Thesis (PhD (Process Engineering))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: Biological agents offer several opportunities to address the many challenges faced in intensive reticulated aquaculture. We therefore isolated and selected Bacillus spp. as potential biological agents, because this group has demonstrated an array of biological activities of possible benefit to aquaculture. They also display advantages in terms of robustness during bioprocessing and end product application. Natural isolates obtained from Cyprinus carpio, selected as a model high-value ornamental fish species, and associated culture environments, were purified and assessed for in vitro efficacy based on the inhibition of growth of pathogenic Aeromonas hydrophila and the decrease in concentrations of ammonium, nitrite, nitrate and phosphate ions, typically found as waste products in aquaculture systems. Based on suitability for aquaculture application, isolates B001, B002 and B003 were selected and further evaluated in vitro and in an in vivo trial with C. carpio. Inhibition of Aer. hydrophila growth and a decrease in concentrations of waste ions were demonstrated in these studies. Based on 16S RNA sequence homology, the isolates were identified as Bacillus subtilis, B. cereus and B. licheniformis, respectively. High sequence homology between B. subtilis and B. anthracis necessitated further safety studies on the best isolate, B. cereus NRRL100132 (B002). The isolate was shown not to contain the anthrax virulence genes pOX1, pOX2 or the B. cereus enterotoxin. Elucidation of the potential modes of action of a biological agent facilitates an understanding of functionality and encourages technology uptake by end users. Competitive exclusion through growth rate and competitive uptake of glucose and iron, the latter facilitated by siderophore production, were shown to be key mechanisms at play in inhibition of Aer. hydrophila by the B. cereus isolate. As production cost is an important consideration in development of commercially relevant biological products, we examined the optimization of nutrient supplementation, which has an impact on high-density production of spores by fermentation. Corn steep liquor (CSL) was identified as a lower cost and more effective nutrient source in comparison to conventional nutrient substrates, in particular yeast extract and nutrient broth. The improved sporulation performance of B. cereus could be related to the increased availability of free amino acids, carbohydrates, and minerals in CSL, which had a positive effect on organism growth and sporulation efficiency. The impact of nutrient concentration on spore yield and productivity was modelled to develop a tool for selection of optimal conditions. Excellent correlation with actual laboratory fermentation data was demonstrated. A cost analysis revealed that production using liquid phytase treated and ultra-filtered CSL was less expensive than spray dried CSL and supported cultivation of B. cereus spores at densities higher than 1×1010 CFU ml 1. Adoption of biological agents in commercial applications is lacking, due to limitations in process and product development that address key end user product requirements such as cost, efficacy, shelf life and convenience. The development of suitable spore recovery, drying, formulation and tablet production process steps was thus performed. Key criteria used for downstream process unit evaluation included spore viability, recovery, spore balance closure, spore re-germination, product intermediate stability, end product stability and efficacy. A process flow sheet comprising vertical tube centrifugation, fluidised bed agglomeration and tablet pressing yielded an attractive product. The formulation included corn steep liquor and glucose to enhance subsequent spore re-germination. Viable spore recovery and spore balance closure across each of the process units was high (>70% and >99% respectively), with improvement in recovery possible by adoption of continuous processing at large scale. Spore re-germination was 97%, whilst a product half-life in excess of 5 years was estimated based on thermal resistance curves. The process resulted in a commercially attractive product and affordable variable cost of production. Functionality of the product, incorporating the B. cereus isolate, was investigated across a range of physiological conditions, including salinity, pH and temperature, based on rearing of C. carpio. Temperature had a significant influence on germination, specific growth rate and increase in cell number of B. cereus, whilst salinity and pH did not have any measurable effect on growth. Controlled studies in bioreactors and modelling of the data to the Arrhenius function indicated the existence of high and low growth temperature domains. The rates of pathogenic Aer. hydrophila suppression and decrease in waste ion concentrations (ammonium, nitrite, nitrate and phosphate) were translated into a linear predictive indicator of efficacy of the B. cereus isolate at different temperatures. This study has resulted in development of an upstream and downstream process for production of a new B. cereus isolate (NRRL 100132) which was shown to be safe, stable, functional, robust and cost effective for application in aquaculture. / AFRIKAANSE OPSOMMING: Biologiese middels bied verskeie maniere om die veelvoudige