SEARCH · PubMed Health

Results for “stepped gradients”

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 19 recordsLinked to original sources

PubMed1987

Zone formation in ion-pair reversed-phase liquid chromatography. III. Step-gradient elution of oligodeoxyribonucleotides.

Step-gradient elution by decrease of the counter-ion concentration or increase of the co-ion concentration was studied in an ion-pair reversed-phase system. As analytes, polyvalently negatively charged oligodeoxyribonucleotides were used. In the co-ion step-gradient technique, the retention volumes can be predicted by use of a simple equation. This technique gives a drastic decrease in peak width, which makes it possible to decrease the separation time by using an optimized composition of the two eluents used. Furthermore, the detectability of organic ions is considerably improved. The time for the introduction of the second eluent, containing the co-ion, into the column after the sample injection is critical.

Adsorption↗

PubMed1996

Protein crystallization in low gravity by step gradient diffusion method.

Two-step crystallization experiments were conducted in low gravity employing a liquid-liquid diffusion method in an effort to eliminate problems associated with protein crystal growth under the supersaturating conditions required for nucleation. Experiments were performed in diffusion cells formed by the sliding of blocks on orbit. Step gradient diffusion experiments consisted of first exposing protein solutions in diffusion half-wells for brief periods to initiating buffer solutions of high precipitant concentrations to induce nucleation followed by expoure of the same protein solutions to solutions of lower precepitant concentration to promote growth of induced nuclei into crystals. To avoid convective disturbances that occur when solutions of discrepant densities are interfaced at normal gravity, crystallization of hen egg-white lysozyme and rabbit skeletal muscle aldolase by step gradient diffusion was investigated in low gravity on four NASA space shuttle flights. In general, the largest ctystals of both proteins formed at the highest initiating precipitant concentration used, which is consistent with nuclei formation upon brief exposure to high precipitant concentration, and that these nuclei are competent for sustained growth at lower precipitant concentration. The two-step approach dissociates nucleation events from crystal growth allowing parameters affecting nucleation kinetics such as time, precipitant concentration and temperature of nucleation to be varied separately from conditions used for post-nucleation growth.

Animals↗

PubMed1997

Step-gradient capillary electrochromatography.

The analytical benefits of using a step-gradient in capillary electrochromatography (CEC) are demonstrated. The application of step-gradient CEC to the analysis of six diuretics of widely differing lipophilicities was evaluated and shown to result in a marked reduction in the analysis time and an improvement in the peak shape for later-eluting lipophilic components. When the step-gradient approach was performed in an automated mode, the retention time RSD for repeated injections was below 1%.

Diuretics↗

PubMed2004

Separation and determination of carbonyl compounds in indoor air using two-step gradient capillary electrochromatography.

A method of two-step gradient capillary electrochromatography (CEC) was developed to measure 12 carbonyls (aldehydes and ketones) in indoor air samples. The carbonyls were derivatized with 2,4-dinitrophenylhydrazine (DNPH) and then separated by a two-step gradient CEC on a C8 column. Effects of various instrumental conditions on the separation, including buffer concentration, organic modifiers, voltage, and cassette temperature, were investigated. The method detection limits for the 12 carbonyls ranged from 0.2 microg to 1.6 microg per sample and the recoveries were generally between 90 and 120%. A subset of 30 indoor air samples containing formaldehyde and acetaldehyde from 75 randomly selected homes in the city of Ottawa, Canada were measured using the CEC method. The concentrations of formaldehyde and acetaldehyde in these indoor air samples ranged from 5.8 microg/m3 to 85 microg/m3, and from 4.4 microg/m3 to 38 microg/m3, respectively. The comparison between CEC and the traditional HPLC method shows a good agreement in measured values.

Journal Article↗

PubMed1988

Rapid step-gradient purification of mitochondrial DNA.

A convenient modification of the step gradient (CsCl/ethidium bomide) procedure is described. This rapid method allows isolation of covalently closed circular DNA separated from contaminating proteins, RNA and chromosomal DNA in ca. 5 h. Large scale preparations can be performed for circular DNA from eukaryotic organelles (mitochondria). The protocol uses organelle pelleting/NaCl-sarcosyl incubation steps for mitochondria followed by a CsCl step gradient and exhibits yields equal to the conventional procedures. It results in DNA sufficiently pure to be used for restriction endonuclease analysis, subcloning, 5'-end labeling, gel retention assays, and various types of hybridization.

Animals↗

PubMed2005

Detection of myofibrillar proteins using a step gradient minigel with an ambiguous interface.

