Studies on fluid dynamics of the flow field and gas transfer in orbitally shaken tubes

Orbitally shaken cylindrical bioreactors [OrbShake bioreactors (OSRs)] without an impeller or sparger are increasingly being used for the suspension cultivation of mammalian cells. Among small volume OSRs, 50‐mL tubes with a ventilated cap (OSR50), originally derived from standard laboratory centrifuge tubes with a conical bottom, have found many applications including high‐throughput screening for the optimization of cell cultivation conditions. To better understand the fluid dynamics and gas transfer rates at the liquid surface in OSR50, we established a three‐dimensional simulation model of the unsteady liquid forms (waves) in this vessel. The studies verified that the operating conditions have a large effect on the interfacial surface. The volumetric mass transfer coefficient (k_La) was determined experimentally and from simulations under various working conditions. We also determined the liquid‐phase mass transfer coefficient (k_L) and the specific interfacial area (a) under different conditions to demonstrate that the value of a affected the gas transfer rate more than did the value of k_L. High oxygen transfer rates, sufficient for supporting the high‐density culture of mammalian cells, were found. Finally, the average axial velocity of the liquid was identified to be an important parameter for maintaining cells in suspension. Overall these studies provide valuable insights into the preferable operating conditions for the OSR50, such as those needed for cell cultures requiring high oxygen levels. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:192–200, 2017     

Characterizing the fluid dynamics in the flow fields of cylindrical orbitally shaken bioreactors with different geometry sizes

Orbitally shaken bioreactors (OSRs) are commonly used for the cultivation of mammalian cells in suspension. To aid the geometry designing and optimizing of OSRs, we conducted a three‐dimensional computational fluid dynamics (CFD) simulation to characterize the flow fields in a 10 L cylindrical OSR with different vessel diameters. The liquid wave shape captured by a camera experimentally validated the CFD models established for the cylindrical OSR. The geometry size effect on volumetric mass transfer coefficient (k_La) and hydromechanical stress was analyzed by varying the ratio of vessel diameter (d) to liquid height at static (h_L), d/h_L. The highest value of k_La about 30 h^?1 was observed in the cylindrical vessel with the d/h_L of 6.35. Moreover, the magnitudes of shear stress and energy dissipation rate in all the vessels tested were below their minimum values causing cells damage separately, which indicated that the hydromechanical‐stress environment in OSRs is suitable for cells cultivation in suspension. Finally, the CFD results suggested that the d/h_L higher than 8.80 should not be adopted for the 10 L cylindrical OSR at the shaking speed of 180 rpm because the “out of phase” state probably will happen there.     

A comparison of orbitally‐shaken and stirred‐tank bioreactors: pH modulation and bioreactor type affect CHO cell growth and protein glycosylation

Orbitally shaken bioreactors (OSRs) support the suspension cultivation of animal cells at volumetric scales up to 200 L and are a potential alternative to stirred‐tank bioreactors (STRs) due to their rapid and homogeneous mixing and high oxygen transfer rate. In this study, a Chinese hamster ovary cell line producing a recombinant antibody was cultivated in a 5 L OSR and a 3 L STR, both operated with or without pH control. Effects of bioreactor type and pH control on cell growth and metabolism and on recombinant protein production and glycosylation were determined. In pH‐controlled bioreactors, the glucose consumption and lactate production rates were higher relative to cultures grown in bioreactors without pH control. The cell density and viability were higher in the OSRs than in the STRs, either with or without pH control. Volumetric recombinant antibody yields were not affected by the process conditions, and a glycan analysis of the antibody by mass spectrometry did not reveal major process‐dependent differences in the galactosylation index. The results demonstrated that OSRs are suitable for recombinant protein production from suspension‐adapted animal cells. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1174–1180, 2016     

Efficient and reproducible mammalian cell bioprocesses without probes and controllers?

