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Bioeng
Kinds of Bioeng Selected AbstractsModeling of protein breakthrough performance in cryogel columns by taking into account the overall axial dispersionJOURNAL OF SEPARATION SCIENCE, JSS, Issue 15-16 2009Junxian Yun Abstract A model considering the overall axial dispersion for describing protein adsorption and breakthrough in monolithic cryogel beds has been developed. The microstructure of cryogels was characterized by tortuous capillaries with a normal diameter distribution but a constant pore wall thickness. The axial dispersion within cryogel columns was described by using the overall axial dispersion coefficient, which can be easily obtained by matching the experimental breakthrough curves without adsorption or measuring residence time distributions (RTDs). Experimental breakthrough curves of lysozyme within a metal-chelated affinity cryogel by Persson et al. (Biotechnol. Bioeng. 2004, 88, 224,236) and a cation-exchange cryogel by Yao et al. (J. Chromatogr. A 2007, 1157, 246,251) were employed as examples to test the model. The results showed that by using the axial dispersion coefficient and assuming uniform radial concentration profile at a given cross-section of the cryogel along the bed height, the model can describe the detailed behaviors of the in-bed overall axial dispersion, the in-pore mass transfer, as well as the protein adsorption and breakthrough. For a known overall axial dispersion coefficient, the lumped parameter of the mass transfer coefficient between the bulk liquid and the capillary wall can be determined by fitting the protein breakthrough curve at a known chromatographic condition. Once this parameter is determined, the model can be used to predict the protein breakthrough profiles under different conditions based on the basic physical parameters of the cryogel bed and the properties of the fluid and protein. The effective capillary diameters employed in the model are close to the actual pore sizes observed from the images by SEM. The model predictions of lysozyme breakthrough profiles at various flow rates are also in good agreement with the experimental data in both the metal-chelated affinity and cation-exchange cryogel columns. [source] A novel silicon patch-clamp chip permits high-fidelity recording of ion channel activity from functionally defined neuronsBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Christophe Py Abstract We report on a simple and high-yield manufacturing process for silicon planar patch-clamp chips, which allow low capacitance and series resistance from individually identified cultured neurons. Apertures are etched in a high-quality silicon nitride film on a silicon wafer; wells are opened on the backside of the wafer by wet etching and passivated by a thick deposited silicon dioxide film to reduce the capacitance of the chip and to facilitate the formation of a high-impedance cell to aperture seal. The chip surface is suitable for culture of neurons over a small orifice in the substrate with minimal leak current. Collectively, these features enable high-fidelity electrophysiological recording of transmembrane currents resulting from ion channel activity in cultured neurons. Using cultured Lymnaea neurons we demonstrate whole-cell current recordings obtained from a voltage-clamp stimulation protocol, and in current-clamp mode we report action potentials stimulated by membrane depolarization steps. Despite the relatively large size of these neurons, good temporal and spatial control of cell membrane voltage was evident. To our knowledge this is the first report of recording of ion channel activity and action potentials from neurons cultured directly on a planar patch-clamp chip. This interrogation platform has enormous potential as a novel tool to readily provide high-information content during pharmaceutical assays to investigate in vitro models of disease, as well as neuronal physiology and synaptic plasticity. Biotechnol. Bioeng. 2010;107:593,600. © 2010 Wiley Periodicals, Inc. [source] Binding modules alter the activity of chimeric cellulases: Effects of biomass pretreatment and enzyme source,BIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Tae-Wan Kim Abstract Improving the catalytic activity of cellulases requires screening variants against solid substrates. Expressing cellulases in microbial hosts is time-consuming, can be cellulase specific, and often leads to inactive forms and/or low yields. These limitations have been obstacles for improving cellulases in a high-throughput manner. We have developed a cell-free expression system and used it to express 54 chimeric bacterial and archaeal endoglucanases (EGs), with and without cellulose binding modules (CBMs) at either the N- or C-terminus, in active enzyme yields of 100,350,µg/mL. The platform was employed to systematically study the role of CBMs in cellulose hydrolysis toward a variety of natural and pretreated solid substrates, including ionic-liquid pretreated Miscanthus and AFEX-pretreated corn stover. Adding a CBM generally increased activity against crystalline Avicel, whereas for pretreated substrates the effect of CBM addition depended on the source of cellulase. The cell-free expression platform can thus provide insights into cellulase structure-function relationships for any substrate, and constitutes a powerful discovery tool for evaluating or engineering cellulolytic enzymes for biofuels production. Biotechnol. Bioeng. 2010;107:601,611. © 2010 Wiley Periodicals, Inc. [source] Valorization of an industrial organosolv,sugarcane bagasse lignin: Characterization and use as a matrix in biobased composites reinforced with sisal fibersBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Elaine C. Ramires Abstract In the present study, the main focus was the characterization and application of the by-product lignin isolated through an industrial organosolv acid hydrolysis process from sugarcane bagasse, aiming at the production of bioethanol. The sugarcane lignin was characterized and used to prepare phenolic-type resins. The analysis confirmed that the industrial sugarcane lignin is of HGS type, with a high proportion of the less substituted aromatic ring p -hydroxyphenyl units, which favors further reaction with formaldehyde. The lignin,formaldehyde resins were used to produce biobased composites reinforced with different proportions of randomly distributed sisal fibers. The presence of lignin moieties in both the fiber and matrix increases their mutual affinity, as confirmed by SEM images, which showed good adhesion at the biocomposite fiber/matrix interface. This in turn allowed good load transference from the matrix to the fiber, leading to biobased composites with good impact strength (near 500,J,m,1 for a 40,wt% sisal fiber-reinforced composite). The study demonstrates that sugarcane bagasse lignin obtained from a bioethanol plant can be used without excessive purification in the preparation of lignocellulosic fiber-reinforced biobased composites displaying high mechanical properties. Biotechnol. Bioeng. 