Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Yield stability”

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 253 records · Page 14Linked to original sources
PubMed2003

Direct measurement of antigen binding properties of CD1 proteins using fluorescent lipid probes.

CD1 proteins are antigen-presenting molecules that bind foreign and self-lipids and stimulate specific T cell responses. In the current study, we investigated ligand binding by CD1 proteins by developing a fluorescent probe binding approach using soluble recombinant human CD1 proteins. To increase stability and yield, soluble group 1 CD1 (CD1b and CD1c) and group 2 CD1 (CD1d) proteins were produced as single chain secreted CD1 proteins in which beta2-microglobulin was fused to the N termini of the CD1 heavy chains by a flexible peptide linker sequence. Analysis of ligand binding properties of single chain secreted CD1 proteins by using fluorescent lipid probes indicated significant differences in ligand preference and in pH dependence of binding by group 1 versus group 2 CD1 proteins. Whereas group 1 CD1 isoforms (CD1b and CD1c) show stronger binding of nitrobenzoxadiazole (NBD)-labeled dialkyl-based ligands (phosphatidylcholine, sphingomyelin, and ceramide), group 2 CD1 (CD1d) proteins were stronger binders of small hydrophobic probes such as 1-anilinonaphthalene-8-sulfonic acid and 4,4'-dianilino-1,1'-naphthyl-5,5'-disulfonic acid. Competition studies indicated that binding of fluorescent lipid probes involved association of the probe with the hydrophobic ligand binding groove of CD1 proteins. Analysis of selected alanine substitution mutants of human CD1b known to inhibit antigen presentation showed that NBD-labeled lipid probe binding could be used to distinguish mutations that interfere with ligand binding from those that affect T cell receptor docking. Our findings provide further evidence for the functional specialization of different CD1 isoforms and demonstrate the value of the fluorescent lipid probe binding method for assisting structure-based studies of CD1 function.

Amino Acid Sequence↗
PubMed2005

A novel versatile phosphoramidite building block for the synthesis of 5'- and 3'-hydrazide modified oligonucleotides.

We introduce a novel versatile phosphoramidite building block for the modification of oligonucleotides (ONs) with acyl hydrazides on the 5'- or 3'-terminus, or both. The reaction of these hydrazide functionalized ONs with 4-methoxyphenylaldehyde is demonstrated for solution derivatization. Hydrazides are considered nowadays as promising reactants, which show enhanced reactivity at neutral and slightly acidic conditions and higher stability of yielding products as compared to the aliphatic amines, which are broadly used for ONs derivatization. Our method to introduce hydrazides into ONs employs a phosphoramidite modifier designed to split, during ammonia or lithium hydroxide treatment, into two hydrazides via beta-elimination of a central bis-2-carbonylethoxysulfone unit. It allows the creation of ONs derivatized with a hydrazide moiety at the 5'-, 3'- and both 5'- and 3'-termini, as well as two different hydrazide containing ONs at the same time, viz. in one sequence on the same solid support In latter case one can, for example, synthesize two hydrazide containing ONs, where one is 5'-modified and second one is 3'-modified.

Chromatography, High Pressure Liquid↗
PubMed2005

European plant science: a field of opportunities.

Plants have a pivotal role in eco- and agricultural systems. Genomics is driving a rapid expansion of our understanding of how genes, individually and in networks, determine plant function. Technological developments in breeding and genomics are providing strategies to translate this knowledge into crop improvement. The possibilities range from improvement of existing crops and the systematic use of natural diversity through to the domestication of completely new species. As examples of possible goals, it is discussed how profiling of composition will integrate plant breeding and agronomic practice with emerging knowledge about nutrition and health, how improved and novel crops will contribute to the creation of new bio-based economies revolving around plant products, and how advances in our knowledge about plant-environment and plant-pathogen interactions will provide novel strategies to stabilize agricultural yield in a fluctuating environment and contribute to integrated approaches in which modern agriculture is carried out in concert with the environment. In addition, knowledge generated by plant science will be needed to monitor, understand, and cope with climate change and its impact on agriculture and ecosystems. Realization of these goals will require close interactions with related disciplines including agronomy and ecology. Further, it will be important to continue and deepen open support for research in the developing world.

