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Thesis (Ph.D.)--Michigan State University. Genetics, 2008. / Title from PDF t.p. (viewed on July 13, 2009) Includes bibliographical references (p. 90-103). Also issued in print.

No description available.

Escherichia coli (E.coli) 0157:H7, a pathogen belonging to the enterohemorrhagic group of E.coli, has long been a concern to human health. The pathogen causes a myriad of symptoms in humans, ranging from diarrhea and malaise to renal failure. Human infection with the spread of the pathogen is mainly attributed to consumption of contaminated food material such as meat. Decontamination of meat via sprays have to date been the most commonly practiced method to reduce contamination, which now has little relevance in the face of developing resistance by the pathogen. In the following study we investigated FlhC mediated gene regulation in E. coli 0157:H7 on the surface of meat, in an attempt to recognize FlhC regulated targets, which may ultimately serve as targets for the development of novel decontaminating sprays. Microarray experiments were conducted to compare gene expression levels between a parental E. coli 0157:H7 strain and its isogenic flhC mutant, both grown on meat. Putative FlhC targets were then grouped based on their function. Realtime PCR experiment was done to confirm the regulation. Additionally, experiments were done to investigate the phenotypic effects of the regulation. To test the effect of FlhC on biofilm formation, an ATP based assay was first developed in E.coli K-12, which has been detailed in the following dissertation. This assay was used to quantify biofilm biomass in E. coli 0157. Microarray experiments revealed 287 genes as being down regulated by FlhC. These genes belonged to functions relating to cell division, metabolism, biofilm formation and pathogenicity. Real-time PCR confirmed the regulation of 87% of the tested genes. An additional 13 genes were tested with real-time PCR. These belonged to the same functional groups, but were either not spotted on the microarray chips or had missing data points and were hence not included in the analysis. All 13 of these genes appeared to be regulated by FlhC. The phenotypic experiments performed elucidated that the FlhC mutants divided to 20 times higher cell densities, formed five times more biofilm biomass and were twice as pathogenic in a chicken embryo lethality assay, when compared to the parental strain. The following dissertation also reports the development of a combination assay for the quantification of biofilm that takes advantage of the previously mentioned ATP assay and the PhenotypeMicroarray TM (PM) system. The assay was developed using the parental E. coli strain AJW678 and later applied to its isogenic flhD mutant to elaborate on the differences in nutritional requirements between the two strains during biofilm formation. Metabolic modeling and statistical testing was also applied to the data obtained. This assay will be used in the future to study biofilm formation by the parental strain E. coli 0157:H7 strain and its isogenic FlhC mutants on single carbon sources, hence identifying potential metabolites which differentially support biofilm formation in the parental and the mutant strain.