2010;107:612,621. © 2010 Wiley Periodicals, Inc. [source] Mechanism of antibody reduction in cell culture production processesBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Yung-Hsiang Kao Abstract We recently observed a significant disulfide reduction problem during the scale-up of a manufacturing process for a therapeutic antibody using a CHO expression system. Under certain conditions, extensive reduction of inter-chain disulfide bonds of an antibody produced by CHO cell culture may occur during the harvest operations and/or the protein A chromatography step, resulting in the observation of antibody fragments (light chain, heavy chain, and various combination of both) in the protein A pools. Although all conditions leading to disulfide reduction have not been completely identified, an excessive amount of mechanical cell lysis generated at the harvest step appears to be an important requirement for antibody reduction (Trexler-Schmidt et al., 2010). We have been able to determine the mechanism by which the antibody is reduced despite the fact that not all requirements for antibody reduction were identified. Here we present data strongly suggesting that the antibody reduction was caused by a thioredoxin system or other reducing enzymes with thioredoxin-like activity. The intracellular reducing enzymes and their substrates/cofactors apparently were released into the harvest cell culture fluid (HCCF) when cells were exposed to mechanical cell shear during harvest operations. Surprisingly, the reducing activity in the HCCF can last for a long period of time, causing the reduction of inter-chain disulfide bonds in an antibody. Our findings provide a basis for designing methods to prevent the antibody reduction during the manufacturing process. Biotechnol. Bioeng. 2010;107:622,632. © 2010 Wiley Periodicals, Inc. [source] Application of solid,liquid TPPBs to the production of L -phenylacetylcarbinol from benzaldehyde using Candida utilisBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Tanya R. Khan Abstract The biotransformation of benzaldehyde and glucose to L -phenylacetylcarbinol (PAC) using Candida utilis was demonstrated in a solid,liquid two-phase partitioning bioreactor (TPPB) with the aim of reducing substrate, product, and by-product toxicity via sequestration. Previous work in the field had used octanol as the sequestering phase of liquid,liquid TPPBs but was limited by the toxic effects of octanol on C. utilis. To improve solvent selection in any future studies, the critical log,P of C. utilis was determined in the current study to be 4.8 and can be used to predict biocompatible solvents. Bioavailability tests showed alkanes and alkenes to be non-bioavailable. As polymers are biocompatible and non-bioavailable, a wide range of commercially available polymers was screened and it was demonstrated that polymer softness plays a key role in absorptive capability. The polymer Hytrel G3548L was selected as the second phase to sequester benzaldehyde, PAC, and benzyl alcohol, with partition coefficients of 35, 7.5, and 10, respectively. With a 9% by volume partitioning phase, 13.6,g/L biomass of C. utilis achieved an overall PAC concentration of 11,g/L, a 1.9-fold improvement over the single-phase case. Benzyl alcohol concentration was 4.5,g/L, a 1.6-fold reduction. The volumetric productivity was 0.85,g/L,h, a 1.2-fold improvement over the single-phase system. These results demonstrate a promising starting point for solid,liquid TPPBs for PAC production. Biotechnol. Bioeng. 2010;107:633,641. © 2010 Wiley Periodicals, Inc. [source] Efficient phase separation and product recovery in organic-aqueous bioprocessing using supercritical carbon dioxideBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Christoph Brandenbusch Abstract Biphasic hydrocarbon functionalizations catalyzed by recombinant microorganisms have been shown to be one of the most promising approaches for replacing common chemical synthesis routes on an industrial scale. However, the formation of stable emulsions complicates downstream processing, especially phase separation. This fact has turned out to be a major hurdle for industrial implementation. To overcome this limitation, we used supercritical carbon dioxide (scCO2) for both phase separation and product purification. The stable emulsion, originating from a stereospecific epoxidation of styrene to (S)-styrene oxide, a reaction catalyzed by recombinant Escherichia coli, could be destabilized efficiently and irreversibly, enabling complete phase separation within minutes. By further use of scCO2 as extraction agent, the product (S)-styrene oxide could be obtained with a purity of 81% (w/w) in one single extraction step. By combining phase separation and product purification using scCO2, the number of necessary workup steps can be reduced to one. This efficient and easy to use technique is generally applicable for the workup of biphasic biocatalytic hydrocarbon functionalizations and enables a cost effective downstream processing even on a large scale. Biotechnol. Bioeng. 