bluuebunny/crossref_metadata_2025_split huggingface dataset:
Slit Scanning of Saccharomyces cerevisiae Cells: Quantification of Asymmetric Cell Division and Cell Cycle Progression in Asynchronous Culture
Authors: Block David E. , Eitzman Philip D. , Wangensteen Jeffrey D. , Srienc Friedrich 
Published: March 2005

AbstractSlit scanning flow cytometry has been applied to the analysis of the cell cycle and cellcycle‐dependent events in Saccharomyces cerevisiae, yielding information on the low‐resolution spatial distribution of cellular components in single cells of unperturbed cell populations. Because this process is rapid, large numbers of cells can be analyzed to give distributions of parameters in a given population. To study asymmetric cell division and cell cycle progression, forward‐angle light scattering (FALS) signals together with fluorescence signals from acriflavine‐stained nuclei have been measured in cells from exponentially growing yeast populations. An algorithm has been developed that assigns the position of the bud neck in the FALS signals so that both FALS and DNA signals can be analyzed in terms of the contributions from the mother cell and the cell bud. The data indicate that mother cell FALS, on average, remains constant while FALS due to the cell bud increases as a cell progresses through the cell cycle. By identifying mitotic cells and measuring their properties, we have found that the coefficient of variation for the distribution of FALS is smallest within the dividing cell population and largest within the newborn cell population, in accordance with the critical size control mechanism of yeast cell growth. The use of this experimental approach to provide data for statistical population models is discussed.
Influence of Medium Exchange Schedules on Metabolic, Growth, and GM‐CSF Secretion Rates of Genetically Engineered NIH‐3T3 Cells
Authors: Caldwell Jerry , Locey Betty , Clarke Michael F. , Emerson Stephen G. , Palsson Bernhard O. 
Published: March 2005

AbstractThe metabolic and secretory characteristics of NIH‐3T3 fibroblasts transfected with a cDNA encoding human granulocyte‐macrophage colony stimulating factor (GM‐CSF) were examined as a function of the culture medium exchange schedule. The rates of glucose and glutamine consumption and of lactate and ammonia production were measured over exchange schedules ranging from complete medium replacement weekly (1/week) to complete medium replacement daily (7/week). All measured metabolic rates increased with increased medium exchange rates and accelerated sharply between exchange rates of 3.5/week and 7/week. The lactate/glucose and ammonia/glutamine yield coefficients, however, remained invariant at about 1.9 and 1.0 mol/mol, respectively, under all medium perfusion conditions. A shift‐up in medium perfusion rates from 3.5/week to 7/week resulted in increased metabolic rates that resembled those observed in the cultures that were exchanged at the 7/week rate throughout, showing that the metabolic rates could be directly controlled by the perfusion rate. Differential regulation of medium versus serum perfusion demonstrated that increased NIH‐3T3 cell metabolism was directly proportional to the serum flux to which the cells were exposed. Thus a limiting serum component is responsible for the altered metabolic and growth rates. The GM‐CSF production by the transfected 3T3 cells was stable but exhibited substantial transient increases during periods of cell proliferation, demonstrating that the secretion of transfected gene products can be highly modulated even when the cDNA is driven from a constitutive promoter. These studies show that the metabolic and secretory behavior of genetically engineered cells is influenced by the medium exchange schedule.
Identifying Rate‐Controlling Enzymes in Metabolic Pathways without Kinetic Parameters
Authors: Delgado Javier P. , Liao James C. 
Published: March 2005

AbstractThe flux control coefficients, originally defined by Kacser and Burns, provide a sound theoretical basis for identifying rate‐controlling enzymes in metabolic pathways. However, the calculation of these quantities requires kinetic parameters, which are usually unavailable in practical systems. This article presents a method for evaluating the flux control coefficients by using measurements of metabolite concentrations in a transient state. The basis of this approach is the relationship identified here between transient fluxes and the flux control coefficients. Principal component analysis in the form of singular value decomposition is used to identify such relationships and evaluate the flux control coefficients. The approach does not require kinetic parameters and depends only on the knowledge of pathway stoichiometry, which is generally available.
Solubility of Globular Proteins in Polysaccharide Solutions
Authors: Guo Meining , Narsimhan Ganesan 
Published: March 2005