Bioprocesses for recombinant protein production with mammalian cells are typically controlled for several physicochemical parameters including the pH and dissolved oxygen concentration (DO) of the culture medium. Here we studied whether these controls are necessary for efficient and reproducible bioprocesses in an orbitally shaken bioreactor (OSR). Mixing, gas transfer, and volumetric power consumption (P(V)) were determined in both a 5-L OSR and a 3-L stirred-tank bioreactor (STR). The two cultivation systems had a similar mixing intensity, but the STR had a lower volumetric mass transfer coefficient of oxygen (k(L)a) and a higher P(V) than the OSR. Recombinant CHO cell lines expressing either tumor necrosis factor receptor as an Fc fusion protein (TNFR:Fc) or an anti-RhesusD monoclonal antibody were cultivated in the two systems. The 5-L OSR was operated in an incubator shaker with 5% CO(2) in the gas environment but without pH and DO control whereas the STR was operated with or without pH and DO control. Higher cell densities and recombinant protein titers were obtained in the OSR as compared to both the controlled and the non-controlled STRs. To test the reproducibility of a bioprocess in a non-controlled OSR, the two CHO cell lines were each cultivated in parallel in six 5-L OSRs. Similar cell densities, cell viabilities, and recombinant protein titers along with similar pH and DO profiles were achieved in each group of replicates. Our study demonstrated that bioprocesses can be performed in OSRs without pH or DO control in a highly reproducible manner, at least at the scale of operation studied here.     

k(L)a as a predictor for successful probe-independent mammalian cell bioprocesses in orbitally shaken bioreactors

The aim of this study was to gain a better understanding of orbitally shaken bioreactors (OSRs) operated without controllers for pH and dissolved oxygen (DO) concentration. We used cylindrical OSRs with working volumes ranging from 250mL to 200L to determine that the volumetric mass transfer coefficient of oxygen (k(L)a) is a good predictor of the performance of OSRs at different scales. We showed that k(L)a values of 7-10hour(-1) were required to avoid DO limitations and to prevent conditions of low pH during the cultivation of CHO cells. Overall, cell cultures in probe-independent OSRs of different nominal volumes ranging from 250mL to 200L achieved similar cell densities, recombinant protein concentrations, and pH and DO profiles when having the same k(L)a. We conclude that k(L)a is a key parameter for probe-independent bioprocesses in OSRs and can be used as a scale-up factor for their operation.     

Oxygen mass transfer and scale-up studies in baffled roller bioreactors

Oxygen mass transfer was studied in conventional, bead mill and baffled roller bioreactors. Using central composite rotational design, impacts of size, rotation speed and working volume on the oxygen mass transfer were evaluated. Baffled roller bioreactor outperformed its conventional and bead mill counterparts, with the highest k _L a obtained in these configurations being 0.58, 0.19, 0.41 min^?1, respectively. Performances of the bead mill and baffled roller bioreactor were only comparable when a high bead loading (40 %) was applied. Regardless of configuration increase in rotation speed and decrease in working volume improved the oxygen mass transfer rate. Increase in size led to enhanced mass transfer and higher k _L a in baffled roller bioreactor (0.49 min^?1 for 2.2 L and 1.31 min^?1 for 55 L bioreactors). Finally, the experimentally determined k _L a in the baffled roller bioreactors of different sizes fit reasonably well to an empirical correlation describing the k _L a in terms of dimensionless numbers.     

Composition and Activity of Marine Alkane-Degrading Bacterial Communities in the Transition from Suboxic to Anoxic Conditions

The impact of the oxygen supply rate (OSR) on the metabolic activity and on the composition of hexadecane-degrading bacterial communities in a quasi-anoxic milieu (nominal DOT=0%) was studied in continuous cultures containing intertidal sediment. The dilution rate was kept constant at 0.035 h⁻¹. The OSR was stepwise reduced from 3.5 mmol O₂L⁻¹ h⁻¹ to 0.06 mmol O₂L⁻¹ h⁻¹. Activity was determined by analyzing the respiration quotient (RQ) and the rates of hexadecane degradation (Q_Hex), of hexadecane mineralization, and of protein production (PPR). The community composition and size were investigated by fluorescence in situ hybridization (FISH), by dilution plating (colony forming units or CFU), and by most probable number (MPN). The culture showed an aerobic hexadecane metabolism down to an OSR of 0.35 mmol O₂L⁻¹ h⁻¹. Below this OSR, anaerobic metabolism was initiated. The relationship among the RQ, PPR, Q_Hex, and the OSR can be approximated by hyperbola (Michaelis-Menten kinetics). We suggest that the metabolic adaptation of the culture to low OSRs is due to regulation of protein expression and enzyme activity. Reducing the OSR resulted in minor but significant changes in the concentration of different physiological and phylogenetic groups. This means that, in addition to protein expression and activity regulation, the adaptation of the population to low OSRs is due to changes in the community composition.     

