Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “GELS”

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 199 records · Page 11Linked to original sources
PubMed1995

Organisation and gel contraction by human colonic carcinoma (HCA-7) sublines grown in 3-dimensional collagen gel.

The role of cell-matrix interactions in controlling phenotypic heterogeneity in human colonic carcinoma sublines has been investigated. Four cell lines (colony 1, colony 3, colony 6 and colony 30) previously isolated from a single human colonic carcinoma cell line, HCA-7, were grown in 3-dimensional collagen gels. In collagen, the growth of the 4 sublines ranged from well-organised glandular structures (colony 30) to elongated branching structures (colony 3). The capability of cells to organise into glandular structures in collagen correlated with the degree of differentiation observed in their xenografts. Certain sublines, most notably colony 3, were able to contract the collagen gel. Gel contraction could be partially inhibited by a function-blocking antibody directed to the alpha 2 integrin chain but not by an antibody directed to the alpha 3 integrin chain demonstrating a role for alpha 2 integrin in the contraction process. In addition, colony 3 cultures treated with the function-blocking alpha 2 antibody formed more compact structures with limited outgrowth, suggesting a role for alpha 2 integrin in cell migration. Gel contraction and cell migration in collagen gel was largely restricted to 1 subline, colony 3. The subsequent demonstration that alpha 2 integrin is involved in both of these processes suggests that integrin expression and function has a role in generating the phenotypic heterogeneity exhibited by these cell lines.

Collagen↗
PubMed2004

Efficient in-gel digestion procedure using 5-cyclohexyl-1-pentyl-beta-D-maltoside as an additive for gel-based membrane proteomics.

A cycloalkyl aliphatic saccharide, 5-cyclohexyl-1-pentyl-beta-D-maltoside (CYMAL-5), was evaluated as a novel additive in a high-throughput in-gel protein digestion system using 96-well plates. Addition of 0.1% CYMAL-5 (final concentration) during trypsin treatment was compatible with both matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis, and gave a better digestion efficiency than n-octylglucoside, which we previously reported. In-gel reduction and alkylation of Cys residues under denaturing conditions also improved the sequence coverage of peptides. In-gel tryptic digestion with the optimum combination of 0.5 mm thick gels, negative staining, alkylation under denaturing conditions (6 M guanidine hydrochloride), and digestion in the presence of CYMAL-5, gave excellent performance especially for membrane protein analysis, where recovery of hydrophobic peptides was markedly enhanced. The new protocol is simple and convenient, and should be widely applicable to gel-based proteomics.

Alkylation↗
PubMed1996

Visualization of DNA in agarose gels as migrating colored bands: applications for preparative gels and educational demonstrations.

Visualization of DNA in electrophoretic gels typically requires UV radiation and the fluorescent dye ethidium bromide. Alternatively, we report here that by inclusion of visible dyes in standard agarose gels, DNA bands are observable in ambient light as they are separating. Such bands can be directly recovered from gels (approximately 50% yield) and used in standard enzymatic reactions (ligation, endonucleolytic cleavage, random labeling, PCR, and cycle-sequencing) without purification. Of 14 common commercially available stains that could visualize fractionating DNA, Nile blue was chosen for more extensive analysis as it gave the sharpest and most persistent bands and is not known to be toxic. Bands containing greater than 40 ng DNA could be detected by direct visual inspection of gels during electrophoresis. Drying the gels increased sensitivity to 4 ng. We describe relevant molecular features of these dyes and detail simple assays that may be employed to find other useful, and perhaps superior, dyes. This method also lends itself to situations in which easy visualization and convenience of DNA electrophoresis are important, such as classroom demonstrations.

Blotting, Southern↗
PubMed1997

Sequencing of N-linked oligosaccharides directly from protein gels: in-gel deglycosylation followed by matrix-assisted laser desorption/ionization mass spectrometry and normal-phase high-performance liquid chromatography.

A generally applicable, rapid, and sensitive method for profiling and sequencing of glycoprotein-associated N-linked oligosaccharides from protein gels was developed. The method employed sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for protein separation and purification and in-gel deglycosylation using PNGase F for glycan release. Profiles of the neutral glycans from bovine ribonuclease B, chicken ovalbumin, and human immunoglobulin G (IgG), as well as sialic acid-containing sugars (following esterification of the acidic groups) of bovine fetuin and bovine alpha1-acid glycoprotein, were obtained by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) and by normal-phase high-performance liquid chromatography following fluorescent labeling. Oligosaccharides were sequenced using specific exoglycosidases, and digestion products were analyzed by MALDI MS. Between 50 and 100 pmol (1.5 to 15 microg) of glycoprotein applied to the gel was sufficient to characterize its oligosaccharide contents. The identity of all glycoproteins investigated could be confirmed after deglycosylation by in-gel trypsin treatment followed by MALDI MS mass mapping and matching the measured molecular weights to a sequence database. The technique was used for the characterization of the glycan moieties of human immunodeficiency virus recombinant gp120 (Chinese hamster ovary cells) and to monitor changes in the glycosylation of this glycoprotein when produced in the presence of a glucosidase I inhibitor. Furthermore, since heavy and light chains of IgG became separated by SDS-PAGE, it could be established that most glycans were associated with the heavy chains.

