Bioprocess Applications Research Articles

Current progress in high cell density yeast bioprocesses for bioethanol production.

High capital costs and low reaction rates are major challenges for establishment of fermentation-based production systems in the bioeconomy. Using high cell density cultures is an efficient way to increase the volumetric productivity of fermentation processes, thereby enabling faster and more robust processes and use of smaller reactors. In this review, we summarize recent progress in the application of high cell density yeast bioprocesses for first and second generation bioethanol production. High biomass concentrations obtained by retention of yeast cells in the reactor enables easier cell reuse, simplified product recovery and higher dilution rates in continuous processes. High local cell density cultures, in the form of encapsulated or strongly flocculating yeast, furthermore obtain increased tolerance to convertible fermentation inhibitors and utilize glucose and other sugars simultaneously, thereby overcoming two additional hurdles for second generation bioethanol production. These effects are caused by local concentration gradients due to diffusion limitations and conversion of inhibitors and sugars by the cells, which lead to low local concentrations of inhibitors and glucose. Quorum sensing may also contribute to the increased stress tolerance. Recent developments indicate that high cell density methodology, with emphasis on high local cell density, offers significant advantages for sustainable second generation bioethanol production.

Cost-efficient entrapment of β-glucosidase in nanoscale latex and silicone polymeric thin films for use as stable biocatalysts

β-Glucosidase is an ubiquitous enzyme which has enormous biotechnological applications. Its deficiency in natural enzyme preparations is often overcome by exogenous supplementation, which further increases the enzyme utilization cost. Enzyme immobilization offers a potential solution through enzyme recycling and easy recovery. In the present work Aspergillus niger β-glucosidase is immobilized within nanoscale polymeric materials (polyurethane, latex and silicone), through entrapment, and subsequently coated onto a fibrous support. Highest apparent activity (90Ug−1 polymer) was observed with latex, while highest entrapment efficiency (93%) was observed for the silicone matrix. Immobilization resulted in the thermo-stabilization of the β-glucosidase with an increase in optimum temperature and activation energy for cellobiose hydrolysis. Supplementation to cellulases also resulted in an increased cellulose hydrolysis, while retaining more than 70% functional stability. Hence, the current study describes novel preparations of immobilized β-glucosidase as highly stable and active catalysts for industrial food- and bio-processing applications.

Quantitative proteomic analysis of the cellulolytic system of Clostridium termitidis CT1112 reveals distinct protein expression profiles upon growth on α-cellulose and cellobiose

Clostridium termitidis CT1112 is an anaerobic, mesophilic, cellulolytic bacterium with potential applications in consolidated bioprocessing of lignocellulosic biomass. To understand how C. termitidis degrades lignocellulose, iTRAQ-based 2D HPLC-MS/MS proteomics was used to measure protein expression in cell lysates and extracellular (secretome) fractions of C. termitidis grown on α-cellulose and cellobiose at both exponential and stationary growth phases. Exoglucanases (GH48, GH9), endoglucanases (GH5, GH8, GH9), hemicellulases including xylanases (GH8, GH10, GH11, GH30) and mannanase (GH26) as well as extracellular adhesion proteins and cellulosome associated proteins, exhibited higher expression on cellulose-grown cells. The expression of these proteins increased with a decrease in growth rate. Non-cellulosomal proteins however did not change significantly between substrate conditions, although there were a few exceptions. Collectively, these would contribute to hydrolysis of lignocellulosic material for uptake through ABC sugar transport proteins. On cellobiose, chitinases (GH18) were expressed abundantly. Although a large number of proteins were shared between the fractions analyzed, some proteins were detected exclusively in the cellular fraction, while others were detected in the secretome. This study reports for the first time on the cellulolytic machinery employed by C. termitidis to hydrolyze cellulosic substrate and provides an understanding of how this microbe deconstructs biomass. Biological significanceThe genome of C. termitidis CT1112 contains genes for a wide variety of carbohydrate active enzymes. Based on bioinformatics analyses, many of these genes appear to encode cellulosome-associated proteins, while others may be secreted extracellularly. To understand how C. termitidis degrades and depolymerizes cellulosic substrates, cells were grown on simple and complex carbohydrates, and quantitative 4-plex iTRAQ-based 2D HPLC-MS/MS proteomics was applied to measure protein expression levels in biological replicates of both cell lysates and extracellular protein (secretome) fractions, at exponential and stationary phases of growth. The resulting data have provided insight into the range of substrates that may be hydrolyzed by C. termitidis, and may be useful in determining potential industrial applications of C. termitidis in biomass to bioenergy production via consolidated bioprocessing.

