SEARCH · PubMed Health

Results for “Process optimization”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17Linked to original sources

PubMed1999

The Design of Leadlike Combinatorial Libraries.

The optimization of low-potency leads into drugs is often accompanied by an increase in molecular weight (M(r)) and lipophilicity, as a consequence of affinity enhancement. Hits with affinity at µM levels discovered by screening leadlike libraries allow scope for this optimization process, as shown schematically by the distributions of M(r) for a leadlike library (1), oral drugs (2), and a typical combinatorial chemistry library (3). y=percentage with a particular molecular weight.

Journal Article↗

PubMed2000

Green fluorescent protein in Saccharomyces cerevisiae: real-time studies of the GAL1 promoter.

Green fluorescent protein (GFP) was used to study the regulation of the galactose-inducible GAL1 promoter in yeast Saccharomyces cerevisiae strains. GFP was cloned into the pGAL110 vector and transformed into the yeast strains. Time course studies comparing culture fluorescence intensity and GFP concentration were conducted along with on-line monitoring of GFP expression. Our results demonstrated that GFP fluorescence could be used as a quantifiable on-line reporter gene in yeast strains. The effect of an integrated GAL10p-GAL4 transcription cassette was investigated. Induction time studies showed that there was no significant difference in GFP expression level by adding galactose at different culture times. A wide range of galactose concentrations was used to study the initial galactose concentration effect on GFP expression kinetics. A minimum of 0.05 g/L galactose doubled the GFP fluorescence signal as compared to the control, whereas 0.1 g/L gave the highest specific GFP yield. A simple analytical model was proposed to describe GFP expression kinetics based on the experimental results. In addition, this GFP-based approach was shown to have potential use for high-throughput studies. The use of GFP as a generic tool provided important insights to the GAL expression system and has great potential for further process optimization applications.

Blotting, Western↗

PubMed2001

An evaluation of the detection limits possible for competitive capillary electrophoretic immunoassays.

Using a high-affinity antibody for estradiol, thermodynamic and experimental limitations on detection limits for competitive capillary electrophoretic immunoassays were examined. Theoretical modeling of the dose-response curves for such assays allowed for optimization of experimental conditions. Through the examination of experimental and theoretical results generalizations could be made as to the ability of capillary electrophoretic immunoassays to achieve low detection limits. An experimental detection limit of 310 pM, corresponding to 2100 molecules, was achieved. A minimum theoretical detection limit for the antibody of interest was approximated to be 125-525 pM depending on the standard deviation. An overview of the optimization process is given as well as commentary on theoretical predictions.

Antibodies↗

PubMed2026

Engineering the Vero Cell Lineage: Toward a Programmable Vaccine Manufacturing Platform.

Vero cells remain an indispensable continuous substrate for human viral vaccine manufacturing. Despite decades of empirical process optimization, intrinsic genomic instability, including segmental aneuploidy and dynamic chromatin rearrangements, continues to limit the durability of engineered phenotypes under sustained viral burden and bioreactor stress. Here, we review the expanding engineering toolkit for the Vero lineage across a three-layered functional framework: the membrane interface, cytoplasmic foundry, and nuclear blueprint, evaluating translational prospects at each level. Receptor transplantation and morphological reprogramming have broadened viral entry range and enabled suspension-adapted culture formats, while metabolic flux management and temporally controlled apoptosis modulation have addressed intracellular production bottlenecks, albeit often with trade-offs between productivity, biosafety, and long-term population stability. At the genomic level, targeted perturbations of transcriptional regulators and emerging epigenetic interventions offer more durable gains, yet expression drift, clonal heterogeneity, and karyotypic instability during extended passaging highlight the need for locus-level precision rather than constitutive trait installation. Looking forward, infection-responsive dynamic logic circuits and the systematic identification of Vero-specific genomic safe harbors could shift the paradigm toward a conditionally responsive manufacturing architecture. Collectively, these advances suggest a pathway for transitioning the Vero lineage from a passive, empirically optimized biological substrate into a conditionally responsive, genomically stable, and programmable platform for modern vaccine preparedness.