AbstractA statistical thermodynamic model based on the lattice model proposed by Baskir et al. (1987) was employed to predict the solubilities of globular proteins such as ovalbumin and lysozyme at their isoelectric points in dextran solutions of different molecular weights. The model accounted for protein‐polysaccharide and polysaccharide‐solvent interactions as well as entropy of mixing, and it employed simplifying assumptions such as a linear homogeneous polysaccharide molecule and a spherical globular protein molecule of uniform surface properties. The protein‐polysaccharide interaction parameter χs, obtained by fitting the model to experimental data for one molecular weight of dextran, was found to be 0.132 and 0.115 for ovalbumin and lysozyme, respectively. Solubilities of ovalbumin and lysozyme in dextran solutions of different molecular weights exhibited a shallow maximum at intermediate dextran concentrations and compared well with model predictions. Protein solubility was found to be very sensitive to protein‐polysaccharide interactions and increase with more favorable protein‐polysaccharide interactions (larger χs), less favorable polysaccharide‐solvent interactions (larger χ), smaller size protein molecule, and lower molecular weight polysaccharide.
Immobilization of Escherichia coli JM103[pUC8] in κ‐Carrageenan Coupled with Recombinant Protein Release by in Situ Cell Membrane Permeabilization
Authors: Ryan Wen , Parulekar Satish J. 
Published: March 2005

AbstractImmobilization of Escherichia coli JM103[pUC8] was carried out with κ‐carrageenan as the support matrix. Substantial natural excretion of β‐lactamase, attributable to the less intact membrane of plasmid‐harboring cells, was observed in immobilized cell cultures. Nevertheless, a significant portion of the β‐lactamase produced was retained in the cells. As compared to suspension cultures, much higher β‐lactamase activities, especially in the extracellular liquid, and much longer retention of plasmid‐bearing cells (improved plasmid stability) were observed in immobilized cell cultures. Further enhancement in excretion of the recombinant protein (β‐lactamase) was achieved by permeabilization of cell membrane by periodic exposure of the immobilized cell cultures to ethylenediaminetetraacetic acid (EDTA). While the presence of EDTA led to some suppression of cell growth in suspension cultures, cell growth in gel beads was not affected by EDTA to the same extent, possibly due to lesser exposure of immobilized cells to EDTA. Exposure of immobilized cell cultures to EDTA presumably inhibited plasmid replication and led in turn to diversion of cellular resources for the support of expression of plasmid genes. Indeed, treatment of the immobilized cell cultures with EDTA resulted in increased production of β‐lactamase when compared to the enzyme production in EDTA‐free cultures. More frequent addition of EDTA increased the period of retention of plasmid‐bearing cells in these cultures but did not have any noticeable adverse effect on synthesis of β‐lactamase. Improvement in plasmid stability in EDTA‐treated immobilized cell cultures was ascribed to the reduction in the growth rate differential between plasmid‐free and plasmid‐bearing cells, since plasmid‐free cells were subject to more reduction in specific growth rate than were plasmid‐bearing cells.
Convective Mass Transfer in Large Porous Biocatalysts: Plant Organ Cultures
Authors: Prince C. L. , Bringi V. , Shuler M. L. 
Published: March 2005

AbstractThe importance of convective contributions to the total rate of mass transfer into porous biological catalysts has been insufficiently appreciated. For liquid systems, diffusion within large particles is generally slow relative to reaction, especially for sparingly soluble nutrients such as oxygen. We report experimental evidence demonstrating that oxygen consumption within porous root culture clumps is normally restricted by the rate of convective mass transfer within the clump. Increasing liquid flow rates around spheres of entangled rootlets induces higher rates of internal convective mass transfer and gives rise to increased total rates of oxygen consumption. Minimum external velocities for full nutrient sufficiency on the interior are not predicted well by creeping external flow models and, especially for larger biocatalysts, inertial effects must be taken into account. For higher Reynolds number external flow, form drag may be used to suggest the dependence of internal convection on external flow conditions. The minimum external liquid velocity for nutrient sufficiency is then seen to be a strong and unpredictable function of catalyst size and catalyst density. Implications for organ culture reactor design are discussed.
Effect of Self‐Association on the Transport of α‐Chymotrypsin across Microporous Membranes
Authors: Zanapalidou R. H. , Domach M. M. 
Published: March 2005

