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Stability and parameter dependency analysis of a facilitation tectal column (FTC) model.

Mathematical models and computer simulations have been widely used to study the spatio-temporal characteristics of the processing of information carried out by the central nervous system. When trying to show whether or not a neural model accounts for the phenomena under study, if the number of parameters whose values need to be calculated becomes large, then computer simulations alone become very inefficient to define such values. Here, we developed stability and parameter dependency analyses of the mathematical representation of a single facilitation tectal column (FTC) model, to show how by using techniques from non-linear systems theory we can define the ranges of parameter values under which the model would explain the required performance of the neural net model. The benefits of these analyses can be grouped in two parts: first, the advantage of using non-linear systems techniques to analyze, analytically, the dynamics of neural net models; and second, we get a deeper understanding of why the hypotheses embedded in the models yield the appropriate behaviors and what are the critical situations (parametric combinations) under which these behaviors are displayed.

Action Potentials↗

Estimating the uncertainty of stability for matrix CRMs.

The new version of ISO Guide 34 requires producers of certified reference materials (CRMs) to include contributions of possible instability to the overall CRM uncertainty, to obtain a value for the uncertainty in compliance with the Guide to the Expression of the Uncertainty in Measurement (GUM). A pragmatic approach to estimating the uncertainty of stability is presented. It relies on regression analysis of stability data with subsequent testing of the slope of the regression line for significance. If the slope is found to be statistically insignificant, a shelf life is chosen and the uncertainty connected with this time is estimated via the standard deviation of the slope. This uncertainty is included in the overall uncertainty of the CRM. This approach is explained with examples showing its applicability to matrix CRMs.

Chemistry Techniques, Analytical↗

The role of context on alpha-helix stabilization: host-guest analysis in a mixed background peptide model.

The helix content of a series of peptides containing single substitutions of the 20 natural amino acids in a new designed host sequence, succinyl-YSEEEEKAKKAXAEEAEKKKK-NH2, has been determined using CD spectroscopy. This host is related to one previously studied, in which triple amino acid substitutions were introduced into a background of Glu-Lys blocks completely lacking alanine. The resulting free energies show that only Ala and Glu- prove to be helix stabilizing, while all other side chains are neutral or destabilizing. This agrees with results from studies of alanine-rich peptide modela, but not the previous Glu-Lys block oligomers in which Leu and Met also stabilize helix. The helix propensity scale derived from the previous block oligomers correlated well with the frequencies of occurrence of different side chains in helical sequences of proteins, whereas the values from the present series do not. The role of context in determining scales of helix propensity values is discussed, and the ability of algorithms designed to predict helix structure from sequence is compared.

Algorithms↗

Multilocus DNA fingerprint analysis of cell banks: stability studies and culture identification in human B-lymphoblastoid and mammalian cell lines.

The technique of multilocus DNA fingerprinting has great potential for the authentication of animal cell cultures and in identification of cross-contamination. The Alec Jeffreys probes 33.6 and 33.15 were used as multilocus probes to demonstrate the consistent DNA fingerprint profiles in human peripheral blood and its derivative Epstein-Barr virus (EBV) transformed B-lymphoblastoid cultures maintained by repeated subculture for six months. However, fingerprint analysis of EBV transformed cultures generated from small numbers of cells showed that the majority (seven of eight cultures) had anomalous profiles. Some of these altered profiles shared common features not seen in the peripheral blood pattern. Analysis of seven murine hybridoma clones from a single fusion experiment revealed only two clones which could not be distinguished using probe 33.15. Further studies of master and distribution cell banks for eleven cell lines demonstrated consistent fingerprint profiles in all cases except one (U937). However, this cell line showed only minor differences in the master and distribution bank profiles. These data indicate that, while changes in fingerprint profile may be identified in exceptional instances, the multilocus fingerprinting method using probes 33.6 and 33.15 is a powerful and reliable tool in the quality control of animal cell cultures.