Patterns of Aggression and Operational Sex Ratio Within Alternative Male Phenotypes in Atlantic Salmon

The intensity of male–male aggression during mating is predicted to increase with the operational sex ratio (OSR) (the ratio of sexually active males to females). We observed aggressive behaviour in relation to OSR within alternative phenotypes (large anadromous males and small ‘sneaker’ mature male parr) of Atlantic salmon, Salmo salar, as they competed for access to anadromous females in large outdoor arenas immediately prior to spawning events as well as throughout the spawning season. Anadromous males were primarily aggressive outside of spawning events, and their aggression increased with OSR over a narrow range of 0.08–4. By contrast, mature male parr were aggressive just prior to spawning, with a decrease in aggression over a broad range of OSRs from 1 to 7.4. Similarly, literature data for three other salmonid species indicated a decrease in aggression with increasing OSRs over a range of 1–6.33. These observations suggest that there is considerable variability in competitive behaviour, even within alternative phenotypes. Because our data are derived from repeated observations on the same individuals of different genetic origin, further confirmation of these findings is desirable. Nevertheless, our study underscores the importance of measuring competitive behaviour and OSR at ecologically relevant spatial and temporal scales, both of which may differ between alternative maturation phenotypes.     

Behavioral Tactics of Male Sockeye Salmon (Oncorhynchus nerka) under Varying Operational Sex Ratios

Previous studies have demonstrated several reproductive-behavior patterns in male salmon, including competitive and sneaking tactics, the formation of hierarchies, and non-hierarchical aggregations around ripe females. Through behavioral observations at varying spatial and temporal scales, we examined the hypothesis that operational sex ratio (OSR) determines male sockeye salmon (Oncorhynchus nerka) distribution and breeding tactics. Patterns of male distribution and behavior varied over both coarse and fine scales, associated with apparent shifts in reproductive opportunities, the physical characteristics of the breeding sites, and the deterioration of the fish as they approached death. Females spawned completely within a few days of arriving on the spawning grounds, whereas males courted the available ripe females from the date of their arrival on the spawning ground until their death. This difference in reproductive lifespans tended to elevate late-season OSRs but was partially counterbalanced by male departures and the arrival of other ripe females. The proportion of males able to dominate access to ripe females decreased and the number of large courting groups increased over the course of the season, apparently related to both increasing OSR and the deteriorating physical condition of males. However, great variation in OSR was observed within the spawning sites on a given day. OSRs were generally higher in shallow than in deep water, perhaps because larger females or more desirable breeding sites were concentrated in shallow water. The aggregations of males courting females were not stable (i.e. many arrivals and departures took place) and male aggression varied with group size. Aggression was most frequent at low OSRs and in groups of intermediate size (2–4 males per female), and much less frequent in larger groups, consistent with the needs of maximizing reproductive opportunities while minimizing unproductive energy expenditure. These results indicate that, while OSR strongly influences male distribution and behavior, other factors such as physical condition, limited movement and habitat choice may also affect male reproductive opportunities.     

