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  • Biochemistry and Biotechnology  (39)
  • Engineering General  (31)
  • 1995-1999  (70)
  • 1
    Electronic Resource
    Electronic Resource
    Cell cycle dependence of retroviral transduction: An issue of overlapping time scales (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 272-281 
    Details
    ISSN: 0006-3592
    Keywords: gene transfer ; retrovirus ; cell cycle ; intracellular stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Recombinant retroviruses are currently used as gene delivery vehicles for the purpose of gene therapy. It is generally believed that the efficiency of retroviral transduction depends on the cell cycle status of the target cells. However, it has been reported that this is not the case for the transduction of human and murine fibroblasts, in contrast to other cell types such as lymphocytes. The predictions of a mathematical model that we constructed, offer an explanation of this contradiction, based on the dynamics of the underlying processes of target cell growth and the intracellular decay of retroviral vectors. The model suggests that the utility of synchronization experiments, that are usually employed to study cell cycle specificity, is severely limited when the time scales of the above kinetic events are comparable to each other. The predictions of the model also suggest the use of retroviral vectors as cell cycle markers, as an alternative way to detect cell cycle dependence of retroviral transduction. This method obviates the need for cell synchronization and therefore, it does not perturb the cell cycle or interfere with the life cycle of retroviral vectors. Moreover, it does not depend on the intracellular stability of retroviral vectors. Our results show that in contrast to previously reported results, transduction of murine fibroblasts is cell cycle dependent, and they are consistent with the current notion that mitosis is the phase that confers transduction susceptibility. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:272-281, 1998.
    Additional Material: 7 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    How will bioinformatics influence metabolic engineering? (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 162-169 
    Details
    ISSN: 0006-3592
    Keywords: bioinformatics ; metabolic engineering ; genetic engineering ; mathematical analysis ; stoichiometry ; enzyme kinetics ; modal analysis ; genetic circuits ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Ten microbial genomes have been fully sequenced to date, and the sequencing of many more genomes is expected to be completed before the end of the century. The assignment of function to open reading frames (ORFs) is progressing, and for some genomes over 70% of functional assignments have been made. The majority of the assigned ORFs relate to metabolic functions. Thus, the complete genetic and biochemical functions of a number of microbial cells may be soon available. From a metabolic engineering standpoint, these developments open a new realm of possibilities. Metabolic analysis and engineering strategies can now be built on a sound genomic basis. An important question that now arises; how should these tasks be approached? Flux-balance analysis (FBA) has the potential to play an important role. It is based on the fundamental principle of mass conservation. It requires only the stoichiometric matrix, the metabolic demands, and some strain specific parameters. Importantly, no enzymatic kinetic data is required. In this article, we show how the genomically defined microbial metabolic genotypes can be analyzed by FBA. Fundamental concepts of metabolic genotype, metabolic phenotype, metabolic redundancy and robustness are defined and examples of their use given. We discuss the advantage of this approach, and how FBA is expected to find uses in the near future. FBA is likely to become an important analysis tool for genomically based approaches to metabolic engineering, strain design, and development. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:162-169, 1998.
