Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Stability analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 1,009 records · Page 56Linked to original sources
PubMed1981

High-performance liquid chromatographic analysis of chemical stability of 5-aza-2'-deoxycytidine.

The chemical stability of 5-aza-2'-deoxycytidine (I) in acidic, neutral, and alkaline solutions was analyzed by high-performance liquid chromatography. In alkaline solution, I underwent rapid reversible decomposition to N-(formylamidino)-N'-beta-D-2-deoxyribofuranosylurea (II), which decomposed irreversibly to form 1-beta-D-2'-deoxyribofuranosyl-3-guanylurea (III). The pseudo-first-order rate constants for this reaction were determined. The decomposition of I in alkaline solution was identical to that reported previously for the related analog, 5-aza-cytidine. However, in neutral solution (or water), there was a marked difference in the decomposition of I and 5-azacytidine. The same decomposition products were formed from 5-azacytidine in neutral solution as in alkaline solution. However, in neutral solution, I decomposed to II and three unknown compounds that were chromophoric at 254 nm. Compound I was most stable when stored in neutral solution at low temperature.

Azacitidine↗
PubMed1992

Qualitative analysis of the stability of the oxazine ring of various benzoxazine and pyridooxazine derivatives with proton nuclear magnetic resonance spectroscopy.

A series of 3,4-dihydro-1,3-benzoxazine and 3,4-dihydro-1,3-pyridooxazine derivatives was synthesized, and the hydrolysis of the derivatives was studied with proton nuclear magnetic resonance spectroscopy. The oxazine derivatives underwent various degrees of hydrolysis when H2O was added to dimethyl sulfoxide solutions of the compounds. The rates and extents of decomposition of the oxazine ring systems depended on the electronic effects of substituents within the molecules. Examination of the proton nuclear magnetic resonance spectra that were generated during decomposition of the oxazines and trends in stability of the oxazine derivatives suggest the formation of an intermediate in the hydrolysis mechanism.

Drug Stability↗
PubMed1993

Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability.

We have chosen two members of the microbial RNase family, barnase and binase, which have 85% identity (17 substitutions and 1 deletion) and almost identical three-dimensional structure, to study the evolution of protein stability. The 17 residues that differ are scattered throughout the molecule. Each of the 17 differing residues has been mutated independently and the effect on protein stability analysed. Each point mutation has an effect on protein stability that ranges from +1.1 to -1.1 kcal mol-1. These changes in energy are additive. There is no clear correlation between the type of mutation and the effect on protein stability. A multiple mutant having six of the single mutations that increase the stability of barnase is 3.3 kcal mol-1 more stable than wild type and has the same activity. There could be selective pressure to maintain proteins at a certain stability and, consequently, mutations that decrease stability tend to be counterbalanced by stabilizing mutations. Alternatively, there could simply be pressure to maintain stability above a certain level, and any further increases in stability need not be maintained during evolution. These results suggest a simple way to improve the stability of proteins: choose two homologous proteins that have high similarity, mutate individually all of the residues that differ between the two, and combine the mutations that increase the stability in a multiple mutant.

Amino Acid Sequence↗
PubMed1999

Acquired immunity of a schistosomiasis transmission model--analysis of the stabilizing effects.

A semi-stochastic model for schistosomiasis was developed based on the immune response built up by human host after elapsing a fixed period of time L from the first infection, and on the parasite infection with multiple occurrences. Both acquired immunity and multiple parasite infections reproduced a great endemic stability for the disease and a high value for the basic reproduction ratio.

Animals↗
PubMed2002

Analysis of the stability of stored adenosine 5'-monophosphate used for bronchoprovocation.

Adenosine 5'-monophosphate (AMP) bronchial challenge has been shown to be very useful tool in the diagnosis of asthma. Freshly test solutions are prepared just prior to each test in most of the studies. The objective of this study was to assess the stability of AMP solutions at different temperatures using a reversed-phase high-performance liquid chromatography assay. Sodium salt AMP solutions in concentrations of 0.03 mg/ml and 400 mg/ml were analyzed. One aliquot was kept at room temperature (20-25 degrees C) and the others were refrigerated at 4 degrees C. Room temperature stored samples were analyzed daily. Refrigerated stored samples were analyzed daily for first 15 days and then weekly. The duration of the study was 25 weeks. Samples were injected into the chromatograph column in quadruplicate and quantification was based on the arithmetic mean and standard deviation (+/-SD) of four measurements. Room temperature stored samples at concentrations of 0.03 mg/ml showed a mean percent variation greater than 10% at day 9 and greater than 75% at day 14. Samples at concentrations of 400 mg/ml maintained almost the initial concentration during the first 10 days, but decomposition occurred thereafter. In contrast, there was no significant degradation of refrigerated stored samples throughout the study period. We conclude the exposure to room temperature of AMP solutions results in a substantial loss of the initial concentration, but the shelf life of adequately prepared stock AMP solutions stored at 4 degrees C is at least 25 weeks.

Adenosine Monophosphate↗
PubMed1994

Flow cytometric analysis of the stability of antibody production by human x human x mouse heterohybridoma subclones.