Animals↗

The contribution of cross-links to protein stability: a normal mode analysis of the configurational entropy of the native state.

The vibrational entropy of native BPTI, with three disulfide bonds, was determined by use of normal mode calculations and compared with that of folded variants having either one less disulfide bond or lacking a peptide bond at the trypsin-reactive site. Favorable contributions to the free energy of 2.5-5.1 kcal/mol at 300 K were calculated for the reduction of disulfide bonds in the folded state, whereas no favorable contribution was found for the hydrolysis of the peptide bond cleaved by trypsin. This is on the order of the effect of disulfides in the unfolded state. The implications of these results for the stabilization of a folded protein by the introduction of cross-links are discussed.

Aprotinin↗

Kinetic analysis of the thermal stability of the photosynthetic reaction center from Rhodobacter sphaeroides.

The temperature-induced denaturation of the photosynthetic reaction center from Rhodobacter sphaeroides has been studied through the changes that occur in the absorption spectrum of the bound chromophores on heating. At elevated temperatures, the characteristic absorbance bands of the bacteriochlorins bound to the polypeptides within the reaction center are lost, and are replaced by features typical of unbound bacteriochlorophyll and bacteriopheophytin. The kinetics of the spectral changes cannot be explained by a direct conversion from the functional to the denatured form of the protein, and require the presence of at least one intermediate. Possible mechanisms for the transformation via an intermediate are examined using a global analysis of the kinetic data, and the most likely mechanism is shown to involve a reversible transformation between the native state and an off-pathway intermediate, coupled to an irreversible transformation to the denatured state. The activation energies for the transformations between the three components are calculated from the effect of temperature on the individual rate constants, and the likely structural changes of the protein during the temperature-induced transformation are discussed.

Kinetics↗

Whole blood analysis of reticulated platelets: improvements of detection and assay stability.

The flow cytometric analysis of reticulated platelets based on the fluorescent derivatization of their RNA content is increasingly used for the diagnostic classification of patients with thrombocytopenia as well as the monitoring of thrombopoiesis recovering under therapy. Many different modifications of the analytical protocol have been published following the first description in 1990 but consensus on the method has not yet been established. We have now reevaluated the assay's methodology in order to optimize sensitivity and specificity and reduce the time length of incubation and washing procedures. In the modified experimental approach native whole blood is incubated for 15 min with an increased amount of thiazole orange (1 microg/ml) in the presence of phycoerythrin labeled antibodies directed against the constitutively surface expressed antigen GPlb. Data acquisition on the flow cytometer can be started immediately after stopping and stabilization of the reaction by paraformaldehyde fixation. Thiazole orange fluorescence was not significantly changed in thrombin-activated, degranulated platelets compared to resting platelets indicating no significant non-specific staining of platelet granules under the selected test conditions. In addition, experiments employing RNAse digestion demonstrated specificity of thiazole orange staining for platelet RNA.

Blood Cell Count↗

Posterior decompression and stabilization for spinal metastases. Analysis of sixty-seven consecutive patients.