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  • 3
    Electronic Resource
    Electronic Resource
    Different measures of human hematopoietic cell culture performance are optimized under vastly different conditions (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 505-513 
    Details
    ISSN: 0006-3592
    Keywords: bone marrow ; hematopoiesis ; perfusion ; culture optimization ; stroma ; stem cells ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Hematopoiesis, the formation of mature blood cells from stem (LTC-IC) and progenitor (CFU-GM) cells in the bone marrow, is a complex tissue-forming process that leads to many important physiological functionalities. Consequently, a functioning ex vivo hematopoietic system has a variety of basic scientific and clinical uses. The design and operation of such a system presents the tissue engineer with challenges and choices. In this study, three culture variables were used to control ex vivo human hematopoiesis. Systematic variation of inoculum density (ID), medium exchange interval (MEI), and the use of preformed stroma (PFS) showed that (1) all three variables significantly influenced culture performance, (2) the three variables interacted strongly, and (3) the variables could be manipulated to achieve the optimization of different performance criteria. Donor-to-donor variability in culture performance was great at low ID but was minimized at higher ID. PFS had a large positive effect on cell and CFU-GM output at low ID, but had minimal effect at higher ID. In fact, PFS caused a decrease in LTC-IC output at high ID. The effects of PFS indicated that stromal cell elements became more limiting than proliferative cell elements as ID was reduced.In cultures without PFS, maximum cell output was obtained with high ID using a short MEI, whereas the greatest cell expansion ratio was obtained at low ID with an intermediate MEI. Maximum CFU-GM output was obtained from cultures with high ID using a short to intermediate MEI, whereas the greatest CFU-GM expansion ratio was obtained at intermediate ID with an intermediate MEI. The addition of PFS altered the locations of these maxima. In general, PFS moved the maxima to lower ID, and culture output became more sensitive to MEI. Therefore, the optimization of one performance criterion always resulted in a decline of the others. This study demonstrates that ex vivo tissue function is sensitive to many culture variables in an interactive fashion and that systematic multivariable studies are required to characterize tissue function. Once the effects of individual variables and their interactions are known, this knowledge can be used to optimize tissue performance with respect to desired criteria. © 1996 John Wiley & Sons, Inc.
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  • 4
    Electronic Resource
    Electronic Resource
    Production of recombinant bacterial endoglucanase as a co-product with ethanol during fermentation using derivatives of Escherichia coli KO11 (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 547-555 
    Details
    ISSN: 0006-3592
    Keywords: ethanol ; cellulose ; hemicellulose ; endoglucanase ; cellulase ; lignocellulose ; biomass ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: This study demonstrates a new approach to reduce the amount of fungal cellulase required for the conversion of cellulose into ethanol. Escherichia coli KO11, a biocatalyst developed for the fermentation of hemicellulose syrups, was used to produce recombinant endoglucanase as a co-product with ethanol. Seven different bacterial genes were expressed from plasmids in KO11. All produced cell-associated endoglucanase activity. KO11(pLOI1620) containing Erwinia chrysanthemi celZ (EGZ) produced the highest activity, 3,200 IU endoglucanase/L fermentation broth (assayed at pH 5.2 and 35°C). Recombinant EGZ was solubilized from harvested cells by treatment with dilute sodium dodecyl sulfate (12.5 mg/ml, 10 min, 50°C) and tested in fermentation experiments with commercial fungal cellulase (5 filter paper units/g cellulose) and purified cellulose (100 g/L). Using Klebsiella oxytoca P2 as the biocatalyst, fermentations supplemented with EGZ as a detergent-lysate of KO11(pLOI1620) produced 14%-24% more ethanol than control fermentations supplemented with a detergent-lysate of KO11(pUC18). These results demonstrate that recombinant bacterial endoglucanase can function with fungal cellulase to increase ethanol yield during the simultaneous saccharification and fermentation of cellulose. © 1997 Wiley & Sons, Inc. Biotechnol Bioeng 55: 547-555, 1997.
