In situ microscopy for online monitoring of cell concentration in Pichia pastoris cultivations

Non-Invasive Characterization of Different Saccharomyces Suspensions with Ultrasound

In fermentation processes, changes in yeast cell count and substrate concentration are indicators of yeast performance. Therefore, monitoring the composition of the biological suspension, particularly the dispersed solid phase (i.e., yeast cells) and the continuous liquid phase (i.e., medium), is a prerequisite to ensure favorable process conditions. However, the available monitoring methods are often invasive or restricted by detection limits, sampling requirements, or susceptibility to masking effects from interfering signals. In contrast, ultrasound measurements are non-invasive and provide real-time data. In this study, the suitability to characterize the dispersed and the liquid phase of yeast suspensions with ultrasound was investigated. The ultrasound signals collected from three commercially available Saccharomyces yeast were evaluated and compared. For all three yeasts, the attenuation coefficient and speed of sound increased linearly with increasing yeast concentrations (0.0-1.0 wt%) and cell counts (R2 > 0.95). Further characterization of the dispersed phase revealed that cell diameter and volume density influence the attenuation of the ultrasound signal, whereas changes in the speed of sound were partially attributed to compositional variations in the liquid phase. This demonstrates the ability of ultrasound to monitor industrial fermentations and the feasibility of developing targeted control strategies.

Label-free detection and enumeration of Giardia cysts in agitated suspensions using in situ microscopy

Laboratory procedures performed in water treatment studies frequently require the characterization of (oo)cyst suspensions. Standard methods commonly used are laborious, expensive and time-consuming, besides requiring well-trained personnel to prepare samples with fluorescent staining and perform analysis under fluorescence microscopy. In this study, an easy cost-effective in situ microscope was assessed to acquire images of Giardia cysts directly from agitated suspensions without using any chemical labels or sample preparation steps. An image analysis algorithm analyzes the acquired images, and automatically enumerates and provides morphological information of cysts within 10 min. The proposed system was evaluated at different cyst concentrations, achieving a limit of detection of ~30 cysts/mL. The proposed system overcomes cost, time and labor demands by standard methods and has the potential to be an alternative technique for the characterization of Giardia cyst suspensions in resource-limited facilities, since it is independent of experts and free of consumables.

Morphometric quantification of a pseudohyphae forming Saccharomyces cerevisiae strain using in situ microscopy and image analysis

Yeast morphology and counting are highly important in fermentation as they are often associated with productivity and can be influenced by process conditions. At present, time-consuming and offline methods are utilized for routine analysis of yeast morphology and cell counting using a haemocytometer. In this study, we demonstrate the application of an in situ microscope to obtain a fast stream of pseudohyphae images from agitated sample suspensions of a Saccharomyces cerevisiae strain, whose morphology in cell clusters is frequently found in the bioethanol fermentation industry. The large statistics of microscopic images allow for online determination of the principal morphological characteristics of the pseudohyphae, including the number of constituent cells, cell-size, number of branches, and length of branches. The distributions of these feature values are calculated online, constituting morphometric monitoring of the pseudohyphae population. By providing representative data, the proposed system can improve the effectiveness of morphological characterization, which in turn can help to improve the understanding and control of bioprocesses in which pseudohyphal-like morphologies are found.

Application of In-Situ and Soft-Sensors for Estimation of Recombinant P. pastoris GS115 Biomass Concentration: A Case Analysis of HBcAg (Mut+) and HBsAg (MutS) Production Processes under Varying Conditions

Microbial biomass concentration is a key bioprocess parameter, estimated using various labor, operator and process cross-sensitive techniques, analyzed in a broad context and therefore the subject of correct interpretation. In this paper, the authors present the results of P. pastoris cell density estimation based on off-line (optical density, wet/dry cell weight concentration), in-situ (turbidity, permittivity), and soft-sensor (off-gas O₂/CO₂, alkali consumption) techniques. Cultivations were performed in a 5 L oxygen-enriched stirred tank bioreactor. The experimental plan determined varying aeration rates/levels, glycerol or methanol substrates, residual methanol levels, and temperature. In total, results from 13 up to 150 g (dry cell weight)/L cultivation runs were analyzed. Linear and exponential correlation models were identified for the turbidity sensor signal and dry cell weight concentration (DCW). Evaluated linear correlation between permittivity and DCW in the glycerol consumption phase (<60 g/L) and medium (for Mut⁺ strain) to significant (for Mut^S strain) linearity decline for methanol consumption phase. DCW and permittivity-based biomass estimates used for soft-sensor parameters identification. Dataset consisting from 4 Mut⁺ strain cultivation experiments used for estimation quality (expressed in NRMSE) comparison for turbidity-based (8%), permittivity-based (11%), O₂ uptake-based (10%), CO₂ production-based (13%), and alkali consumption-based (8%) biomass estimates. Additionally, the authors present a novel solution (algorithm) for uncommon in-situ turbidity and permittivity sensor signal shift (caused by the intensive stirrer rate change and antifoam agent addition) on-line identification and minimization. The sensor signal filtering method leads to about 5-fold and 2-fold minimized biomass estimate drifts for turbidity- and permittivity-based biomass estimates, respectively.

