Synthetic co-culture in an interconnected two-compartment bioreactor system: violacein production with recombinant E. coli strains

The concept of modular synthetic co-cultures holds considerable potential for biomanufacturing, primarily to reduce the metabolic burden of individual strains by sharing tasks among consortium members. However, current consortia often show unilateral relationships solely, without stabilizing feedback control mechanisms, and are grown in a shared cultivation setting. Such 'one pot' approaches hardly install optimum growth and production conditions for the individual partners. Hence, novel mutualistic, self-coordinating consortia are needed that are cultured under optimal growth and production conditions for each member. The heterologous production of the antibiotic violacein (VIO) in the mutually interacting E. coli-E. coli consortium serves as an example of this new principle. Interdependencies for growth control were implemented via auxotrophies for L-tryptophan and anthranilate (ANT) that were satisfied by the respective partner. Furthermore, VIO production was installed in the ANT auxotrophic strain. VIO production, however, requires low temperatures of 20-30 °C which conflicts with the optimum growth temperature of E. coli at 37 °C. Consequently, a two-compartment, two-temperature level setup was used, retaining the mutual interaction of the cells via the filter membrane-based exchange of medium. This configuration also provided the flexibility to perform individualized batch and fed-batch strategies for each co-culture member. We achieved maximum biomass-specific productivities of around 6 mg (g h)-1 at 25 °C which holds great promise for future applications.

Self-Buffering system for Cost-Effective production of lactic acid from glucose and xylose using Acid-Tolerant Issatchenkia orientalis

This study presents a cost-effective strategy for producing organic acids from glucose and xylose using the acid-tolerant yeast, Issatchenkia orientalis. I. orientalis was engineered to produce lactic acid from xylose, and the resulting strain, SD108XL, successfully converted sorghum hydrolysates into lactic acid. In order to enable low-pH fermentation, a self-buffering strategy, where the lactic acid generated by the SD108XL strain during fermentation served as a buffer, was developed. As a result, the SD108 strain produced 67 g/L of lactic acid from 73 g/L of glucose and 40 g/L of xylose, simulating a sugar composition of sorghum biomass hydrolysates. Moreover, techno-economic analysis underscored the efficiency of the self-buffering strategy in streamlining the downstream process, thereby reducing production costs. These results demonstrate the potential of I. orientalis as a platform strain for the cost-effective production of organic acids from cellulosic hydrolysates.

Assessing the feasibility and sustainability of a surfactin production process: a techno-economic and environmental analysis

Biosurfactants have been profiled as a sustainable replacement for chemical-based surfactants since these bio-based molecules have higher biodegradability. Few research papers have focused on assessing biosurfactant production to elucidate potential bottlenecks. This research aims to assess the techno-economic and environmental performance of surfactin production in a potential scale of 65m3, considering different product yields and involving the European energy crisis of 2021-2022. The conceptual design, simulation, techno-economic, and environmental assessments were done by applying process engineering concepts and software tools such as Aspen Plus v.9.0 and SimaPro v.8.3.3. The results demonstrated the high economic potential of surfactin production since the higher values in the market offset the low fermentation yields, low recovery efficiency, and high capital investment. The sensitivity analysis of the economic assessment elucidated a minimum surfactin selling price between 29 and 31 USD/kg of surfactin, while a minimum processing scale for economic feasibility between 4 and 5 kg/h is needed to reach an equilibrium point. The environmental performance must be improved since the carbon footprint was 43 kg CO2eq/kg of surfactin. The downstream processing and energy demand are the main bottlenecks since these aspects contribute to 63 and 25% of the total emissions. The fermentation process and downstream process are key factors for future optimization and research.