Concentration Measurement with Refractive Index

Genetic Engineering & Biotechnology NewsVol. 35, No. 8 Bioprocessing TutorialConcentration Measurement with Refractive IndexUtilizing Index of Refraction Monitors in Biopharmaceutical Downstream Processing and PurificationMike W. Johnson and Eric IsbergMike W. JohnsonMike W. Johnson (E-mail Address: mike_johnson@entegris.com) is global bioprocess applications manager and Eric Isberg is bioprocess business development director at Entegris. Website: www.EntegrisLifeSciences.com.Search for more papers by this author and Eric IsbergMike W. Johnson (E-mail Address: mike_johnson@entegris.com) is global bioprocess applications manager and Eric Isberg is bioprocess business development director at Entegris. Website: www.EntegrisLifeSciences.com.Search for more papers by this authorPublished Online:16 Jun 2020https://doi.org/10.1089/gen.35.08.15AboutSectionsView articleView Full TextPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail View articleFiguresReferencesRelatedDetails Volume 35Issue 8Apr 2015 Information© 2015 by GEN PublishingTo cite this article:Mike W. Johnson and Eric Isberg.Concentration Measurement with Refractive Index.Genetic Engineering & Biotechnology News.Apr 2015.26-27.http://doi.org/10.1089/gen.35.08.15Published in Volume: 35 Issue 8: June 16, 2020PDF download

Buffer-free therapeutic antibody preparations provide a viable alternative to conventionally buffered solutions: from protein buffer capacity prediction to bioprocess applications.

Protein therapeutics, including monoclonal antibodies (mAbs), have significant buffering capacity, particularly at concentrations>50 mg/mL. This report addresses pH-related issues critical to adoption of self-buffered monoclonal antibody formulations. We evaluated solution conditions with protein concentrations ranging from 50 to 250 mg/mL. Samples were both buffer-free and conventionally buffered with citrate. Samples were non-isotonic or adjusted for isotonicity with NaCl or trehalose. Studies included accelerated temperature stability tests, shaking stability studies, and pH changes in infusion media as protein concentrate is added. We present averaged buffering slopes of capacity that can be applied to any mAb and present a general method for calculating buffering capacity of buffer-free, highly concentrated antibody liquid formulations. In temperature stability tests, neither buffer-free nor conventionally buffered solution conditions showed significant pH changes. Conventionally buffered solutions showed significantly higher opalescence than buffer-free ones. In general, buffer-free solution conditions showed less aggregation than conventionally buffered solutions. Shaking stability tests showed no differences between buffer-free and conventionally buffered solutions. "In-use" preparation experiments showed that pH in infusion bag medium can rapidly approximate that of self-buffered protein concentrate as concentrate is added. In summary, the buffer capacity of proteins can be predicted and buffer-free therapeutic antibody preparations provide a viable alternative to conventionally buffered solutions.

Nanobiocatalyst advancements and bioprocessing applications.

The nanobiocatalyst (NBC) is an emerging innovation that synergistically integrates advanced nanotechnology with biotechnology and promises exciting advantages for improving enzyme activity, stability, capability and engineering performances in bioprocessing applications. NBCs are fabricated by immobilizing enzymes with functional nanomaterials as enzyme carriers or containers. In this paper, we review the recent developments of novel nanocarriers/nanocontainers with advanced hierarchical porous structures for retaining enzymes, such as nanofibres (NFs), mesoporous nanocarriers and nanocages. Strategies for immobilizing enzymes onto nanocarriers made from polymers, silicas, carbons and metals by physical adsorption, covalent binding, cross-linking or specific ligand spacers are discussed. The resulting NBCs are critically evaluated in terms of their bioprocessing performances. Excellent performances are demonstrated through enhanced NBC catalytic activity and stability due to conformational changes upon immobilization and localized nanoenvironments, and NBC reutilization by assembling magnetic nanoparticles into NBCs to defray the high operational costs associated with enzyme production and nanocarrier synthesis. We also highlight several challenges associated with the NBC-driven bioprocess applications, including the maturation of large-scale nanocarrier synthesis, design and development of bioreactors to accommodate NBCs, and long-term operations of NBCs. We suggest these challenges are to be addressed through joint collaboration of chemists, engineers and material scientists. Finally, we have demonstrated the great potential of NBCs in manufacturing bioprocesses in the near future through successful laboratory trials of NBCs in carbohydrate hydrolysis, biofuel production and biotransformation.

