Effects of dissolved oxygen availability and culture biomass at induction upon the intracellular expression of monoamine oxidase by recombinant E. coli in fed batch bioprocesses

The effects of oxygen availability and induction culture biomass upon production of an industrially important monoamine oxidase (MAO) were investigated in fed-batch cultures of a recombinant E. coli. For each induction cell biomass 2 different oxygenation methods were used, aeration and oxygen enriched air. Induction at higher biomass levels increased the culture demand for oxygen, leading to fermentative metabolism and accumulation of high levels of acetate in the aerated cultures. Paradoxically, despite an almost eight fold increase in acetate accumulation to levels widely reported to be highly detrimental to protein production, when induction wet cell weight (WCW) rose from 100% to 137.5%, MAO specific activity in these aerated processes showed a 3 fold increase. By contrast, for oxygenated cultures induced at WCW's 100% and 137.5% specific activity levels were broadly similar, but fell rapidly after the maxima were reached. Induction at high biomass levels (WCW 175%) led to very low levels of specific MAO activity relative to induction at lower WCW's in both aerated and oxygenated cultures. Oxygen enrichment of these cultures was a useful strategy for boosting specific growth rates, but did not have positive effects upon specific enzyme activity. Based upon our findings, consideration of the amino acid composition of MAO and previous studies on related enzymes, we propose that this effect is due to oxidative damage to the MAO enzyme itself during these highly aerobic processes. Thus, the optimal process for MAO production is aerated, not oxygenated, and induced at moderate cell density, and clearly represents a compromise between oxygen supply effects on specific growth rate/induction cell density, acetate accumulation, and high specific MAO activity. This work shows that the negative effects of oxygen previously reported in free enzyme preparations, are not limited to these acellular environments but are also discernible in the sheltered environment of the cytosol of E. coli cells.

Development of a pilot-scale bacterial fermentation for plasmid-based biopharmaceutical production using a stoichiometric medium

The recognition of the potential efficacy of plasmid DNA (pDNA) molecules as vectors in the treatment and prevention of emerging diseases has birthed the confidence to combat global pandemics. This is due to the close-to-zero safety concern associated with pDNA vectors compared to viral vectors in cell transfection and targeting. Considerable attention has been paid to the potential of pDNA vectors but comparatively less thought has been given to the practical challenges in producing large quantities to meet current rising demands. A pilot-scale fermentation scheme was developed by employing a stoichiometrically-designed growth medium whose exceptional plasmid yield performance was attested in a shake flask environment for pUC19 and pEGFP-N1 transformed into E. coliDH5α and E. coliJM109, respectively. Batch fermentation of E. coliDH5α-pUC19 employing the stoichiometric medium displayed a maximum plasmid volumetric and specific yield of 62.6 mg/L and 17.1 mg/g (mg plasmid/g dry cell weight), respectively. Fed-batch fermentation of E. coliDH5α-pUC19 on a glycerol substrate demonstrated one of the highest ever reported pilot-scale plasmid specific yield of 48.98 mg/g and a volumetric yield of 0.53 g/L. The attainment of high plasmid specific yields constitutes a decrease in plasmid manufacturing cost and enhances the effectiveness of downstream processes by reducing the proportion of intracellular impurities. The effect of step-rise temperature induction was also considered to maximize ColE1-origin plasmid replication.

High-level expression of Rhodotorula gracilis d-amino acid oxidase in Pichia pastoris

By combining gene design and heterologous over-expression of Rhodotorula gracilis D-amino acid oxidase (RgDAO) in Pichia pastoris, enzyme production was enhanced by one order of magnitude compared to literature benchmarks, giving 350 kUnits/l of fed-batch bioreactor culture with a productivity of 3.1 kUnits/l h. P. pastoris cells permeabilized by freeze-drying and incubation in 2-propanol (10% v/v) produce a highly active (1.6 kUnits/g dry matter) and stable oxidase preparation. Critical bottlenecks in the development of an RgDAO catalyst for industrial applications have been eliminated.