Online monitoring of the cell-specific oxygen uptake rate with an in situ combi-sensor

In a biotechnological process, standard monitored process variables are pH, partial oxygen pressure (pO₂), and temperature. These process variables are important, but they do not give any information about the metabolic activity of the cell. The ISICOM is an in situ combi-sensor that is measuring the cell-specific oxygen uptake rate (qOUR) online. This variable allows a qualitative judgement of metabolic cell activity. The measuring principle of the ISICOM is based on a volume element enclosed into a small measuring chamber. Inside the measuring chamber, the pO₂ and the scattered light is measured. Within a defined measuring interval, the chamber closes, and the oxygen supply for the cells is interrupted. The decreasing oxygen concentration is recorded by the pO₂ optode. This measuring principle, known as the dynamic method, determines the oxygen uptake rate (OUR). Together with the scattered light signal, the cell concentration is estimated and the qOUR is available online. The design of the ISICOM is focused on functionality, sterility, long-term stability, and response time behavior so the sensor can be used in bioprocesses. With the ISICOM, measurement of online and in situ measurement of the OUR is possible. The OUR and qOUR online measurement of an animal cell batch cultivation is demonstrated, with maximum values of OUR = 2.5 mmol L^-1 h^-1 and a qOUR = 9.5 pmol cell^-1 day^-1. Information about limitation of the primary and secondary substrate is derived by the monitoring of the metabolic cell activity of bacteria and yeast cultivation processes. This sensor contributes to a higher process understanding by offering an online view on to the cell behavior. In the sense of process analytical technology (PAT), this important information is needed for bioprocesses to realize a knowledge base process control.

In situ microscopy as online tool for detecting microbial contaminations in cell culture

Microbial contamination in mammalian cell cultures causing rejected batches is costly and highly unwanted. Most methods for detecting a contamination are time-consuming and require extensive off-line sampling. To circumvent these efforts and provide a more convenient alternative, we used an online in situ microscope to estimate the cell diameter of the cellular species in the culture to distinguish mammalian cells from microbial cells depending on their size. A warning system was set up to alert the operator if microbial cells were present in the culture. Hybridoma cells were cultured and infected with either Candida utilis or Pichia stipitis as contaminant. The warning system could successfully detect the introduced contamination and alert the operator. The results suggest that in situ microscopy could be used as an efficient online tool for early detection of contaminations in cell cultures.

Real-time monitoring of the budding index in Saccharomyces cerevisiae batch cultivations with in situ microscopy

BACKGROUND

The morphology of yeast cells changes during budding, depending on the growth rate and cultivation conditions. A photo-optical microscope was adapted and used to observe such morphological changes of individual cells directly in the cell suspension. In order to obtain statistically representative samples of the population without the influence of sampling, in situ microscopy (ISM) was applied in the different phases of a Saccharomyces cerevisiae batch cultivation. The real-time measurement was performed by coupling a photo-optical probe to an automated image analysis based on a neural network approach.

RESULTS

Automatic cell recognition and classification of budding and non-budding cells was conducted successfully. Deviations between automated and manual counting were considerably low. A differentiation of growth activity across all process stages of a batch cultivation in complex media became feasible. An increased homogeneity among the population during the growth phase was well observable. At growth retardation, the portion of smaller cells increased due to a reduced bud formation. The maturation state of the cells was monitored by determining the budding index as a ratio between the number of cells, which were detected with buds and the total number of cells. A linear correlation between the budding index as monitored with ISM and the growth rate was found.

CONCLUSION

It is shown that ISM is a meaningful analytical tool, as the budding index can provide valuable information about the growth activity of a yeast cell, e.g. in seed breeding or during any other cultivation process. The determination of the single-cell size and shape distributions provided information on the morphological heterogeneity among the populations. The ability to track changes in cell morphology directly on line enables new perspectives for monitoring and control, both in process development and on a production scale.

Engineering strategies for enhanced production of protein and bio-products in Pichia pastoris: A review

Pichia pastoris has been recognized as one of the most industrially important hosts for heterologous protein production. Despite its high protein productivity, the optimization of P. pastoris cultivation is still imperative due to strain- and product-specific challenges such as promoter strength, methanol utilization type and oxygen demand. To address the issues, strategies involving genetic and process engineering have been employed. Optimization of codon usage and gene dosage, as well as engineering of promoters, protein secretion pathways and methanol metabolic pathways have proved beneficial to innate protein expression levels. Large-scale production of proteins via high cell density fermentation additionally relies on the optimization of process parameters including methanol feed rate, induction temperature and specific growth rate. Recent progress related to the enhanced production of proteins in P. pastoris via various genetic engineering and cultivation strategies are reviewed. Insight into the regulation of the P. pastoris alcohol oxidase 1 (AOX1) promoter and the development of methanol-free systems are highlighted. Novel cultivation strategies such as mixed substrate feeding are discussed. Recent advances regarding substrate and product monitoring techniques are also summarized. Application of P. pastoris to the production of biodiesel and other value-added products via metabolic engineering are also reviewed. P. pastoris is becoming an indispensable platform through the use of these combined engineering strategies.