uitdagings van intensiewe netsgewyse akwakultuur aan te spreek. Gevolglik het ons uitgesoekte Bacillus spesies as potensiële biologiese middels geïsoleer, omdat hierdie groep verskeie biologiese aktiwiteite demonstreer wat van potensiële waarde kan wees in akwakultuur. Die groep toon ook voordele in terme van robuustheid gedurende bioprosessering en eind-toepassings. Natuurlike bakteriële isolate vanuit Cyprinus carpio geassosieerde kultuur omgewings, geselekteer as 'n hoë-waarde model ornamentele spesie, is gesuiwer. Die in vitro doeltreffendheid van die isolate is bepaal gebasseerd op die groei inhibisie van patogeniese Aeromons hydrophila asook die afname in konsentrasies van ammonium, nitriete, nitrate en fosfaat ione wat as tipiese afval produkte gevind word in akwakultuur sisteme. Isolate B001, B002 en B003 is geselekteer op grond van geskiktheid en verder evalueer in in vitro en in vivo proewe met C. carpio. Groei inhibisie van Aer. hydrophila asook 'n afname in konsentrasies van afval ione was tydens die studies gedemonstreer is. Die isolate is identifiseer as Bacillus subtilis, B. cereus en B. licheniformis, respektiewelik, op grond van 16S RNS volgorde homologie. Die hoë volgorde homologie tussen B. subtilis en B. anthracis het verdere veiligheidstudies op die beste isolaat, B. cereus NRRL100132 (B002) genoodsaak. Die isolaat het nie die antraks virulensie plasmied pOX1, pOX2 of die B. cereus enterotoksien getoon nie. Uitklaring van die potensiële meganismes van aksie van biologiese middels fasiliteer 'n begrip van funksionaliteit en moedig tegnologie aanvaarding deur eind-gebruikers aan. Mededingende uitsluiting deur groeitempo en mededingende opname van glukose asook die produksie van siderofore is bewys as sleutel meganismes betrokke in die inhibisie van Aer. hydrophila deur die B. cereus isolaat. Aangesien koste 'n belangrike oorweging is in die ontwikkeling van kommersiële toepaslike biologiese produkte, is die optimisering van voedingstof aanvullings wat 'n impak het op hoëdigtheid produksie van spore deur fermentasie ondersoek. Week-vloeistof van mielie prosessering (CSL) is identifiseer as 'n lae koste en effektiewe voedingsbron in vergelyking met konvensionele voeding substrate, veral gisekstrak en voedingsboeljon. Die verbeterde sporulering prestasie van B. cereus kon toegeskryf word aan die verhoogde beskikbaarheid van vrye aminosure, koolhidrate en minerale in CSL, wat 'n postitewe effek op organisme groei en sporulerings effektiwiteit getoon het. Die impak van voedingstof konsentrasie op spoor opbrengs en produktiwiteit is gemodelleer om 'n werktuig vir die selektering van optimale kondisies te ontwikkel. Uitstekende korrelasie met werklike laboratorium data is gedemonstreer. Koste analises het getoon dat produksie deur middel van vloeibare fitase-behandelde en ultra-filtreerde CSL goedkoper is as sproei-gedroogde CSL en ondersteun verder die kultivering van B. cereus spore teen digthede hoër as 1 x 1010 kolonie vormende eenhede.ml-1. Die opname van biologiese middels in kommersiële toepassings skiet tekort as gevolg van beperkinge in proses en produk ontwikkeling wat belangrike eind-gebruiker vereistes soos koste, doeltreffendheid, rak leeftyd en gerieflikheid aanspreek. Die ontwikkeling van toepaslike prosesse vir spoor herwinning, droging, formulering en tablet produksie is gevolglik uitgevoer. Belangrike maatstawwe wat gebruik is vir stroomaf proseseenheid-ontwikkeling het lewensvatbaarheid, herwinning, spoor balans sluiting, spoor her-ontkieming, intermediêre produk stabiliteit, eindproduk stabiliteit en doeltreffendheid ingesluit. 'n Proses vloeidiagram bestaande uit vertikale buis sentrifugasie, vloeibare bed agglomerasie en tablet persing het 'n aantreklike produk voortgebring. Die formulering het ook CSL en glukose ingesluit om gevolglike spoor herontkieming te verbeter. Lewensvatbare spoor herwinning en spoor balans sluiting oor elke proses eenheid was hoog (>70% en 99% respektiewelik) met verbetering in herwinning wat moontlik gemaak is deur die gebruik van aaneenlopende prosessering op groot skaal. Spoor her-ontkieming was 97%, terwyl produk halfleeftyd langer as 5 jaar beraam is, gebasseer op termiese weerstand grafieke. Die proses het gelei tot 'n kommersiële aantreklike produk asook bekostigbare veranderbare produksie koste. Die funksionaliteit van die tablet-produk met die ingeslote B. cereus isolaat is ondersoek oor 'n reeks fisiologiese kondisies insluitend soutgehalte, pH en temperatuur, gebasseer op die kultivering van C. carpio. Temperatuur het 'n betreklike invloed op ontkieming, spesifieke groeitempo en toename in sel hoeveelheid van B. cereus gehad, terwyl soutgehalte en pH nie enige meetbare effek op groei gehad het nie. Gekontrolleerde studies in bioreaktors en modellering van die data op die Arrhenius funksie het hoë en lae groei temperatuur domeins gewys. Die tempo van patogeniese Aer. hydrophila onderdrukking en afname in konsentrasies van afval-ione (ammonium, nitriete, nitrate en fosfaat) is herlei na 'n liniêre voorspellende aanwysing van effektiwiteit van B. cereus isolate by verskillende temperature. Die studie het gelei tot die ontwikkeling van stroomop- en stroomaf-prosesse vir die produksie van 'n nuwe B. cereus isolaat (NRRL 100132) wat bewys is as veilig, stabiel, funksioneel, robuust en koste effektiewe vir toepassing in akwakultuur.