Stepwise engineering of a Pichia pastoris D-amino acid oxidase whole cell catalyst

Trigonopsis variabilis D-amino acid oxidase (TvDAO) is a well characterized enzyme used for cephalosporin C conversion on industrial scale. However, the demands on the enzyme with respect to activity, operational stability and costs also vary with the field of application. Processes that use the soluble enzyme suffer from fast inactivation of TvDAO while immobilized oxidase preparations raise issues related to expensive carriers and catalyst efficiency. Therefore, oxidase preparations that are more robust and active than those currently available would enable a much broader range of economically viable applications of this enzyme in fine chemical syntheses. A multi-step engineering approach was chosen here to develop a robust and highly active Pichia pastoris TvDAO whole-cell biocatalyst. As compared to the native T. variabilis host, a more than seven-fold enhancement of the intracellular level of oxidase activity was achieved in P. pastoris through expression optimization by codon redesign as well as efficient subcellular targeting of the enzyme to peroxisomes. Multi copy integration further doubled expression and the specific activity of the whole cell catalyst. From a multicopy production strain, about 1.3 x 103 U/g wet cell weight (wcw) were derived by standard induction conditions feeding pure methanol. A fed-batch cultivation protocol using a mixture of methanol and glycerol in the induction phase attenuated the apparent toxicity of the recombinant oxidase to yield final biomass concentrations in the bioreactor of >or= 200 g/L compared to only 117 g/L using the standard methanol feed. Permeabilization of P. pastoris using 10% isopropanol yielded a whole-cell enzyme preparation that showed 49% of the total available intracellular oxidase activity and was notably stabilized (by three times compared to a widely used TvDAO expressing Escherichia coli strain) under conditions of D-methionine conversion using vigorous aeration. Stepwise optimization using a multi-level engineering approach has delivered a new P. pastoris whole cell TvDAO biocatalyst showing substantially enhanced specific activity and stability under operational conditions as compared to previously reported preparations of the enzyme. The production of the oxidase through fed-batch bioreactor culture and subsequent cell permeabilization is high-yielding and efficient. Therefore this P. pastoris catalyst has been evaluated for industrial purposes.

Model-based analysis and optimization of bioreactor for hematopoietic stem cell cultivation

One of the problems to be solved in attaining the full potentials of hematopoietic stem cell (HSC) applications is the limited availability of the cells. Growing HSCs in a bioreactor offers an alternative solution to this problem. Besides, it also offers the advantages of eliminating labour intensive process as well as the possible contamination involved in the periodic nutrient replenishments in the traditional T-flask stem cell cultivation. In spite of this, the optimization of HSC cultivation in a bioreactor has been barely explored. This manuscript discusses the development of a mathematical model to describe the dynamics in nutrient distribution and cell concentration of an ex vivo HSC cultivation in a microchannel perfusion bioreactor. The model was further used to optimize the cultivation by proposing three alternative feeding strategies in order to prevent the occurrence of nutrient limitation in the bioreactor. The evaluation of these strategies, the periodic step change increase in the inlet oxygen concentration, the periodic step change increase in the media inflow, and the feedback control of media inflow, shows that these strategies can successfully improve the cell yield of the bioreactor. In general, the developed model is useful for the design and optimization of bioreactor operation.

Plasmid DNA purification via the use of a dual affinity protein

Methods are presented for the production, affinity purification and analysis of plasmid DNA (pDNA). Batch fermentation is used for the production of the pDNA, and expanded bed chromatography, via the use of a dual affinity glutathione S-transferase (GST) fusion protein, is used for the capture and purification of the pDNA. The protein is composed of GST, which displays affinity for glutathione immobilized to a solid-phase adsorbent, fused to a zinc finger transcription factor, which displays affinity for a target 9-base pair sequence contained within the target pDNA. A Picogreen™ fluorescence assay and/or anx ethidium bromide agarose gel electrophoresis assay can be used to analyze the eluted pDNA.