Myosin heavy chain (MHC), actin, titin, and nebulin are four major myofibrillar proteins that interact with each other. However, it is difficult to analyze the four proteins simultaneously on the same minigel due to their broad range of molecular weights. Numerous gradient gels are normally used to detect these myofibrillar proteins. The conventional step gradient gel provides better separation of the four major proteins, but several proteins accumulate at the interfaces between different gradient layers. To eliminate the obvious interfaces, we employed a plastic syringe filled with 12 and 4% acrylamide solutions simultaneously and then established an improved step gradient minigel with an ambiguous interface. It was determined by blue dextran in-gel visualization and scanning densitometry that the acrylamide concentration at the ambiguous interface gradually changed. Coomassie blue staining and immunoblotting revealed that the four proteins were successfully separated and transferred for analysis. This gel system is simple to prepare and easy to use, and it is a reliable method for analyzing myofibrillar proteins or other protein mixtures with broad molecular masses.

Actins↗

PubMed1995

A novel vertebrate svp-related nuclear receptor is expressed as a step gradient in developing rhombomeres and is affected by retinoic acid.

The protein encoded by the zebrafish gene svp[40] belongs to a distinct group within the steroid hormone receptor superfamily that includes Drosophila seven-up and several vertebrate orphan receptors. Svp[40] shares a particularly high degree of amino acid sequence identity (approximately 86%) with the mammalian transcription factors ARP-1 and COUP. The gene is expressed in specific regional and segmental domains within the developing brain. Correspondence between this expression pattern and early sites of neuronal differentiation and axonogenesis in the rostral brain may reflect an involvement in neural patterning. During the early embryonic stages when hindbrain rhombomeres are formed, a segmental expression pattern is established as a step gradient. The single steps of this gradient coincide directly with the four anteriormost segments suggesting a role in controlling rhombomere-specific expression of genes contributing to cell differentiation in the hindbrain. Since COUP/ARP-1 and retinoic acid receptors (RARs/RXRs) are known to have similar DNA-binding specificities, different levels of Svp[40] might modulate retinoid signaling through competition for binding to specific RAREs in the promoters of target genes. Treatment of zebrafish embryos with retinoic acid affects the svp[40] step gradient and causes an elimination of a regional expression domain in the retina. These observations are consistent with svp[40] being an integral part of the retinoid signaling network during hindbrain and eye development.

Amino Acid Sequence↗

PubMed2005

Evaluation of multidimensional (ion-exchange/reversed-phase) protein separations using linear and step gradients in the first dimension.

The performance characteristics of multidimensional liquid chromatographic protein separations were evaluated using on-line electrospray mass detection, and a novel workflow for automated LC/MS data processing. Two-dimensional ion exchange/reversed-phase LC separations of Escherichia coli cytosol were conducted using either a continuous linear or discontinuous step gradient in the first dimension. Chromatographic profiles of the top 100 most abundant components were characterized to assess overall separation reproducibility within each mode, and to characterize differences in component distribution between the two modes of operation. Analysis of the resulting data indicates that multidimensional separations of complex protein mixtures can be done reproducibly. Furthermore, under the conditions employed within this study, a linear first dimension gradient was more effective at fractionating the protein mixture, distributing fewer major components to multiple second dimension cycles than an equivalent step gradient. The application of on line mass spectrometry, and automated processing of the resulting data, proved valuable for producing component level analysis of multidimensional protein separations.

Chromatography, Ion Exchange↗

PubMed2024

Gradient-Elution Nanoflow Liquid Chromatography Without a Binary Pump: Smoothed Step Gradients Enable Reproducible, Sensitive, and Low-Cost Separations for Single-Cell Proteomics.

Mass spectrometry-based proteome profiling of trace analytes including single cells benefits from liquid chromatography separations operated at low flow rates (e.g., <50 nl/min). However, high-pressure binary pumps needed to achieve such flow rates are not commercially available, and instead require splitting of the gradient flow to achieve low-nanoliter-per-minute flow rates. Gradient flow splitting can waste solvent and lead to flow inconsistencies. To address this, we have developed a method for creating gradients by combining segments of mobile phase having increasing solvent strength together in an open capillary, and then relying on Taylor dispersion to form the desired smooth gradient profile. Our method dramatically reduces costs, as only a single isocratic high-pressure pump is required. Following development of gradient profiles for both 10- and 20-min active gradients, we measured 200 pg injections of HeLa digest using a timsTOF mass spectrometer. Finally, we investigated differences in protein expression between single cells originating from two different colonies of ATG-KO HeLa cells. Thousands of proteins were quantified, and a potential mechanism explaining differential immune responses of these two colonies upon exposure to viral DNA treatment was determined.

Humans↗

PubMed2003

Linear two-step gradient counter-current chromatography analysis based on a recursive solution of an equilibrium stage model.