OptMSP: A toolbox for designing optimal multi-stage (bio)processes

One central goal of bioprocess engineering is to maximize the production of specific chemicals using microbial cell factories. Many bioprocesses are one-stage (batch) processes (OSPs), in which growth and product synthesis are coupled. However, OSPs often exhibit low volumetric productivities due to the competition for substrate for biomass and product synthesis implying trade-offs between biomass and product yields. Two-stage or, more generally, multi-stage processes (MSPs) offer the potential to tackle this trade-off for improved efficiency of bioprocesses, for example, by separating growth and production. MSPs have recently gained much attention, also because of a rapidly growing toolbox for the dynamic control of metabolic fluxes. Despite these promising advancements, computational tools specifically tailored for the optimal design of MSPs in the field of biotechnology are still lacking. Here, we present OptMSP, a new Python-based toolbox for identifying optimal MSPs maximizing a user-defined process metrics (such as volumetric productivity, yield, and titer or combinations thereof) under given constraints. In contrast to other methods, our framework starts with a set of well-defined modules representing relevant stages or sub-processes. Experimentally determined parameters (such as growth rates, substrate uptake and product formation rates) are used to build suitable ODE models describing the dynamic behavior of each module. OptMSP finds then the optimal combination of those modules, which, together with the optimal switching time points, maximize a given objective function. We demonstrate the applicability and relevance of the approach with three different case studies, including the example of lactate production by E. coli in a batch setup, where an aerobic growth phase can be combined with anaerobic production phases with or without growth and with or without enhanced ATP turnover.

Modeling the behavior of monoclonal antibodies on hydrophobic interaction chromatography resins

Monoclonal antibodies (mAbs) require a high level of purity for regulatory approval and safe administration. High-molecular weight (HMW) species are a common impurity associated with mAb therapies. Hydrophobic interaction chromatography (HIC) resins are often used to remove these HMW impurities. Determination of a suitable HIC resin can be a time and resource-intensive process. In this study, we modeled the chromatographic behavior of seven mAbs across 13 HIC resins using measurements of surface hydrophobicity, surface charge, and thermal stability for mAbs, and hydrophobicity and zeta-potential for HIC resins with high fit quality (adjusted R2 > 0.80). We identified zeta-potential as a novel key modeling parameter. When using these models to select a HIC resin for HMW clearance of a test mAb, we were able to achieve 60% HMW clearance and 89% recovery. These models can be used to expedite the downstream process development for mAbs in an industry setting.

Recombinant therapeutic proteins degradation and overcoming strategies in CHO cells

Mammalian cell lines are frequently used as the preferred host cells for producing recombinant therapeutic proteins (RTPs) having post-translational modified modification similar to those observed in proteins produced by human cells. Nowadays, most RTPs approved for marketing are produced in Chinese hamster ovary (CHO) cells. Recombinant therapeutic antibodies are among the most important and promising RTPs for biomedical applications. One of the issues that occurs during development of RTPs is their degradation, which caused by a variety of factors and reducing quality of RTPs. RTP degradation is especially concerning as they could result in reduced biological functions (antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity) and generate potentially immunogenic species. Therefore, the mechanisms underlying RTP degradation and strategies for avoiding degradation have regained an interest from academia and industry. In this review, we outline recent progress in this field, with a focus on factors that cause degradation during RTP production and the development of strategies for overcoming RTP degradation. KEY POINTS: • The recombinant therapeutic protein degradation in CHO cell systems is reviewed. • Enzymatic factors and non-enzymatic methods influence recombinant therapeutic protein degradation. • Reducing the degradation can improve the quality of recombinant therapeutic proteins.

Recent advances in methanol production from methanotrophs

Methanol, the simplest aliphatic molecule of the alcohol family, finds diverse range of applications as an industrial solvent, a precursor for producing other chemicals (e.g., dimethyl ether, acetic acid and formaldehyde), and a potential fuel. There are conventional chemical routes for methanol production such as, steam reforming of natural gas to form syngas, followed by catalytic conversion into methanol; direct catalytic oxidation of methane, or hydrogenation of carbon dioxide. However, these chemical routes are limited by the requirement for expensive catalysts and extreme process conditions, and plausible environmental implications. Alternatively, methanotrophic microorganisms are being explored as biological alternative for methanol production, under milder process conditions, bypassing the requirement for chemical catalysts, and without imposing any adverse environmental impact. Methanotrophs possess inherent metabolic pathways for methanol production via biological methane oxidation or carbon dioxide reduction, thus offering a surplus advantage pertaining to the sequestration of two major greenhouse gases. This review sheds light on the recent advances in methanotrophic methanol production including metabolic pathways, feedstocks, metabolic engineering, and bioprocess engineering approaches. Furthermore, various reactor configurations are discussed in view of the challenges associated with solubility and mass transfer limitations in methanotrophic gas fermentation systems.

