Thesis (Ph.D.)--Duquesne University, 2007. / Title from document title page. Abstract included in electronic submission form. Includes bibliographical references (p. 136-146).

Thesis (M.S.)--Duquesne University, 2003. / Title from document title page. Abstract included in electronic submission form. Includes bibliographical references (p. 46-54) and abstract.

Os manguezais são considerados um ecossistema único, devido sua particular combinação de condições ambientais, influenciados pela sua localização na interface entre o continente e oceano. O estudo deste ecossistema se torna urgente uma vez que os manguezais estão desaparecendo em todo mundo, e sua diversidade de grupos microbianos é ainda pouco conhecida. Dentro dessa temática, o presente projeto visa descrever a possível funcionalidade de bactérias pertencentes ao filo Planctomycetes nos manguezais. Tais organismos são ainda pouco estudados, de difícil cultivo, sendo obtidos principalmente em ambientes marinhos, tratamento de água e locais de criação de peixes. Dentro desse filo são encontrados microrganismos pertencentes a gêneros descritos como capazes de realizar a oxidação anaeróbica do íon amônio (anammox), uma importante transformação do nitrogênio em ambientes com baixa disponibilidade de oxigênio. E ainda, visamos descrever a possível funcionalidade de bactérias pertencentes ao filo Planctomycetes nos manguezais. Para isso, foi inicialmente realizada uma comparação dos genomas de Planctomycetes com as sequências obtidas por análises de metagenômica e metatranscriptômica, onde foram encontradas sequências similares às afiliadas a funções desconhecidas (putative protein) e a sulfatases. Tais enzimas são descritas como hidrolíticas, que catalizam a clivagem de ésteres de sulfato, liberando o enxofre na forma assimilável. A análise de sequências de uma biblioteca metagenômica (obtida de um manguezal contaminado com petróleo) permitiu a visualização de fragmentos genômicos de Planctomycetes. Esta análise revelou também a ocorrência de genes relacionados a produção de sulfatases, além de indicar arranjos gênicos distintos dos descritos nos genomas de organismos deste grupo, possivelmente indicando a ocorrência de endemismo de Planctomycetes em manguezais. Esta observação foi reforçada pelo cultivo de isolados afiliados a este grupo, os quais tiveram sua afiliação confirmada pelo sequenciamento parcial do gene ribossomal 16S DNAr. Alguns destes isolados formaram clusters diferenciados dentro do filo Planctomycetes, indicando que podem ser estes novas espécies. Sendo assim, a caracterização desse grupo de microrganismos numa combinação de análises in sílico e in vivo, possibilitou a confirmação da ocorrência de tais organismos nos manguezais, e gerou as primeiras informações sobre sua funcionalidade neste sistema, onde parece ocorrer de forma diferenciada aos demais ambientes onde já foram descritos. / Mangroves are considered an unique ecosystem due to its particular combination of environmental conditions, influenced by its location at the interface between land and ocean. The study of this ecosystem becomes urgent since mangroves are disappearing worldwide, and its diversity of microbial groups is still poorly understood. Within this theme, this project aims to describe the possible functionality of bacteria belonging to the phylum Planctomycetes in mangroves. Such organisms are still poorly studied, difficult to cultivate and mainly isolated from marine environments, water treatment and fish farming sites. Within this phylum are found microorganisms belonging to genera described as capable of performing the anaerobic oxidation of ammonium (anammox), a major transformation of nitrogen in environments with low oxygen availability. Here we aimed to describe the possible functionality of bacteria belonging to the phylum Planctomycetes in the mangroves. In order to achieve the target, it was initially performed a comparison of the Planctomycetes genomes with sequences obtained by metagenomics and metatranscriptomics, revealing the presence of sequences with similarity to those affiliated to unknown function and sulfatases. These are hydrolytic enzymes, which catalyze the cleavage of sulfate esters, releasing sulfur on its available form. The analysis of sequences from a metagenomic library (obtained from an oil-contaminated mangrove) allowed the visualization of genomic fragments related to Planctomycetes. It also revealed the presence of genes related with the production of sulfatases, besides the indication of specific genome arrangements, distinct from those describe in organisms allocated in this group, possibly indicating the occurrence of endemicity for Planctomycetes in mangroves. It was reinforced by the cultivation of isolates affiliated to this groups, whose have their affiliation confirmed by the partial sequencing of the 16S rDNA gene. Some isolates clustered composed new clusters within the Planctomycetes phylum, indicating the occurrence of new species. In sum, the characterization of this group by combining in sílico and in vivo analyses, allowed the confirmation of the occurrence of these organisms in mangroves, and generated the first insights about its functioning on this system, where it seems to occur in a differentiated form from those observed in other environments where it has been described.