The neurological function, survival, and rehabilitation of sixty-seven consecutive patients who had been managed operatively for spinal metastases with epidural compression were assessed. The epidural compression was in the thoracic spine in forty-one patients and in the lumbar spine in twenty-six. According to the system of Frankel et al. for the assessment of neurological function, twenty-six patients had a major neurological deficit (grade B or C), thirty-two had a minor deficit (grade D), and nine had no deficit (grade E). None of the patients had an operation to treat a pathological vertebral fracture without epidural compression. The operative treatment included wide decompression through a posterior approach followed by stabilization without bone-grafting. A Cotrel-Dubousset device was used in thirty-two patients; an Olerud posterior fixator, in sixteen; an Isola device, in twelve; and another device, in seven. The most common complication was wound infection (eleven patients). There were no perioperative or immediate postoperative deaths (within fourteen days). The rate of survival was 51 per cent (thirty-four of sixty-seven) at six months and 22 per cent (fifteen of sixty-seven) at twelve months. Over-all, forty-four of the fifty-eight patients who had had a neurological deficit preoperatively had complete or partial neurological recovery within the first two weeks postoperatively. The nine patients who had not had a neurological deficit preoperatively retained normal neurological function postoperatively. Thirty-eight of the forty-four patients who were alive at three months and twenty-nine of the thirty-four who were alive at six months were still able to walk. Thirty-nine of the forty-nine patients who survived more than two months were able to return home for a median of seven months. Fourteen patients had a reoperation on the spine. Six of these patients had recurrent epidural compression at another level of the spine, and five had recurrent compression at the previously treated level. Three patients had a reoperation because of loosening of the implant. The results of this study suggest that neurological function can be maintained or improved by decompression and stabilization through a posterior approach as treatment for spinal metastases.

Adult↗

Pralidoxime chloride stability-indicating assay and analysis of solution samples stored at room temperature for ten years.

A high-performance liquid chromatographic (HPLC) method is described for quantitation of pralidoxime chloride and its decomposition products 2-carboxy-, 2-formyl-, and 2-(aminocarbonyl)-1-methylpyridinium chloride. These decomposition products and 2-cyano- and 2-(hydroxymethyl)-1-methylpyridinium chloride and 1-methyl-2(1H)-pyridinone were separated from pralidoxime chloride on a silica gel column using a mobile phase of acetonitrile:water (86:14) in which the aqueous component was 8.36 mM in tetraethylammonium chloride and 52.5 mM in acetic acid. This method allows quantitation of the relatively low levels of 2-formyl-1-methylpyridinium chloride formed in acidic solution at room temperature. Sensitivity was shown to be at least 5 ng of the pralidoxime chloride and 15 ng of the 2-carboxy-, 2-formyl-, and 2-(aminocarbonyl)-1-methylpyridinium chloride injected on column. The coefficient of variation was 4% or less for all components measured. Autoinjectors containing 300 mg/mL of pralidoxime chloride in water were stored at room temperature for 8-10 years, followed by analysis for hydrogen cyanide using an ion-selective electrode. Less than 15 micrograms of cyanide per autoinjector was detected. The HPLC analysis of the solutions after being stored an additional 3-4 years at approximately 5 degrees C demonstrated that greater than 90% of the total of all measured components consisted of pralidoxime chloride. The remaining percentage was made up of 2-carboxy-, 2-formyl-, and 2-(aminocarbonyl)-1-methylpyridinium chloride.

Chromatography, High Pressure Liquid↗

Analysis of the CoIE1 stability determinant Rcd.

Multimer formation is an important cause of instability for many multicopy plasmids. Plasmid CoIE1 is maintained stably because multimers are converted to monomers by Xer-mediated site-specific recombination at the cer site. However, multimer resolution is not the whole story; inactivation of a promoter (Pcer) within cer causes plasmid instability even though recombination is unaffected. The promoter directs the synthesis of a short transcript (Rcd) which is proposed to delay the division of multimer-containing cells. Mapping of the 5' terminus of Rcd confirms that transcription initiates from Pcer. The 3' terminus shows considerable heterogeneity, consistent with a primary transcript of 95 nt being degraded via intermediates of 79 and 70 nt. Secondary structure predictions for Rcd are presented. Of four mutations which abolish Rcd-mediated growth inhibition, one reduces the activity of Pcer while the other three map to the rcd coding sequence and reduce the steady-state level of the transcript. RNA folding analysis suggests that these three mutant transcripts adopt a common secondary structure in which the major stem-loop differs from that of wild-type Rcd. A survey of 24 cer-like multimer resolution sites revealed six which contain Pcer-like sequences. The putative transcripts from these sites have similar predicted secondary structures to Rcd and contain a highly conserved 15 base sequence. To test the hypothesis that Rcd acts as an anti-sense RNA, interacting with its target gene(s) through the 15 nt sequence, we used DNA hybridization and sequence analysis to find matches to this sequence in the Escherichia coli chromosome. Our failure to find plausible anti-sense targets has led to the suggestion that Rcd may interact directly with a protein target.