Agriculture↗
PubMed1982

Isolation of the catalytic core of DNA polymerase alpha from rabbit bone marrow.

Modification of the purification procedures for rabbit bone marrow DNA polymerase [Byrnes, J.J., & Black, V.L. (1978) Biochemistry 17, 4226-4231] has increased the yield and stability of the enzyme thus allowing further purification. In particular, the higher molecular weight form, alpha 1, has been more abundant. Additional purification has been obtained upon phosphocellulose and chromatofocusing column chromatography. SDS slab gel electrophoretic analyses of the eluates demonstrate a 135,000 molecular weight polypeptide in nearly pure form which correlates with DNA polymerase activity. Approximately 200,000 nmol of thymidine monophosphate is incorporated into DNA (mg of protein) -1h -1 at 37 degrees C. Similar to DNA polymerase alpha from other sources this enzyme is an acidic protein, is very sensitive to aphidicolin, and has no detectable 3' to 5' nuculease activity.

Animals↗
PubMed1980

DNA-like duplexes with repetitions. I. Properties of concatemer duplexes formed by d(T-G-C-A-C-A-T-G).

A new class of synthetic DNA duplexes containing repeating oligonucleotide sequences, double-helical concatemers, is characterized. The UV-absorption and circular dichroism of a concatemer formed in self-association of d(T-G-C-A-C-A-T-G) have been studied. The thermodynamical parameters of complex formation are the following: delta Ho1 = -9.2 +/- 0.3 kcal/mol, delta So1 = -27 +/- 1 e.u. The data obtained show that pseudopolymeric duplexes having structures that are similar to DNA-B-type helices are formed in solutions of d(T-G-C-A-C-A-T-G). Polymerization of 32P-d(pT-G-C-A-C-A-T-G) induced by water-soluble carbodiimide has been carried out under the conditions of concatemer stability. The yield of the dimer, a 16-member oligonucleotide, was 13%.

Carbodiimides↗
PubMed1997

Two amino acid mutations in an anti-human CD3 single chain Fv antibody fragment that affect the yield on bacterial secretion but not the affinity.

Recombinant antibody fragments directed against cell surface antigens have facilitated the development of novel therapeutic agents. As a first step in the creation of cytotoxic immunoconjugates, we constructed a single-chain Fv fragment derived from the murine hybridoma OKT3, that recognizes an epitope on the epsilon-subunit of the human CD3 complex. Two amino acid residues were identified that are critical for the high level production of this scFv in Escherichia coli. First, the substitution of glutamic acid encoded by a PCR primer at position 6 of VH framework 1 by glutamine led to a more than a 30-fold increase in the production of soluble scFv. Second, the substitution of cysteine by a serine in the middle of CDR-H3 additionally doubled the yield of soluble antibody fragment without any adverse effect on its affinity for the CD3 antigen. The double mutant scFv (Q,S) proved to be very stable in vitro: no loss of activity was observed after storage for 1 month at 4 degrees C, while the activity of scFv containing a cysteine residue in CDR-H3 decreased by more than half. The results of production yield, affinity, stability measurements and analysis of three-dimensional models of the structure suggest that the sixth amino acid influences the correct folding of the VH domain, presumably by affecting a folding intermediate, but has no effect on antigen binding.

Amino Acid Sequence↗
PubMed1995

In vivo system for the detection of low level activity barnase mutants.

We report the design of a new tightly controlled barnase system which allows the existence of the barnase gene in host cells without a signal sequence. When expression of barnase is turned on by gene inversion in vivo, the lethal effect of barnase (or its mutants) is not compromised either by coexpression of its polypeptide inhibitor (barstar), or by extracellular secretion. This serves as a rapid, sensitive in vivo test for the detection of any very low residual activity of the barnase mutants. Active-site mutants His102Lys, Glu73Asp and Arg87Lys, and a mutant which greatly reduces the stability and yield of protein, Arg83Lys, produce enough activity to be detectable by this test. In contrast, when expressed on a secretion vector, these mutants do not yield detectable activity in a solution assay. Truly inactive mutants, such as those of His102 to Gly, Ala or Leu, were completely harmless when expressed in this system.

Bacterial Proteins↗
PubMed1983

Assessment of negative and positive symptoms in schizophrenia.