2010;107:642,651. © 2010 Wiley Periodicals, Inc. [source] Increasing the activity of monoclonal antibody therapeutics by continuous chromatography (MCSGP)BIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010T. Müller-Späth Abstract The charged monoclonal antibody (mAb) variants of the commercially available therapeutics Avastin®, Herceptin® and Erbitux® were separated by ion-exchange gradient chromatography in batch and continuous countercurrent mode (MCSGP process). Different stationary phases, buffer conditions and two MCSGP configurations were used in order to demonstrate the broad applicability of MCSGP in the field of charged protein variant separation. Batch chromatography and MCSGP were compared with respect to yield, purity, and productivity. In the case of Herceptin®, also the biological activity of the product stream was taken into account as performance indicator. The robustness of the MCSGP process against feed composition variations was confirmed experimentally and by model simulations. Biotechnol. Bioeng. 2010;107:652,662. © 2010 Wiley Periodicals, Inc. [source] Crystallization of recombinant human growth hormone at elevated pressures: Pressure effects on PEG-induced volume exclusion interactionsBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Ryan L. Crisman Abstract Crystallization of recombinant human growth hormone (rhGH) at elevated pressures was investigated in the presence of 6,000 molecular weight poly(ethylene glycol; PEG-6000). Crystallization of rhGH at atmospheric pressure occurred at a protein concentration of 15,mg/mL in 6% PEG-6000. Crystallization did not occur in the same solutions at 250,MPa. In contrast, at a pressure of 250,MPa in the presence of 8% PEG-6000, rhGH readily crystallized from solutions containing 35,mg/mL rhGH, whereas amorphous precipitate formed in the same solutions at atmospheric pressure. Osmotic virial coefficients were determined from static light scattering measurements and combined with a hard-sphere activity coefficient model to predict rhGH activity coefficients as a function of pressure and PEG concentration. Predicted activity coefficients quantitatively matched those determined from equilibrium solubility measurements. The ability to adjust the thermodynamic non-ideality with pressure provides a valuable tool to study protein crystallization in addition to providing a methodology for obtaining crystals at elevated pressures. Biotechnol. Bioeng. 2010;107:663,672. © 2010 Wiley Periodicals, Inc. [source] Production of succinic acid at low pH by a recombinant strain of the aerobic yeast Yarrowia lipolyticaBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Tigran V. Yuzbashev Abstract Biotechnological production of weak organic acids such as succinic acid is most economically advantageous when carried out at low pH. Among naturally occurring microorganisms, several bacterial strains are known to produce considerable amounts of succinic acid under anaerobic conditions but they are inefficient in performing the low-pH fermentation due to their physiological properties. We have proposed therefore a new strategy for construction of an aerobic eukaryotic producer on the basis of the yeast Yarrowia lipolytica with a deletion in the gene coding one of succinate dehydrogenase subunits. Firstly, an original in vitro mutagenesis-based approach was proposed to construct strains with Ts mutations in the Y. lipolytica SDH1 gene. These mutants were used to optimize the composition of the media for selection of transformants with the deletion in the Y. lipolytica SDH2 gene. Surprisingly, the defects of each succinate dehydrogenase subunit prevented the growth on glucose but the mutant strains grew on glycerol and produced succinate in the presence of the buffering agent CaCO3. Subsequent selection of the strain with deleted SDH2 gene for increased viability allowed us to obtain a strain capable of accumulating succinate at the level of more than 45,g,L,1 in shaking flasks with buffering and more than 17,g,L,1 without buffering. The possible effect of the mutations on the utilization of different substrates and perspectives of constructing an industrial producer is discussed. Biotechnol. Bioeng. 2010;107:673,682. © 2010 Wiley Periodicals, Inc. [source] Three-dimensional culture systems for the expansion of pluripotent embryonic stem cellsBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Michael P. Storm Abstract Mouse embryonic stem cell (ESC) lines, and more recently human ESC lines, have become valuable tools for studying early mammalian development. Increasing interest in ESCs and their differentiated progeny in drug discovery and as potential therapeutic agents has highlighted the fact that current two-dimensional (2D) static culturing techniques are inadequate for large-scale production. The culture of mammalian cells in three-dimensional (3D) agitated systems has been shown to overcome many of the restrictions of 2D and is therefore likely to be effective for ESC proliferation. Using murine ESCs as our initial model, we investigated the effectiveness of different 3D culture environments for the expansion of pluripotent ESCs. Solohill Collagen, Solohill FACT, and Cultispher-S microcarriers were employed and used in conjunction with stirred bioreactors. Initial seeding parameters, including cell number and agitation conditions, were found to be critical in promoting attachment to microcarriers and minimizing the size of aggregates formed. While all microcarriers supported the growth of undifferentiated mESCs, Cultispher-S out-performed the Solohill microcarriers. When cultured for successive passages on Cultispher-S microcarriers, mESCs maintained their pluripotency, demonstrated by self-renewal, expression of pluripotency markers and the ability to undergo multi-lineage differentiation. When these optimized conditions were applied to unweaned human ESCs, Cultispher-S microcarriers supported the growth of hESCs that retained expression of pluripotency markers including SSEA4, Tra-1,60, NANOG, and OCT-4. Our study highlights the importance of optimization of initial seeding parameters and provides proof-of-concept data demonstrating the utility of microcarriers and bioreactors for the expansion of hESCs. Biotechnol. Bioeng. 