CPV of the Future: AI-Powered Continued Process Verification for Bioreactor Processes

According to the standard guidelines by the FDA, process validation in biopharma manufacturing encompasses a life cycle consisting of three stages: process design (PD), process qualification (PQ), and continued process verification (CPV). The validity and efficiency of the analytics methods employed during the CPV require extensive knowledge of the process. However, for new processes and new drugs, such knowledge is often not available from Process performance qualification and Validation (PPQV). In this work, the suitability of methods based on machine learning/artificial intelligence (ML/AI) for the CPV applied in bioprocess monitoring and cell physiological control of the yeast Pichia pastoris (Komagataella phaffii) was studied with limited historical data. In particular, the production of recombinant Candida rugosa lipase 1 (Crl1) under hypoxic conditions in fed-batch cultures was considered as a case study. Supervised and unsupervised machine learning models using data from fed-batch bioprocesses with different gene dosage clones under normoxic and hypoxic conditions were evaluated. Firstly, a multivariate anomaly detection (isolation forest) model was applied to the batch phase of the bioprocess. Secondly, a supervised random forest model for prediction of required operator's control actions during the semiautomated fed-batch phase under hypoxic conditions was assessed to maintain the respiratory quotient (RQ) within the desired range for maximizing the specific production rate (q_P ). The performance of these models was tested on historical data using independent evaluation of the process by the process control engineer (subject matter expert-SME), and on real-time data in the case of manual action prediction, where the model was implemented to guide the control of the bioprocess. The work presented here constitutes a proof-of-concept that multivariate analytics methods, based on machine learning, can be a valuable tool for real-time monitoring and control of biopharma manufacturing bioprocesses to improve its efficiency and to assure product quality.

Genome-guided approaches and evaluation of the strategies to influence bioprocessing assisted morphological engineering of Streptomyces cell factories

Streptomyces genera serve as adaptable cell factories for secondary metabolites with various and distinctive chemical structures that are relevant to the pharmaceutical industry. Streptomyces' complex life cycle necessitated a variety of tactics to enhance metabolite production. Identification of metabolic pathways, secondary metabolite clusters, and their controls have all been accomplished using genomic methods. Besides this, bioprocess parameters were also optimized for the regulation of morphology. Kinase families were identified as key checkpoints in the metabolic manipulation (DivIVA, Scy, FilP, matAB, and AfsK) and morphology engineering of Streptomyces. This review illustrates the role of different physiological variables during fermentation in the bioeconomy coupled with genome-based molecular characterization of biomolecules responsible for secondary metabolite production at different developmental stages of the Streptomyces life cycle.

Strategies for Controlling Afucosylation in Monoclonal Antibodies during Upstream Manufacturing

Core fucosylation is a highly prevalent and significant feature of N-glycosylation in therapeutic monoclonal antibodies produced by mammalian cells where its absence (afucosylation) plays a key role in treatment safety and efficacy. Notably, even slight changes in the level of afucosylation can have a considerable impact on the antibody-dependent cell-mediated cytotoxicity. Therefore, implementing control over afucosylation levels is important in upstream manufacturing to maintain consistent quality across batches of product, since standard downstream processing does not change afucosylation. In this review, the influences and strategies to control afucosylation are presented. In particular, there is emphasis on upstream manufacturing culture parameters and media supplementation, as these offer particular advantages as control strategies over alternative approaches such as cell line engineering and chemical inhibitors. The review discusses the relationship between the afucosylation influences and the underlying cellular metabolism to promote increased process understanding. Also, briefly highlighted is the value of empirical and mechanistic models in evaluating and designing control methods for core fucosylation. This article is protected by copyright. All rights reserved.