Thesis (MSc)--University of Stellenbosch, 2000. / ENGLISH ABSTRACT: Esterases play a variety of roles in nearly every aspect of life ranging from cellular metabolism, signal transduction to defence mechanisms in plants. One aspect of esterases that recently is receiving more attention is the role esterases play in the .degradation of plant material. With fossil fuels (coal and oil) estimated to run out in the next 20 to 30 years, renewable sources such as plant biomass are becoming increasingly important. Plant biomass contains hemicellulosic and cellulosic materials that need to be degraded to their different constituents before they can be optimally used for the production of commodities. Although the enzymes needed to hydrolyse the xylan backbone (xylanases and P-xylosidases) are important, enzymes that remove side chains from the polymer are equally important. They facilitate hydrolysis by xylanases and P-xylosidases and will improve the availability of monomeric sugars for utilisation when used in conjunction with other xylanolytic enzymes. Many of these side-chains are esters and they need to be removed through the action of esterases, either directly from the xylan backbone or from shorter xylo-oligomers. An existing genomic DNA library of Bacil/us pumilus in Escherichia coli was screened for the presence of an acetyl esterase encoding gene. Positive clones were identified by the formation of clearing zones on plates containing glucose pentaacetate. Plasmid DNA was isolated from a positive E. coli clone. The DNA insert was sequenced and found to contain two open reading frames, one of which encoded a novel esterase (estA). Using different primers the gene was amplified by polymerase chain reaction and inserted into an inducible expression vector (pKK223- 3) for expression in E. coli. The plasmid was introduced into E coli and the esterase activity determined, using the chromogenic substrate a-naphthyl acetate. Activity levels decreased shortly after induction with IPTG and therefore plasmid pAP4 was used for enzymatic assays. Cultures containing plasmid pAP4 produced extracellular activity of 2.5 nkatal/ml. The pH and temperature optima as well as temperature stability of the enzyme was determined. The enzyme exhibited optimal activity at pH 6 and 60°C and was stable at 60°C after 2 h. Enzyme assays on different substrates yielded activity on methylumbelliferyl butyrate and methylumbelliferyl acetate in addition to the glucose pentaacetate and a-naphthyl acetate. The estA gene was cloned into a yeast expression vector between the PGK promoter and terminator sequences for expression of the gene in Saccharomyces cerevisiae. The estA open reading frame was also fused to the MFa 1 secretion signal for secretion of the protein from S. cerevisiae. The expression vector was successfully transformed into S. cerevisiae, but no extracellular activity was detected. Only low intracellular activity of 0.260 nkatal/ml was detected in S. cerevisiae. / AFRIKAANSE OPSOMMING: Esterases speel 'n verskeidenheid van rolle in feitlik elke aspek van lewe, van sel metabolisme, sein transduksie tot verdedigingsmeganismes in plante. Een aspek van esterases wat al hoe meer aandag geniet, is die rol wat esterases in die afbraak van plant en plantmateriaal speel. Met olie- en steenkoolbronne wat na beraming oor 20 tot 30 jaar tot niet sal gaan, raak die rol wat hernubare bronne speel al hoe belangriker. Plantbiomassa bevat sellulose en hemisellulose wat tot die verskillende komponente afgebreek moet word voordat dit optimaal vir die vervaardiging van produkte aangewend kan word. Alhoewel die ensieme wat vir die hidrolise van die xilaanruggraat benodig word, (xilanases en ~-xulosidases) belangrik is, is die ensieme wat die sygroepe vanaf die polimeer verwyder ewe belangrik aangesien hulle die hidrolise deur xilanases en ~-xulosidases bevorder. Wanneer hulle saam met die ander xilanolitiese ensieme gebruik word, sal hulle die beskikbaarheid van monomeriese suikers vir fermentasie verhoog. Baie van hierdie sygroepe is esters en hulle word deur die aksie van esterases verwyder, of direk van die ruggraat, ofvanafkorter xilo-oligosakkariede. 'n Bestaande genoom DNA biblioteek van Bacillus pumilus in Escherichia coli is vir die teenwoordigheid van 'n asetielesterase-koderende geen gesif. Positiewe klone is deur die vorming van 'n sone op plate wat glukose pentaasetaat bevat, geïdentifiseer. Die DNA-invoeging van die positiewe E. coli-kloon se DNA-volgorde is bepaal en twee oopleesrame is gevind waarvan een vir 'n unieke esterase (estA) kodeer. Met behulp van verskillende inleiers is die geen met die polimerasekettingreaksie (PKR) geamplifiseer en in 'n induseerbare promotor vir uitdrukking in E. coli gekloneer. Die plasmied is getransformeer in E. coli en aktiwiteit is bepaal deur cc-naftielasetaatte gebruik. Vlakke van aktiwiteit het kort na induksie met IPTG weer gedaal en daarom was plasmied pAP4 vir ensiematiese toetse gebruik. E. coli-transformante met plasmied pAP4 het ekstrasellulêre aktiwiteit van 2.5 nkatal/ml gelewer. Die pH en temperatuur optima sowel as die temperatuurstabiliteit van die ensiem was bepaal. Die ensiem toon optimale aktiwiteit by pH 6 en 'n temperatuur van 60°C. Aktiwiteitstoetse op verskillende substrate het aktiwiteit op metielumbelliferielasetaat en metielumbelliferielbutiraat bo-en-behalwe die glukosepentaasetaat en c-naftielasetaar getoon. Die estA geen is in uitdrukkingskasette bevattende die PGKpromotor en-termineerder vir uitdrukking in Saccharomyces cerevisiae gekloneer. Dit is ook agter die MFal-sekresiesein gekoppel vir sekresie vanuit S. cerevisiae. Geen ekstrasellulêre aktiwiteit is gevind nie. Slegs intrasellulêre aktiwiteit van 0.26 nanokatal per mililiter was bepaal.

