence has been optimized according to the codon usage of S. cerevisiae. In such studies, two mutations in the synthetic gene were confirmed. The first mutation of valine for leucine residue at position 483 synthetic gene led to the production of friedelin, β-amyrin and tararexol, while the second mutation of leucine to threonine residue, at the same position, produced exclusively β-amyrin. The same mutations were performed using the gene of friedelin synthase of Maytenus ilicifolia. The compound identities were confirmed by gas chromatography and mass spectrometry. The results suggested that the ratio of protein production-enzyme function, involved in the production of friedelin, may be associated with the active cavity of the enzyme setting, when an amino acid residue of the active site is replaced for smaller, expanding the cavity to provide the prior stabilization of the carbocation in the biosynthetic pathway of triterpenes to produce β-amyrin. Thus, these data contribute to understand the specificity of such enzyme. Furthemore, this studie was the first one to show the importance of each amino acid in the active site of the enzyme to produce a pentacyclic triterpene with the highest number of rearrangements and was the basis for future studies of enzyme engeenering to increase productivity of such compounds. / Mestre

abstract: A synbody is a newly developed protein binding peptide which can be rapidly produced by chemical methods. The advantages of the synbody producing process make it a potential human proteome binding reagent. Most of the synbodies are designed to bind to specific proteins. The peptides incorporated in a synbody are discovered with peptide microarray technology. Nevertheless, the targets for unknown synbodies can also be discovered by searching through a protein mixture. The first part of this thesis mainly focuses on the process of target searching, which was performed with immunoprecipitation assays and mass spectrometry analysis. Proteins are pulled down from the cell lysate by certain synbodies, and then these proteins are identified using mass spectrometry. After excluding non-specific bindings, the interaction between a synbody and its real target(s) can be verified with affinity measurements. As a specific example, the binding between 1-4-KCap synbody and actin was discovered. This result proved the feasibility of the mass spectrometry based method and also suggested that a high throughput synbody discovery platform for the human proteome could be developed. Besides the application of synbody development, the peptide microarray technology can also be used for immunosignatures. The composition of all types of antibodies existing in one's blood is related to an individual's health condition. A method, called immunosignaturing, has been developed for early disease diagnosis based on this principle. CIM10K microarray slides work as a platform for blood antibody detection in immunosignaturing. During the analysis of an immunosignature, the data from these slides needs to be validated by using landing light peptides. The second part of this thesis focuses on the validation of the data. A biotinylated peptide was used as a landing light on the new CIM10K slides. The data was collected in several rounds of tests and indicated that the variation among landing lights was significantly reduced by using the newly prepared biotinylated peptide compared with old peptide mixture. Several suggestions for further landing light improvement are proposed based on the results. / Dissertation/Thesis / M.S. Biological Design 2011

As an emerging area, systems biology provides a new paradigm not only for studying the cellular organization and regulation, but also for investigating how the systemic behaviors emerge in biological systems. One of the main objectives of systems biology is to understand mechanism and principle of the strategy that is applied in the metabolic network response to the environment and resources availability. Mass spectrometry (MS) was employed as the high-throughput technique tools to collect reliable data to obtain a quantitative understanding of the regulation of metabolic network in different cases. A LC-MS based method was developed and optimized for the measurement of central carbon metabolites in Escherichia coli. It could avoid the leakage problem and the "false high level" caused by the metabolites excreted to the medium, and provides better coverage as well as more accurate quantitative results of intracellular metabolites from different conditions. The developed method was employed to investigate the metabolic response to the nutrition stress. Intracellular concentrations of central carbon metabolites were measured under different nutrition conditions. The FBP concentration revealed the carbon influx because it served as a sensor of glycolytic flux and the α-ketoglutarate served as a coordinator of carbon and nitrogen flux response to the nutrient availabilities. A scenario was made that cell coordinated the catabolic and anabolic metabolism under different conditions by α-ketoglutarate and cAMP signaling. The overflow metabolism of E. coli was studied. A robust linear relation between acetate excretion rate and growth rate was observed. Gene expression level and quantitative proteomics approach were employed under perturbations such as mutants and increased energy demand (drained the energy by DNP). Acetate overflow in E. coli results from the tradeoff between efficient utilization of carbon resources by respiration and efficient utilization of proteome resources by fermentation. The physiology-driven approach was employed to investigate the potential targets of sRNA RyhB and the function of chaperon Hfq. Construction of a truncated RyhB mutant (RyhBt) was performed to confirm the necessity of hfq to RyhB. The expression of RyhB and RyhBt can both slow the growth rate. However, after the deletion of hfq, the growth defects induced by RyhB disappeared but still existed in the RyhBt strain without Hfq. It indicated that RyhB played its function by binding with Hfq at the special regions. Proteomics approach discovered some target genes of RyhB and RyhBt in both TCA cycle and nitrogen assimilation pathway. The relative abundance of proteins reflected that the RyhB and RyhBt affected the target differently because they had different binding sites with chaperons or targets. It will provided valuable information for revealing the inner mechanism of the physiology changes caused by sRNAs. GC-MS method was developed to identify and quantify the metabolites in E.coli cells. Three different derivatization methods for GC-MS were compared and optimized. The pool size of glutamine and glutamate was stable in the wild type strain at certain conditions but changed significantly in the GOGAT- strain especially the nitrogen was limited.

Heparan sulfate (HS) is a class of linear, sulfated polysaccharides located on cell surface, secretory granules, and in extracellular matrices found in all animal organ systems. It consists of alternately repeating disaccharide units, expressed in animal species ranging from hydra to higher vertebrates including humans. HS binds and mediates the biological activities of over 300 proteins, including growth factors, enzymes, chemokines, cytokines, adhesion and structural proteins, lipoproteins and amyloid proteins. The binding events largely depend on the fine structure - the arrangement of sulfate groups and other variations - on HS chains. With the activated electron dissociation (ExD) high-resolution tandem mass spectrometry technique, researchers acquire rich structural information about the HS molecule. Using this technique, covalent bonds of the HS oligosaccharide ions are dissociated in the mass spectrometer. However, this information is complex, owing to the large number of product ions, and contains a degree of ambiguity due to the overlapping of product ion masses and lability of sulfate groups; as a result, there is a serious barrier to manual interpretation of the spectra. The interpretation of such data creates a serious bottleneck to the understanding of the biological roles of HS. In order to solve this problem, I designed HS-SEQ - the first HS sequencing algorithm using high-resolution tandem mass spectrometry. HS-SEQ allows rapid and confident sequencing of HS chains from millions of candidate structures and I validated its performance using multiple known pure standards. In many cases, HS oligosaccharides exist as mixtures of sulfation positional isomers. I therefore designed MULTI-HS-SEQ, an extended version of HS-SEQ targeting spectra coming from more than one HS sequence. I also developed several pre-processing and post-processing modules to support the automatic identification of HS structure. These methods and tools demonstrated the capacity for large-scale HS sequencing, which should contribute to clarifying the rich information encoded by HS chains as well as developing tailored HS drugs to target a wide spectrum of diseases.