Recombinant antibodies aggregation and overcoming strategies in CHO cells

Mammalian cell lines are frequently used as the preferred host cells for producing recombinant therapeutic proteins (RTPs) having post-translational modified modifications similar to those observed in proteins produced by human cells. Nowadays, most RTPs approved for marketing are produced in Chinese hamster ovary (CHO) cells. Recombinant therapeutic antibodies (RTAs) are among the most important and promising RTPs for biomedical applications. A major limitation associated with the use of RTAs is their aggregation, which can be caused by a variety of factors; this results in a reduction of quality. RTA aggregations are especially concerning as they can trigger human immune responses in humans and may be fatal. Therefore, the mechanisms underlying RTA aggregation and measures for avoiding aggregation are interesting topics in RTAs research. In this review, we discuss recent progress in the field of RTAs aggregation, with a focus on factors that cause aggregation during RTA production and the development of strategies for overcoming RTA aggregation. KEY POINTS: • The recombinant antibody aggregation in mammalian cell systems is reviewed. • Intracellular environment and extracellular parameters influence recombinant antibody aggregation. • Reducing the aggregations can improve the quality of recombinant antibodies.

Enhancing microbial lipids yield for biodiesel production by oleaginous yeast Lipomyces starkeyi fermentation: A review

The enhanced production of microbial lipids suitable for manufacturing biodiesel from oleaginous yeast Lipomyces starkeyi is critically reviewed. Recent advances in several aspects involving the biosynthetic pathways of lipids, current conversion efficiencies using various carbon sources, intensification strategies for improving lipid yield and productivity in L. starkeyi fermentation, and lipid extraction approaches are analyzed from about 100 papers for the past decade. Key findings on strategies are summarized, including (1) optimization of parameters, (2) cascading two-stage systems, (3) metabolic engineering strategies, (4) mutagenesis followed by selection, and (5) co-cultivation of yeast and algae. The current technical limitations are analyzed. Research suggestions like examination of more gene targets via metabolic engineering are proposed. This is the first comprehensive review on the latest technical advances in strategies from the perspective of process and metabolic engineering to further increase the lipid yield and productivity from L. starkeyi fermentation.

Metabolic engineering of Yarrowia lipolytica for improving squalene production

The aim of this present research is to enhance the squalene production in Yarrowia lipolytica using pathway engineering and bioprocess engineering. Firstly, to improve the production of squalene, the endogenous HMG-CoA reductase (HMG1) was overexpressed in Y. lipolytica to yield 208.88 mg/L squalene. Secondly, the HMG1 and diacylglycerol acyltranferase (DGA1) were co-overexpressed, the derived recombinant Y. lipolytica SQ-1 strain produced 439.14 mg/L of squalene. Thirdly, by optimizing the fermentation medium, the improved titer of squalene with 514.34 mg/L was obtained by the engineered strain SQ-1 grown on YPD-80 medium. Finally, by optimizing the addition concentrations of acetate, citrate and terbinafine, the 731.18 mg/L squalene was produced in the engineered strain SQ-1 with the addition of 0.5 mg/L terbinafine. This work describes the highest reported squalene titer in Y. lipolytica to date. This study will provide the foundation for further engineering Y. lipolytica capable of cost-efficiently producing squalene.

History and Evolution of Modeling in Biotechnology: Modeling & Simulation, Application and Hardware Performance

Biological systems are typically composed of highly interconnected subunits and possess an inherent complexity that make monitoring, control and optimization of a bioprocess a challenging task. Today a toolset of modeling techniques can provide guidance in understanding complexity and in meeting those challenges. Over the last four decades, computational performance increased exponentially. This increase in hardware capacity allowed ever more detailed and computationally intensive models approaching a “one-to-one” representation of the biological reality. Fueled by governmental guidelines like the PAT initiative of the FDA, novel soft sensors and techniques were developed in the past to ensure product quality and provide data in real time. The estimation of current process state and prediction of future process course eventually enabled dynamic process control. In this review, past, present and envisioned future of models in biotechnology are compared and discussed with regard to application in process monitoring, control and optimization. In addition, hardware requirements and availability to fit the needs of increasingly more complex models are summarized. The major techniques and diverse approaches of modeling in industrial biotechnology are compared, and current as well as future trends and perspectives are outlined.