Synthesis and characterization of robust magnetic carriers for bioprocess applications

Abstract Magnetic carriers are an effective option to withdraw selected target molecules from complex mixtures or to immobilize enzymes. This paper describes the synthesis of robust silica magnetic microparticles (SMMps), particularly designed for applications in bioprocesses. SMMps were synthesized in a micro-emulsion, using sodium silicate as the silica source and superparamagnetic iron oxide nanoparticles as the magnetic core. Thermally resistant particles, with high and accessible surface area, narrow particle size distribution, high saturation magnetization, and with superparamagnetic properties were obtained. Several reaction conditions were tested, yielding materials with saturation magnetization between 45 and 63 emu g −1 , particle size between 2 and 200 μm and average diameter between 11.2 and 15.9 μm, surface area between 49 and 103 m 2 g −1 and pore diameter between 2 and 60 nm. The performance of SMMps in a bioprocess was evaluated by the immobilization of Pseudomonas fluorescens lipase on to octyl modified SMMp, the biocatalyst obtained was used in the production of butyl butyrate with good results.

Silica-based strong anion exchange media for protein purification

The main objective of our research was to develop silica-based, polymer-functionalized ion exchange materials for single-use bioprocess applications, with the ultimate goal of achieving maximal binding capacity for target proteins. Herein we report the utilization of Grace® wide pore silica gel and bonding the silica with cationic polymers. The strong anion exchange materials have been prepared by a two-step process involving initial bonding with two trimethoxysilanes and subsequent aqueous solution radical polymerization with quaternary ammonium ion containing monomers and an azo initiator. Using the binding capacities for bovine serum albumin (BSA), a model protein for the evaluation of the new materials, we optimized the processes with regard to the median pore size of the silica gel, as well as polymer composition and ratios, which were determined by reagent ratios and reaction conditions. The products were also characterized by both chemical and physical methods. It has been found that higher binding capacities are associated with lower ligand density and higher molecular weight for the attached polymers, with over 20% higher in both static and dynamic binding capacity values with the same amount of attached polymers. The advantages of a large pore size distribution and optimal median pore size for the base silica are discussed. Optimal pore size range of 500–1500Å and distribution of Span 90 for over 1.0 give the highest BSA binding capacities. Silica-based strong anion exchange materials showed excellent flow characteristics when packed into a column and were superior to commercial agarose-based strong anion exchange material with respect to dynamic binding capacity, elution of proteins, and baseline separation of a mixture of three model proteins.

Liquid Perfluorochemicals as Flexible and Efficient Gas Carriers Applied in Bioprocess Engineering: An Updated Overview and Future Prospects

Abstract Fully synthetic, biochemically inert and water-immiscible liquid perfluorochemicals (PFCs) are recognised as flexible liquid carriers/scavengers of gaseous compounds (respiratory gases mainly, i.e. O2 and CO2) and increasingly applied in bioprocess engineering. A range of unmatched physicochemical properties of liquid PFCs, i.e. outstanding chemo- and thermostability, extremely low surface tension, simultaneous hydro- and lipophobicity, which result from carbon chain substitution with fluorine atoms (the most electronegative chemical element) and the presence of intramolecular C-F bonds (the strongest single bond known in organic chemistry) have been described in detail. Exceptional propensity to solubility of respiratory gases in liquid perfluorinated compounds has been widely discussed. Advantages and disadvantages of bioprocess applications of liquid PFCs in the form of a pure PFC as well as in an emulsified form have been pointed out. A liquid PFC-mediated mass transfer intensification in various types of microbial, plant cell and animal cell culture systems: from miniaturised microlitre-scale cultures, via biomaterial-based scaffolds containing culture systems, to litre-scale bioreactors, has been reviewed and elaborated on bearing in mind the benefits of bioprocesses.