Reliable, convenient rating scales to assess negative and positive symptoms in schizophrenia are necessary to evaluate further the theoretical and clinical importance of this division of symptoms and signs. The authors describe the application of the Rasch model, a probabilistic, item-independent, and sample-independent test construction procedure to the development of scales for both types of symptoms. The scales for negative and positive symptoms, which are based separately on the Schedule for Affective Disorders and Schizophrenia-Current (SADS-C) and the Nurses' Observation Scale for Inpatient Evaluation (NOSIE), demonstrated excellent reliability and temporal stability (i.e., yielded a rank order of patients that remained stable over time). The pattern of interscale correlations supports the view that positive symptoms, cognitive-affective negative symptoms, and social withdrawal are independent of one another.

Adult↗
PubMed1995

Microcirculatory perfusion during volume therapy. A comparative study using crystalloid or colloid in awake animals.

BACKGROUND: Because of the passage of water and salt molecules into the interstitial space, volume replacement with crystalloid solutions requires an amount at least four times that of lost blood. The resulting tissue edema may interfere with nutritive capillary perfusion and oxygen delivery. To prove this hypothesis, the effects of isovolemic hemodilution (hematocrit 30%) with Ringer's lactate solution or dextran 60 on tissue perfusion and oxygenation were investigated in awake Syrian golden hamsters. METHODS: Experiments were performed by using a chronic dorsal skinfold window giving access to skeletal muscle tissue (musculus cutaneus) with in vivo microscopy, quantitative video image analysis, and surface oxygen partial pressure electrodes. Central venous and arterial pressures were measured by means of chronically implanted jugular venous and carotid catheters. RESULTS: Isovolemic exchange of blood with dextran caused no significant changes in arterial or central venous pressure, heart rate, capillary flow velocity, functional capillary density, or surface oxygen partial pressure during the 1-h observation period. A volume of Ringer's solution equal to four times of the amount of blood lost maintained arterial pressure and heart rate when central venous pressure was kept at predilution control values. However, tissue perfusion determined by counting perfused capillaries per terminal arteriole was reduced by 62%, and mean tissue oxygen partial pressure decreased from 19 to 8 mmHg. CONCLUSIONS: In this model, volume replacement with artificial colloids yielded hemodynamic stability and adequate tissue oxygen supply, whereas administration of crystalloids alone jeopardized tissue perfusion and oxygenation.

Animals↗
PubMed1995

Contrast sensitivity in Alzheimer's disease: a 1-year longitudinal analysis.

Spatial contrast sensitivity was evaluated in normal elderly adults and a group with probable Alzheimer's disease (AD) in three sessions over a 1-year period. There was evidence of a reduction over 1 year in contrast sensitivity for static, high spatial frequencies in both groups of subjects. A striking difference between the subject groups was observed in their response to flickered stimuli. Although normal elderly adults yielded good stability in sensitivity for both static and flickered spatial frequencies over the 1 year, AD patients experienced a significant decline in response to flickered (7.5 Hz) stimuli. The significant decline in sensitivity for low contrast, high temporal events in AD patients is consistent with reports of cell loss at the retinal and cortical levels of the magnocellular (M) channel in AD. Thus, the spatial contrast sensitivity change in AD may reflect a more rapid loss of cells specifically in the M channel over a 1-year period.

Adult↗
PubMed1999

Intratype sequence variation among clinical isolates of the human papillomavirus type 6 L1 ORF: clustering of mutations and identification of a frequent amino acid sequence variant.

Human papillomavirus type 6 (HPV-6) is the causative agent of condyloma acuminata, a common sexually transmitted disease. Virus-like particles (VLPs) assembled from the L1 major capsid protein represent promising candidates for prophylactic vaccines. However, any intratype sequence variation among HPV-6 L1 ORFs will influence which sequence is used for a vaccine according to its prevalence in the population and its propensity for VLP production. Therefore, we have analysed the entire L1 nucleotide sequence of 17 clinical isolates of HPV-6 from the London area. We found 28 positions where changes from the prototype HPV-6b L1 occurred, showing that HPV-6 L1 intratype variation is greater than previously reported. The most frequently observed substitutions are clustered into three discrete regions: R1 (nt 5920-6075), R2 (nt 6590-6670) and R3 (nt 7070-7230). Indeed, most of the nucleotide substitutions within the HPV-6 L1 reported worldwide also map to these regions. The R3 region contains predominantly non-silent substitutions, the most common of which is a G-to-C substitution at position 7079. This results in a Glu-to-Gln change at aa 431, although this change had no effect on VLP yield or stability. This substitution defines a new HPV-6 L1 amino acid sequence that is more abundant in the isolates examined than any other reported sequence.

