Biology subjects

Cruz Bournazou, M. N.

Publications and source records attributed to Cruz Bournazou, M. N..

4 recordsLinked to original sources

bioRxiv2024

Self-driving development of perfusion processes for monoclonal antibody production

The development of autonomous agents in bioporcess development is crucial for advancing biopharma innovation, as it can significantly reduce the time and resources required to transition from product to process. While robotics and machine learning have greatly accelerated drug discovery and initial screening, the later stages of development have primarily benefited from experimental automation, lacking advanced computational tools for experimental planning and execution. For example, in the development of new monoclonal antibodies, the search for optimal upstream conditions (such as feeding strategy, pH, temperature, and media composition) is often conducted using sophisticated high-throughput (HT) mini-bioreactor systems, while the integration of machine learning tools for experimental design and operation in these systems have not matured accordingly. In this work, we introduce an integrated user-friendly software framework that combines a Bayesian experimental design algorithm, a cognitive digital twin of the cultivation system, and an advanced 24-parallel mini-bioreactor perfusion experimental setup. This results in an autonomous experimental machine capable of: (1) embedding existing process knowledge, (2) learning during experimentation, utilizing information from similar processes, (4) predicting future events, and (5) autonomously operating the parallel cultivation setup to achieve challenging objectives. As proof of concept, we present experimental results from 27-day-long cultivations operated by the autonomous software agent, which successfully achieved challenging goals such as increasing the viable cell volume (VCV) and maximizing the viability throughout the experiment.

bioengineering↗

bioRxiv2023

Modeling of enzyme-mediated glucose release to facilitate continuous feed in miniaturized cultivations

When striving for maximal throughput at minimal volumes while cultivating close to industrial conditions, simple and robust feeding strategies offer important advantages. Enzyme-mediated glucose cleavage from dextrin is an easy way of imitating continuous fed-batch in the small scale, with no complex equipment required. While the release rate - and thus the feed rate - can be controlled by adapting the enzyme concentration, it strongly depends on the concentration of the involved substances and the environmental conditions. Thus, it is a challenge to use the technology for controlling the specific growth rate, as it is commonly done with feed pumps. For solving this problem, we present here a mathematical model that extends simple Michaelis-Menten kinetics by considering different substrate fractions and can be applied to control the glucose release rate even in high throughput experiments. The fitted model was used during automated microbial cultivations to control the growth rate in quasi-continuous fed-batch processes and to realize different exponential growth rates by intermittent additions of enzyme and dextrin by a liquid handling robot system. We thus present an approach for defined biocatalytically controlled glucose supply of small-scale systems, where - if at all - continuous feeding was only possible with low accuracy or high technical efforts until now.

bioengineering↗

bioRxiv2021

Optimal operation of parallel mini-bioreactors in bioprocess development using multi-stage MPC

Bioprocess development is commonly characterized by long development times, especially in the early screening phase. After promising candidates have been pre-selected in screening campaigns, an optimal operating strategy has to be found and verified under conditions similar to production. Cultivating cells with pulse-based feeding and thus exposing them to oscillating feast and famine phases has shown to be a powerful approach to study microorganisms closer to industrial bioreactor conditions. In view of the large number of strains and the process conditions to be tested, high-throughput cultivation systems provide an essential tool to sample the large design space in short time. We have recently presented a comprehensive platform, consisting of two liquid handling stations coupled with a model-based experimental design and operation framework to increase the efficiency in High Throughput bioprocess development. Using calibrated macro-kinetic growth models, the platform has been successfully used for the development of scale-down fed-batch cultivations in parallel mini-bioreactor systems. However, it has also been shown that parametric uncertainties in the models can significantly affect the prediction accuracy and thus the reliability of optimized cultivation strategies. To tackle this issue, we implemented a multi-stage Model Predictive Control (MPC) strategy to fulfill the experimental objectives under tight constraints despite the uncertainty in the parameters and the measurements. Dealing with uncertainties in the parameters is of major importance, since constraint violation would easily occur otherwise, which in turn could have adverse effects on the quality of the heterologous protein produced. Multi-stage approaches build up scenario tree, based on the uncertainty that can be encountered and computing optimal inputs that satisfy the constrains despite of such uncertainties. Using the feedback information gained through the evolution along the tree, the control approach is significantly more robust than standard MPC approaches without being overly conservative. We show in this study that the application of multi-stage MPC can increase the number of successful experiments, by applying this methodology to a mini-bioreactor cultivation operated in parallel.

bioengineering↗

bioRxiv2020

Suspension of A Point-Mass-Loaded Filament in Non-uniform Flows: Passive Dynamics of a Ballooning Spider

Spiders utilize their fine silk fibres for their aerial dispersal, known as ballooning. With this method, spiders can disperse hundreds of kilometres, reaching as high as 4.5 km. However, the passive dynamics of a ballooning model (a highly flexible filament and a spider body at the end of it) are not well understood. The previous study (Rouse model: without taking into account anisotropic drag of a fibre) suggested that the flexible and extendible fibres reduce the settling speed of the ballooning model in homogeneous turbulence. However, the exact cause of the reduction of the settling speed is not explained and the assumed isotropic drag of a fibre is not realistic in the low Reynolds number flow. Here we introduce a bead-spring model that takes into account the anisotropic drag of a fibre to investigate the passive behaviour of the ballooning model in the various non-uniform flows (a shear flow, a periodic vortex flow field and a homogeneous turbulent flow). For the analysis of the wide range of parameters, we defined a dimensionless parameter, which is called a ballooning number. The ballooning number means the ratio of Stokes fluid-dynamic force on a fibre by the non-uniform flow field to the gravitational force of a body at the end of the fibre. Our simulation shows that the settling speed of the present model in the homogeneous turbulent flows shows the biased characters of slow settling as the influence of the turbulent flow increases. The causes of this slow settling are investigated by simulating it in a wide range of shear flows. We revealed that the cause of this is the drag anisotropy of the filament structure (spider silk). In more detail, the cause of reduced settling speed lies not only in the deformed geometrical shape of the ballooning silk but also in its generation of fluid-dynamic force in a non-uniform flow (shear flow). Additionally, we found that the ballooning structure could become trapped in a vortex flow. This seemed to be the second reason why the ballooning structure settles slowly in the homogeneous turbulent flow. These results can help deepen our understanding of the passive dynamics of spiders ballooning in the atmospheric boundary layer.

biophysics↗