2010;107:683,695. © 2010 Wiley Periodicals, Inc. [source] Stoichiometric model and metabolic flux analysis for Leptospirillum ferrooxidansBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010M.P. Merino Abstract A metabolic model for Leptospirillum ferrooxidans was developed based on the genomic information of an analogous iron oxidizing bacteria and on the pathways of ferrous iron oxidation, nitrogen and CO2 assimilation based on experimental evidence for L. ferrooxidans found in the literature. From this metabolic reconstruction, a stoichiometric model was built, which includes 86 reactions describing the main catabolic and anabolic aspects of its metabolism. The model obtained has 2 degrees of freedom, so two external fluxes were estimated to achieve a determined and observable system. By using the external oxygen consumption rate and the generation flux biomass as input data, a metabolic flux map with a distribution of internal fluxes was obtained. The results obtained were verified with experimental data from the literature, achieving a very good prediction of the metabolic behavior of this bacterium at steady state. Biotechnol. Bioeng. 2010;107:696,706. © 2010 Wiley Periodicals, Inc. [source] A microfluidic bioreactor with integrated transepithelial electrical resistance (TEER) measurement electrodes for evaluation of renal epithelial cellsBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Nicholas Ferrell Abstract We have developed a bilayer microfluidic system with integrated transepithelial electrical resistance (TEER) measurement electrodes to evaluate kidney epithelial cells under physiologically relevant fluid flow conditions. The bioreactor consists of apical and basolateral fluidic chambers connected via a transparent microporous membrane. The top chamber contains microfluidic channels to perfuse the apical surface of the cells. The bottom chamber acts as a reservoir for transport across the cell layer and provides support for the membrane. TEER electrodes were integrated into the device to monitor cell growth and evaluate cell,cell tight junction integrity. Immunofluorescence staining was performed within the microchannels for ZO-1 tight junction protein and acetylated ,-tubulin (primary cilia) using human renal epithelial cells (HREC) and MDCK cells. HREC were stained for cytoskeletal F-actin and exhibited disassembly of cytosolic F-actin stress fibers when exposed to shear stress. TEER was monitored over time under normal culture conditions and after disruption of the tight junctions using low Ca2+ medium. The transport rate of a fluorescently labeled tracer molecule (FITC-inulin) was measured before and after Ca2+ switch and a decrease in TEER corresponded with a large increase in paracellular inulin transport. This bioreactor design provides an instrumented platform with physiologically meaningful flow conditions to study various epithelial cell transport processes. Biotechnol. Bioeng. 2010;107:707,716. © 2010 Wiley Periodicals, Inc. [source] Cre recombinase-mediated site-specific modification of a cellular genome using an integrase-defective retroviral vectorBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Shuohao Huang Abstract Retroviral integrase is an enzyme responsible for the integration of retroviruses. A single mutation in the integrase core domain can severely compromise its integration ability, leading to the accumulation of circular retroviral cDNA in the nuclei of infected cells. We therefore attempted to use those cDNA as substrates for Cre recombinase to perform a recombinase-mediated cassette exchange (RMCE), thereby targeting retroviral vectors to a predetermined site. An expression unit containing a promoter, an ATG codon and marker genes (hygromycin resistance gene and red fluorescent protein gene) flanked by wild-type and mutant loxP sites was first introduced into cellular chromosome to build founder cell lines. We then constructed another plasmid for the production of integrase-defective retroviral vectors (IDRV), which contains an ATG-deficient neomycin resistance gene and green fluorescent protein gene, flanked by a compatible pair of loxPs. After providing founder cells with Cre and infecting with IDRV later, effective RMCE occurred, resulting in the appearance of G418-resistant colonies and a change in the color of fluorescence from red to green. Southern blot and PCR analyses on selected clones further confirmed site-specific recombination. The successful substitution of the original viral integration machinery with a non-viral mechanism could expand the application of retroviral vectors. Biotechnol. Bioeng. 2010;107:717,729. © 2010 Wiley Periodicals, Inc. [source] Lentivirus-mediated knockdown of aggrecanase-1 and -2 promotes chondrocyte-engineered cartilage formation in vitroBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Zheng-Hui Wang Abstract Chondrocyte-based tissue engineering has emerged as a promising approach for repair of injured cartilage tissues that have a poor self-healing capacity. However, this technique faces a major limitation: dedifferentiation of chondrocytes occurs following several passages in culture. Aggrecan, a major component of cartilage extracellular matrix, plays an essential role in chondrocyte differentiation. The aim of this study is to determine whether inhibition of chondrocyte aggrecanases, key degradative enzymes for aggrecan in cartilage, could benefit chondrocyte differentiation and the preservation of chondrocyte phenotype within a long-term period. Lentivirus-mediated RNA interference (RNAi) was employed to target both aggrecanase-1 and -2 in primary rat chondrocytes, and the transduced cells were seeded into chitosan,gelatin three-dimensional scaffolds. Histological, morphological, and biochemical analyses were performed at 1,8 weeks post-implantation to study chondrocyte survival, differentiation, and function. We found that lentivirus-mediated RNAi notably decreased the abundance of aggrecanase transcripts in chondrocytes but did not affect cell viability. Most importantly, compared to the control constructs seeded with untransduced chondrocytes, the aggrecanase inhibition increased chondrocyte proliferation and reinforced the production of glycosaminoglycans and total collagen, indicative of chondrocyte differentiation. The mRNA expression of chondrocyte marker genes (collagen II and aggrecan) was enhanced by aggrecanase silencing relative to the control. Together our data demonstrate that inhibition of endogenous aggrecanases facilitates chondrocyte differentiation and chondrocyte-engineered cartilage formation in vitro. The combination of lentiviral delivery system and genetic manipulation techniques provides a useful tool for modulation of chondrocyte phenotype in cartilage engineering. Biotechnol. Bioeng. 