OPERATIONAL SEX RATIO BUT NOT DENSITY AFFECTS SEXUAL SELECTION IN A FISH

The operational sex ratio (OSR) and density are considered important factors affecting the strength of sexual selection. Although there is increasing evidence that OSR and density affect the potential for sexual selection, few studies have addressed whether this is realized in phenotypic selection and how the two factors interact. We manipulated OSR (three levels) and male density (two levels) in 36 experimental breeding populations of Gobiusculus flavescens—a fish with paternal care. We measured mating competition behavior, the opportunity for selection (I), and selection on four morphological traits in males. We found sexual selection on two male traits, with the strongest selection being 20% of I. As predicted from OSR theory, increasing female scarcity caused males to become more competitive, concomitant with an increase in I and selection on morphological traits. Model simulations of I based on random mating (I_min) and maximum mate monopolization (I_max) demonstrated that the potential for sexual selection was close to its theoretical maximum across the range of OSRs. However, male density and its interaction with the OSR did not affect sexual selection. We argue that a multifaceted approach, combining mating behavior and selection analyses, can help us to understand how ecological factors affect sexual selection.     

Scale‐up analysis for a CHO cell culture process in large‐scale bioreactors

Bioprocess scale‐up is a fundamental component of process development in the biotechnology industry. When scaling up a mammalian cell culture process, it is important to consider factors such as mixing time, oxygen transfer, and carbon dioxide removal. In this study, cell‐free mixing studies were performed in production scale 5,000‐L bioreactors to evaluate scale‐up issues. Using the current bioreactor configuration, the 5,000‐L bioreactor had a lower oxygen transfer coefficient, longer mixing time, and lower carbon dioxide removal rate than that was observed in bench scale 5‐ and 20‐L bioreactors. The oxygen transfer threshold analysis indicates that the current 5,000‐L configuration can only support a maximum viable cell density of 7 × 10⁶ cells mL^?1. Moreover, experiments using a dual probe technique demonstrated that pH and dissolved oxygen gradients may exist in 5,000‐L bioreactors using the current configuration. Empirical equations were developed to predict mixing time, oxygen transfer coefficient, and carbon dioxide removal rate under different mixing‐related engineering parameters in the 5,000‐L bioreactors. These equations indicate that increasing bottom air sparging rate is more efficient than increasing power input in improving oxygen transfer and carbon dioxide removal. Furthermore, as the liquid volume increases in a production bioreactor operated in fed‐batch mode, bulk mixing becomes a challenge. The mixing studies suggest that the engineering parameters related to bulk mixing and carbon dioxide removal in the 5,000‐L bioreactors may need optimizing to mitigate the risk of different performance upon process scale‐up. Biotechnol. Bioeng. 2009;103: 733–746. © 2009 Wiley Periodicals, Inc.     

Operational sex ratio and density do not affect directional selection on male sexual ornaments and behavior

Demographic parameters including operational sex ratio (OSR) and population density may influence the opportunity for, and strength of sexual selection. Traditionally, male-biased OSRs and high population densities have been thought to increase the opportunity for sexual selection on male sexual traits due to increased male competition for mates. Recent experimental evidence, however, suggests that male-biased OSRs might reduce the opportunity for sexual selection due to increased sexual coercion experienced by females. How OSR, density, and any resultant changes in the opportunity for sexual selection actually affect selection on male sexual traits is unclear. In this study, we independently manipulated OSR and density in the guppy (Poecilia reticulata) without altering the number of males present. We recorded male and female behavior and used DNA microsatellite data to assign paternity to offspring and estimate male reproductive success. We then used linear selection analyses to examine the effects of OSR and density on directional sexual selection on male behavioral and morphological traits. We found that females were pursued more by males in male-biased treatments, despite no change in individual male behavior. There were no differences in sexual behavior experienced by females or performed by males in relation to density. Neither OSR nor density significantly altered the opportunity for sexual selection. Also, Although there was significant multivariate linear selection operating on males, neither OSR nor density altered the pattern of sexual selection on male traits. Our results suggest that differences in either OSR or density (independent of the number of males present) are unlikely to alter directional evolutionary change in male sexual traits.     