The implementation of gradients in continuously operated chromatographic counter-current processes has recently attracted considerable interest as a method to improve the performance of this effective separation method. If liquid mobile phases are applied it is advantageous to set the solvent strength in the desorbent stream higher than that in the feed stream. As a consequence. the components to be separated are more retained in the adsorption zones and more easily eluted in the desorption zones. Due to the additional degrees of freedom the design and the optimization of such a two-step gradient counter-current process is difficult. In this paper a steady state equilibrium stage model is used to simulate the process under linear conditions. A simple solution of the underlying model equations is presented capable to describe efficiently the unit for large stage numbers typically encountered in chromatographic columns. Due to the rapidity of the algorithm developed a broad range of operating conditions can be evaluated systematically for different types of gradients. The impact of (a) the functional dependence of the adsorption equilibrium constants on the solvent composition, (b) the number of equilibrium stages and (c) the specification of purity requirements is illustrated and discussed based on results of parametric calculations. The results achieved emphasize the potential of two-step gradient counter-current chromatography.

Countercurrent Distribution↗

PubMed1985

Rapid analysis of the major classes of retinoids by step gradient reversed-phase high-performance liquid chromatography using retinal (O-ethyl) oxime derivatives.

A rapid step-gradient reversed-phase high-performance liquid chromatography (HPLC) method is presented for analysis of the major classes of retinoids in tissues. Retinal was converted into a new derivative, retinal (O-ethyl) oxime, since the standard derivative, retinaloxime, co-elutes with retinol on reversed-phase HPLC. The most abundant naturally occurring retinyl esters, retinyl palmitate and retinyl stearate, were eluted within 12 min to complete the separation. Retinoids were extracted in the presence of an antioxidant, butylated hydroxytoluene, and a lipid carrier, cholesterol. Recoveries of 98-100% were obtained from tissue samples by internal addition for the retinoids tested (retinol, retinal and retinyl palmitate); and the absolute recovery of endogenous retinal from rat eyecups was confirmed by spectrophotometric measurements of rhodopsin. Extraction was carried out in an air atmosphere and under subdued incandescent light rather than requiring inert atmosphere and safe-light conditions used in most methods. Cis-trans isomers were not separated under the reversed-phase HPLC conditions employed. Quantitation was carried out using retinyl acetate as internal standard and the day to day precision was better than 3.5%. A sensitivity of about 1 ng is obtained for all retinoids using absorbance monitoring at 325 nm and a C18 5 micrometers column with 12% reversed-phase loading. The tocopherols can also be separated and detected simultaneously with similar sensitivity by this method using a fluorescence detector in series [G. J. Handelman, L. J. Machlin, K. Fitch, J. J. Weiter and E. A. Dratz, J. Nutr., 115 (1985) 807].

Animals↗

PubMed2001

Rapid and sensitive step gradient assays of glutamate, glycine, taurine and gamma-aminobutyric acid by high-performance liquid chromatography-fluorescence detection with o-phthalaldehyde-mercaptoethanol derivatization with an emphasis on microdialysis samples.

We developed a rapid step-gradient HPLC method for determination of glutamate, glycine and taurine, and a separate method for determination of gamma-aminobutyric acid (GABA) in striatal microdialysates. The amino acids were pre-column derivatized with o-phthalaldehyde-2-mercaptoethanol by using an automated refrigerated autoinjector. Separation of the amino acids was established with a non-porous ODS-II HPLC column, late-eluting substances were washed out with a one-step low-pressure gradient. Concentrations of the amino acids were determined with a fixed-wavelength fluorescence detector. The detection limit for GABA was 80 fmol in a 15 microl sample, detection limits for glutamate, glycine and taurine were not determined because their concentrations in striatal perfusates were far above their detection limits. Total analysis time was less than 12 min, including the wash-out step. The methods described are relatively simple, sensitive, inexpensive, and fast enough to keep up with the microdialysis sampling.

Chromatography, High Pressure Liquid↗

PubMed1991

Using sodium chloride step gradients to fractionate DNA fragments.

A method is described for the separation of DNA fragments by ultracentrifugation through a sodium chloride step gradient. The gradients are quickly and easily prepared and require a five- to six-hour centrifugation. Fractionated samples of DNA may be directly examined by agarose gel electrophoresis, then further analyzed by Southern transfer and hybridization. A simple ethanol precipitation followed by several ethanol washes yields fragments that ligate efficiently to vector DNA. The method has been applied to separate chromosomal DNA restriction fragments as well as bacteriophage lambda arms from insert DNA.

Bacillus subtilis↗

PubMed2003

[Sodium chloride step gradients centrifuge to fractionate foreign DNA fragment for microinjection].