A dissertation submitted to the Faculty of Science, University of' the Witwatersrand, in partial fulfilment of the requirements of the Degree of Master of Science in the field ·of Biotechnology. February 1991. / Nocardioform bacteria were studied for their ability to interconvert bile acids. From the studies of utilisation and resistance curves, the most suitable donor and recipient strains for complementary gene cloning, were Arthrobacter oxydans strain C1 and Rhodococcus erythropolis strain ATCC 4217-1 respectively. [Abbreviated Abstract. Open document to view full version] / MT2016

by Pong Tsang Wai Hai. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1993. / Includes bibliographical references (leaves 98-105). / Acknowledgements --- p.i / Abstract --- p.ii / Abbreviations --- p.v / Chapter Chapter 1 --- Introduction / Chapter 1.1 --- Biological functions and structure of GH --- p.1 / Chapter 1.2 --- Application of recombinant GH --- p.2 / Chapter 1.3 --- Expression of eukaryotic gene in E.coli --- p.4 / Chapter 1.4 --- Methods for increasing expression of a cloned gene --- p.6 / Chapter 1.4.1 --- Changing the 5' end codons of the cDNA to E.coli preferred codons --- p.6 / Chapter 1.4.2 --- Optimization of distance between SD sequence and the initiation codons --- p.6 / Chapter 1.4.3 --- "Construction of a short ""dummy"" cistron at the 5' end of the cloned gene to improve attachment of ribosome" --- p.7 / Chapter 1.4.4 --- Increasing the copy number of recombinant expression plasmid --- p.8 / Chapter 1.4.5 --- Optimizing high density cell expression --- p.9 / Chapter 1.5 --- Quantitating the expression of cloned gene --- p.10 / Chapter 1.6 --- Inclusion bodies formation --- p.11 / Chapter 1.7 --- The purification of eukaryotic polypeptides synthesized as inclusion bodies --- p.12 / Chapter 1.7.1 --- Solubilization of the inclusion bodies --- p.13 / Chapter 1.7.2 --- Refolding the polypetides and disulfide bond formation --- p.13 / Chapter 1.8 --- Expression of secreted recombinant protein --- p.14 / Chapter 1.9 --- Purpose of present study --- p.15 / Chapter Chapter 2 --- Materials and Methods / Chapter 2.1 --- General techniques --- p.16 / Chapter 2.1.1 --- Chemical Synthesis of DNA linkers and primers --- p.16 / Chapter 2.1.2 --- Manipulation of DNA --- p.16 / Chapter 2.1.3 --- Electro-elution of DNA from Agarose Gel --- p.17 / Chapter 2.1.4 --- Preparation of Competent Cells and Transformation --- p.18 / Chapter 2.1.5 --- Screening of the Expressed Clones --- p.19 / Chapter 2.1.6 --- Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) --- p.21 / Chapter 2.1.7 --- Western blot analysis --- p.21 / Chapter 2.2 --- Purification procedures --- p.23 / Chapter 2.2.1 --- Growing up the cells in large scale --- p.23 / Chapter 2.2.2 --- Harvesting of cells from large scale culture --- p.23 / Chapter 2.2.3 --- Sonication of the cells --- p.24 / Chapter 2.2.4 --- Washing of the inclusion body --- p.24 / Chapter 2.2.5 --- Solubilization of the inclusion bodies --- p.25 / Chapter 2.2.6 --- Renaturation of r-gcGH --- p.26 / Chapter 2.2.6.1 --- Step down dilution mehtod --- p.26 / Chapter 2.2.6.2 --- Rapid dilution method --- p.26 / Chapter 2.2.7 --- Separation by reverse phase chromatography --- p.27 / Chapter 2.2.7.1 --- Octadodecylsilica (ODS) column