AbstractThe dependence of the rate of α‐chymotrypsin transport across microporous, polycarbonate membranes on enzyme concentration was investigated. It was of interest to determine whether self‐association, the extent of which is concentration‐dependent, would have a significant effect on the mass transfer coefficient. When the enzyme was solubilized in pH 6.2 and I 0.2 buffer, a significant decrease in the mass transfer coefficient accompanied an increase in solute concentration. Furthermore, when the pH and ionic strength of the solvent were altered, it was found that the concentration dependence of the mass transfer coefficient reflected the degree of self‐association known to occur in the different solvents. An analysis of the potential effects of osmotic backflow and excluded volume indicates that self‐association is responsible for the observed changes in the mass transfer coefficient. From the practical standpoint, these results suggest that self‐association could be promoted in order to alter a solute's rejection coefficient, and membrane transport studies could complement the results of moving boundary and light scattering experiments.
Concentration of Spirulina Suspensions by Radial Migration with Flow Through Vertical Tees
Authors: Rakow Allen L. , Fernald Daniel 
Published: March 2005

AbstractSuspensions of Spirulina platensis, a microalga, were pumped in laminar flow through vertical tubes. Reynolds numbers in the high end of the laminar regime were maintained along with sufficient length of tube in most cases to allow the particles to migrate to a region close to the tube axis. An equidiameter tee‐branch was employed to direct the dilute outer region of the flow through the branches while the central region of concentrated particles flowed on through the main channel. A 0.01 % dry mass (DM) suspension can be concentrated 100‐fold in a 650‐μm diameter system to approximately 1 % DM in the equivalent of 6 passes (the upper limit of concentration on the basis of a rod exclusion model is about 2.5% DM). The concentration factor decreases exponentially with inlet concentration ranging from a value near 3 at low inlet concentration to a value near 1 at the highest concentration tested to date.
Catalytic Peptide Synthesis by Trypsin Modified with Polystyrene in Chloroform
Authors: Ito Yoshihiro , Fujii Hajime , Imanishi Yukio 
Published: March 2005

AbstractTrypsin was modified with a hydrophobic synthetic polymer, polystyrene. The attachment was achieved by first coupling free amines in the trypsin with azobis(4‐cyanovaleric acid) and then irradiating the product in the presence of styrene. Decomposition of the azo structure provided free radical initiation of styrene polymerization, with the trypsin thus becoming part of the end group for the polymer chain initiated. That the modified trypsin retained catalytic activity when dissolved in chloroform was demonstrated by using it to catalyze the formation of a peptide linkage between amino acids. The catalytic reaction was stereoselective.
Fractional Factorial Study of Hybridoma Behavior. 2. Kinetics of Nutrient Uptake and Waste Production
Authors: Gaertner John G. , Dhurjati Prasad 
Published: March 2005

AbstractA fractional factorial experimental method was used to identify important variables and variable interactions which affect nutrient uptake and waste production. The variables studied include glucose, glutamine, base medium, lactate, and ammonium. Cellular glucose uptake was stimulated by glucose and glutamine and inhibited by lactate. Glucose, base medium, and glutamine all had large stimulative effects on lactate production. Glucose uptake and lactate production both exhibited Monod‐type dependencies on the glucose concentration. Ammonium production was sensitive to the glucose and lactate concentrations at levels below about 8 and 20 mM, respectively. Mathematical descriptions of glucose uptake and of lactate and ammonium production were developed. These experimental results have significant implications for the optimization of hybridoma growth in bioreactors.
Modeling and Simulation of Anaerobic Wastewater Treatment and Its Application to Control Design: Case Whey
Authors: Ryhiner Gerhard B. , Heinzle Elmar , Dunn Irving J. 
Published: March 2005