Thesis (MScEng (Process Engineering))--University of Stellenbosch, 2005. / The development of non-replicating vaccines is an emerging option for safe, effective vaccines, several of which contain virus-like particles (VLPs). Many recombinant expression systems have been evaluated as hosts for VLP production for the prevention of infectious diseases. The filamentous fungi Aspergillus niger has emerged as a potential alternative expression system for cost effective VLP vaccine production. Hepatitis B surface antigen (HBsAg) was used as a model VLP product to benchmark A. niger’s production capacity with those of Saccharomyces cerevisiae, Pichia pastoris and Hansenula polymorpha. Bioprocessing strategies were used to optimise VLP production by recombinant A. niger in batch culture. In particular, the effect of the parameters culture temperature, inoculum concentration, agitation intensity, dissolved oxygen (dO2) concentration and culture pH on biomass formation, morphology and VLP (HBsAg) production concentration was quantified. At an optimum agitation of 100 rpm and optimum dO2 concentration of 50 %, HBsAg production levels were increased 9-fold compared to yields obtained in shakeflask cultivation. Highest HBsAg production levels of 3.6 mg.ℓculture -1 and 350 μg.gDW -1 were recorded, at a biomass concentration of 10.5 gDW.ℓculture -1. These production levels compare favourable with those obtained by other production systems under similar conditions. HBsAg VLPs mostly accumulated intracellularly, although under optimum bioreactor conditions significant HBsAg accumulation in the cytoplasm and culture supernatant was also observed. The impact of these process parameters on VLP production and cell morphology was attributed to environmental stress conditions. Volumetric biomass and HBsAg production levels were maximised under conditions of lowest environmental stress, resulting in the most optimal small-pelleted morphology. These results indicate a substantial potential for further engineering of the A. niger production system for the high level of intracellular and extracellular VLP production.