Vero cells↗

PubMed1987

Promoter recognition and promoter strength in the Escherichia coli system.

The strength of Escherichia coli promoters in vivo as well as the rates of association between RNA polymerase and promoter sequences differ by more than an order of magnitude. Since efficient promoter recognition and rapid binding of the enzyme might be a prerequisite for exceptional promoter strength we have determined the forward rate constants kon (as well as koff) for nine promoters including PL, PA1, and PN25 from phages lambda, T7, and T5, respectively as well as Pbla and PlacUV5 from E. coli. The second order forward rate constants span a 30-fold range from 1 X 10(7) M-1 s-1 for Pbla and PL up to 2.9 X 10(8) M-1 S-1 for PN25. Little correlation between 'promoter recognition' as defined by the rate of complex formation of a promoter sequence with RNA polymerase and its strength in vivo as defined by the rate of RNA synthesis has been found. This adds to the evidence that the complex functional pathway encoded in a promoter sequence can be limited at various levels and that promoter strength in vivo is the result of an optimization process involving more than just one functional parameter.

Bacteriophage lambda↗

PubMed1990

The effects of a biosurfactant on oxygen transfer in a cyclone column reactor.

A laboratory-scale cyclone column reactor was tested to determine how its oxygen transfer characteristics were affected by surfactants in the liquid medium. The volumetric oxygen transfer coefficient was greatly decreased by small quantities of the synthetic surfactants dodecyltrimethylammonium bromide and sodium dodecylsulfate, and the biosurfactant surfactin produced by Bacillus subtilis (ATCC 21332). Since the gas holdup fraction was generally increased due to foaming, the effectiveness of the surfactants was probably due to an increase in the interfacial film resistance. B. subtilis was grown in the cyclone column to 0.6 g dm-3 with a significant level of surfactin produced while maintaining at least 75% oxygen saturation in the broth. Process optimization and scale-up of surfactin production will have to consider oxygen transfer as a key parameter.

Bacillus subtilis↗

PubMed1998

Optimal design of gradient coils in MR imaging: optimizing coil performance versus minimizing cost functions.

The "forward" method of an optimal gradient coil design provides a coil that has the minimal cost function value. It is shown in this study that the solution obtained by minimizing the cost function is directly dependent on the specified cost function and generally results in a deviation from the most desirable coil design. In this paper, a gradient coil design approach for obtaining the best achievable coil performance for pre-determined imaging applications is presented. Through this approach, all intermediate coil performance values calculated during an optimization process, using a simulated annealing algorithm, are stored and presented in a three-dimensional data set. Using this three-dimensional data set, a coil designer is able to make a balance between different coil performance parameters and to select a coil that is the most desirable for the pre-determined imaging applications.

Algorithms↗

PubMedDate not supplied

Quantitative magnetic resonance spectroscopy by optimized numerical curve fitting.

A technique is reported for generating the quantitative area under selected peaks within a 31P NMR spectrum. A numerical iterative method generates the fitted curve so as to minimize the RMS deviation between the fit and the experimental data. The curve is constructed from elemental grains of spectral density ('spexels'), each of which represents an elemental Lorentzian distribution, where the centre frequency and line width of the spexel may be varied within predetermined limits. This provides a fit that in principle is not restricted to a Lorentzian model. The method allows peak areas to be estimated, including the case of overlapping peaks. The method has been tested using simulated spectra containing six overlapping spectral lines each of known amplitude (ranging from 367 to 661 mV) and area; together with additional Gaussian noise with a standard deviation ranging from 30 to 646 mV. The results of fitting both unfiltered and filtered spectra were compared. The variation of quality of fit with spectral noise and filtering has been evaluated. In all cases, the method fitted the peak amplitudes to within 1% of the simulated value. The optimization processes provide an excellent non-linear spectrum filtering algorithm. Provided the noise in the spectra did not exceed ca 400 mV, prefiltered data could be adequately fitted.