separation --- p.27 / Chapter 2.2.7.2 --- Fast performance Liquid Chromatography(FPLC) --- p.28 / Chapter 2.3 --- Characterization methods --- p.29 / Chapter 2.3.1 --- Radioimmunoassay --- p.29 / Chapter 2.3.1.1 --- Iodination of r-gcGH --- p.29 / Chapter 2.3.1.2 --- Binding assay --- p.31 / Chapter 2.3.2 --- Preparation of anti-r-gcGH serum --- p.32 / Chapter 2.3.3 --- Determination of amino acid composition and N-terminal sequence of r-gcGH --- p.32 / Chapter Chapter 3 --- Results / Chapter 3.1 --- Recombinant plasmids construction --- p.34 / Chapter 3.1.1 --- Basic construction of plasmid producing gcGH in E.coli --- p.34 / Chapter 3.1.2 --- N-terminal modification of gcGH cDNA --- p.38 / Chapter 3.1.3 --- Constuction of a short 'dummy' cistron at the 5'end of gcGH cDNA --- p.40 / Chapter 3.1.4 --- Optimization of distance between ribosomal binding site and initiation codon --- p.42 / Chapter 3.1.5 --- Increasing expression level by increasing plasmid copy number --- p.44 / Chapter 3.1.6 --- Optimizing the high density expression by changing the promoter --- p.48 / Chapter 3.1.7 --- Construction of excretion plasmid for gcGH production from E. coli --- p.48 / Chapter 3.2 --- Quantitation and qualitation of the expressed protein --- p.51 / Chapter 3.3 --- Effect of IPTG on induction of r-gcGH in pp5 --- p.57 / Chapter 3.4 --- Stability of overproducing strain pp5 during continuous culture --- p.59 / Chapter 3.5 --- Stability of overproducing strain ppADH4 during continuous culture --- p.61 / Chapter 3.6 --- "Optimization of culture condition for high level expression strains,pp5 and ppADH4" --- p.64 / Chapter 3.7 --- Purification of r-gcGH --- p.67 / Chapter 3.7.1 --- Distribution of r-gcGH as Soluble and insoluble protein in E. coli --- p.67 / Chapter 3.7.2 --- Isolation and cleaning of the inclusion bodies --- p.69 / Chapter 3.7.3 --- Solubilization and renaturation of r-gcGH --- p.71 / Chapter 3.7.4 --- Purification of r-gcGH by chromatography --- p.73 / Chapter 3.8 --- Characterization of r-gcGH --- p.78 / Chapter 3.8.1 --- Amino acid composition and N-terminal sequence determination --- p.78 / Chapter 3.8.2 --- Immunological property of r-gcGH --- p.81 / Chapter 3.8.3 --- Physical Property of r-gcGH --- p.84 / Chapter 3.8.4 --- Stability of r-gcGH --- p.84 / Chapter 3.9 --- Expression and purification of r-gcGH in excretion vector ppSP14 --- p.86 / Chapter Chapter 4 --- Discussion / Chapter 4.1 --- Evaluation of expression strains --- p.88 / Chapter 4.1.1 --- Strain pKgcGH2 --- p.88 / Chapter 4.1.2 --- Strain pKgcGH2-17 --- p.88 / Chapter 4.1.3 --- Strain pSD78 --- p.89 / Chapter 4.1.4 --- "Strains pLl,pL2 and pL4" --- p.90 / Chapter 4.1.5 --- "Strains pp5,pplA,pp2I and pp4Q" --- p.90 / Chapter 4.1.6 --- Strain ppADH4 --- p.91 / Chapter 4.1.7 --- Strain ppSP14 --- p.91 / Chapter 4.2 --- Disulfide bond formation during refolding process --- p.92 / Chapter 4.2.1 --- Renaturaion in the presence of L-arginine and thiol reagent in oxidized form --- p.93 / Chapter 4.2.2 --- Renaturation in the presence of thiol reagent and 3M guanidine hydrochloride --- p.94 / Chapter 4.3 --- Stability of the r-gcGH --- p.94 / Chapter 4.4 --- Further studies --- p.96 / References --- p.98

Graduation date: 1995

Graduation date: 1994

Graduation date: 1993