Mass transfer and hydrodynamic characteristics of unbaffled stirred bio-reactors: Influence of impeller design

Unbaffled stirred tanks are increasingly recognized as a viable alternative to common baffled tanks for a range of processes where the presence of baffles is undesirable for some reason. For instance, in the case of shear sensitive cell cultivation (e.g. human cells), unbaffled tanks have been recently found to be able to provide sufficient mass transfer through the free surface vortex. As a consequence the need for bubble formation and subsequent bursting, along with relevant cells damage, is conveniently avoided. In this work the influence of impeller geometry on mass transfer performance and power demand of an unbaffled stirred vessel operating both in sub-critical conditions (the free surface vortex has not yet reached the impeller) and in super-critical conditions (the free surface vortex has reached the impeller and a gas phase is ingested and dispersed inside the reactor) is presented.Experimental results show that the mass transfer performance of unbaffled systems is mainly affected by specific power consumption. Among the stirrer geometries investigated a simple PBT was found to provide the most interesting oxygen transfer performance in the sub-critical regime, and can therefore be regarded as a particularly suitable stirrer for shear sensitive cultures. As regards the super-critical regime, unbaffled tanks are found to provide a performance comparable with that of the standard (baffled) bioreactors, hence resulting in a viable alternative also for fermentations involving robust cells.     

Evaluation of criteria for bioreactor comparison and operation standardization for mammalian cell culture

Development of bioprocesses with mammalian cell culture deals with different bioreactor types and scales. The bioreactors might be intended for generation of cell inoculum and production, research, process development, validation, or transfer purposes. During these activities, not only the difficulty of up and downscaling might lead to failure of consistency in cell growth, but also the use of different bioreactor geometries and operation conditions. In such cases, criteria for bioreactor design and process transfer should be carefully evaluated in order to select appropriate cultivation parameters. In this work, power input, mixing time, impeller tip speed, and Reynolds number have been compared systematically for the cultivation of the human cell line AGE1.HN within three partner laboratories using five different bioreactor systems. Proper operation ranges for the bioreactors were identified using the maximal cell‐specific growth rate (μ_max) as indicator. Common optimum values for process transfer criteria were found in these geometrically different bioreactors, in which deviations of μ_max between cultivation systems can be importantly reduced. The data obtained in this work are used for process standardization and comparability of results obtained in different bioreactor systems, i.e. to guarantee lab‐to‐lab consistency for systems biology approaches using mammalian cells.     

Time efficient way to calculate oxygen transfer areas and power input in cylindrical disposable shaken bioreactors

Disposable orbitally shaken bioreactors are a promising alternative to stirred or wave agitated systems for mammalian and plant cell cultivation, because they provide a homogeneous and well‐defined liquid distribution together with a simple and cost‐efficient design. Cultivation conditions in the surface‐aerated bioreactors are mainly affected by the size of the volumetric oxygen transfer area (a) and the volumetric power input (P∕V_L) that both result from the liquid distribution during shaking. Since Computational Fluid Dynamics (CFD)—commonly applied to simulate the liquid distribution in such bioreactors—needs high computing power, this technique is poorly suited to investigate the influence of many different operating conditions in various scales. Thus, the aim of this paper is to introduce a new mathematical model for calculating the values of a and P∕V_L for liquids with water‐like viscosities. The model equations were derived from the balance of centrifugal and gravitational forces exerted during shaking. A good agreement was found among calculated values for a and P∕V_L, CFD simulation values and empirical results. The newly proposed model enables a time efficient way to calculate the oxygen transfer areas and power input for various shaking frequencies, filling volumes and shaking and reactor diameters. All these parameters can be calculated fast and with little computing power. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1441–1456, 2014     

Characterization of the localized hydrodynamic shear forces and dissolved oxygen distribution in sparged bioreactors

Detailed, high-resolution numerical simulations of the bubbly flows, used for oxygen delivery and mixing in mammalian cell suspensions, have been performed. The hydrodynamics, shear and normal forces, mass transfer and mass transport from and around individual bubbles and bubble clusters were resolved for different operating conditions, that is, Weber, Morton, and Schmidt numbers. Suspended animal (e.g., mammalian, insect) cells are known to be susceptible to damage potentially leading to cell death, caused by hydrodynamic stresses and oxygen deprivation. Better knowledge of the magnitude of the shear forces and the extent of mixing of the dissolved oxygen in sparged bioreactors can have a significant impact on their future design and optimization. Therefore, the computed liquid-phase velocity fields were used to calculate and compare the local shear in different types of single bubble wakes and in bubble clusters. Oxygen mass transfer and dissolved oxygen transport were resolved to examine oxygen supply to the cells in the different types of flows.     