Cost analysis based on bioreactor cultivation conditions: Production of a soluble recombinant protein using Escherichia coli BL21(DE3)

The impact of cultivation strategy on the cost of recombinant protein production is crucial for defining cost-effective bioreactor operation conditions. This paper presents a methodology to estimate and compare cost impacts related to utilities as well as medium composition, using simple design equations and accessible data. Data from batch bioreactor cultures were used as case study involving the production of pneumococcal surface protein A, a soluble recombinant protein, employing E. coli BL21(DE3). Cultivation strategies and corresponding process costs covered a wide range of operational conditions, including different media, inducers, and temperatures. The core expenses were related to the medium and cooling. When the price of peptone was above the threshold value of US$ 30/kg, defined medium became the best choice. IPTG and temperatures around 32 °C led to shorter cultures and lower PspA4Pro production costs. The procedure offers a simple, accessible theoretical tool to identify cost-effective production strategies using bioreactors.

Effect of alternating electrical current on denitrifying bacteria in a microbial electrochemical system: biofilm viability and ATP assessment

The present study considers the impact of the alternating electric current on the viability and biological activity of denitrifying bacteria in a microbial electrochemical system (MES). The bio-stimulation using low-frequency low-voltage alternating current (AC) was studied in terms of the adenosine triphosphate (ATP) level of bacteria, viability, morphological characteristics, cell size, and complexity. Apoptosis assays by flow cytometry revealed that 81-95% of the cells were non-apoptotic, and cell membrane damage occurred < 18%. The applied AC could affect the bacterial metabolic activity and ATP content in the denitrifying bacteria depending on characteristics of the alternating electric current. Scanning electron microscopy (SEM) analysis of cell morphology illustrated low cell deformations under AC stimulation. The obtained results revealed that the applied alternating electrical current could increase the metabolic activity of denitrifying bacteria, leading to a better denitrification. Graphical abstract ᅟ.

Metabolic engineering strategies for enhanced shikimate biosynthesis: current scenario and future developments

Shikimic acid is an important intermediate for the manufacture of the antiviral drug oseltamivir (Tamiflu®) and many other pharmaceutical compounds. Much of its existing supply is obtained from the seeds of Chinese star anise (Illicium verum). Nevertheless, plants cannot supply a stable source of affordable shikimate along with laborious and cost-expensive extraction and purification process. Microbial biosynthesis of shikimate through metabolic engineering and synthetic biology approaches represents a sustainable, cost-efficient, and environmentally friendly route than plant-based methods. Metabolic engineering allows elevated shikimate production titer by inactivating the competing pathways, increasing intracellular level of key precursors, and overexpressing rate-limiting enzymes. The development of synthetic and systems biology-based novel technologies have revealed a new roadmap for the construction of high shikimate-producing strains. This review elaborates the enhanced biosynthesis of shikimate by utilizing an array of traditional metabolic engineering along with novel advanced technologies. The first part of the review is focused on the mechanistic pathway for shikimate production, use of recombinant and engineered strains, improving metabolic flux through the shikimate pathway, chemically inducible chromosomal evolution, and bioprocess engineering strategies. The second part discusses a variety of industrially pertinent compounds derived from shikimate with special reference to aromatic amino acids and phenazine compound, and main engineering strategies for their production in diverse bacterial strains. Towards the end, the work is wrapped up with concluding remarks and future considerations.

Perspectives for the microbial production of methyl propionate integrated with product recovery

A new approach was studied for bio-based production of methyl propionate, a precursor of methyl methacrylate. Recombinant E. coli cells were used to perform a cascade reaction in which 2-butanol is reduced to butanone using alcohol dehydrogenase, and butanone is oxidized to methyl propionate and ethyl acetate using a Baeyer-Villiger monooxygenase (BVMO). Product was removed by in situ stripping. The conversion was in line with a model comprising product formation and stripping kinetics. The maximum conversion rates were 1.14 g-butanone/(L h), 0.11 g-ethyl acetate/(L h), and 0.09 g-methyl propionate/(L h). The enzyme regioselectivity towards methyl propionate was 43% of total ester. Starting from biomass-based production of 2-butanol, full-scale ester production with conventional product purification was calculated to be competitive with petrochemical production if the monooxygenase activity and regioselectivity are enhanced, and the costs of bio-based 2-butanol are minimized.