Os manguezais são considerados um ecossistema único, devido sua particular combinação de condições ambientais, influenciados pela sua localização na interface entre o continente e oceano. O estudo deste ecossistema se torna urgente uma vez que os manguezais estão desaparecendo em todo mundo, e sua diversidade de grupos microbianos é ainda pouco conhecida. Dentro dessa temática, o presente projeto visa descrever a possível funcionalidade de bactérias pertencentes ao filo Planctomycetes nos manguezais. Tais organismos são ainda pouco estudados, de difícil cultivo, sendo obtidos principalmente em ambientes marinhos, tratamento de água e locais de criação de peixes. Dentro desse filo são encontrados microrganismos pertencentes a gêneros descritos como capazes de realizar a oxidação anaeróbica do íon amônio (anammox), uma importante transformação do nitrogênio em ambientes com baixa disponibilidade de oxigênio. E ainda, visamos descrever a possível funcionalidade de bactérias pertencentes ao filo Planctomycetes nos manguezais. Para isso, foi inicialmente realizada uma comparação dos genomas de Planctomycetes com as sequências obtidas por análises de metagenômica e metatranscriptômica, onde foram encontradas sequências similares às afiliadas a funções desconhecidas (putative protein) e a sulfatases. Tais enzimas são descritas como hidrolíticas, que catalizam a clivagem de ésteres de sulfato, liberando o enxofre na forma assimilável. A análise de sequências de uma biblioteca metagenômica (obtida de um manguezal contaminado com petróleo) permitiu a visualização de fragmentos genômicos de Planctomycetes. Esta análise revelou também a ocorrência de genes relacionados a produção de sulfatases, além de indicar arranjos gênicos distintos dos descritos nos genomas de organismos deste grupo, possivelmente indicando a ocorrência de endemismo de Planctomycetes em manguezais. Esta observação foi reforçada pelo cultivo de isolados afiliados a este grupo, os quais tiveram sua afiliação confirmada pelo sequenciamento parcial do gene ribossomal 16S DNAr. Alguns destes isolados formaram clusters diferenciados dentro do filo Planctomycetes, indicando que podem ser estes novas espécies. Sendo assim, a caracterização desse grupo de microrganismos numa combinação de análises in sílico e in vivo, possibilitou a confirmação da ocorrência de tais organismos nos manguezais, e gerou as primeiras informações sobre sua funcionalidade neste sistema, onde parece ocorrer de forma diferenciada aos demais ambientes onde já foram descritos. / Mangroves are considered an unique ecosystem due to its particular combination of environmental conditions, influenced by its location at the interface between land and ocean. The study of this ecosystem becomes urgent since mangroves are disappearing worldwide, and its diversity of microbial groups is still poorly understood. Within this theme, this project aims to describe the possible functionality of bacteria belonging to the phylum Planctomycetes in mangroves. Such organisms are still poorly studied, difficult to cultivate and mainly isolated from marine environments, water treatment and fish farming sites. Within this phylum are found microorganisms belonging to genera described as