At-line analysis of high cell density Escherichia coli fermentation using near-infrared spectroscopy (NIRS).

Liu, Haijing.Thesis (M.Phil.)--Chinese University of Hong Kong, 2010.Includes bibliographical references (leaves 112-116).Abstracts in English and Chinese.Acknowledgements --- p.iAbstract --- p.iii摘要 --- p.vTable of contents --- p.viList of figures --- p.xiiList of tables --- p.xvList of abbreviations --- p.xviChapterChapter 1 --- IntroductionChapter 1.1 --- Fermentation --- p.1Chapter 1.1.1 --- Biopharmaceutical production --- p.1Chapter 1.1.2 --- History of fermentation --- p.1Chapter 1.1.3 --- Fermentation Technology --- p.2Chapter 1.1.3.1 --- Fermentation process --- p.2Chapter 1.1.3.2 --- Fermenter --- p.4Chapter "1,1.3.3" --- Mode of fermentation process --- p.5Chapter 1.1.3.4 --- Bacterial growth --- p.6Chapter 1.1.4 --- High cell density fermentation for plasmid DNA production --- p.7Chapter 1.1.4.1 --- Porcine growth hormone releasing factor (pGRF) --- p.8Chapter 1.1.4.2 --- H5N1 avian influenza viruses DNA vaccine --- p.9Chapter 1.1.4.3 --- Fed-batch high-cell-density fermentation --- p.9Chapter 1.1.5 --- Fermentation process monitoring --- p.11Chapter 1.2 --- Near-infrared spectroscopy (NIRS) --- p.12Chapter 1.2.1 --- Basic near-infrared spectroscopy --- p.13Chapter 1.2.1.1 --- Rationale of near-infrared spectroscopy --- p.13Chapter 1.2.1.2 --- NIR spectra acquisition --- p.16Chapter 1.2.1.3 --- Interpretation of NIR spectra --- p.18Chapter 1.2.2 --- Multivariate calibration --- p.20Chapter 1.2.2.1 --- Why multivariate calibration --- p.22Chapter 1.2.2.2 --- The problem of collinearity --- p.25Chapter 1.2.2.3 --- Spectral range selection --- p.26Chapter 1.2.2.4 --- Signal optimization --- p.26Chapter 1.2.2.5 --- Spectral pretreatment --- p.27Chapter 1.2.2.6 --- Parameter selection --- p.28Chapter 1.2.3 --- Applications of NIRS in high cell density E. coli fermentation --- p.31Chapter 1.2.4 --- Adaptive calibration strategy --- p.33Chapter 1.3 --- Aims of study --- p.34Chapter 2 --- Materials and methodsChapter 2.1 --- High cell density fermentation of plasmid DNA --- p.35Chapter 2.1.1 --- Fermentation system --- p.35Chapter 2.1.2 --- pGRF fermentation --- p.38Chapter 2.1.2.1 --- Prepare seed flask --- p.38Chapter 2.1.2.2 --- Reagents for bacterial culture by fermenter --- p.38Chapter 2.1.2.2.1 --- LB based complex fermentation medium --- p.38Chapter 2.1.2.2.2 --- Batch fermentation medium --- p.39Chapter 2.1.2.2.3 --- Feeding medium-1 --- p.41Chapter 2.1.2.2.4 --- Base feed --- p.41Chapter 2.1.2.3 --- Fermentation methods --- p.42Chapter 2.1.2.3.1 --- Fermenter set-up --- p.42Chapter 2.1.2.3.2 --- Inoculate seed culture into the fermenter --- p.43Chapter 2.1.2.3.3 --- Transfer the feeding medium --- p.44Chapter 2.1.2.3.4 --- Heat induction --- p.44Chapter 2.1.2.3.5 --- Fermentation harvest --- p.44Chapter 2.1.2.4 --- Scale-up fermentation and large scale production 45Chapter 2.1.3 --- H5N1 fermentation --- p.45Chapter 2.1.4 --- Reference analytical testing --- p.45Chapter 2.1.4.1 --- Optical density --- p.45Chapter 2.1.4.2 --- Cell dry weight --- p.45Chapter 2.1.4.3 --- Specific plasmid DNA yield --- p.46Chapter 2.1.4.3.1 --- Plasmid DNA isolation --- p.46Chapter 2.1.4.3.2 --- Plasmid DNA measurement --- p.46Chapter 2.1.4.3.3 --- Plasmid DNA identification --- p.46Chapter 2.1.4.4 --- Analysis of glycerol and acetate --- p.46Chapter 2.1.4.4.1 --- Standard samples --- p.46Chapter 2.1.4.4.2 --- Enzymatic test kits --- p.47Chapter 2.1.4.4.3 --- Automatic biochemistry analyzer --- p.47Chapter 2.1.5 --- Summary of all fermentation batches --- p.48Chapter 2.2 --- Full factorial design and semi-synthetic samples --- p.49Chapter 2.2.1 --- Adaptive calibration samples --- p.49Chapter 2.2.1.1 --- Matrix 1 calibration samples --- p.49Chapter 2.2.1.2 --- Matrix 2 calibration samples --- p.50Chapter 2.2.1.3 --- Matrix 3 calibration samples --- p.50Chapter 2.2.2 --- Summary of all samples --- p.51Chapter 2.3 --- NIR sample presentation and spectral acquisition --- p.52Chapter 2.3.1 --- NIR spectrophotometers --- p.52Chapter 2.3.2 --- Cuvettes for transmittance spectral acquisition --- p.53Chapter 2.3.3 --- Bottles for reflectance spectral acquisition --- p.54Chapter 2.3.4 --- Spectral acquisition --- p.55Chapter 2.3.4.1 --- Transmittance --- p.55Chapter 2.3.4.2 --- Reflectance --- p.55Chapter 2.4 --- Multivariate calibration and validation --- p.56Chapter 2.4.1 --- Spectral preprocessing --- p.56Chapter 2.4.2 --- Multivariate calibration --- p.57Chapter 2.4.3 --- Model validation --- p.57Chapter 3 --- Results and discussionChapter 3.1 --- Sample presentation and NIR spectrum --- p.59Chapter 3.1.1 --- Transmission measurement --- p.60Chapter 3.1.2 --- Reflectance measurement --- p.63Chapter 3.1.3 --- Spectral responses and pre-treatment method --- p.64Chapter 3.1.4 --- Design of experiments for calibration sample preparation --- p.67Chapter 3.1.5 --- Summary --- p.68Chapter 3.2 --- Adaptive calibration --- p.69Chapter 3.2.1 --- Selection of Multivariate calibration model --- p.70Chapter 3.2.1.1 --- Matrix 1 calibration models --- p.70Chapter 3.2.1.2 --- Matrix 2 calibration models --- p.74Chapter 3.2.1.3 --- Matrix 3 calibration models --- p.76Chapter 3.2.1.4 --- Summary --- p.78Chapter 3.2.2 --- Model validation --- p.79Chapter 3.2.2.1 --- Performance of Reference analytical methods --- p.79Chapter 3.2.2.1.1 --- Enzymatic test kits --- p.79Chapter 3.2.2.1.2 --- Automatic biochemistry anaylyzer (Bioprofile) --- p.81Chapter 3.2.2.1.3 --- Summary --- p.83Chapter 3.2.2.2 --- Model validation using external test samples --- p.83Chapter 3.2.2.2.1 --- Matrix 1 models --- p.83Chapter 3.2.2.2.2 --- Matrix 2 models --- p.87Chapter 3.2.2.2.3 --- Matrix 3 models --- p.89Chapter 3.2.2.2.4 --- Overall NIR measurement errors --- p.90Chapter 3.2.2.2.5 --- Summary --- p.91Chapter 3.3 --- Use of calibrated NIRS in at-line monitoring and control of fermentation --- p.93Chapter 3.3.1 --- Analysis of small-scale fermentation --- p.94Chapter 3.3.1.1 --- pGRF plasmid DNA production --- p.94Chapter 3.3.1.2 --- H5N1 plasmid DNA production --- p.95Chapter 3.3.1.3 --- Summary --- p.97Chapter 3.3.2 --- Analysis of large scale fermentation --- p.97Chapter 3.3.2.1 --- 30 L clinical production of H5N1 plasmid DNA --- p.97Chapter 3.3.2.2 --- 80 L scale-up production of H5N1 plasmid DNA --- p.99Chapter 3.3.2.3 --- Summary --- p.100Chapter 3.3.3 --- Effective control of fermentation production using at-line NIR analysis --- p.101Chapter 3.3.3.1 --- At-line monitoring of Batch 11 --- p.101Chapter 3.3.3.2 --- At-line monitoring of Batch 12 X --- p.102Chapter 3.3.3.3 --- Summary --- p.104Chapter 3.4 --- General discussion and conclusion --- p.105Chapter 3.5 --- Future prospects --- p.108References --- p.112Appendix 1 --- p.117Appendix 2 --- p.118Appendix 3 --- p.123Appendix 4 --- p.131Appendix 5 --- p.13