Recent Advances in Pichia pastoris as Host for Heterologous Expression System for Lipases: A Review

The production of heterologous lipases is one of the most promising strategies to increase the productivity of the bioprocesses and to reduce costs, with the final objective that more industrial lipase applications could be implemented.In this chapter, an overview of the new success in synthetic biology, with traditional molecular genetic techniques and bioprocess engineering in the last 5 years in the cell factory Pichia pastoris, the most promising host system for heterologous lipase production, is presented.The goals get on heterologous Candida antarctica, Rhizopus oryzae, and Candida rugosa lipases, three of the most common lipases used in biocatalysis, are showed. Finally, new cell factories producing heterologous lipases are presented.

Magnetic immobilization of bacteria using iron oxide nanoparticles

Bacterial cell immobilization is a novel technique used in many areas of biosciences and biotechnology. Iron oxide nanoparticles have attracted much attention in bacterial cell immobilization due to their unique properties such as superparamagnetism, large surface area to volume ratio, biocompatibility and easy separation methodology. Adhesion is the basis behind many immobilization techniques and various types of interactions determine bacterial adhesion. Efficiency of bacterial cell immobilization using iron oxide nanoparticles (IONs) generally depends on the physicochemical properties of the IONs and surface properties of bacterial cells as well as environmental/culture conditions. Bacteria exhibit various metabolic responses upon interaction with IONs, and the potential applications of iron oxide nanoparticles in bacterial cell immobilization will be discussed in this work.

Additive Biotech-Chances, challenges, and recent applications of additive manufacturing technologies in biotechnology

The diversity and complexity of biotechnological applications are constantly increasing, with ever expanding ranges of production hosts, cultivation conditions and measurement tasks. Consequently, many analytical and cultivation systems for biotechnology and bioprocess engineering, such as microfluidic devices or bioreactors, are tailor-made to precisely satisfy the requirements of specific measurements or cultivation tasks. Additive manufacturing (AM) technologies offer the possibility of fabricating tailor-made 3D laboratory equipment directly from CAD designs with previously inaccessible levels of freedom in terms of structural complexity. This review discusses the historical background of these technologies, their most promising current implementations and the associated workflows, fabrication processes and material specifications, together with some of the major challenges associated with using AM in biotechnology/bioprocess engineering. To illustrate the great potential of AM, selected examples in microfluidic devices, 3D-bioprinting/biofabrication and bioprocess engineering are highlighted.

Advances in analytical methodologies to guide bioprocess engineering for bio-therapeutics

This study was performed to monitor the glycoform distribution of a recombinant antibody fusion protein expressed in CHO cells over the course of fed-batch bioreactor runs using high-throughput methods to accurately determine the glycosylation status of the cell culture and its product. Three different bioreactors running similar conditions were analysed at the same five time-points using the advanced methods described here. N-glycans from cell and secreted glycoproteins from CHO cells were analysed by HILIC-UPLC and MS, and the total glycosylation (both N- and O-linked glycans) secreted from the CHO cells were analysed by lectin microarrays. Cell glycoproteins contained mostly high mannose type N-linked glycans with some complex glycans; sialic acid was α-(2,3)-linked, galactose β-(1,4)-linked, with core fucose. Glycans attached to secreted glycoproteins were mostly complex with sialic acid α-(2,3)-linked, galactose β-(1,4)-linked, with mostly core fucose. There were no significant differences noted among the bioreactors in either the cell pellets or supernatants using the HILIC-UPLC method and only minor differences at the early time-points of days 1 and 3 by the lectin microarray method. In comparing different time-points, significant decreases in sialylation and branching with time were observed for glycans attached to both cell and secreted glycoproteins. Additionally, there was a significant decrease over time in high mannose type N-glycans from the cell glycoproteins. A combination of the complementary methods HILIC-UPLC and lectin microarrays could provide a powerful and rapid HTP profiling tool capable of yielding qualitative and quantitative data for a defined biopharmaceutical process, which would allow valuable near 'real-time' monitoring of the biopharmaceutical product.