Batch Verification of Validity of Bids in Homomorphic E-auction

Bid opening in e-auction is efficient when a homomorphic secret sharing function is employed to seal the bids and homomorphic secret reconstruction is employed to open the bids. However, this high efficiency is based on an assumption: the bids are valid (e.g., within a special range). An undetected invalid bid can compromise correctness and fairness of the auction. Unfortunately, validity verification of the bids is ignored in the auction schemes employing homomorphic secret sharing (called homomorphic auction in this paper). In this paper, an attack against the homomorphic auction in the absence of bid validity check is presented and a necessary bid validity check mechanism is proposed. Then a batch cryptographic technique is introduced and applied to improve the efficiency of bid validity check.

Clarification of cane juice for fermentation

Fermentation feedstocks in the sugar industry are based on cane juice, B molasses or final molasses. Brazil has been producing ethanol by directing sugarcane juice to fermentation directly or using lower quality juice as a diluent with B molasses to prepare the fermentation broth. One issue that has received only limited interest particularly from outside Brazil is the most appropriate conditions for clarification of the juice going to fermentation. Irrespective of whether the juice supply is the total flow from the milling tandem or a diffuser station or a part of the total flow, removal of the insoluble solids is essential. However, the standard defecation process used by sugar factories around the world to clarify juice can introduce unwanted calcium ions and remove other nutrients such as phosphorus and nitrogen that are considered essential for the fermentation process. An investigation was undertaken by SRI to assess the effects on the constituents of cane juice when subjected to the typical clarification process in an Australian factory and what conditions would be needed to provide a clarified juice suitable for fermentation. Typical juices from one factory were clarified in laboratory trials under a range of pH conditions and the resulting clarified juices analysed. The results indicated that pH had a major effect on the residual concentrations of key constituents in the clarified juice and that the selected clarification conditions are determined by the nominated quality criteria of clarified juice feedstock for fermentation. Further trials were conducted in overseas factories to confirm the results obtained in Australia. It became apparent that the preferred specifications for clarified juice going to fermentation varied from country to country. Each supplier of fermentation technology had criteria applying to clarified juice feedstock that would have a major impact on the standard of clarification required to achieve compliance with the criteria.

Applied batch cryptography

The material presented in this thesis may be viewed as comprising two key parts, the first part concerns batch cryptography specifically, whilst the second deals with how this form of cryptography may be applied to security related applications such as electronic cash for improving efficiency of the protocols. The objective of batch cryptography is to devise more efficient primitive cryptographic protocols. In general, these primitives make use of some property such as homomorphism to perform a computationally expensive operation on a collective input set. The idea is to amortise an expensive operation, such as modular exponentiation, over the input. Most of the research work in this field has concentrated on its employment as a batch verifier of digital signatures. It is shown that several new attacks may be launched against these published schemes as some weaknesses are exposed. Another common use of batch cryptography is the simultaneous generation of digital signatures. There is significantly less previous work on this area, and the present schemes have some limited use in practical applications. Several new batch signatures schemes are introduced that improve upon the existing techniques and some practical uses are illustrated. Electronic cash is a technology that demands complex protocols in order to furnish several security properties. These typically include anonymity, traceability of a double spender, and off-line payment features. Presently, the most efficient schemes make use of coin divisibility to withdraw one large financial amount that may be progressively spent with one or more merchants. Several new cash schemes are introduced here that make use of batch cryptography for improving the withdrawal, payment, and deposit of electronic coins. The devised schemes apply both to the batch signature and verification techniques introduced, demonstrating improved performance over the contemporary divisible based structures. The solutions also provide an alternative paradigm for the construction of electronic cash systems. Whilst electronic cash is used as the vehicle for demonstrating the relevance of batch cryptography to security related applications, the applicability of the techniques introduced extends well beyond this.