Cartilage tissue engineering is an emerging treatment option for osteoarthritis and trauma related joint injuries. A continuing challenge for cartilage tissue engineering is increasing construct extracellular matrix production and material properties. Shear stress and oxygen tension play an important role in tissue engineering of cartilage. In this select stimulatory conditions using combinations of shear stress and oxygen tension have been used to enhance the construct extracellular matrix deposition and material properties. Additionally, a perfusion concentric cylinder bioreactor has been developed to incorporate multiple fluid flow regimes through the construct. This thesis attempts to elucidate the effect of shear stress and biochemical conditions on cartilage development in vitro to provide functional tissue engineered constructs.

Biocatalysts offer advantages over their chemical counterparts in terms of their high enantioselectivity and the opportunity to develop more environmentally friendly processes. However, the widespread adoption of biocatalytic processes is hampered by the long development times for enzymes with novel and sufficient activity and adequate stability under operating conditions. Protein engineering, while extremely useful for modifying the properties of protein catalysts in select cases, still cannot be performed rapidly enough for many applications. In order for biocatalysts to become a competitive alternative to chemical catalysts, new tools to make the tailoring of biocatalysts by protein engineering methods speedier and more efficient are necessary. The aim of this work was to develop methods to aid in the faster production of novel biocatalysts. Protein engineering involves two steps: the generation of diversity and the screening or selection of variants with the desired properties. Both of these must be targeted to create a faster protein engineering process. In the case of the former, this work sought to clone and overexpress some template enzymes which would create smaller, more manageable libraries of mutants with a higher likelihood of function by the manipulation of a few focused amino acid residues. For the latter, this work developed and validated a Monte-Carlo simulation model of pooling to increase screening throughput and created a set of vectors to aid in high-throughput screening by eliminating unwanted mutants from the assay procedure entirely.

Thesis (Ph.D)--Biology, Georgia Institute of Technology, 2009. / Committee Chair: Alfred H. Merrill, Jr; Committee Member: John Cairney; Committee Member: M. Cameron Sullards; Committee Member: Marion B. Sewer; Committee Member: Yuhong Fan. Part of the SMARTech Electronic Thesis and Dissertation Collection.

Thesis (D.Tech.: Biotechnology)-Dept. of Biotechnology, Durban University of Technology, 2007 xi, 209 leaves / Protein engineering technologies, such as directed evolution and DNA recombination, are often used to modify enzymes on a genetic level for the creation of useful industrial catalysts. Pre-treatment of paper pulps with xylanases have been shown to decrease the amounts of toxic chlorine dioxide used to bleach pulp. This study was undertaken to improve the thermal and alkaline stabilities of the xylanase from the fungus Thermomyces lanuginosus using ep-PCR and DNA shuffling.

The purpose of this study was to develop an incremental field exercise test of disability to use in the assessment of functional capacity in patients with chronic airways limitation (CAL). The test was modified from the 20m shuttle running test, employed to predict the maximal oxygen uptake of sporting individuals. The protocol devised for the patients was adapted from the running speeds proposed by Leger and Lambert (1982). The shuttle walking test requires patients to walk up and down a 10m course at speeds dictated by a series of audio signals played from a tape cassette, increasing each minute to a symptom limited maximum performance. Examination of the reproducibility of the test revealed strong test/retest reliability, after just one practice walk. The mean between trial difference (test 2 vs test 3) was -2m,(n=10), (95% CI -21.9 to 17.9m). The shuttle walking test was validated against the traditional measurement of peak oxygen uptake (Vo2pmk) measured conventionally during an incremental maximal treadmill test with Douglas bags (n=19). The results from this exercise test were compared against the patients' performance (distance achieved) on the shuttle walking test (after one practice walk) and revealed a strong relationship between the two variables (r=0.88). The validity and the resistance to breathing, of a portable oxygen consumption meter was examined. Validation, again in comparison to Douglas bag measurements, involved four cohorts (two healthy and two patient groups). After some modifications to the equipment, measurements of lib2 by the two different methods were not significantly different. The patients' response to the shuttle walking test was examined (n=10). The heart rate, ventilation and 7Orck2 increased gradually in response to the increasing intensity of the shuttle walking test. Again Vo 2wa measurements related strongly to the patients performance (r=0.81). A further study employing a treadmill test and shuttle walking test confirmed that the latter provided a comparable metabolic and physiological challenge to the patients as the conventional treadmill test. Comparison with the 6 minute walking test (6MWT), one of the most commonly employed field exercise tests in this patient population) revealed that the heart rate response was significantly higher in the shuttle walking test than the 6 MWT and graded, a response not observed in the 6MWT. The shuttle test reflected the true extent of the patients disability more accurately than the 6MWT. The shuttle walking test provides a simple, reproducible exercise test of disability in patients with CAL that relates well to Vb2puk . The external pacing of the test allows more valid intra- and inter- subject comparison than has previously been possible with field tests alone.