2010;107:730,736. © 2010 Wiley Periodicals, Inc. [source] Design of cellular porous biomaterials for wall shear stress criterionBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Yuhang Chen Abstract The microfluidic environment provided by implanted prostheses has a decisive influence on the viability, proliferation and differentiation of cells. In bone tissue engineering, for instance, experiments have confirmed that a certain level of wall shear stress (WSS) is more advantageous to osteoblastic differentiation. This paper proposes a level-set-based topology optimization method to regulate fluidic WSS distribution for design of cellular biomaterials. The topological boundary of fluid phase is represented by a level-set model embedded in a higher-dimensional scalar function. WSS is determined by the computational fluid dynamics analysis in the scale of cellular base cells. To achieve a uniform WSS distribution at the solid,fluid interface, the difference between local and target WSS is taken as the design criterion, which determines the speed of the boundary evolution in the level-set model. The examples demonstrate the effectiveness of the presented method and exhibit a considerable potential in the design optimization and fabrication of new prosthetic cellular materials for bioengineering applications. Biotechnol. Bioeng. 2010;107:737,746. © 2010 Wiley Periodicals, Inc. [source] Synthesis and utilization of E. coli -encapsulated PEG-based microdroplet using a microfluidic chip for biological applicationBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2010Kyoung G. Lee Abstract We report herein an effective strategy for encapsulating Escherichia coli in polyethylene glycol diacrylate (PEGDA) microdroplets using a microfluidic device and chemical polymerization. PEGDA was employed as a reactant due to the biocompatibility, high porosity, and hydrophilic property. The uniform size and shape of microdroplets are obtained in a single-step process using microfluidic device. The size of microdroplets can be controlled through the changing continuous flow rate. The combination of microdroplet generation and chemical polymerization techniques provide unique environment to produce non-toxic ways of fabricating microorganism-encapsulated hydrogel microbeads. Due to these unique properties of micro-sized hydrogel microbeads, the encapsulated E. coli can maintain viability inside of microbeads and green fluorescent protein (GFP) and red fluorescent protein (RFP) genes are efficiently expressed inside of microbeads after isopropyl- , - D -thiogalactopyranoside induction, suggesting that there is no low-molecular weight substrate transfer limitation inside of microbeads. Furthermore, non-toxic, gentle, and outstanding biocompatibility of microbeads, the encapsulated E. coli can be used in various applications including biotransformation, biosensing, bioremediation, and engineering of artificial cells. Biotechnol. Bioeng. 2010;107:747,751. © 2010 Wiley Periodicals, Inc. [source] Systematizing the generation of missing metabolic knowledgeBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Jeffrey D. Orth Abstract Genome-scale metabolic network reconstructions are built from all of the known metabolic reactions and genes in a target organism. However, since our knowledge of any organism is incomplete, these network reconstructions contain gaps. Reactions may be missing, resulting in dead-ends in pathways, while unknown gene products may catalyze known reactions. New computational methods that analyze data, such as growth phenotypes or gene essentiality, in the context of genome-scale metabolic networks, have been developed to predict these missing reactions or genes likely to fill these knowledge gaps. A growing number of experimental studies are appearing that address these computational predictions, leading to discovery of new metabolic capabilities in the target organism. Gap-filling methods can thus be used to improve metabolic network models while simultaneously leading to discovery of new metabolic gene functions. Biotechnol. Bioeng. 2010;107: 403,412. © 2010 Wiley Periodicals, Inc. [source] Construction of cellobiose phosphorylase variants with broadened acceptor specificity towards anomerically substituted glucosidesBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Manu R.M. De Groeve Abstract The general application of glycoside phosphorylases such as cellobiose phosphorylase (CP) for glycoside synthesis is hindered by their relatively narrow substrate specificity. We have previously reported on the creation of Cellulomonas uda CP enzyme variants with either modified donor or acceptor specificity. Remarkably, in this study it was found that the donor mutant also displays broadened acceptor specificity towards several ,-glucosides. Triple mutants containing donor (T508I/N667A) as well as acceptor mutations (E649C or E649G) also display a broader acceptor specificity than any of the parent enzymes. Moreover, further broadening of the acceptor specificity has been achieved by site-saturation mutagenesis of residues near the active site entrance. The best enzyme variant contains the additional N156D and N163D mutations and is active towards various alkyl ,-glucosides, methyl ,-glucoside and cellobiose. In comparison with the wild-type C. uda CP enzyme, which cannot accept anomerically substituted glucosides at all, the obtained increase in substrate specificity is significant. The described CP enzyme variants should be useful for the synthesis of cellobiosides and other glycosides with prebiotic and pharmaceutical properties. Biotechnol. Bioeng. 