Amino Acid Sequence↗
PubMed2001

Cavity approach to noisy learning in nonlinear perceptrons.

We analyze the learning of noisy teacher-generated examples by nonlinear and differentiable student perceptrons using the cavity method. The generic activation of an example is a function of the cavity activation of the example, which is its activation in the perceptron that learns without the example. Mean-field equations for the macroscopic parameters and the stability condition yield results consistent with the replica method. When a single value of the cavity activation maps to multiple values of the generic activation, there is a competition in learning strategy between preferentially learning an example and sacrificing it in favor of the background adjustment. We find parameter regimes in which examples are learned preferentially or sacrificially, leading to a gap in the activation distribution. Full phase diagrams of this complex system are presented, and the theory predicts the existence of a phase transition from poor to good generalization states in the system. Simulation results confirm the theoretical predictions.

Biophysical Phenomena↗
PubMed2004

Falling films and the Marangoni effect.

The instability of a falling liquid film of an aqueous surfactant solution along a vertical slope with surfactant adsorption-desorption at its open surface originating surface stresses (Marangoni effect) is investigated. The diffusion of surfactant to the film surface from the bulk and desorption of surfactant to the gas phase are taken into account. The Navier-Stokes and Fick equations are reduced to a system of simpler hence, analytically and numerically, more tractable nonlinear evolution equations albeit with nine dimensionless parameters. The linear stability analysis yields a dispersion equation that is numerically solved and eigenvalues are obtained for various values of significant dimensionless parameters. A very rich picture of instabilities appears. In addition to the earlier known (Kapitza) hydrodynamic mode there are up to four new (Marangoni-driven) diffusion modes. Two modes travel with the liquid velocity on the film surface and the other two travel on their own downstream and upstream, respectively. One diffusion mode could be identified, in the reference frame moving with the liquid on the film surface, as a monotonic instability mode hence leading to a patterned film surface. All other modes are oscillatory ones. Resonance of modes is also predicted for suitable combinations of the parameters of the problem. The mode observed depends upon the surface stress (in terms of a dimensionless Marangoni number), the particular choice of the adsorption-desorption kinetics, and the surface tension state equation at the open surface of the film.

Journal Article↗
PubMed2005

Langevin simulation of the chirally decomposed sine-Gordon model.

A large class of quantum and statistical field theoretical models, encompassing relevant condensed matter and non-Abelian gauge systems, are defined in terms of complex actions. As the ordinary Monte Carlo methods are useless in dealing with these models, alternative computational strategies have been proposed along the years. The Langevin technique, in particular, is known to be frequently plagued with difficulties such as strong numerical instabilities or subtle ergodic behavior. Regarding the chirally decomposed version of the sine-Gordon model as a prototypical case for the failure of the Langevin approach, we devise a truncation prescription in the stochastic differential equations which yields numerical stability and is assumed not to spoil the Berezinskii-Kosterlitz-Thouless transition. This conjecture is supported by a finite size scaling analysis, whereby a massive phase ending at a line of critical points is clearly observed for the truncated stochastic model.

Journal Article↗
PubMed2006

Competition of pattern forming instabilities due to phase front curvature in an optical system.

In this paper we analyze experimentally and theoretically the competition between two pattern forming instabilities in a single mirror feedback scheme with sodium vapor as the nonlinear medium. Two types of structures with different transverse wave numbers are observed experimentally, if the spatial phase modulation of the light field is varied. This phenomenon results from the combination of a nonlinear self-lensing effect on the one hand and of the externally controlled phase front curvature of the light field on the other. A linear stability analysis yields two instabilities whose length scales match quite well the experimental findings. Further analysis reveals the mechanism of length-scale selection in this system and demonstrates the possibly crucial role of phase front curvature in optical pattern formation.