Computer Simulation↗

PubMed1996

Cryopreservation of an attenuated vaccine strain of the protozoan parasite Toxoplasma gondii.

Toxoplasma gondii is a protozoan parasite that infects birds and mammals, including humans. T. gondii T-263 is an attenuated mutant strain that is being developed as a live vaccine to protect cats from shedding oocysts. A cryopreservation procedure for T. gondii T-263 bradyzoites has been developed to meet the requirement for product stability. A Me2SO-based procedure for the cryopreservation of tachyzoites was used as a basis for process optimization. A modified cell culture plaque assay was used to determine the effects of selected cryobiological parameters on bradyzoite viability. The major parameters evaluated were: (i) cooling rates; (ii) intermediate plunge temperature; and (iii) thawing and dilution rates and temperatures. The optimized cryopreservation protocol comprised incubation in 12.5% Me2SO and 4% BSA for 30 min at room temperature, cooling at 1 degree C min-1 to -40 degrees C, followed by direct transfer into liquid nitrogen. Rapid thawing (approximately 120 degrees C min-1) followed by slow dilution of cryoprotectant over 15 min resulted in the highest survival. The optimized procedure increased survival 10,000-fold over that obtained using an established tachyzoite protocol. This procedure is to be adapted for the large-scale cryopreservation of T. gondii T-263 bradyzoites in individual vaccine doses.

Animals↗

PubMed1996

Fitness spectrum among random mutants on Mt. Fuji-type fitness landscape.

Statistical properties of a Mt. Fuji-type fitness landscape on a multi-valued sequence space were analysed. We constructed the model landscape based on additivity of the free energy contributed by each residue on a biopolymer, introducing "tolerance functions" that describe tolerance to residue substitution at each site. The fitness spectrum among a random mutant population around a wild-type sequence was theoretically obtained as the probability density distribution function of fitness. As the Hamming distance from the wild-type to the mutants increases, the mean fitness of the mutant population gradually decreases, and the variance of the fitness increases. These features are originated from the anisotropy of the landscape. On the assumption that the free energy is statistically additive around a wild-type in a sequence space of a real biopolymer, one can estimate the Hamming distance from the wild-type to the optimal biopolymer and the fitness of the optimum. Two sets of experimental data were analysed: (1) a promoter strength spectrum of a mutant population produced by the random mutagenesis of a wild-type lac promoter; (2) four stepwise optimization processes of different peptide mixtures evaluated with ligand binding affinity. Analysis of both experiments showed the compatibility with the hypothesis that local fitness landscapes around contemporary biopolymers are near Mt. Fuji-type. The mean slope of each of the four affinity landscapes for (2) was estimated as delta In K(d)/delta d = 1.3 approximately 2.3, where d denotes the Hamming distance from the optimum and K(d) represents the mean dissociation constant of sequences located at the Hamming distance of d. Mt. Fuji-type landscape can be regarded as a zero-th order approximation to the real local landscape just like an "ideal gas". We showed a method to gauge statistically the shape of a near Mt. Fuji-type landscape by measuring mutant fitness spectra.

Animals↗

PubMed2001

Recycling probability and dynamical properties of germinal center reactions.

We introduce a new model for the dynamics of centroblasts and centrocytes in a germinal center. The model reduces the germinal center reaction to the elements considered as essential and embeds proliferation of centroblasts, point mutations of the corresponding antibody types represented in a shape space, differentiation to centrocytes, selection with respect to initial antigens, differentiation of positively selected centrocytes to plasma or memory cells and recycling of centrocytes to centroblasts. We use exclusively parameters with a direct biological interpretation such that, once determined by experimental data, the model gains predictive power. Based on the experiment of Han et al. (1995b) we predict that a high rate of recycling of centrocytes to centroblasts is necessary for the germinal center reaction to work reliably. Furthermore, we find a delayed start of the production of plasma and memory cells with respect to the start of point mutations, which turns out to be necessary for the optimization process during the germinal center reaction. The dependence of the germinal center reaction on the recycling probability is analysed.