Enhanced Expansion and Sustained Inductive Function of Skin-Derived Precursor Cells in Computer-Controlled Stirred Suspension Bioreactors

Endogenous dermal stem cells (DSCs) reside in the adult hair follicle mesenchyme and can be isolated and grown in vitro as self‐renewing colonies called skin‐derived precursors (SKPs). Following transplantation into skin, SKPs can generate new dermis and reconstitute the dermal papilla and connective tissue sheath, suggesting they could have important therapeutic value for the treatment of skin disease (alopecia) or injury. Controlled cell culture processes must be developed to efficiently and safely generate sufficient stem cell numbers for clinical use. Compared with static culture, stirred‐suspension bioreactors generated fivefold greater expansion of viable SKPs. SKPs from each condition were able to repopulate the dermal stem cell niche within established hair follicles. Both conditions were also capable of inducing de novo hair follicle formation and exhibited bipotency, reconstituting the dermal papilla and connective tissue sheath, although the efficiency was significantly reduced in bioreactor‐expanded SKPs compared with static conditions. We conclude that automated bioreactor processing could be used to efficiently generate large numbers of autologous DSCs while maintaining their inherent regenerative function. Stem Cells Translational Medicine2017;6:434–443

A global RNA-seq-driven analysis of CHO host and production cell lines reveals distinct differential expression patterns of genes contributing to recombinant antibody glycosylation

Boehringer Ingelheim uses two CHO-DG44 lines for manufacturing biotherapeutics, BI-HEX-1 and BI-HEX-2, which produce distinct cell type-specific antibody glycosylation patterns. A recently established CHO-K1 descended host, BI-HEX-K1, generates antibodies with glycosylation profiles differing from CHO-DG44. Manufacturing process development is significantly influenced by these unique profiles. To investigate the underlying glycosylation related gene expression, we leveraged our CHO host and production cell RNA-seqtranscriptomics and product quality database together with the CHO-K1 genome. We observed that each BI-HEX host and antibody producing cell line has a unique gene expression fingerprint. CHO-DG44 cells only transcribe Fut10, Gfpt2 and ST8Sia6 when expressing antibodies. BI-HEX-K1 cells express ST8Sia6 at host cell level. We detected a link between BI-HEX-1/BI-HEX-2 antibody galactosylation and mannosylation and the gene expression of the B4galt gene family and genes controlling mannose processing. Furthermore, we found major differences between the CHO-DG44 and CHO-K1 lineages in the expression of sialyl transferases and enzymes synthesizing sialic acid precursors, providing a rationale for the lack of immunogenic NeuGc/NGNA synthesis in CHO. Our study highlights the value of systems biotechnology to understand glycoprotein synthesis and product glycoprofiles. Such data improve future production clone selection and process development strategies for better steering of biotherapeutic product quality.

Open and continuous fermentation: products, conditions and bioprocess economy

Microbial fermentation is the key to industrial biotechnology. Most fermentation processes are sensitive to microbial contamination and require an energy intensive sterilization process. The majority of microbial fermentations can only be conducted over a short period of time in a batch or fed-batch culture, further increasing energy consumption and process complexity, and these factors contribute to the high costs of bio-products. In an effort to make bio-products more economically competitive, increased attention has been paid to developing open (unsterile) and continuous processes. If well conducted, continuous fermentation processes will lead to the reduced cost of industrial bio-products. To achieve cost-efficient open and continuous fermentations, the feeding of raw materials and the removal of products must be conducted in a continuous manner without the risk of contamination, even under 'open' conditions. Factors such as the stability of the biological system as a whole during long cultivations, as well as the yield and productivity of the process, are also important. Microorganisms that grow under extreme conditions such as high or low pH, high osmotic pressure, and high or low temperature, as well as under conditions of mixed culturing, cell immobilization, and solid state cultivation, are of interest for developing open and continuous fermentation processes.

Metabolic modeling of synthesis gas fermentation in bubble column reactors

BACKGROUND

A promising route to renewable liquid fuels and chemicals is the fermentation of synthesis gas (syngas) streams to synthesize desired products such as ethanol and 2,3-butanediol. While commercial development of syngas fermentation technology is underway, an unmet need is the development of integrated metabolic and transport models for industrially relevant syngas bubble column reactors.