Diarrhoea risk factors in enterally tube fed critically ill patients : a retrospective audit

Objective: Diarrhoea in the enterally tube fed (ETF) intensive care unit (ICU) patient is a multifactorial problem. Diarrhoeal aetiologies in this patient cohort remain debatable; however, the consequences of diarrhoea have been well established and include electrolyte imbalance, dehydration, bacterial translocation, peri anal wound contamination and sleep deprivation. This study examined the incidence of diarrhoea and explored factors contributing to the development of diarrhoea in the ETF, critically ill, adult patient. ---------- Method: After institutional ethical review and approval, a single centre medical chart audit was undertaken to examine the incidence of diarrhoea in ETF, critically ill patients. Retrospective, non-probability sequential sampling was used of all emergency admission adult ICU patients who met the inclusion/exclusion criteria. ---------- Results: Fifty patients were audited. Faecal frequency, consistency and quantity were considered important criteria in defining ETF diarrhoea. The incidence of diarrhoea was 78%. Total patient diarrhoea days (r = 0.422; p = 0.02) and total diarrhoea frequency (r = 0.313; p = 0.027) increased when the patient was ETF for longer periods of time. Increased severity of illness, peripheral oxygen saturation (Sp02), glucose control, albumin and white cell count were found to be statistically significant factors for the development of diarrhoea. ---------- Conclusion: Diarrhoea in ETF critically ill patients is multi-factorial. The early identification of diarrhoea risk factors and the development of a diarrhoea risk management algorithm is recommended.

Probiotics and diarrhoea management in enterally tube fed critically ill patients : what is the evidence?

Objective: The aim of this literature review is to identify the role of probiotics in the management of enteral tube feeding (ETF) diarrhoea in critically ill patients.---------- Background: Diarrhoea is a common gastrointestinal problem seen in ETF patients. The incidence of diarrhoea in tube fed patients varies from 2% to 68% across all patients. Despite extensive investigation, the pathogenesis surrounding ETF diarrhoea remains unclear. Evidence to support probiotics to manage ETF diarrhoea in critically ill patients remains sparse.---------- Method: Literature on ETF diarrhoea and probiotics in critically ill, adult patients was reviewed from 1980 to 2010. The Cochrane Library, Pubmed, Science Direct, Medline and the Cumulative Index of Nursing and Allied Health Literature (CINAHL) electronic databases were searched using specific inclusion/exclusion criteria. Key search terms used were: enteral nutrition, diarrhoea, critical illness, probiotics, probiotic species and randomised clinical control trial (RCT).---------- Results: Four RCT papers were identified with two reporting full studies, one reporting a pilot RCT and one conference abstract reporting an RCT pilot study. A trend towards a reduction in diarrhoea incidence was observed in the probiotic groups. However, mortality associated with probiotic use in some severely and critically ill patients must caution the clinician against its use.---------- Conclusion: Evidence to support probiotic use in the management of ETF diarrhoea in critically ill patients remains unclear. This paper argues that probiotics should not be administered to critically ill patients until further research has been conducted to examine the causal relationship between probiotics and mortality, irrespective of the patient's disease state or projected prophylactic benefit of probiotic administration.

‘They get fed up with playing.’ Parents’ views on play-based learning in the Preparatory Year

Within early childhood education two ideas are firmly held: play is the best way for children to learn and parents are partners in the child’s learning. While these ideas have been explored, limited research to date has investigated the confluence of the two - how parents of young children view the concept of play. This paper investigates parents’ views on play by analysing the views of small group of parents of Prep Year children in Queensland, Australia. The parents in this study held varying definitions of what constitutes play, and complex and contradictory notions of its value. Positive views of play were linked to learning without knowing it, engaging in hands-on activities, and preparation for Year One through a strong focus on academic progress. Some parents held that Prep was play-based, while others did not. The complexities and diversity of parental opinion in this study echo the ongoing commentary about how play ought to be defined. Moreover, the notion that adults may interpret play in different ways is also reflected here. The authors suggest that for early childhood educators these complexities require an ongoing engagement, debate and reconceptualisation of the place of play in light of broader curricular and socio-political agendas.