DNA microinjection is the most popular and reliable method of producing transgenic animals. The purity of foreign DNA plays an important role for the success of microinjection. In this study, we introduced the use of sodium chloride step gradients in fractionating foreign DNA fragment for microinjection. The data demonstrated that,compared with the conventional agarose gel extraction method, NaCl purification scheme of toreign DNA could improve the treated embryo survival and foreign DNA intergration rate markedly.

English Abstract↗

PubMed2004

Fractionation of grape anthocyanin classes using multilayer coil countercurrent chromatography with step gradient elution.

Grape anthocyanins from rosé wine pomace and grape skins were fractionated by multilayer coil countercurrent chromatography (MLCCC). Tert-butyl methyl ether/n-butanol/acetonitrile/water acidified with trifluoroacetic acid (2/2/x/5) was chosen as the solvent system because of its demonstrated efficiency in separating anthocyanins. A method combining MLCCC and step gradient elution has been developed. This method enabled the fractionation of anthocyanins as series of glucosides, and the corresponding acetylated, coumaroylated, and caffeoylated derivatives. The different anthocyanins were identified on the basis of their UV spectra, their elution time on reversed-phase HPLC as well as by mass spectrometry. A polar-colored fraction free of anthocyanin monomers and corresponding to the material remaining in the stationary phase after the completion of the gradient was recovered.

Anthocyanins↗

PubMed1986

Simple step gradient elution of the major high-energy compounds and their catabolites in cardiac muscle using high-performance liquid chromatography.

The majority of high-energy nucleotides and their catabolites are separated in a single 13-min run using reversed-phase high-performance liquid chromatography. Economical step gradient elution of these compounds with a Nova Pak-A C18, 5-microns, 10 cm X 8 mm column accomplishes this separation with recoveries of 94-100% and sensitivities of 1-5 pmol. Furthermore, the total adenine nucleotide pool can now be quantitated precisely in a simple and easily automated procedure.

Adenine Nucleotides↗

PubMed1992

Neurite outgrowth on a step gradient of chondroitin sulfate proteoglycan (CS-PG).

Sulfated proteoglycans (PGs) may play a significant role in the regulation of neurite outgrowth. They are present in axon-free regions of the developing nervous system and repel elongating neurites in a concentration-dependent manner in vitro. The addition of growth-promoting molecules, such as laminin, can modify the inhibitory effect of PGs on neurite outgrowth (Snow, Steindler, and Silver, 1990b). Substrata containing a high-PG/low-laminin ratio completely inhibit neurite outgrowth, while normal, unimpeded outgrowth is observed on low-PG/high-laminin substrata. Therefore, different patterns of neurite outgrowth may result from regulation of the ratio of growth-promoting molecules to growth-inhibiting molecules. Using video microscopy, embryonic chicken dorsal root ganglia neurons (DRG), chicken retinal ganglia neurons (RGC), and rat forebrain neurons (FB) were analyzed as they extended processes from a substratum consisting of laminin alone onto a step gradient of increasing concentrations of chondroitin sulfate proteoglycan (CS-PG) bound to laminin. In contrast to neurite outgrowth inhibition that occurs at the border of a single stripe of high concentration of CS-PG (Snow et al., 1990b and this study), growth cones grew onto and up CS-PG presented in a step-wise graded distribution. Although the behavior of the different cell types was unique, a common behavior of each cell type was a decrease in the rate of neurite outgrowth with increasing CS-PG concentration. These data suggest that appropriate concentrations of growth-promoting molecules combined with growth-inhibiting molecules may regulate the direction and possibly the timing of neurite outgrowth in vivo. The different responses of different neuronal types suggest that the presence of sulfated PG may have varying effects on different aspects of neuronal development.

Aggrecans↗

PubMed1997

Application of mixed mobile phases and a step gradient method in capillary electrochromatography for the separation of isomeric polycyclic aromatic hydrocarbon-deoxyribonucleoside adduct mixtures prepared in vitro.

Capillary electrochromatography (CEC) was used for the analysis of mixtures of neutral isomeric compounds derived from the reaction of carcinogenic hydrocarbon (benzo[g]chrysene and 5,6-dimethylchrysene) dihydrodiol epoxides with calf thymus deoxyribonucleic acid (DNA). The CEC analysis demonstrated higher resolution, greater speed and lower analyte consumption than high-performance liquid chromatography (HPLC) in the analysis of the same samples using the same type of stationary phase. Proper selection of the mixed mobile phases was critical for the separation of these complex mixtures with enhanced speed and selectivity. The use of a step gradient further improved the speed of the CEC analysis resulting in electrochromatograms that required only 25-70% of the corresponding HPLC analysis times.

DNA Adducts↗