Bacteriocin Plasmids↗

Use of real-time quantitative PCR for the analysis of phiLC3 prophage stability in lactococci.

Bacteriophages are a common and constant threat to proper milk fermentation. It has become evident that lysogeny is widespread in lactic acid bacteria, and in this work the temperate lactococcal bacteriophage phi LC3 was used as a model to study prophage stability in lactococci. The stability was analyzed in six phi LC3 lysogenic Lactococcus lactis subsp. cremoris host strains when they were growing at 15 and 30 degrees C. In order to perform these analyses, a real-time PCR assay was developed. The stability of the phi LC3 prophage was found to vary with the growth phase of its host L. lactis IMN-C1814, in which the induction rate increased during the exponential growth phase and reached a maximum level when the strain was entering the stationary phase. The maximum spontaneous induction frequency of the phi LC3 prophage varied between 0.32 and 9.1% (28-fold) in the six lysogenic strains. No correlation was observed between growth rates of the host cells and the spontaneous prophage induction frequencies. Furthermore, the level of extrachromosomal phage DNA after induction of the prophage varied between the strains (1.9 to 390%), and the estimated burst sizes varied up to eightfold. These results show that the host cells have a significant impact on the lytic and lysogenic life styles of temperate bacteriophages. The present study shows the power of the real-time PCR technique in the analysis of temperate phage biology and will be useful in work to reveal the impact of temperate phages and lysogenic bacteria in various ecological fields.

Attachment Sites, Microbiological↗

Poroelastic analysis of lumbar spinal stability in combined compression and anterior shear.

OBJECTIVE: A three-dimensional poroelastic finite element (FE) L2-L3 model was developed to study lumbar spinal instability and intrinsic parameters in the intervertebral disc (IVD). METHODS: The FE model took into consideration poroelasticity of the IVD and viscoelasticity of the annulus fibers and ligaments to predict the time-dependent behavior. To simulate a holding task, the motion segment was subjected to a combined loading of constant compressive load (1600 N) and anterior shear (200 N) for 2 hours, and the role of facet joints and ligaments in the biomechanical response was investigated by removal of unilateral/bilateral facets, posterior ligaments (supraspinous and interspinous), and facets and ligaments. RESULTS: The results show the stabilizing role of the facets and ligaments in resisting anterior shear and sagittal rotation under combined loading over time. The main pathway of fluid movement was found to permeate through the central region of the endplate, and the fluid diffusion occurred earlier at the posterior nucleus than the anterior nucleus. The fluid loss from the nucleus dictated the time-dependent motion under the sustained loading, whereas the intrinsic properties of ligaments/annulus fibers played a role only in the early stage of the loading. CONCLUSION: The predicted results using poroelastic elements provide new insight into the IVD in providing the spinal stiffness under combined loading.

Body Fluids↗

Analysis of the structural stability of the multidomain enzyme flavocytochrome P-450 BM3.