Flow cytometry has been utilized to evaluate the stability of antibody production by unstable subclones of a human x human x mouse heterohybridoma. Heterogeneity of cell-associated immunoglobulin heavy chain expression was demonstrated in different subclones and an increased frequency of cells containing low levels of heavy chain was found to correlate with low antibody productivity. However, the majority of cells were not completely devoid of heavy chains suggesting that the genetic information for the gamma chain was not lost. In contrast, the gene encoding the kappa light chain was shown to be absent from the subclones expressing low levels of heavy chain and these subclones also contained substantially reduced levels of heavy chain mRNA, suggesting that the production of this protein was controlled at the level of transcription or mRNA stability. In conclusion, the correlation of staining intensity as observed by flow cytometry antibody productivity makes flow cytometry a suitable technique for the rapid evaluation of heterohybridoma cell lines used for antibody production.

Animals↗
PubMed1989

Analysis of the stabilizing effect of epsilon-aminocaproic acid by electrophoretic techniques and immunoblotting.

The effect of epsilon-aminocaproic acid (EACA) on the degradation of aqueous pollen extracts was studied by isoelectric focusing, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and immunoblotting. The extracts were stored at 4 degrees C for 7 days and at 37 degrees C for 1, 4, and 7 days. Addition of 0.1 mol/L of EACA before storage partly protected the extract from degradation. The protective effect of EACA could be demonstrated most clearly by immunoblotting, suggesting that more epitopes were preserved in an antigenic configuration. The stabilizing effect increased with higher EACA concentrations.

Aminocaproates↗
PubMed1990

Analysis of RNA stability and (-) strand content in viral infections using biotinylated RNA probes.

Non-radioactive biotinylated RNA probes specific for plus (+) and minus (-) sense RNAs of brome mosaic virus (BMV) were synthesized in vitro from a plasmid bearing a 200 base pair fragment complementary to the 3' terminus of each of the three genomic RNAs of the virus. Using virion RNAs isolated from BMV infected barley plants, the sensitivity of biotinylated RNAs as hybridization probes was compared with that of 32P-labeled probes in Northern hybridization assays. Although the sensitivity of biotinylated and 32P-labeled probes is similar (approximately 5 pg), the time required to detect the RNA bands was much less than for autoradiography; (-) sense RNAs could be detected in 30 min whereas 48 h or more were required by autoradiography. The value of biotinylated probes for following RNA stability was exemplified by the detection of supplied inocula in protoplasts 24 h post-inoculation. Quantitation of relative accumulation of progeny (+) and (-) sense RNAs by densitometry of the Northern blots probed with biotinylated RNAs paralleled that of radiolabeled probes. The application of these probes was extended to the detection of RNAs in barley protoplasts and BMV infected plant sap by dot hybridization. In these tests, viral RNAs were detected in as few as 250 protoplasts and sap dilutions up to 1:2000. The merits of these non-radioactive probes in monitoring the replication events by the detection and quantitation of mutant progeny RNAs of BMV are discussed.

Biotin↗
PubMed2003

Analysis of the stability of amino acids derivatized with naphthalene-2,3-dicarboxaldehyde using high-performance liquid chromatography and mass spectrometry.

The stability of amino acids derivatized with naphthalene-2,3-dicarboxaldehyde (NDA) was investigated using a combination of high-performance liquid chromatography, solid-phase extraction, photodiode array spectrophotometric detection, and mass spectrometric (MS) characterization. The degradation of amino acid derivatives, generated using beta-mercaptoethanol as a nucleophile, was characterized under a variety of environmental influences, with a focus on understanding the degradation kinetics and identifying the degradation products. The predominant degradation product observed under most reaction conditions was the nonfluorescent lactam form of the originally fluorescent isoindole derivative. First, the time-dependent degradation of the isoindole derivative L-serine-NDA-beta-mercaptoethanol was found to follow pseudo-first order kinetics with a half-life of 2.0 min at pH 9.2 and room temperature. The isoindole derivative was observed to react further with methanol to form a more stable fluorescent methoxy-isoindole, shedding new light on the basis for enhanced stability of these derivatives in methanol. Tandem mass spectrometry (MS/MS) experiments were used to demonstrate unimolecular degradation of the protonated isoindole in the absence of solvent or atmosphere, suggesting an intramolecular reaction mechanism involving the hydroxyethylthio group. Finally, in photobleaching studies, NDA derivatives rapidly degraded into a variety of products within the first 2 min of photobleaching versus timed controls, with the predominant product being the lactam. These results suggest that the degradation pathway for NDA derivatives is similar to the previously reported pathway for o-phthalaldehyde derivatives and clearly identifies the reaction and degradation products under a variety of conditions.

Amino Acids↗
PubMed2005

Analysis of the stability and function of nucleoplasmin through cysteine mutants.