Dyestuffs are widely used industrial chemicals, yet surprisingly little is known about their fate in the environment. The potential modes of transformation and removal of reactive dyes in treatment and in the environment are principally through anaerobic and aerobic biodegradation and photodegradation. The research herein describes the use of LC-MS analysis with laboratory simulations to develop a better understanding of the occurrence and fate of reactive dyes and their degradation products in the aquatic environment. One reason for the lack of information on the environmental fate of reactive dyes has been the paucity of robust analytical methods suitable for the determination of dyes in aqueous samples. Robust analytical methods were optimised to provide LC-MS and MSMS identification of degradation products. Additionally, interpretation of the MSMS spectra of known reactive dyes provided novel characteristic fragment ions indicative of the triazine reactive group of reactive dyes . Fibre reactive dyes are designed to have a degree of photostability and therefore their photodegradation behaviour has not been widely investigated. Little is known of their stability to daylight over prolonged periods of irradiation in dilute aqueous solutions and in the presence of humic substances. The kinetics of photodegradation of an anthraquinone dye (Reactive Blue H4R) and azo dye (Reactive Yellow P5G) were evaluated. The former underwent rapid and extensive degradation 01/2 1.5 h). The major products formed were identified using LC-MSMS and a photodegradation pathway proposed. By comparison, the photodegradation of the azo dye was significantly slower, 01/2 30 h). The addition of humic substancesa ppearedt o have little effect on the rate of photodegradationu nder the conditions used. The reduction of azo dyes under anaerobic treatment has been extensively studied, but the subsequent fate of the initial reduction products when exposed to air are not understood. Three relatively simple azo dyes, Amaranth, Sunset Yellow and Naphthol Blue-Black, were reduced and their autoxidation products identified by LC-MS. These were subsequently used to predict the autoxidation products of a more complex azo reactive dye: Reactive Red 3.1. Additionally, a persistent degradation product from the anaerobicaerobic treatment of Reactive Red 3.1 was identified from LC-MS data. Azo reactive dyes are generally regarded as being resistant to aerobic degradation and there are few published data regarding degradation pathways for reactive anthraquinone dyes. Pure cultures of Pseudomonas docunhae, A 9046 and A texaco and mixed bacterial consortia (semi-continuous activated sludge, SCAS) aerobic degradation of azo and anthraquinone reactive dyes was studied. Two azo dyes were degraded by pure cultures of A docunhae and A 9046, suggesting that azo dyes can be aerobically degraded given favourable conditions. The antraquinone dye was extensively degraded by SCAS and pure culture biodegradation. Metabolites were identified by LC-MS and a degradation pathway proposed.

Bioprocessing applications are gaining importance in the traditional chemical industries. With environmental, political, and economical concerns growing, research efforts have recently focused on the substitution of petroleum-derived transportation fuels and materials. As possible products and feedstocks are being investigated, it is important to ensure the new processes are also sustainable. There are several aspects to developing sustainable processes: minimize waste, use environmentally-benign chemicals, find renewable feedstocks, and limit the number of processing steps. This thesis examines ways to enhance the sustainability of bioprocesses. Novel, alternative solvent systems are studied and applied to a variety of bioprocesses. Downstream processing steps and waste can be minimized by designing systems that combine reactions and separations into one process unit. This is accomplished by designing new reactor systems and by replacing currently used solvents. Additional studies, involving analytical techniques that reduce the use of organic solvents, are tested and applied to industrial problems. Finally, new solvent systems are examined for potential processes using renewable carbohydrate feedstock.

Thesis (Ph. D.)--Rutgers University, 2010. / "Graduate Program in Chemical and Biochemical Engineering." Includes bibliographical references (p. 209-237).