AbstractModeling and simulation of the anaerobic treatment of whey wastewater was studied. A model inpluding five groups of organisms, whey substrate, butyric, propionic, and acetic acids, CO2, H2, and CH4, was developed for single‐ and two‐stage anaerobic fluidized bed reactors. It included thermodynamic limitations for the acetogenesis reaction, acid‐base equilibria of dissociating compounds (organic acids and CO2) for variable and constant pH situations, gas‐liquid phase mass transfer, and measurement dynamics. The model was adequate to describe both the steady‐state and dynamic behavior of the reactors and was used to study various control schemes. In all cases the feed flow rate was the manipulated variable. Controls of pH, dissolved hydrogen, and organic acids were all successful in simulation and experiment. Simulations were used to determine optimal control parameters for conventional proportional—integral (PI) or proportional—integral—differential (PID) control. The experimentally found optimal values were in close agreement with predetermined simulated values. Simple control using gas analysis results did not give stable control, either in the simulation or in the experiment.
A Computer Model Based on Reaction‐Diffusion Equations for the Growth of Filamentous Fungi on Solid Substrate
Authors: Molin Paul , Gervais Patrick , Lemiere Jean‐Pierre 
Published: March 2005

AbstractA model of two reaction‐diffusion equations for biomass production and glucose consumption was developed. Experiments were carried out in order to estimate the different constants of the model and to compare the behavior of the system using two species of fungi, Rhizopus oligosporus and Trichoderma viride T.S. A mathematical study of the equations was performed. The model provides good predictive values, and the parameters have a precise biological significance. From the study of the phase plane biomass‐glucose, in the case of Rhizopus oligosporus the existence of a secondary metabolism for the growth when glucose consumption is almost complete is proposed.
Modeling of Isotope Distributions and Intracellular Fluxes in Metabolic Networks Using Atom Mapping Matrices
Authors: Zupke C. , Stephanopoulos G. 
Published: March 2005

AbstractThe modeling of isotope distributions can be used to evaluate intracellular fluxes and to investigate cellular metabolism. A method of modeling isotope distributions in biochemical networks that addresses some of the shortcomings of conventional methods is presented. Matrix equations representing steady state isotope balances are formulated for each metabolite and solved iteratively via computer. The key feature of this method is the use of atom mapping matrices, which decouple the generation of the steady state equations from the details of the transfer of carbon atoms from reactants to products. The use of atom mapping matrices results in a clear, intuitive description of metabolic networks that is easy to develop, check, and modify. A network representing energy metabolism in a hybridoma cell line was developed and presented as an example of the method. A program that uses the atom mapping matrix method to calculate the isotope distribution in the network as a function of the intracellular fluxes was written. Calculations showed that a single nuclear magnetic resonance (NMR) experiment with 13C‐labeled glucose should be able to uniquely determine two important TCA cycle flux ratios. These results demonstrate how in vitro NMR can be used to study cellular metabolism or to validate the flux estimates obtained from other methods.
A Mathematical Model To Predict the Partitioning of Peptides and Peptide‐Modified Proteins in Aqueous Two‐Phase Systems
Authors: Eiteman Mark A. , Hassinen Cynthia , Veide Andres 
Published: March 2005

AbstractA mathematical procedure was developed to predict the partition coefficients of the peptides AIIP, AWWP, AIIPAIIP and AWWPAWWP in poly(ethylene glycol) (PEG)/ phosphate aqueous two‐phase systems from amino acid hydrophobicities. In general, peptides containing tryptophan partition more into the PEG‐enriched upper phase than analogous peptides containing isoleucine. Specifically, as the PEG concentration difference between the phases increased in a PEg/potassium phosphate aqueous two‐phase system, the peptide AIIP was observed to have a partition coefficient ranging from 1.2 to 1.6, AIIPAIIP from 2.4 to 5.7, AWWP from 13.5 to 32.2, and AWWPAWWP from 43 to 170. The model was extended to predict the partitioning of a staphylococcal protein A derivative (ZZ) modified with these four peptides. As predicted, the protein modified with isoleucine‐containing peptides had lower partition coefficients than the protein modified with tryptophan‐containing peptides. The partition coefficient of the ZZ protein ranged from 0.35 to 0.20, that of ZZAIIPAIIP from 0.58 to 0.48, and that of ZZAWWPAWWP from 3.5 to 5.3 in these systems. The results show that short peptide handles can significantly enhance the partitioning of proteins in aqueous two‐phase systems. The relationship between the model and the surface exposure of peptide handles and the utility of the model to aid in the design of such handles to enhance purifications are also discussed.
Measurement of Adhesion and Spreading Kinetics of Baby Hamster Kidney and Hybridoma Cells Using an Integrated Optical Method
Authors: Li S. ‐Y. , Ramsden J. J. , Prenosil J. E. , Heinzle E. 
Published: March 2005

