Developing a scalable model of recombinant protein yield from Pichia pastoris:the influence of culture conditions, biomass and induction regime

Background The optimisation and scale-up of process conditions leading to high yields of recombinant proteins is an enduring bottleneck in the post-genomic sciences. Typical experiments rely on varying selected parameters through repeated rounds of trial-and-error optimisation. To rationalise this, several groups have recently adopted the 'design of experiments' (DoE) approach frequently used in industry. Studies have focused on parameters such as medium composition, nutrient feed rates and induction of expression in shake flasks or bioreactors, as well as oxygen transfer rates in micro-well plates. In this study we wanted to generate a predictive model that described small-scale screens and to test its scalability to bioreactors. Results Here we demonstrate how the use of a DoE approach in a multi-well mini-bioreactor permitted the rapid establishment of high yielding production phase conditions that could be transferred to a 7 L bioreactor. Using green fluorescent protein secreted from Pichia pastoris, we derived a predictive model of protein yield as a function of the three most commonly-varied process parameters: temperature, pH and the percentage of dissolved oxygen in the culture medium. Importantly, when yield was normalised to culture volume and density, the model was scalable from mL to L working volumes. By increasing pre-induction biomass accumulation, model-predicted yields were further improved. Yield improvement was most significant, however, on varying the fed-batch induction regime to minimise methanol accumulation so that the productivity of the culture increased throughout the whole induction period. These findings suggest the importance of matching the rate of protein production with the host metabolism. Conclusion We demonstrate how a rational, stepwise approach to recombinant protein production screens can reduce process development time.

The relative performance of scalable load balancing algorithms in loosely-coupled distributed systems. Available in 2 volumes.

The computer systems of today are characterised by data and program control that are distributed functionally and geographically across a network. A major issue of concern in this environment is the operating system activity of resource management for different processors in the network. To ensure equity in load distribution and improved system performance, load balancing is often undertaken. The research conducted in this field so far, has been primarily concerned with a small set of algorithms operating on tightly-coupled distributed systems. More recent studies have investigated the performance of such algorithms in loosely-coupled architectures but using a small set of processors. This thesis describes a simulation model developed to study the behaviour and general performance characteristics of a range of dynamic load balancing algorithms. Further, the scalability of these algorithms are discussed and a range of regionalised load balancing algorithms developed. In particular, we examine the impact of network diameter and delay on the performance of such algorithms across a range of system workloads. The results produced seem to suggest that the performance of simple dynamic policies are scalable but lack the load stability of more complex global average algorithms.

Improved production of industrially relevant recombinant proteins: application of multi-factorial design of experiments and scalable process modelling

The work described in this thesis focuses on the use of a design-of-experiments approach in a multi-well mini-bioreactor to enable the rapid establishments of high yielding production phase conditions in yeast, which is an increasingly popular host system in both academic and industrial laboratories. Using green fluorescent protein secreted from the yeast, Pichia pastoris, a scalable predictive model of protein yield per cell was derived from 13 sets of conditions each with three factors (temperature, pH and dissolved oxygen) at 3 levels and was directly transferable to a 7 L bioreactor. This was in clear contrast to the situation in shake flasks, where the process parameters cannot be tightly controlled. By further optimisating both the accumulation of cell density in batch and improving the fed-batch induction regime, additional yield improvement was found to be additive to the per cell yield of the model. A separate study also demonstrated that improving biomass improved product yield in a second yeast species, Saccharomyces cerevisiae. Investigations of cell wall hydrophobicity in high cell density P. pastoris cultures indicated that cell wall hydrophobin (protein) compositional changes with growth phase becoming more hydrophobic in log growth than in lag or stationary phases. This is possibly due to an increased occurrence of proteins associated with cell division. Finally, the modelling approach was validated in mammalian cells, showing its flexibility and robustness. In summary, the strategy presented in this thesis has the benefit of reducing process development time in recombinant protein production, directly from bench to bioreactor.

An accurate and scalable analytical model for IEEE 802.15.4 slotted CSMA/CA networks

In this paper a Markov chain based analytical model is proposed to evaluate the slotted CSMA/CA algorithm specified in the MAC layer of IEEE 802.15.4 standard. The analytical model consists of two two-dimensional Markov chains, used to model the state transition of an 802.15.4 device, during the periods of a transmission and between two consecutive frame transmissions, respectively. By introducing the two Markov chains a small number of Markov states are required and the scalability of the analytical model is improved. The analytical model is used to investigate the impact of the CSMA/CA parameters, the number of contending devices, and the data frame size on the network performance in terms of throughput and energy efficiency. It is shown by simulations that the proposed analytical model can accurately predict the performance of slotted CSMA/CA algorithm for uplink, downlink and bi-direction traffic, with both acknowledgement and non-acknowledgement modes.