capable of performing the anaerobic oxidation of ammonium (anammox), a major transformation of nitrogen in environments with low oxygen availability. Here we aimed to describe the possible functionality of bacteria belonging to the phylum Planctomycetes in the mangroves. In order to achieve the target, it was initially performed a comparison of the Planctomycetes genomes with sequences obtained by metagenomics and metatranscriptomics, revealing the presence of sequences with similarity to those affiliated to unknown function and sulfatases. These are hydrolytic enzymes, which catalyze the cleavage of sulfate esters, releasing sulfur on its available form. The analysis of sequences from a metagenomic library (obtained from an oil-contaminated mangrove) allowed the visualization of genomic fragments related to Planctomycetes. It also revealed the presence of genes related with the production of sulfatases, besides the indication of specific genome arrangements, distinct from those describe in organisms allocated in this group, possibly indicating the occurrence of endemicity for Planctomycetes in mangroves. It was reinforced by the cultivation of isolates affiliated to this groups, whose have their affiliation confirmed by the partial sequencing of the 16S rDNA gene. Some isolates clustered composed new clusters within the Planctomycetes phylum, indicating the occurrence of new species. In sum, the characterization of this group by combining in sílico and in vivo analyses, allowed the confirmation of the occurrence of these organisms in mangroves, and generated the first insights about its functioning on this system, where it seems to occur in a differentiated form from those observed in other environments where it has been described.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1970. / Vita. Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references.

No description available.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2006. / Härtill 5 uppsatser.

Lau Kin Chong. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 149-158). / Abstracts in English and Chinese. / Abstract --- p.i / 摘要 --- p.iii / Acknowledgements --- p.v / Table of Contents --- p.vi / List of Tables --- p.xii / List of Figures --- p.xiii / List of Appendices --- p.xv / Abbreviations --- p.xvi / Chapter 1 --- Introduction / Chapter 1.1 --- Mucopolysaccharidosis type II as a lysosomal storage disease --- p.1 / Chapter 1.1.1 --- Prevalence of MPS II --- p.2 / Chapter 1.1.2 --- Pathophysiology of MPS II --- p.4 / Chapter 1.1.3 --- Clinical features of MPS II --- p.4 / Chapter 1.1.4 --- Clinical management of MPS II --- p.6 / Chapter 1.1.4.1 --- Diagnostic methods for MPS II --- p.6 / Chapter 1.1.4.2 --- Treatments for MPS II --- p.7 / Chapter 1.2 --- Iduronate-2-sulfatase protein (IDS) --- p.9 / Chapter 1.2.1 --- Role in GAG degradation --- p.9 / Chapter 1.2.2 --- Post-translational modifications --- p.11 / Chapter 1.2.2.1 --- Formylglycine formation --- p.11 / Chapter 1.2.2.2 --- Glycosylation --- p.12 / Chapter 1.2.2.3 --- Proteolysis --- p.12 / Chapter 1.2.3 --- Iduronate-2-sulfatase gene (IDS) --- p.14 / Chapter 1.2.3.1 --- Properties of IDS mutations --- p.15 / Chapter 1.2.3.2 --- Methylation patterns are