Hydrolysis of Hazelnut Shells as a Carbon Source for Bioprocessing Applications and Fermentation

Abstract Hazelnut shells are generated in large amounts from hazelnut processing. Currently, it is used as fuel. However, reuse in bioprocessing can release remarkable content of sugars, which can be used for production of additives such as enzymes widely used in the food industry. Thus, the present study was undertaken to determine the effect of single and combined chemical and enzymatic hydrolysis on the production of fermentable sugars from hazelnut shells. Batch hydrolysis was carried out under various conditions to select optimal conditions. The results revealed that an optimal sugar concentration of about 19.2 g/l was achieved after 3.42% (w/w) dilute acid pretreatment conducted at 130°C for 31.7 min and enzymatic load of 200 U/g for 24 h. The overall sugar yield was calculated as 72.4% (g reducing sugar/g total carbohydrate). Therefore, hazelnut shells can be considered a suitable feedstock to compete with synthetic sugars used in fermentations.

The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications.

First isolated in 1926, Clostridium thermocellum has recently received increased attention as a high utility candidate for use in consolidated bioprocessing (CBP) applications. These applications, which seek to process lignocellulosic biomass directly into useful products such as ethanol, are gaining traction as economically feasible routes toward the production of fuel and other high value chemical compounds as the shortcomings of fossil fuels become evident. This review evaluates C. thermocellum's role in this transitory process by highlighting recent discoveries relating to its genomic, transcriptomic, proteomic, and metabolomic responses to varying biomass sources, with a special emphasis placed on providing an overview of its unique, multivariate enzyme cellulosome complex and the role that this structure performs during biomass degradation. Both naturally evolved and genetically engineered strains are examined in light of their unique attributes and responses to various biomass treatment conditions, and the genetic tools that have been employed for their creation are presented. Several future routes for potential industrial usage are presented, and it is concluded that, although there have been many advances to significantly improve C. thermocellum's amenability to industrial use, several hurdles still remain to be overcome as this unique organism enjoys increased attention within the scientific community.

A systematic strain selection approach for halotolerant and halophilic bioprocess development: a review.

Halotolerant and halophilic microorganisms have potential applications in a number of very relevant environmental and industrial bioprocesses, from wastewater treatment to production of value-added chemicals. While numerous microbial strains have been identified and studied in the literature, the number of those successfully used in industrial applications is comparatively small. Literature is abundant in terms of characterisation of specific strains under a microbiology perspective; however, there is a need for studies tackling the selection of strains for bioprocess applications. This review presents a database of over 200 halophilic and halotolerant prokaryote strains compiled from taxonomic microbiological resources and classified by trophic groups as well as by their salinity, pH and temperature tolerance and optimum ranges, all under a process development perspective. In addition to this database, complementary systematic approaches for the selection of suitable strains for a given trophic activity and environmental conditions are also presented. Both the database and the proposed selection approaches together constitute a general tool for process development that allows researchers to systematically search for strains capable of specific substrate degradations under specific conditions (pH, T, salinity). Many exiting established halotolerant and halophilic environmental and industrial bioprocesses appear to have been developed following strategies in line with the systematic approaches proposed here.

Verification of a new biocompatible single-use film formulation with optimized additive content for multiple bioprocess applications.

Single-use bioprocessing bags and bioreactors gained significant importance in the industry as they offer a number of advantages over traditional stainless steel solutions. However, there is continued concern that the plastic materials might release potentially toxic substances negatively impacting cell growth and product titers, or even compromise drug safety when using single-use bags for intermediate or drug substance storage. In this study, we have focused on the in vitro detection of potentially cytotoxic leachables originating from the recently developed new polyethylene (PE) multilayer film called S80. This new film was developed to guarantee biocompatibility for multiple bioprocess applications, for example, storage of process fluids, mixing, and cell culture bioreactors. For this purpose, we examined a protein-free cell culture medium that had been used to extract leachables from freshly gamma-irradiated sample bags in a standardized cell culture assay. We investigated sample bags from films generated to establish the operating ranges of the film extrusion process. Further, we studied sample bags of different age after gamma-irradiation and finally, we performed extended media extraction trials at cold room conditions using sample bags. In contrast to a nonoptimized film formulation, our data demonstrate no cytotoxic effect of the S80 polymer film formulation under any of the investigated conditions. The S80 film formulation is based on an optimized PE polymer composition and additive package. Full traceability alongside specifications and controls of all critical raw materials, and process controls of the manufacturing process, that is, film extrusion and gamma-irradiation, have been established to ensure lot-to-lot consistency. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1171–1176, 2014

Newly derived GH43 gene from compost metagenome showing dual xylanase and cellulase activities.