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  • 5
    Electronic Resource
    Electronic Resource
    Photosynthetic performance of a helical tubular photobioreactor incorporating the cyanobacterium spirulina platensis (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 47 (1995), S. 261-269 
    Details
    ISSN: 0006-3592
    Keywords: photosynthesis ; global warming ; CO2 fixation ; photobioreactor ; Spirulina platensis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The photosynthetic performance of a helical tubular photobioreactor (“Biocoil”), incorporating the filamentous cyanobacterium Spirulina platensis, was investigated. The photobioreactor was constructed in a cylindrical shape (0.9 m high) with a 0.25-m2basal area and a photostage comprising 60 m of transparent PVC tubing of 1.6-cm inner diameter (volume = 12.1 L). The inner surface of the cylinder (area = 1.32 m2) was illuminated with cool white fluorescent lamps; the energy input of photosynthetically active radiation(PAR, 400 to 700 nm) into the photobioreactor was 2920 kJ per day. An air-lift system ncorporating 4%CO2 was used to circulate the growth medium in the tubing. The maximum productivity achieved in batch culture was 7.18 g dry biomass per day [0.51 g · d biomass/L · day, or 5.44 g · d biomass/m2(inner surface of cylindrical shape)/day] which corresponded to a photosynthetic (PAR) efficiency of 5.45%. The CO2 was efficiently removed from the gaseous stream; monitoring the CO2 the outlet and inlet gas streams showed a 70% removal of CO2 from the inlet gas over an 8-h period with almost maximum growth rate. © 1995 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260470218
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  • 6
    Electronic Resource
    Electronic Resource
    Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 45 (1995), S. 69-79 
    Details
    ISSN: 0006-3592
    Keywords: E. coli ; linear optimization ; metabolic fluxes ; stoichiometry ; sensitivity analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Stoichiometrically based flux balance models provide a method to quantify the metabolic pathway fluxes within a living cell. Predictions of flux balance models are expected to have applications in pathway engineering as well as in bioprocess design and control. These models utilize optimality principles applied to metabolic pathway stoichiometry along with the metabolic requirements for growth to determine the flux distribution in a metabolic network. A flux balance model has been developed for Escherichia coli W3110 using five experimentally determined strain-specific parameters. In this report, we determine the sensitivity of the predictions of the flux balance model to these five strain-specific parameters. Model predictions are shown to be sensitive to the two parameters describing metabolic capacity, while they are relatively insensitive to the three parameters that describe the metabolic requirements for growth. Thus, when stoichiometrically based models are formulated for additional strains one needs to measure the metabolic capacity (maximum rates of nutrient and oxygen utilization) accurately. Determination of metabolic capacity from batch experiments is relatively easy to perform. On the other hand, the harder to determine maintenance parameters need not be as accurately determined. © 1995 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/bit.260450110
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  • 7
    Electronic Resource
    Electronic Resource
    Controlling enzyme-catalyzed regioselectivity in sugar ester synthesis (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 45 (1995), S. 426-434 
    Details
    ISSN: 0006-3592
    Keywords: regioselectivity of enyzmatic catalysis ; sucrose acylation in organic solvents ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The rational control over enzyme-catalyzed regioselectivity has been studied using sucrose acylation by vinyl esters in organic media as a model. Subtilisins BPN' and Carlsberg preferentially acylate at the 1′-hydroxyl of sucrose with some acylation observed at the 6-hydroxyl. The preference for the 1′-hydroxyl is strongly affected by the hydrophobicity of the organic solvent and the chain length of the vinyl ester. Increasingly hydrophobic solvents and longer chain lengths lower the favorable formation of the 1′-acylation and improve 6-acylation. Molecular modeling of sucrose in the binding pocket of subtilisin BPN' shows that the 1′-acylation is favored in solvents that can solvate sugars (such as pyridine) as the glucose moiety is exposed to the medium, whereas 6-acylation leaves the entire sucrose molecule buried within the enzyme's binding pocket. Thus, 1′-acylation is sterically more favorable than 6-acylation. Increasingly hydrophobic solvents affect regioselectivity by changing the degree of solvation of the glucose moiety in the medium and forcing the sucrose 1′-ester completely into the binding pocket. In a related modeling, the vinyl ester chain length was shown to modulate regioselectivity by controlling the bond angles between the resulting acylenzymes and the sucrose thereby affecting the positioning of the sucrose in the binding pocket of subtilisin BPN'. This study shows that control over enzymic regioselectivity can be achieved by rational choices of substrate and solvent. © 1995 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/bit.260450507
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  • 8
    Electronic Resource
    Electronic Resource