correlated with transitional mutations --- p.17 / Chapter 1.2.3.3 --- Genotype-phenotype correlations between IDS gene and MPS II --- p.19 / Chapter 1.3 --- In this study --- p.21 / Chapter 1.3.1 --- Mutational analysis --- p.21 / Chapter 1.3.2 --- In vitro expression of mutant IDS --- p.22 / Chapter 1.3.3 --- Maturation of IDS polypeptides --- p.23 / Chapter 2 --- Materials & Methods / Chapter 2.1 --- Mutation screening for MPS II patients --- p.24 / Chapter 2.1.1 --- Patients --- p.24 / Chapter 2.1.2 --- Genomic DNA extraction --- p.24 / Chapter 2.1.2.1 --- Materials --- p.24 / Chapter 2.1.2.2 --- Methods --- p.25 / Chapter 2.1.3 --- IDS exons amplification by Polymerase Chain Reaction (PCR) --- p.26 / Chapter 2.1.3.1 --- Materials --- p.26 / Chapter 2.1.3.1.1 --- PCR --- p.26 / Chapter 2.1.3.1.2 --- Agarose gel electrophoresis --- p.27 / Chapter 2.1.3.1.3 --- PCR fragments purification --- p.29 / Chapter 2.1.3.2 --- Methods --- p.29 / Chapter 2.1.3.2.1 --- Amplifying IDS exons by PCR --- p.29 / Chapter 2.1.3.2.2 --- Purifying PCR fragments --- p.30 / Chapter 2.1.4 --- DNA sequencing for detecting IDS mutations --- p.30 / Chapter 2.1.4.1 --- Materials --- p.30 / Chapter 2.1.4.2 --- Methods --- p.30 / Chapter 2.1.4.2.1 --- Sequencing reaction --- p.30 / Chapter 2.1.4.2.2 --- Purifying sequencing products --- p.31 / Chapter 2.1.4.2.3 --- Analyzing sequencing results --- p.31 / Chapter 2.1.5 --- Fragment restriction endonuclease analysis --- p.31 / Chapter 2.1.5.1 --- Materials --- p.31 / Chapter 2.1.5.2 --- Methods --- p.32 / Chapter 2.2 --- Isolation of IDS cDNA from peripheral blood --- p.34 / Chapter 2.2.1 --- Materials --- p.34 / Chapter 2.2.1.1 --- Total RNA extraction --- p.34 / Chapter 2.2.1.2 --- Reverse-transcriptase PCR (RT-PCR) --- p.35 / Chapter 2.2.1.3 --- PCR for amplifying IDS cDNA --- p.35 / Chapter 2.2.2 --- Methods --- p.37 / Chapter 2.2.2.1 --- Extracting total RNA by QIAamp RNeasy Mini Kit --- p.37 / Chapter 2.2.2.2 --- Converting IDS mRNA into cDNA by RT-PCR --- p.38 / Chapter 2.2.2.3 --- Isolating IDS cDNA by PCR --- p.39 / Chapter 2.2.2.4 --- Isolating firefly luciferase gene by PCR --- p.39 / Chapter 2.3 --- Introducing IDS cDNA into Gateway Cloning System --- p.40 / Chapter 2.3.1 --- Materials --- p.40 / Chapter 2.3.1.1 --- Directional cloning --- p.40 / Chapter 2.3.1.2 --- LB medium/ agar with antibiotics preparation --- p.42 / Chapter 2.3.1.3 --- Plasmids purification from transformed cells --- p.42 / Chapter 2.3.1.4 --- Validation of IDS inserted plasmids --- p.43 / Chapter 2.3.2 --- Methods --- p.43 / Chapter 2.3.2.1 --- TOPO cloning reaction --- p.43 / Chapter 2.3.2.2 --- Transformation --- p.44 / Chapter 2.3.2.3 --- Small-scale plasmids preparation by QIAprep Miniprep Kit --- p.44 / Chapter 2.3.2.4 --- Sequencing the plasmids --- p.45 / Chapter 2.3.2.5 --- QuikChange II XL site-directed mutagenesis --- p.46 / Chapter 2.3.2.5.1 --- Synthesizing mutant strand with desired mutations --- p.46 / Chapter 2.3.2.5.2 --- Digesting parental strand --- p.46 / Chapter 2.3.2.5.3 --- Transformation --- p.47 / Chapter 2.3.2.6 --- Swapping IDS gene from entry clone to expression vectors --- p.47 / Chapter 2.3.2.6.1 --- LR clonase reaction --- p.47 / Chapter 2.3.2.6.2 --- Transformation --- p.48 / Chapter 2.4 --- Introducing IDS cDNA into RTS pIVEX Wheat Germ vector --- p.49 / Chapter 2.4.1 --- Materials --- p.49 / Chapter 2.4.1.1 --- Restriction digestion --- p.49 / Chapter 2.4.1.2 --- Purification of digested products --- p.50 / Chapter 2.4.1.3 --- Ligation of the IDS insert into pIVE´Xؤ1.3_WG --- p.50 / Chapter 2.4.2 --- Methods --- p.50 / Chapter 2.4.2.1 --- Restriction digestion to create sticky ends --- p.50 / Chapter 2.4.2.2 --- Purifying the digested products --- p.51 / Chapter 2.4.2.3 --- Ligating the IDS insert into pIVE´Xؤ1.3_WG --- p.51 / Chapter 2.4.2.4 --- Transformation --- p.51 / Chapter 2.5 --- Transient expression study of IDS constructs --- p.53 / Chapter 2.5.1 --- Materials --- p.53 / Chapter 2.5.2 --- Methods --- p.55 / Chapter 2.5.2.1 --- Cell culturing --- p.55 / Chapter 2.5.2.2 --- Transfecting IDS constructs by lipofection procedures --- p.55 / Chapter 2.5.2.3 --- Harvesting COS-7 cells --- p.56 / Chapter 2.5.2.4 --- Total RNA extraction from transfected COS-7 cells --- p.57 / Chapter 2.5.2.5 --- RT-PCR showing IDS mRNA stability --- p.58 / Chapter 2.5.2.6 --- Endocytosis of expressed IDS products into COS-7 cells --- p.58 / Chapter 2.6 --- Synthesizing IDS by cell-free in vitro expression systems --- p.59 / Chapter 2.6.1 --- Materials --- p.59 / Chapter 2.6.1.1 --- DNA templates for expression --- p.59 / Chapter 2.6.1.2 --- Commercial cell-free expression kits --- p.60 / Chapter 2.6.1.3 --- Supplements --- p.61 / Chapter 2.6.2 --- Methods --- p.64 / Chapter 2.6.2.1 --- Cell-free expression by ExpressWay plus expression system --- p.64 / Chapter 2.6.2.2 --- Cell-free expression by RTS 100 E.coli HY Kit --- p.64 / Chapter 2.6.2.3 --- Cell-free expression by RTS 100 Wheat Germ CECF Kit --- p.64 / Chapter 2.6.2.4 --- Cell-free expression by TnT Coupled Wheat Germ Extract Systems --- p.65 / Chapter 2.6.2.5 --- Cell-free expression by TNT Coupled Reticulocyte Lysate Systems --- p.66 / Chapter 2.7 --- Investigations of IDS protein expression --- p.67 / Chapter 2.7.1 --- Materials --- p.67 / Chapter 2.7.1.1 --- Isolation of Histidine-tagged proteins --- p.67 / Chapter 2.7.1.2 --- Sodium dodecyl sulfate polyacrylamide gel electrophoresis/ SDS-PAGE --- p.67 / Chapter 2.7.1.3 --- Fluorometric activity assay for IDS --- p.69 / Chapter 2.7.1.4 --- Luciferase activity assay --- p.72 / Chapter 2.7.2 --- Methods --- p.72 / Chapter 2.7.2.1 --- Isolating His-tagged IDS from cell-free expression products --- p.72 / Chapter 2.7.2.2 --- Protein staining of expression products --- p.73 / Chapter 2.7.2.2.1 --- Preparation of protein separating gel --- p.73 / Chapter 2.7.2.2.2 --- Preparation of proteins for SDS-PAGE --- p.73 / Chapter 2.7.2.2.3 --- SDS-PAGE analysis --- p.73 / Chapter 2.7.2.3 --- Fluorometric enzyme assay for IDS proteins --- p.74 / Chapter 2.7.2.4 --- Luciferase activity assay --- p.75 / Chapter 3 --- Results / Chapter 3.1 --- Mutational analysis of MPS II and carrier detection --- p.76 / Chapter 3.2 --- Investigating IDS mutants by transient expression --- p.86 / Chapter 3.2.1 --- Fluorometric enzyme assay for measuring IDS activity --- p.86 / Chapter 3.2.2 --- Source of IDS gene for transient expression in COS-7 cells --- p.89 / Chapter 