2010;107: 413,420. © 2010 Wiley Periodicals, Inc. [source] Farnesol production from Escherichia coli by harnessing the exogenous mevalonate pathwayBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Chonglong Wang Abstract Farnesol (FOH) production has been carried out in metabolically engineered Escherichia coli. FOH is formed through the depyrophosphorylation of farnesyl pyrophosphate (FPP), which is synthesized from isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) by FPP synthase. In order to increase FPP synthesis, E. coli was metabolically engineered to overexpress ispA and to utilize the foreign mevalonate (MVA) pathway for the efficient synthesis of IPP and DMAPP. Two-phase culture using a decane overlay of the culture broth was applied to reduce volatile loss of FOH produced during culture and to extract FOH from the culture broth. A FOH production of 135.5,mg/L was obtained from the recombinant E. coli harboring the pTispA and pSNA plasmids for ispA overexpression and MVA pathway utilization, respectively. It is interesting to observe that a large amount of FOH could be produced from E. coli without FOH synthase by the augmentation of FPP synthesis. Introduction of the exogenous MVA pathway enabled the dramatic production of FOH by E. coli while no detectable FOH production was observed in the endogenous MEP pathway-only control. Biotechnol. Bioeng. 2010;107: 421,429. © 2010 Wiley Periodicals, Inc. [source] Effect of varying feedstock,pretreatment chemistry combinations on the formation and accumulation of potentially inhibitory degradation products in biomass hydrolysatesBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Bowen Du Abstract A variety of potentially inhibitory degradation products are produced during pretreatment of lignocellulosic biomass. Qualitative and quantitative interrogation of pretreatment hydrolysates is paramount to identifying potential correlations between pretreatment chemistries and microbial inhibition in downstream bioconversion processes. In the present study, corn stover, poplar, and pine feedstocks were pretreated under eight different chemical conditions, which are representative of leading pretreatment processes. Pretreatment processes included: 0.7% H2SO4, 0.07% H2SO4, liquid hot water, neutral buffer solution, aqueous ammonia, lime, lime with oxygen pressurization, and wet oxidation. Forty lignocellulosic degradation products resulting from pretreatment were analyzed using high performance liquid chromatography in combination with UV spectroscopy or tandem mass spectrometry detection (HPLC-PDA-MS/MS) and ion chromatography (IC). Of these compounds, several have been reported to be inhibitory, including furfural, hydroxymethyl furfural, ferulic acid, 3,4-dihydroxybenzaldehyde, syringic acid among others. Formation and accumulation of monitored compounds in hydrolysates is demonstrated to be a function of both the feedstock and pretreatment conditions utilized. Biotechnol. Bioeng. 2010;107: 430,440. © 2010 Wiley Periodicals, Inc. [source] Alkali-based AFEX pretreatment for the conversion of sugarcane bagasse and cane leaf residues to ethanolBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Chandraraj Krishnan Abstract Sugarcane is one of the major agricultural crops cultivated in tropical climate regions of the world. Each tonne of raw cane production is associated with the generation of 130,kg dry weight of bagasse after juice extraction and 250,kg dry weight of cane leaf residue postharvest. The annual world production of sugarcane is ,1.6 billion tones, generating 279 MMT tones of biomass residues (bagasse and cane leaf matter) that would be available for cellulosic ethanol production. Here, we investigated the production of cellulosic ethanol from sugar cane bagasse and sugar cane leaf residue using an alkaline pretreatment: ammonia fiber expansion (AFEX). The AFEX pretreatment improved the accessibility of cellulose and hemicelluloses to enzymes during hydrolysis by breaking down the ester linkages and other lignin carbohydrate complex (LCC) bonds and the sugar produced by this process is found to be highly fermentable. The maximum glucan conversion of AFEX pretreated bagasse and cane leaf residue by cellulases was ,85%. Supplementation with hemicellulases during enzymatic hydrolysis improved the xylan conversion up to 95,98%. Xylanase supplementation also contributed to a marginal improvement in the glucan conversion. AFEX-treated cane leaf residue was found to have a greater enzymatic digestibility compared to AFEX-treated bagasse. Co-fermentation of glucose and xylose, produced from high solid loading (6% glucan) hydrolysis of AFEX-treated bagasse and cane leaf residue, using the recombinant Saccharomyces cerevisiae (424A LNH-ST) produced 34,36,g/L of ethanol with 92% theoretical yield. These results demonstrate that AFEX pretreatment is a viable process for conversion of bagasse and cane leaf residue into cellulosic ethanol. Biotechnol. Bioeng. 2010;107: 441,450. © 2010 Wiley Periodicals, Inc. [source] High-solids biphasic CO2,H2O pretreatment of lignocellulosic biomassBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Jeremy S. Luterbacher Abstract A high pressure (200,bar) CO2,H2O process was developed for pretreating lignocellulosic biomass at high-solid contents, while minimizing chemical inputs. Hardwood was pretreated at 20 and 40 (wt.%) solids. Switchgrass, corn stover, big bluestem, and mixed perennial grasses (a co-culture of big bluestem and switchgrass) were pretreated at 40 (wt.%) solids. Operating temperatures ranged from 150 to 250°C, and residence times from 20,s to 60,min. At these conditions a biphasic mixture of an H2O-rich liquid (hydrothermal) phase and a CO2 -rich supercritical phase coexist. Following pretreatment, samples were then enzymatically hydrolyzed. Total yields, defined as the fraction of the theoretical maximum, were determined for glucose, hemicellulose sugars, and two degradation products: furfural and 5-hydroxymethylfurfural. Response surfaces of yield as a function of temperature and residence time were compared for different moisture contents and biomass species. Pretreatment at 170°C for 60,min gave glucose yields of 77%, 73%, and 68% for 20 and 40 (wt.%) solids mixed hardwood and mixed perennial grasses, respectively. Pretreatment at 160°C for 60,min gave glucan to glucose yields of 81% for switchgrass and 85% for corn stover. Biotechnol. Bioeng. 