RESULTS

We developed and evaluated a spatiotemporal metabolic model for bubble column reactors with the syngas fermenting bacterium Clostridium ljungdahlii as the microbial catalyst. Our modeling approach involved combining a genome-scale reconstruction of C. ljungdahlii metabolism with multiphase transport equations that govern convective and dispersive processes within the spatially varying column. The reactor model was spatially discretized to yield a large set of ordinary differential equations (ODEs) in time with embedded linear programs (LPs) and solved using the MATLAB based code DFBAlab. Simulations were performed to analyze the effects of important process and cellular parameters on key measures of reactor performance including ethanol titer, ethanol-to-acetate ratio, and CO and H2 conversions.

CONCLUSIONS

Our computational study demonstrated that mathematical modeling provides a complementary tool to experimentation for understanding, predicting, and optimizing syngas fermentation reactors. These model predictions could guide future cellular and process engineering efforts aimed at alleviating bottlenecks to biochemical production in syngas bubble column reactors.

Advances and Practices of Bioprocess Scale-up

: This chapter addresses the update progress in bioprocess engineering. In addition to an overview of the theory of multi-scale analysis for fermentation process, examples of scale-up practice combining microbial physiological parameters with bioreactor fluid dynamics are also described. Furthermore, the methodology for process optimization and bioreactor scale-up by integrating fluid dynamics with biokinetics is highlighted. In addition to a short review of the heterogeneous environment in large-scale bioreactor and its effect, a scale-down strategy for investigating this issue is addressed. Mathematical models and simulation methodology for integrating flow field in the reactor and microbial kinetics response are described. Finally, a comprehensive discussion on the advantages and challenges of the model-driven scale-up method is given at the end of this chapter.

Engineering efficient retinal pigment epithelium differentiation from human pluripotent stem cells

Human embryonic stem cells (hESCs) are a promising source of retinal pigment epithelium (RPE) cells: cells that can be used for the treatment of common and incurable forms of blindness, such as age-related macular degeneration. Although most hESC lines will produce a number of clusters of pigmented RPE cells within 30-50 days when allowed to spontaneously differentiate, the timing and efficiency of differentiation is highly variable. This could prove problematic in the design of robust processes for the large scale production of RPE cells for cell therapy. In this study we sought to identify, quantify, and reduce the sources of variability in hESC-RPE differentiation. By monitoring the emergence of pigmented cells over time, we show how the cell line, passaging method, passage number, and seeding density have a significant and reproducible effect on the RPE yield. To counter this variability, we describe the production of RPE cells from two cell lines in feeder-free, density controlled conditions using single cell dissociation and seeding that is more amenable to scaled up production. The efficacy of small molecules in directing differentiation toward the RPE lineage was tested in two hESC lines with divergent RPE differentiation capacities. Neural induction by treatment with a bone morphogenetic protein inhibitor, dorsomorphin, significantly enhanced the RPE yield in one cell line but significantly reduce it in another, generating instead a Chx10 positive neural progenitor phenotype. This result underlines the necessity to tailor differentiation protocols to suit the innate properties of different cell lines.

Economics of recombinant antibody production processes at various scales: Industry-standard compared to continuous precipitation

Standard industry processes for recombinant antibody production employ protein A affinity chromatography in combination with other chromatography steps and ultra-/diafiltration. This study compares a generic antibody production process with a recently developed purification process based on a series of selective precipitation steps. The new process makes two of the usual three chromatographic steps obsolete and can be performed in a continuous fashion. Cost of Goods (CoGs) analyses were done for: (i) a generic chromatography-based antibody standard purification; (ii) the continuous precipitation-based purification process coupled to a continuous perfusion production system; and (iii) a hybrid process, coupling the continuous purification process to an upstream batch process. The results of this economic analysis show that the precipitation-based process offers cost reductions at all stages of the life cycle of a therapeutic antibody, (i.e. clinical phase I, II and III, as well as full commercial production). The savings in clinical phase production are largely attributed to the fact that expensive chromatographic resins are omitted. These economic analyses will help to determine the strategies that are best suited for small-scale production in parallel fashion, which is of importance for antibody production in non-privileged countries and for personalized medicine.