Xenopus laevis nucleoplasmin is a pentameric nuclear chaperone. The relation between the structure and the multifunctional aspects of the molecule has not yet been clearly established. In the course of analysing a C-terminally His-tagged recombinant version of the region equivalent to the trypsin resistant core (r-NP142) of the molecule, we found that this domain exhibited a substantially decreased oligomerization potential. To better understand the role of the three cysteines of nucleoplasmin on its pentameric functional structure, we have selectively mutated these residues to serine and generated three mutants (C15S, C35S, and C45S) both for the complete recombinant nucleoplasmin (r-NP) and the truncated r-NP142 non-tagged forms. We demonstrate that there are no disulphide bridges stabilizing either the monomer or the pentamer. Neither C15S nor C35S has any structural effects, while the mutation C45S abolishes the ability of r-NP142 to pentamerize. This structural impairment suggests that hydrophobic interactions of Cys 45 are critical for the stability of the protein. Our studies allow to analyse for the first time the structural and functional properties of nucleoplasmin in its monomeric form.

Amino Acid Sequence↗
PubMed2006

High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design.

Recent efforts to design de novo or redesign the sequence and structure of proteins using computational techniques have met with significant success. Most, if not all, of these computational methodologies attempt to model atomic-level interactions, and hence high-resolution structural characterization of the designed proteins is critical for evaluating the atomic-level accuracy of the underlying design force-fields. We previously used our computational protein design protocol RosettaDesign to completely redesign the sequence of the activation domain of human procarboxypeptidase A2. With 68% of the wild-type sequence changed, the designed protein, AYEdesign, is over 10 kcal/mol more stable than the wild-type protein. Here, we describe the high-resolution crystal structure and solution NMR structure of AYEdesign, which show that the experimentally determined backbone and side-chains conformations are effectively superimposable with the computational model at atomic resolution. To isolate the origins of the remarkable stabilization, we have designed and characterized a new series of procarboxypeptidase mutants that gain significant thermodynamic stability with a minimal number of mutations; one mutant gains more than 5 kcal/mol of stability over the wild-type protein with only four amino acid changes. We explore the relationship between force-field smoothing and conformational sampling by comparing the experimentally determined free energies of the overall design and these focused subsets of mutations to those predicted using modified force-fields, and both fixed and flexible backbone sampling protocols.

Carboxypeptidases A↗
PubMed2004

An analysis of exponential stability of delayed neural networks with time varying delays.

This paper derives a new sufficient condition for the exponential stability of the equilibrium point for delayed neural networks with time varying delays by employing a Lyapunov-Krasovskii functional and using Linear Matrix Inequality (LMI) approach. This result establishes a relation between the delay time and the parameters of the network. The result is also compared with the most recent result derived in the literature.

Animals↗
PubMed2005

In vivo analysis of mRNA stability using the Tet-Off system in the chicken embryo.

The rate of mRNA degradation plays an important role in the control of gene expression. The mRNA stability is mainly dependent on cis-regulatory elements contained in the 3' or 5' untranslated region (UTR) of the mature mRNAs, and its regulation is an efficient way to adapt the level of a given transcript in the cell. Although this process has been well studied in cell culture, little is known about mRNA stability during embryonic development. Here, we describe an assay that combines the tetracyclin-dependent inducible system Tet-Off with in ovo electroporation to monitor mRNA stability in the chick neural tube. We show, by using the GFP intensity as an indirect reporter system, that the 3'UTR of Lunatic Fringe strongly destabilizes transcripts, while transcripts bearing the 3'UTR of Fgf8 are much more stable. This simple assay provides a powerful tool to study mRNA dynamics in vivo.

3' Untranslated Regions↗
PubMed1997

Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions.

A combination of conformational search, energy minimization, and energetic evaluation using a continuum solvent treatment has been employed to study the stability of various conformations of the DNA fragment d(CGCAGAA)/d(TTCGCG) containing a single adenine bulge. The extra-helical (looped-out) bulge conformation derived from a published x-ray structure and intra-helical (stacked bulge base) model structures partially based on nuclear magnetic resonance (NMR) data were used as start structures for the conformational search. Solvent-dependent contributions to the stability of the conformations were calculated from the solvent exposed molecular surface area and by using the finite difference Poisson-Boltzmann approach. Three classes (I-III) of bulge conformations with calculated low energies can be distinguished. The lowest-energy conformations were found in class I, corresponding to structures with the bulge base stacked between flanking helices, and class II, composed of structures forming a triplet of the bulge base and a flanking base pair. All extra-helical bulge structures, forming class III, were found to be less stable compared with the lowest energy structures of class I and II. The results are consistent with NMR data on an adenine bulge in the same sequence context indicating an intra-helical or triplet bulge conformation in solution. Although the total energies and total electrostatic energies of the low-energy conformations show only relatively modest variations, the energetic contributions to the stability were found to vary significantly among the classes of bulge structures. All intra-helical bulge structures are stabilized by a more favorable Coulomb charge-charge interaction but destabilized by a larger electrostatic reaction field contribution compared with all extra-helical and most triplet bulge structures. Van der Waals packing interactions and nonpolar surface-area-dependent contributions appear to favor triplet class II structures and to a lesser degree also the intra-helical stacked bulge conformations. The large conformational variation found for class III conformers might add a favorable entropic contribution to the stability of the extra-helical bulge form.

Adenine↗