Journal Article↗
PubMed1973

Regulation of Succinate Dehyrogenase in Higher Plants: I. Some General Characteristics of the Membrane-bound Enzyme.

The spectrophotometric phenazine methosulfate assay of succinate dehydrogenase was adapted to use with cauliflower (Brassica oleracea) and mung bean (Phaseolus aureus) mitochondria with suitable modifications to overcome the permeability barrier to the dye. Procedures in the literature for the isolation and sonic disruption of mitochondria from these sources were modified to assure maximal yield and stability of the enzyme. In tightly coupled mung bean mitochondria, as isolated, about half of the succinate dehydrogenase is in the deactivated state, and the enzyme is further extensively deactivated on sonication or freeze-thawing. In cauliflower mitochondria most of the enzyme is in the deactivated form, and little or no further deactivation occurs on sonication or freeze-thawing. Incubation of mitochondria from either source with succinate leads to full activation of the enzyme. The energy of activation for the conversion of the deactivated to the activated form in membranal preparations under the influence of substrate is about 30,000 cal/mole, essentially the same value as in animal tissues. Activation of the enzyme also occurs under the influence of a variety of other agents, among which the action of anions as activators is documented in the present paper. Activation is accompanied by the release of very tightly bound oxaloacetate. As in animal tissues, the enzyme appears to contain covalently bound flavin (histidyl 8alpha-FAD), and the turnover number is 19,400 moles of succinate oxidized/mole of histidyl flavin at pH 7.5, 38 C.

Journal Article↗
PubMed1978

The mechanism of codon-anticodon interaction in ribosomes. Quantitative study of codon-dependent binding of tRNA to the 30-S ribosomal subunits of Escherichia coli.

The formation of a ternary complex 30-S-subunit . poly(U) . tRNAPhe is discussed and the conditions for its correct description by Langmuir's isotherm are deduced. The affinity constant of the binary complex 30-S-subunit . poly(U) is measured. The reversibility of binding of tRNAPhe to the complex 30-S-subunit . poly(U) is proved in a direct way. The main reason for the heterogeneity of ternary complexes was found to be due to the ability of high-molecular-weight poly(U) to form complicated aggregates with 30-S subunits. If a fraction of poly(U) of moderate molecular weight (30 000) is used, then the ternary complexes are homogeneous in stability and yield the same affinity constants for deacylated, aminoacylated and peptidyl-tRNAPhe (1 X 10(8) M-1 at 20 mM Mg2+, 200 mM NH+4 and 0 degrees C). Ribosomal protein S1 increases the binding constant of poly(U) with 30-S subunits but does not change the binding constant of tRNAPhe with the 30-S-subunit . poly(U) complex. All 30-S subunits, even partially stripped of S1 protein, are active in the binding of both poly(U) and tRNAPhe.

Anticodon↗
PubMed1993

Conditional suicide system of Escherichia coli released into soil that uses the Bacillus subtilis sacB gene.

The sacB gene from Bacillus subtilis confers sucrose sensitivity upon gram-negative bacteria. The gene was investigated for use as a potential conditional suicide system for Escherichia coli released into soil. To ensure against the loss of the cell death function encoded under nonselective conditions, the nptI-sacR-B suicide cassette was inserted into the E. coli chromosome by using a circular nonreplicative integration vector. Stability studies yielded no loss of the suicide cassette in the integrated E. coli EL1026 strain. sacB induction in the absence of a selective pressure resulted in a lysis efficiency of up to 99.9%. The microcosm experiments confirmed the ability of the suicide cassette to limit the growth and reduce the survival of E. coli strains released into soil. Sucrose addition to sterile soil resulted in a 10(-3)-fold reduction of the final E. coli population density. sacB induction prevented the proliferation and triggered the rapid disappearance of E. coli from natural soil. Mutation to sucrose tolerance occurred at a frequency of 10(-5), making E. coli EL1026 a potential counterselectable donor strain for gene transfer studies. Specificity and potential adaptability to a wide range of gram-negative bacteria are additional conveniences of this conditional suicide system for the containment and counterselection of engineered microorganisms.

Bacillus subtilis↗