Animals↗

PubMed2001

Evolutionary engineering of industrially important microbial phenotypes.

The tremendous complexity of dynamic interactions in cellular systems often impedes practical applications of metabolic engineering that are largely based on available molecular or functional knowledge. In contrast, evolutionary engineering follows nature's 'engineering' principle by variation and selection. Thus, it is a complementary strategy that offers compelling scientific and applied advantages for strain development and process optimization, provided a desired phenotype is amenable to direct or indirect selection. In addition to simple empirical strain development by random mutation and direct selection on plates, evolutionary engineering also encompasses recombination and continuous evolution of large populations over many generations. Two distinct evolutionary engineering applications are likely to gain more relevance in the future: first, as an integral component in metabolic engineering of strains with improved phenotypes, and second, to elucidate the molecular basis of desired phenotypes for subsequent transfer to other hosts. The latter will profit from the broader availability of recently developed methodologies for global response analysis at the genetic and metabolic level. These methodologies facilitate identification of the molecular basis of evolved phenotypes. It is anticipated that, together with novel analytical techniques, bioinformatics, and computer modeling of cellular functions and activities, evolutionary engineering is likely to find its place in the metabolic engineer's toolbox for research and strain development. This review presents evolutionary engineering of whole cells as an emerging methodology that draws on the latest advances from a wide range of scientific and technical disciplines.

Biological Evolution↗

PubMed1986

A multicomponent, random walk model of transport and metabolism inside a neuron.

A model of multicomponent transport, consumption, and production of metabolites inside a neuron containing discrete mitochondria and glycolytic enzymes is developed using a random walk model of molecular transport. The ratio of anaerobic to aerobic metabolism which maximizes ATP production under normal, ischemic, and anoxic conditions is calculated. The ratio of the number of mitochondria to glycolytic enzymes which maximizes ATP under normal conditions is also calculated. Because the volume of the neuron is fixed, the sum of the number of mitochondria and glycolytic enzymes is fixed. This constraint is incorporated in the optimization process as an interior penalty function. Some of the advantages of employing the random walk technique are simple stoichiometry can be used to model consumption and production of metabolites, the geometry of the enzyme system and their active sites can be easily included in the model, and saturation of enzymes can be more easily modeled.

Animals↗

PubMed1989

Parameter optimization model of learning in stepping motion.

In this study we combine the representation of motion by a finite number of hardwired functions with parameter optimization to model learning during a stepping motion. Representation of experimental kinematic data by a finite number of predetermined functions and undetermined coefficients was analyzed. Least squares approximation was used to represent experimental data of stepping motions over obstacles of different heights. Functional relationships between coefficients and obstacles heights were also obtained. Learning of stepping over an obstacle was then formulated as a finite dimensional optimization problem. The pattern of foot path, and joint angles trajectories obtained by this learning model, were then compared to the experimental data. The results of the data fitting analysis and of the optimization process as a model for motion learning, indicate that motion can be adequately represented by a set of hardwired functions, and a finite number of task dependent coefficients.

Humans↗

PubMed1987

On visual orientation of dot patterns.

Two-dimensional normally distributed random dot patterns were used in two experiments on visual orientation estimation. In the first experiment the patterns differed in their sample correlation and in dot number. In the second one the number of dots was maintained constant but the patterns were generated as a superposition of two normally distributed orthogonal sets composed of different number of dots. In both experiments the estimated orientation depended on stimuli correlation - with increasing correlation the estimated orientation gets closer to the orientation of the least square distance axis of the pattern. Even at very low unsignificant correlations there still remained a hint about stimulus orientation which was not estimated at random. Equalizing consecutively the number of dots in the two orthogonal dot patterns during the second experiment did not result in chance performance either. The bimodal angular distributions of the obtained responses permitted to approach the problem of orientation ambiguity. The results are discussed in terms of optimization processes taking place in the visual system.