A metagenomic fosmid library was constructed from compost microbial communities that were collected from various farms throughout the Khon Kaen province, Thailand. The library was enriched in carboxymethylcellulose (CM-cellulose)--containing media prior to the screening of clones capable of degrading cellulosic materials. Two clones were selected for further subcloning and sequencing based on different patterns from restriction analysis. Deduced amino acid analysis of possible ORFs revealed one novel gene encoding an enzyme belonging to glycosyl hydrolase family 43 (GH43), which is a GH family rarely found in metagenomic studies. The most notable finding is that this enzyme, designated as Biof1_09, shows dual activities, namely endocellulase and endoxylanase activities. Biof1_09 showed greater than 50% of its activity under acidic conditions ranging from pH 3.5 to 5.5 with a pH optimum of 4.5. The optimum temperature of this enzyme was between 45 and 55 °C with an optimum of 50 °C. The properties of Biof1_09 make this enzyme an attractive candidate for large-scale expression for use in lignocellulose degradation for various bioprocess applications, including bioethanol fermentation.

A green-light inducible lytic system for cyanobacterial cells

BackgroundCyanobacteria are an attractive candidate for the production of biofuel because of their ability to capture carbon dioxide by photosynthesis and grow on non-arable land. However, because huge quantities of water are required for cultivation, strict water management is one of the greatest issues in algae- and cyanobacteria-based biofuel production. In this study, we aim to construct a lytic cyanobacterium that can be regulated by a physical signal (green-light illumination) for future use in the recovery of biofuel related compounds.ResultsWe introduced T4 bacteriophage-derived lysis genes encoding holin and endolysin under the control of the green-light regulated cpcG2 promoter in Synechocystis sp. PCC 6803. When cells harboring the lysis genes were illuminated with both red and green light, we observed a considerable decrease in growth rate, a significant increase in cellular phycocyanin released in the medium, and a considerable fraction of dead cells. These effects were not observed when these cells were illuminated with only red light, or when cells not containing the lysis genes were grown under either red light or red and green light.These results indicate that our constructed green-light inducible lytic system was clearly induced by green-light illumination, resulting in lytic cells that released intracellular phycocyanin into the culture supernatant. This property suggests a future possibility to construct photosynthetic genetically modified organisms that are unable to survive under sunlight exposure. Expression of the self-lysis system with green-light illumination was also found to greatly increase the fragility of the cell membrane, as determined by subjecting the induced cells to detergent, osmotic-shock, and freeze-thaw treatments.ConclusionsA green-light inducible lytic system was constructed in Synechocystis sp. PCC 6803. The engineered lytic cyanobacterial cells should be beneficial for the recovery of biofuels and related compounds from cells with minimal effort and energy, due to the fragile nature of the induced cells. Furthermore, the use of light-sensing two-component systems to regulate the expression of exogenous genes in cyanobacteria promises to replace conventional chemical inducers in many bioprocess applications, impacting the limiting water management issues.

Multimodal chromatography: Characterization of protein binding and selectivity enhancement through mobile phase modulators

The unique selectivity of mixed mode chromatography resins is driving increasing utilization of these novel selectivities into bioprocess applications. There is a need for improved fundamental understanding of protein binding to these stationary phases to enable the development of efficient and robust purification processes. A panel of four monoclonal antibodies and two model proteins were employed to characterize protein interaction with a mixed-mode chromatographic resin comprising a hydrophobic ligand with cation-exchange functionality. Binding of these proteins was studied as a function of salt concentration and pH in the presence of various mobile phase modulators. This knowledge was applied towards screening mobile phase modulators that could selectively decrease host cell protein levels during monoclonal antibody purification.