2010;107: 451,460. © 2010 Wiley Periodicals, Inc. [source] A novel microplate-based screening strategy to assess the cellulolytic potential of Trichoderma strainsBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Stefano Cianchetta Abstract Bioconversion of lignocellulosic biomass to fuel requires a hydrolysis step to obtain fermentable sugars, generally accomplished by fungal enzymes. An assorted library of cellulolytic microbial strains should facilitate the development of optimal enzyme cocktails specific for locally available feedstocks. Only a limited number of strains can be simultaneously assayed in screening based on large volume cultivation methods, as in shake flasks. This study describes a miniaturization strategy aimed at allowing parallel assessment of large numbers of fungal strains. Trichoderma strains were cultivated stationary on microcrystalline cellulose using flat bottom 24-well plates containing an agarized medium. Supernatants obtained by a rapid centrifugation step of the whole culture plates were evaluated for extracellular total cellulase activity, measured as filter paper activity, using a microplate-based assay. The results obtained were consistent with those observed in shake-flask experiments and more than 300 Trichoderma strains were accordingly characterized for cellulase production. Five strains, displaying on shake-flasks at least 80% of the activity shown by the hyper-cellulolytic mutant Trichoderma Rut-C30, were correctly recognized by the screening on 24-well plates, demonstrating the feasibility of this approach. Cellulase activity distribution for the entire Trichoderma collection is also reported. One strain (T. harzianum Ba8/86) displayed the closest profile to the reference strain Rut-C30 in time course experiments. The method is scalable and addresses a major bottleneck in screening programs, allowing small-scale parallel cultivation and rapid supernatant extraction. It can also be easily integrated with high-throughput enzyme assays and could be suitable for automation. Biotechnol. Bioeng. 2010;107: 461,468. © 2010 Wiley Periodicals, Inc. [source] A metal-repressed promoter from gram-positive Bacillus subtilis is highly active and metal-induced in gram-negative Cupriavidus metalliduransBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Gabriela Ribeiro-dos-Santos Abstract A synthetic version of the metal-regulated gene A (mrgA) promoter from Bacillus subtilis, which in this Gram-positive bacterium is negatively regulated by manganese, iron, cobalt, or copper turned out to promote high level of basal gene expression that is further enhanced by Co(II), Cd(II), Mn(II), Zn(II), Cu(II), or Ni(II), when cloned in the Gram-negative bacterium Cupriavidus metallidurans. Promoter activity was monitored by expression of the reporter gene coding for the enhanced green fluorescent protein (EGFP), and cellular intensity fluorescence was quantified by flow cytometry. Expression levels in C. metallidurans driven by the heterologous promoter, here called pan, ranged from 20- to 53-fold the expression level driven by the Escherichia coli lac promoter (which is constitutively expressed in C. metallidurans), whether in the absence or presence of metal ions, respectively. The pan promoter did also function in E. coli in a constitutive pattern, regardless of the presence of Mn(II) or Fe(II). In conclusion, the pan promoter proved to be a powerful tool to express heterologous proteins in Gram-negative bacteria, especially in C. metallidurans grown upon high levels of toxic metals, with potential applications in bioremediation. Biotechnol. Bioeng. 2010;107: 469,477. © 2010 Wiley Periodicals, Inc. [source] The effect of carbon source on microbial community structure and Cr(VI) reduction rateBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Athanasia G. Tekerlekopoulou Abstract In the present work, the effect of the carbon source on microbial community structure in batch cultures derived from industrial sludge and hexavalent chromium reduction was studied. Experiments in aerobic batch reactors were carried out by amending industrial sludge with two different carbon sources: sodium acetate and sucrose. In each of the experiments performed, four different initial Cr(VI) concentrations of: 6, 13, 30 and 115,mg/L were tested. The change of carbon source in the batch reactor from sodium acetate to sucrose led to a 1.3,2.1 fold increase in chromium reduction rate and to a 5- to 9.5-fold increase in biomass. Analysis of the microbial structure in the batch reactor showed that the dominant communities were bacterial species (Acinetobacter lwoffii, Defluvibacter lusatiensis, Pseudoxanthomonas japonensis, Mesorhizium chacoense, and Flavobacterium suncheonense) when sodium acetate was used as carbon source and fungal strains (Trichoderma viride and Pichia jadinii), when sodium acetate was replaced by sucrose. These results indicate that the carbon source is a key parameter for microbial dynamics and enhanced chromium reduction and should be taken into account for efficient bioreactor design. Biotechnol. Bioeng. 2010;107: 478,487. © 2010 Wiley Periodicals, Inc. [source] Sialylation enhancement of CTLA4-Ig fusion protein in Chinese hamster ovary cells by dexamethasoneBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Ying Jing Abstract The importance of glycoprotein sialic acid levels is well known, as increased levels have been shown to increase in vivo serum half-life profiles. Here we demonstrate for the first time that dexamethasone (DEX) was capable of improving the sialylation of a CTLA4-Ig fusion protein produced by Chinese hamster ovary (CHO) cells. DEX was shown to enhance the intracellular addition of sialic acid by sialyltransferases as well as reduce extracellular removal of sialic acid by sialidase cleavage. We illustrated that DEX addition resulted in increased expression of the glycosyltransferases ,2,3-sialyltransferase (,2,3-ST) and ,1,4-galactosyltransferase (,1,4-GT) in CHO cells. Based upon our previous results showing DEX addition increased culture cell viability, we confirmed here that cultures treated with DEX also resulted in decreased sialidase activity. Addition of the glucocorticoid receptor (GR) antagonist mifepristone (RU-486) was capable of blocking the increase in sialylation by DEX which further supports that DEX affected sialylation as well as provides evidence that the sialylation enhancement effects of DEX on recombinant CHO cells occurred through the GR. Finally, the effects of DEX on increasing sialylation were then confirmed in 5-L controlled bioreactors. Addition of 1,µM DEX to the bioreactors on day 2 resulted in harvests with average increases of 16.2% for total sialic acid content and 15.8% in the protein fraction with N-linked sialylation. DEX was found to be a simple and effective method for increasing sialylation of this CTLA4-Ig fusion protein expressed in CHO cells. Biotechnol. Bioeng. 