Spiking neurons that keep the rhythm

Detecting the temporal relationship among events in the environment is a fundamental goal of the brain. Following pulses of rhythmic stimuli, neurons of the retina and cortex produce activity that closely approximates the timing of an omitted pulse. This omitted stimulus response (OSR) is generally interpreted as a transient response to rhythmic input and is thought to form a basis of short-term perceptual memories. Despite its ubiquity across species and experimental protocols, the mechanisms underlying OSRs remain poorly understood. In particular, the highly transient nature of OSRs, typically limited to a single cycle after stimulation, cannot be explained by a simple mechanism that would remain locked to the frequency of stimulation. Here, we describe a set of realistic simulations that capture OSRs over a range of stimulation frequencies matching experimental work. The model does not require an explicit mechanism for learning temporal sequences. Instead, it relies on spike timing-dependent plasticity (STDP), a form of synaptic modification that is sensitive to the timing of pre- and post-synaptic action potentials. In the model, the transient nature of OSRs is attributed to the heterogeneous nature of neural properties and connections, creating intricate forms of activity that are continuously changing over time. Combined with STDP, neural heterogeneity enabled OSRs to complex rhythmic patterns as well as OSRs following a delay period. These results link the response of neurons to rhythmic patterns with the capacity of heterogeneous circuits to produce transient and highly flexible forms of neural activity.     

A study of mass transfer in yeast in a pulsed baffled bioreactor

We report experimental data of mass transfer of oxygen into yeast resuspension in a pulsed baffled bioreactor. The bioreactor consists of a 50-mm-diameter column with the presence of a series of either wall (orifice) or central (disc) baffles or a mixture of both where fluid oscillation can also be supermposed during the experiments. Air bubbles are sparged into the bottom of the pulsed baffled bioreactor, and the kinetics of liquid oxygen concentration in the yeast solution is followed using a dissolved oxygen probe with a fast response time of 3 s together with the dynamic gassing-out technique. Among the three different baffle geometries investigated, the orifice baffles gave the highest and sharpest increase in the oxygen transfer rate, and the trends in the k(L)a measurements are consistent with the fluid mechanics observed within both the systems and previous work. In addition, we have also compared the k(L)a values with those obtained in a stirred tank; an 11% increase in the K(L)a is reported. (c) 1995 John Wiley & Sons, Inc.     

The baffled microtiter plate: Increased oxygen transfer and improved online monitoring in small scale fermentations

Most experiments in screening and process development are performed in shaken bioreactors. Today, microtiter plates are the preferred vessels for small‐scale microbial cultivations in high throughput, even though they have never been optimized for this purpose. To interpret the experimental results correctly and to obtain a base for a meaningful scale‐up, sufficient oxygen supply to the culture liquid is crucial. For shaken bioreactors this problem can generally be addressed by the introduction of baffles. Therefore, the focus of this study is to investigate how baffling and the well geometry affect the maximum oxygen transfer capacity (OTR_max) in microtiter plates. On a 48‐well plate scale, 30 different cross‐section geometries of a well were studied. It could be shown that the introduction of baffles into the common circular cylinder of a microtiter plate well doubles the maximum oxygen transfer capacity, resulting in values above 100 mmol/L/h (k_La > 600 1/h). To also guarantee a high volume for microbial cultivation, it is important to maximize the filling volume, applicable during orbital shaking. Additionally, the liquid height at the well bottom was examined, which is a decisive parameter for online‐monitoring systems such as the BioLector. This technology performs fiber‐optical measurements through the well bottom, therefore requires a constant liquid height at all shaking frequencies. Ultimately, a six‐petal flower‐shaped well geometry was shown to be the optimal solution taking into account all aforementioned criteria. With its favorable culture conditions and the possibility for unrestricted online monitoring, this novel microtiter plate is an efficient tool to gain meaningful results for interpreting and scaling‐up experiments in clone screening and bioprocess development. Biotechnol. Bioeng. 2009;103: 1118–1128. © 2009 Wiley Periodicals, Inc.