3.2.3 --- In vitro expression of IDS and its mutants in COS-7 cells --- p.92 / Chapter 3.2.3.1 --- Analysis of transient expression in terms of IDS activity --- p.92 / Chapter 3.2.3.2 --- Analysis of IDS mRNA stability in COS-7 cells --- p.95 / Chapter 3.2.3.3 --- Analysis of IDS protein stability in COS-7 cells --- p.95 / Chapter 3.3 --- Cell-free in vitro expression for investigating the IDS mutants --- p.98 / Chapter 3.3.1 --- The five cell-free systems involved --- p.98 / Chapter 3.3.2 --- Source of IDS gene for cell-free in vitro expression --- p.98 / Chapter 3.3.3 --- SDS-PAGE analysis of IDS protein stability in cell-free systems --- p.100 / Chapter 3.3.3.1 --- Wheat germ-based cell-free expression system (Roche) --- p.100 / Chapter 3.3.3.2 --- E.coli-based cell-free expression system (Invitrogen) --- p.102 / Chapter 3.3.3.3 --- E.coli-based cell-free expression system (Roche) --- p.102 / Chapter 3.3.4 --- In Vision His-tag In-gel stain for wild-type IDS and its mutant --- p.103 / Chapter 3.3.5 --- Analysis of IDS activity in cell-free expression systems --- p.107 / Chapter 3.3.6 --- Analysis of the cellular uptake of IDS --- p.110 / Chapter 4 --- Discussions / Chapter 4.1 --- Mutational analysis --- p.113 / Chapter 4.1.1 --- Heterogeneity of IDS mutations --- p.113 / Chapter 4.1.2 --- Role of molecular diagnosis for MPS II --- p.113 / Chapter 4.1.3 --- Two novel mutations and one reported mutation were identified --- p.115 / Chapter 4.1.3.1 --- A novel nonsense mutation: Ser369term --- p.115 / Chapter 4.1.3.2 --- A reported nonsense mutation: Gln389term --- p.115 / Chapter 4.1.3.3 --- A novel missense mutation: Leu339Pro --- p.116 / Chapter 4.2 --- Expression studies of the IDS mutants --- p.117 / Chapter 4.2.1 --- Analysis of transient expression in COS-7 cells --- p.117 / Chapter 4.2.1.1 --- Stability of mutant mRNA --- p.119 / Chapter 4.2.1.2 --- IDS catalytic activity --- p.119 / Chapter 4.2.2 --- Analysis of mutant stability by cell-free expression systems --- p.120 / Chapter 4.2.3 --- Structural analysis of amino acids alterations --- p.121 / Chapter 4.2.3.1 --- p.L339P causes conformational change --- p.122 / Chapter 4.2.3.2 --- p.L339R changes overall charge balance --- p.122 / Chapter 4.2.3.3 --- Mutations at Leu339 residue affect substrate binding --- p.123 / Chapter 4.3 --- Analysis of IDS maturation processing --- p.124 / Chapter 4.3.1 --- Active IDS modifications are not completed in lysosomes --- p.124 / Chapter 4.3.2 --- C-terminal proteolysis is essential for active IDS --- p.125 / Chapter 4.3.3 --- Functional role of glycosylation during IDS processing --- p.126 / Chapter 4.4 --- Analysis of cell-free expression systems --- p.128 / Chapter 4.4.1 --- Microbial systems using E.coli cell extracts: insoluble IDS precursors --- p.128 / Chapter 4.4.2 --- Plant system using wheat germ extracts: soluble IDS precursors --- p.129 / Chapter 4.4.3 --- Mammalian system using rabbit reticulocytes extracts: undetectable --- p.129 / Chapter 4.5 --- Role of transfecting IDS constructs --- p.131 / Chapter 4.6 --- Conclusion --- p.132 / Appendices --- p.133 / Electronic-database and computing system --- p.149 / Bibliography --- p.149

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