The unfolding and refolding of flavocytochrome P-450 BM3 and its constituent haem and flavin domains have been analysed, using guanidinium chloride (GdnHCl) as a denaturant. Enzyme activities are lost at GdnHCl concentrations too low to cause major changes in secondary structure (0.1-0.5 M). The losses are primarily due to time-dependent FMN removal. Fluorescence and visible CD spectroscopies show that FMN dissociation is complete by 0.7 M GdnHCl, whereas FAD removal is complete by 1.5 M GdnHCl. Limited regain of activity is achieved by dilution of enzyme from solutions of < or = 0.75 M GdnHCl into fresh buffer. Supplementation of GdnHCl-free assay media with flavins (FAD and FMN) causes small additional regains in flavin domain (cytochrome-c reductase) activity lost at low [GdnHCl]. However, flavin addition during the denaturation step affords greater protection against inactivation, suggesting that conformational changes may occur subsequent to flavin loss and that these changes are not readily reversed on dilution of GdnHCl. Loss of catalytically competent haem ligation occurs over the same [GdnHCl] range for P-450 BM3 and its haem domain. In both cases, the 'denatured' P-420 form accumulates in the reduced/carbon monoxide-bound visible spectrum from 0.5 to 2 M GdnHCl. Secondary structure loss also occurs over similar [GdnHCl] ranges for P-450 BM3 and its two domains (80-90% lost from 0.5-3 M GdnHCl), indicating that there is little mutual stabilisation of domains in the holoenzyme. Differential scanning calorimetry measurements support this conclusion, but show that the haem domain is more thermostable than the flavin domain.

Bacillus megaterium↗

Genetic analysis of transfer and stabilization of Agrobacterium DNA in plant cells.

In an attempt to elucidate the transfer and integration mechanism of Agrobacterium DNA upon crown gall induction, we translocated a borderless T-DNA to different sites of the C58 Ti plasmid. As a result of the physical linkage of the T-DNA onc genes with other Ti plasmid functions, the concerned strain retained tumor-inducing capacity. However, when the borderless T-DNA is separated on an independent replicon while all other pTi functions are provided in trans, the strain can no longer induce tumors on plants. We provide evidence that the right T-DNA border region harbors one or more in cis active functions essential in the transfer and/or stabilization of the T-DNA into plant cells. The strains used in these experiments allowed us to conclude that some function(s) of the Ti plasmid can induce plant cell proliferations independently of the T-DNA transformation event. The results described here indicate that other Ti plasmid sequences than solely the T-region can be transferred to plant cells.

Journal Article↗

Regulatory, design, and analysis aspects of complex stability studies. US Food & Drug Administration.

Drug stability studies are expensive and time consuming. Multiple batches are studied to ensure that a product will consistently remain within specifications for its entire expiration dating period. Some of these studies involve the same drug products in similar packages or in multiple strengths. Application of sound statistical design principles can reduce the amount of testing required. We extend the principles stated in the Food & Drug Administration's 1987 publication Guideline for Submitting Documentation for the Stability of Human Drugs and Biologics to setting expiration dating periods for more complex situations.

Drug Packaging↗

Analysis of the segmental stability of helical peptides by isotope-edited infrared spectroscopy.

Isotope-edited infrared spectroscopy has the ability to probe the segmental properties of long biopolymers. In this work, we have compared the infrared spectra of a model helical peptide ((12)C) Ac-W-(E-A-A-A-R)(6)-A-NH(2), described originally by Merutka et al. (Biochemistry 1991;30:4245-4248) and three derivatives that are (13)C labeled at the backbone carbonyl of alanines. The locations of six isotopically labeled alanines are at the N-terminal, C-terminal, and the middle two repeating units of the peptide. Variation in temperature from 1 degrees to 91 degrees C transformed the peptides from predominantly helical to predominantly disordered state. Amplitude and position of the infrared amide I' absorption bands from (12)C- and (13)C-labeled segments provided information about the helical content. Temperature dependence of infrared spectra was used to estimate segmental stability. As a control measure of overall peptide stability and helicity (independent of labeling), the temperature dependence of circular dichroism spectra in the far-UV range at identical conditions (temperature and solvent) as infrared spectra was measured. The results indicate that the central quarter of the 32 amino acids helix has the maximal helicity and stability. The midpoint of the melting curve of the central quarter of the helix is 5.4 +/- 0.8 degrees C higher than that of the termini. The N-terminal third of the helix is more helical and is 2.0 +/- 1.4 degrees C more stable than the C-terminus.

Alanine↗