2010;107: 488,496. © 2010 Wiley Periodicals, Inc. [source] Microfluidic biolector,microfluidic bioprocess control in microtiter platesBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Matthias Funke Abstract In industrial-scale biotechnological processes, the active control of the pH-value combined with the controlled feeding of substrate solutions (fed-batch) is the standard strategy to cultivate both prokaryotic and eukaryotic cells. On the contrary, for small-scale cultivations, much simpler batch experiments with no process control are performed. This lack of process control often hinders researchers to scale-up and scale-down fermentation experiments, because the microbial metabolism and thereby the growth and production kinetics drastically changes depending on the cultivation strategy applied. While small-scale batches are typically performed highly parallel and in high throughput, large-scale cultivations demand sophisticated equipment for process control which is in most cases costly and difficult to handle. Currently, there is no technical system on the market that realizes simple process control in high throughput. The novel concept of a microfermentation system described in this work combines a fiber-optic online-monitoring device for microtiter plates (MTPs),the BioLector technology,together with microfluidic control of cultivation processes in volumes below 1,mL. In the microfluidic chip, a micropump is integrated to realize distinct substrate flow rates during fed-batch cultivation in microscale. Hence, a cultivation system with several distinct advantages could be established: (1) high information output on a microscale; (2) many experiments can be performed in parallel and be automated using MTPs; (3) this system is user-friendly and can easily be transferred to a disposable single-use system. This article elucidates this new concept and illustrates applications in fermentations of Escherichia coli under pH-controlled and fed-batch conditions in shaken MTPs. Biotechnol. Bioeng. 2010;107: 497,505. © 2010 Wiley Periodicals, Inc. [source] Generation of high rapamycin producing strain via rational metabolic pathway-based mutagenesis and further titer improvement with fed-batch bioprocess optimizationBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Xiangcheng Zhu Abstract Rapamycin is a triene macrolide antibiotic produced by Streptomyces hygroscopicus. Besides its wide application as an effective immunosuppressive agent, other important bioactivities have made rapamycin a potential drug lead for novel pharmaceutical development. However, the low titer of rapamycin in the original producer strain limits further industrialization efforts and restricts its use for other applications. Predicated on knowledge of the metabolic pathways related to rapamycin biosynthesis in S. hygroscopicus, we have rationally designed approaches to generate a rapamycin high producer strain of S. hygroscopicus HD-04-S. These have included alleviation of glucose repression, improved tolerance towards lysine and shikimic acid, and auxotrophy of tryptophan and phenylalanine through the application of stepwise UV mutagenesis. The resultant strain produced rapamycin at 450,mg/L in the shake flask scale. These fermentations were further scaled up in 120 and 20,000,L fermentors, respectively, at the pilot plant. Selected fermentation factors including agitation speed, pH, and on-line supplementation were systematically evaluated. A fed-batch strategy was established to maximize rapamycin production. With these efforts, an optimized fermentation process in the larger scale fermentor was developed. The final titer of rapamycin was 812,mg/L in the 120,L fermentor and 783,mg/L in the 20,000,L fermentor. This work highlights a high rapamycin producing strain derived by mutagenesis and subsequent screening, fermentation optimization of which has now made it feasible to produce rapamycin on an industrial scale by fermentation. The strategies developed here should also be applicable to titer improvement of other important microbial natural products on an industrial scale. Biotechnol. Bioeng. 2010;107: 506,515. © 2010 Wiley Periodicals, Inc. [source] Profiling of N -glycosylation gene expression in CHO cell fed-batch culturesBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Danny Chee Furng Wong Abstract One of the goals of recombinant glycoprotein production is to achieve consistent glycosylation. Although many studies have examined the changes in the glycosylation quality of recombinant protein with culture, very little has been done to examine the underlying changes in glycosylation gene expression as a culture progresses. In this study, the expression of 24 genes involved in N -glycosylation were examined using quantitative RT PCR to gain a better understanding of recombinant glycoprotein glycosylation during production processes. Profiling of the N -glycosylation genes as well as concurrent analysis of glycoprotein quality was performed across the exponential, stationary and death phases of a fed-batch culture of a CHO cell line producing recombinant human interferon-, (IFN-,). Of the 24 N -glycosylation genes examined, 21 showed significant up- or down-regulation of gene expression as the fed-batch culture progressed from exponential, stationary and death phase. As the fed-batch culture progressed, there was also an increase in less sialylated IFN-, glycoforms, leading to a 30% decrease in the molar ratio of sialic acid to recombinant IFN-,. This correlated with decreased expression of genes involved with CMP sialic acid synthesis coupled with increased expression of sialidases. Compared to batch culture, a low glutamine fed-batch strategy appears to need a 0.5,mM glutamine threshold to maintain similar N -glycosylation genes expression levels and to achieve comparable glycoprotein quality. This study demonstrates the use of quantitative real time PCR method to identify possible "bottlenecks" or "compromised" pathways in N -glycosylation and subsequently allow for the development of strategies to improve glycosylation quality. Biotechnol. Bioeng. 2010;107: 516,528. © 2010 Wiley Periodicals, Inc. [source] | ||||||||||