AbstractA novel optical method was used for quantitative characterization and continuous measurement of both the adhesion and spreading of mammalian cells on inorganic surfaces. It is based upon the effective refractive index change caused by cells when they adhere to a planar optical waveguide. We have applied this technique to measure the kinetics of the adhesion and spreading processes of baby hamster kidney (BHK) cells adhering to surfaces coated with fibronectin and under different culture conditions (PBS, medium, serum, EDTA). In comparison, hybridoma cells are only adsorbed to the surface and do not spread at all. Moreover, this technique also allows the mass of an adsorbed protein adlayer to be determined very precisely and thus provides a valuable tool for screening suitable substrata as well as determining the influence of different culture conditions on cell adhesion and spreading. This sensitive test for substrate influence could be important in toxicity tests using adherent animal cells.
Dynamic Mixing and Oxygen Transfer in Small, Airlift Loop Bioreactors: Model and Experimental Verification
Authors: Fraser Randall D. , Ritchie Brian J. , Hill Gordon A. 
Published: March 2005

AbstractA mechanistic model for mixing and mass transfer in both airlift bubble column and loop bioreactors is described. The model is a useful design tool to improve oxygen‐transfer characteristics. It is shown that the model fits mixing and mass‐transfer experimental data closely. The model confirms that the overall oxygen‐transfer coefficient in the riser of a loop airlift fermentor is similar to that in bubble columns and that lower measured transfer rates are due solely to the dead volume in the downcomer. The effects of parameters such as mass‐transfer coefficient, aeration rate, dispersion coefficient, sparger rotation speed, and liquid circulation velocity are presented in terms of both the liquid‐ and gas‐phase oxygen concentrations.
Effects of Skin Pigmentation on Pulse Oximeter Accuracy at Low Saturation
Authors: Bickler Philip E. , Feiner John R. , Severinghaus John W. 
Published: March 2005

Background
It is uncertain whether skin pigmentation affects pulse oximeter accuracy at low HbO2 saturation.

Methods
The accuracy of finger pulse oximeters during stable, plateau levels of arterial oxygen saturation (Sao2) between 60 and 100% were evaluated in 11 subjects with darkly pigmented skin and in 10 with light skin pigmentation. Oximeters tested were the Nellcor N-595 with the OxiMax-A probe (Nellcor Inc., Pleasanton, CA), the Novametrix 513 (Novametrix Inc., Wallingford, CT), and the Nonin Onyx (Nonin Inc., Plymouth, MN). Semisupine subjects breathed air-nitrogen-carbon dioxide mixtures through a mouthpiece. A computer used end-tidal oxygen and carbon dioxide concentrations determined by mass spectrometry to estimate breath-by-breath Sao2, from which an operator adjusted inspired gas to rapidly achieve 2- to 3-min stable plateaus of desaturation. Comparisons of oxygen saturation measured by pulse oximetry (Spo2) with Sao2 (by Radiometer OSM3) were used in a multivariate model to determine the interrelation between saturation, skin pigmentation, and oximeter bias (Spo2 - Sao2).

Results
At 60-70% Sao2, Spo2 (mean of three oximeters) overestimated Sao2 (bias +/- SD) by 3.56 +/- 2.45% (n = 29) in darkly pigmented subjects, compared with 0.37 +/- 3.20% (n = 58) in lightly pigmented subjects (P < 0.0001). The SD of bias was not greater with dark than light skin. The dark-light skin differences at 60-70% Sao2 were 2.35% (Nonin), 3.38% (Novametrix), and 4.30% (Nellcor). Skin pigment-related differences were significant with Nonin below 70% Sao2, with Novametrix below 90%, and with Nellcor at all ranges. Pigment-related bias increased approximately in proportion to desaturation.

Conclusions
The three tested pulse oximeters overestimated arterial oxygen saturation during hypoxia in dark-skinned individuals.