Cybernetics↗

PubMed1980

Pathology of skeletal muscle: principles of reaction patterns and histochemistry and experience with 195 biopsies.

Technique and interpretation of muscle biopsies require the coordinated team work between referring clinician, surgeon, and pathologist so that optimal management of a patient with neuromuscular disease may be attained. Investigation of muscle diseases has advanced so much with an interdisciplinary approach that not only can accurate diagnosis be offered for the benefit of the patient in certain instances, but also genetic counselling provided and pre-natal diagnosis established. The principal reaction patterns and pathogenetic mechanisms of skeletal muscle as a contractile and metabolically active tissue are described; the diagnostic usefulness of enzyme histochemistry and the basic principles of the motor unit are discussed and illustrated. For the practicing pathologist, adequate tissue preparation of a muscle biopsy specimen requires interest and a willingness to dedicate time, effort and funds. While the paraffin-embedded section is still very valuable, enzyme histochemistry provides certain highly diagnostic information not otherwise obtainable. Likewise, there must be an interest in electron microscopy and appreciation for its value in depicting ultrastructural abnormalities when certain reaction patterns are apparent on light microscopic sections, enzyme histochemical stains, or Epon-embedded "thick" sections. Finally, concurrent sural nerve biopsy also requires optimal processing and interpretation.

Biopsy↗

PubMed1981

Scintillation autoradiography at the light microscopic level: a review.

This article reviews the reported attempts to expose autoradiographs, intended for examination by light microscopy, in the presence of scintillation fluid in order to increase efficiency and thus shorten exposure times. The scintillation process is reviewed, together with the use of comparable techniques in the autoradiography of chromatograms and electrophoresis gels. The conflicting reports on the usefulness of scintillation autoradiography in light microscopy are then discussed, and explanations sought for the wide diversity of claims made for the technique. Many of the more optimistic claims can be explained on the basis that the 'normal' autoradiographs used for comparison had unduly low efficiencies caused by inadequate drying of the emulsion and consequent latent image fading. The techniques used are unlikely to have produced any increase in efficiency through the scintillation process. Optimal conditions for obtaining such increases are derived from theoretical considerations.

Animals↗

PubMed1995

Chemical and biological characteristics of a west African weaning food supplemented with compea (Vigna unguiculata).

The effects of cowpea and amino acid supplementation on the protein quality and chemical characteristics of a maize-based West African traditional weaning food were studied. Process optimization for improved nutritive value was also determined. Supplementation of the traditional weaning food with cowpea increased the lysine, tryptophan and threonine content while the sulphur-amino acids decreased with increasing levels of cowpea. Further supplementation of 70:30 maize/cowpea blends with lysine, threonine or methionine did not significantly improve (p > 0.05) protein quality in terms of the biological value (BV) and net protein utilization (NPU), although significant increases in the protein scores were noted. However, considerable improvements in the BV and NPU were recorded in blends fortified with either tryptophan alone or a combination of lysine, tryptophan, methionine and threonine. Cooking whole cowpea seeds for 45 min before incorporating in the blend formulation also significantly improved (p < 0.05) the protein quality of maize/cowpea blends. The BV and NPU of blends containing 30% pre-cooked cowpea increased from 52 to 76% and 50 to 71% respectively compared to pure maize porridge. The protein content increased from 10 to 14% and the utilizable proteins more than doubled. The weight increase of experimental rats fed with these blends was comparable to that of rats on casein diet. A 30% supplementation of the maize-based weaning food with cowpea therefore greatly enhances the nutritive value especially when the cowpea is pre-cooked for 45 min. Use of chemical scores alone for such blends cannot be a reliable index of blend quality.

Africa, Western↗