Characteristics ofStreptomyces griseusbiofilms in continuous flow tubular reactors

The purpose of this study was to investigate the feasibility of cultivating the biotechnologically important bacterium Streptomyces griseus in single-species and mixed-species biofilms using a tubular biofilm reactor (TBR). Streptomyces griseus biofilm development was found to be cyclical, starting with the initial adhesion and subsequent development of a visible biofilm after 24 h growth, followed by the complete detachment of the biofilm as a single mass, and ending with the re-colonisation of the tube. Fluorescence microscopy revealed that the filamentous structure of the biofilm was lost upon treatment with protease, but not DNase or metaperiodate, indicating that the extracellular polymeric substance is predominantly protein. When the biofilm was cultivated in conjunction with Bacillus amyloliquefaciens, no detachment was observed after 96 h, although once subjected to flow detachment. Electron microscopy confirmed the presence of both bacteria in the biofilm and revealed a network of fimbriae-like structures that were much less apparent in single-species biofilm and are likely to increase mechanical stability when developing in a TBR. This study presents the very first attempt in engineering S. griseus biofilms for continuous bioprocess applications.

Efficient secretion of (R)-3-hydroxybutyric acid from Halomonas sp. KM-1 by nitrate fed-batch cultivation with glucose under microaerobic conditions

To establish a sustainable society, commodity chemicals need to be developed from biomass resources. Recently, (R)-3-hydroxybutyric acid ((R)-3-HB), a monomer of bioplastic poly-(R)-3-hydroxybutyric acid (PHB), has attracted attention for its possible use in the chemical industry. Halophilic bacteria have been considered for bioprocess applications due to certain characteristics such as the ability to grow in media containing high levels of the starting carbon source and the ability to be rarely contaminated. A halophilic bacterium Halomonas sp. KM-1 stores PHB intracellularly under aerobic conditions and secretes (R)-3-HB under microaerobic conditions. In this study, we optimized culture conditions to maximize (R)-3-HB secretion by KM-1 cells. By a simple nitrate fed-batch cultivation, Halomonas sp. KM-1 secreted 40.3g/L (R)-3-HB with a productivity of 0.48g L(-1)h(-1) with 20% (w/v) glucose. This level is one of the highest recorded productivity of (R)-3-HB to date.

FunSecKB2: a fungal protein subcellular location knowledgebase

FunSecKB2 is an improved and updated version of the fungal secretome and subcellular proteome, i. e. protein subcellular location, knowledgebase. The fungal protein sequence data were retrieved from UniProtKB, consisting of nearly 2 million entries with 167 species having a complete proteome. The assignments of protein subcellular locations were based on curated information and prediction using seven computational tools. The tools used for subcellular location prediction include SignalP, WoLF PSORT, Phobius, TargetP, TMHMM, FragAnchor, and PS-Scan. Secreted proteins, i.e. secretomes, along with 15 other subcellular proteomes were predicted. The database can be searched by users using several different types of identifiers, gene name or keyword(s). A subcellular proteome from a species can be searched or downloaded. BLAST searching whole fungal protein data or secretomes is available. Community annotation of subcelluar locations based on experimental evidence is also supported. A primary analysis revealed that the secretome size of a fungal species is one of the determining factors to its lifestyle. The Gene Ontology and protein domain analysis of fungal secretomes revealed that fungal secretomes contain a large number of hydrolases, peptidases, oxidoreductases, and lysases, which may have potential applications in bio-processing of chemical wastes or biofuel production. The database provides an important and rich resource for the fungal community looking for protein subcellular location information and performing comparative subcellular proteome analysis. Database URL: http://proteomics.ysu.edu/secretomes/fungi2/index.php

HEK293 cell culture media study: increasing cell density for different bioprocess applications

Background The increasing demand for biopharmaceuticals produced in mammalian cells has lead industries to enhance bioprocess volumetric productivity through different strategies. Among them, media development is of major interest [1]. According to the increasing constraints regarding the use of animal derived components on industrial bioprocesses but also the drawbacks of its depletion from cell culture [2], the main goal of the present work was to provide different cell culture platforms which are suitable for a wide range of applications depending on the type and the final use of the product obtained.