    Modeling biofilm accumulation and mass transport in a porous medium under high substrate loading (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 47 (1995), S. 703-712 
    Details
    ISSN: 0006-3592
    Keywords: biofilm modeling ; detachment ; porous media ; biobarriers ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A packed bed biofilm reactor inoculated with pure culture Pseudomonas aeruginosa was run under high substrate loading and constant flow rate conditions. The 3.1-cm-diameter cylindrical reactor was 5 cm in length and packed with 1-mm glass beads. Daily observations of biofilm thickness, influent and effluent glucose substrate concentration, and effluent dissolved and total organic carbon were made during the 13-day experiment. Biofilm thickness appeared to rech quasi-steady-state condition after 10 days. A published biofilm process simulation program (AQUASIM) was used to analyze experimental data. Comparison of observed and simulated variables revealed three distinct phases of biofilm accumulation during the experiment: an initial phase, a growth phase, and a mature biofilm phase. Different combinations of biofilm and mass transport process variables were found to be important during each phase. Biofilm detachment was highly correlated with shear at the biofilm surface during all three phases of biofilm development. © 1995 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/bit.260470611
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  • 9
    Electronic Resource
    Electronic Resource
    Expanded bed affinity chromatography of dehydrogenases from bakers' yeast using dye-ligand perfluoropolymer supports (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 48 (1995), S. 341-354 
    Details
    ISSN: 0006-3592
    Keywords: affinity chromatography ; perfluoropolymers ; expanded bed ; dye-ligand ; dehydrogenases ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Malate dehydrogenase (MDH) and glucose 6-phosphate dehydrogenase (G6PDH) have been partially purified from preparations of homogenized yeast cells using Procion Yellow H-E3G and Procion Red H-E7B, respectively, immobilized on solid perfluoropolymer supports in an expanded bed. A series of pilot experiments were carried out in small packed beds using clarified homogenate to determine the optimal elution conditions for both MDH and G6PDH. Selective elution of MDH using NADH was effective but the yields obtained were dependent on the concentration of NADH used. Selective elution was found to be most effective when a low concentration of NaCl (0.1 M) was present. MDH could be recovered in 84% yield with a purification factor of 94 when this strategy was adopted. In the case of G6PDH, specific elution using NADP+ was successful in purifying G6PDH 178-fold in 96% yield. The dynamic capacity of both affinity supports was estimated by frontal analysis, in an expanded bed with unclarified homogenate, and corresponded to 17 U MDH/mL of settled Procion Yellow H-E3G perfluoropolymer support and 7.7 U H6PDH/mL of settled Procion Red H-E7B perfluoropolymer support. Expanded bed affinity chromatography of MDH resulted in an eluted fraction containing 89% of the applied activity with a purification factor of 113. Expanded bed affinity chromatography of G6PDH resulted in an eluted fraction containing 84% of the applied activity with a purification factor of 172. With both enzymes, the overall recovery of enzyme activity was greater than 94%, showing that the expanded bed approach to purification was nondenaturing. © 1995 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/bit.260480407
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  • 10
    Electronic Resource
    Electronic Resource
    Influence of substrate oscillations on acetate formation and growth yield in Escherichia coli glucose limited fed-batch cultivations (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 47 (1995), S. 139-146 
    Details
    ISSN: 0006-3592
    Keywords: Escherichia coli ; fed-batch ; acetate ; glucose ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A Large bioreactor is an inhomogenous system with concentration gradients which depend on the fluid dynamics and the mass transfer of the reactor, the feeding strategy, the saturation constant, and the cell density. The responses of Escherichia coli cells to short-term oscillations of the carbon/energy substrate in glucose limited fed-batch cultivations were studied in a two-compartment reactor system consisting of a stirred tank reactor (STR) and an aerated plug flow reactor (PFR) as a recycle loop. Short-term glucose excess or starvation in the PFR was simulated by feeding of glucose to the PFR or to the STR alternatively. The cellular response to repeated short-term glucose excess was a transient increase of glucose consumption and acetate formation. But, there was no accumulation of acetate in the culture, because it was consumed in the STR part where the glucose concentration was growth limiting. However, acetate accumulated during the cultivation if the oxygen supply in the PFR was insufficient, causing higher acetate formation. The biomass yield was then negatively influenced, which was also the case if the PFR was used to simulate a glucose starvation zone. The results suggest that short-term heterogeneities influence the cellular physiology and growth, and can be of major importance for the process performance. © 1995 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/bit.260470204
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