All-optical 40 Gbit/s 2R regeneration in scalable WDM networks

In this paper we propose a 2R regeneration scheme based on a nonlinear optical loop mirror (NOLM) and optical filtering. We numerically investigate wavelength-division multiplexing (WDM) operation at a channel bit rate of 40 Gbit/s. In distinction to our previous work, we focus here on the regenerative characteristics and signal quality after a single transmission section, whose length is varied from 200 to 1000 km. © 2003 IEEE.

All-optical 2R regeneration in scalable 40 Gbit/s wavelength-division multiplexed networks

We propose a 2R regeneration scheme based on a nonlinear optical loop mirror and optical filtering. The feasibility of wavelength-division multiplexing operation at 40 Gbit/s is numerically demonstrated. We examine the characteristics of one-step regeneration and discuss networking applications.

An enhanced scalable probe-based multicast admission control scheme

To guarantee QoS for multicast transmission, admission control for multicast sessions is expected. Probe-based multicast admission control (PBMAC) scheme is a scalable and simple approach. However, PBMAC suffers from the subsequent request problem which can significantly reduce the maximum number of multicast sessions that a network can admit. In this letter, we describe the subsequent request problem and propose an enhanced PBMAC scheme to solve this problem. The enhanced scheme makes use of complementary probing and remarking which require only minor modification to the original scheme. By using a fluid-based analytical model, we are able to prove that the enhanced scheme can always admit a higher number of multicast sessions. Furthermore, we present validation of the analytical model using packet based simulation. Copyright © 2005 The Institute of Electronics, Information and Communication Engineers.

A potentially scalable method for the harvesting of hMSCs from microcarriers

The use of hMSCs for allogeneic therapies requiring lot sizes of billions of cells will necessitate large-scale culture techniques such as the expansion of cells on microcarriers in bioreactors. Whilst much research investigating hMSC culture on microcarriers has focused on growth, much less involves their harvesting for passaging or as a step towards cryopreservation and storage. A successful new harvesting method has recently been outlined for cells grown on SoloHill microcarriers in a 5L bioreactor [1]. Here, this new method is set out in detail, harvesting being defined as a two-step process involving cell 'detachment' from the microcarriers' surface followed by the 'separation' of the two entities. The new detachment method is based on theoretical concepts originally developed for secondary nucleation due to agitation. Based on this theory, it is suggested that a short period (here 7min) of intense agitation in the presence of a suitable enzyme should detach the cells from the relatively large microcarriers. In addition, once detached, the cells should not be damaged because they are smaller than the Kolmogorov microscale. Detachment was then successfully achieved for hMSCs from two different donors using microcarrier/cell suspensions up to 100mL in a spinner flask. In both cases, harvesting was completed by separating cells from microcarriers using a Steriflip® vacuum filter. The overall harvesting efficiency was >95% and after harvesting, the cells maintained all the attributes expected of hMSC cells. The underlying theoretical concepts suggest that the method is scalable and this aspect is discussed too. © 2014 The Authors.

Scalable harmonization of complex networks with local controllers

Computational and communication complexities call for distributed, robust, and adaptive control. This paper proposes a promising way of bottom-up design of distributed control in which simple controllers are responsible for individual nodes. The overall behavior of the network can be achieved by interconnecting such controlled loops in cascade control for example and by enabling the individual nodes to share information about data with their neighbors without aiming at unattainable global solution. The problem is addressed by employing a fully probabilistic design, which can cope with inherent uncertainties, that can be implemented adaptively and which provide a systematic rich way to information sharing. This paper elaborates the overall solution, applies it to linear-Gaussian case, and provides simulation results.

Toward a scalable and consistent manufacturing process for the production of human MSCs

The development of novel, affordable and efficacious therapeutics will be necessary to ensure the continued progression in the standard of global healthcare. With the potential to address previously unmet patient needs as well as tackling the social and economic effects of chronic and age-related conditions, cell therapies will lead the new generation of healthcare products set to improve health and wealth across the globe. However, if many of the small to medium enterprises (SMEs) engaged in much of the commercialization efforts are to successfully traverse the ‘Valley of Death’ as they progress through clinical trials, there are a number of challenges that must be overcome. No longer do the challenges remain biological but rather a series of engineering and manufacturing issues must also be considered and addressed.