1-Deoxynojirimycin↗
PubMed1990

Maintenance of embedded pig pancreatic pseudo-islets in a collagen gel matrix: study of the effect of hydrocortisone, a collagenase inhibitor, and nicotinamide on collagenolysis and the morphogenesis of pancreatic islet-cells in collagen gel matrix.

We describe a method for maintaining neonatal pig pancreatic isletlike cell clusters (as pseudo-islets) embedded in a collagen gel matrix for long periods. The pseudo-islets were formed from single cells of pig pancreas maintained in a suspension culture and then embedded in pepsin-solubilized type I collagen. When the pseudo-islets were cultured in the collagen matrix, the amount of collagen in the culture decreased gradually during the culture period as soluble hydroxyproline-containing material accumulated in the medium. A low concentration of collagen (0.16%) degraded the collagen gels more rapidly than did high concentrations of collagen (0.64%). The degradation of collagen depended both on the number of pseudo-islets embedded in the gel matrix and on the culture conditions used to maintain them. With added nicotinamide, the accumulation of hydroxyproline decreased in the medium and the structure of the gel matrix was well maintained. Hydrocortisone or a specific inhibitor of collagenase did not decrease the solubilization of embedded pseudo-islet cultures and did not help to maintain their structure. These observations indicate the possible utility of long-term maintenance of pseudo-islets in collagen gel matrix in the presence of nicotinamide.

Animals↗
PubMed2001

Submerged gel electrophoresis on Spreadex gels--a new method for APC gene mutation detection.

Familial adenomatous polyposis (FAP) is an autosomal dominant inherited disease. Patients with FAP develop hundreds to thousands of adenomatous polyps in the colon and rectum during their 2nd or 3rd decades, and one or more of them progress to cancer if left without surgical treatment. The gene responsible for FAP was identified in 1991 and termed the APC (adenomatous polyposis coli) gene. Following identification of APC, a number of germ-line mutations responsible for the development of the disease were found. The purpose of this study was to determine the usefulness of a new method, submerged gel electrophoresis, in the detection of the most-frequent mutation of the APC gene [5-base pair (bp) deletion in codon 1309], especially in the presymptomatic diagnosis of FAP. Genomic DNAs were isolated from peripheral blood of patients and their relatives. We used two methods, electrophoresis on polyacrylamide gel and submerged gel electrophoresis, for the identification of APC gene codon 1309 mutation. After only 110 min PCR fragments of 91 bp and 86 bp (5-bp deletion) were completely resolved on a Spreadex EL300 gel. Our results showed that electrophoresis using Spreadex gels provides a simple and rapid non-radioactive method for determination of the most-frequent germ-line mutations in the APC gene.

Adenomatous Polyposis Coli↗
PubMed1998

Culture of chondrocytes in alginate gel: variations in conditions of gelation influence the structure of the alginate gel, and the arrangement and morphology of proliferating chondrocytes.

Sodium alginate, which gels in the presence of calcium ions, is commonly used for culture of anchorage-independent cells, such as chondrocytes. Normally, the gel appears microscopically homogeneous but, depending on the conditions of gelation, it may contain a varying number of small channels that extend inward from the surface. We have examined the influence of these channels on the morphology of cultured chondrocytes entrapped in alginate beads. Growth-plate or articular chondrocytes cultured in alginate normally proliferate and form rounded cell clusters but, in alginate beads containing numerous channels, many chondrocytes become aligned and form columns similar to those in the growth plate in vivo. As the pattern of cellular growth and morphology in alginate is profoundly influenced by the presence of channels in the gel, further studies were conducted to determine what specific conditions of gelation affect their formation. The channels are especially numerous when both the alginate and the gelling solutions lack sodium ions or other monovalent cations. The channels are cavities in the gel formed by particulate blocking of the rapid diffusion of calcium ions from the gelling solution into the boundary of the calcium alginate solution, and hence they extend inward from cells at the surface of the alginate gel. An understanding of the conditions under which these channels develop makes it possible either to avoid their formation or, alternatively, to enhance the number of channels in order to encourage proliferating cells to grow in radial columns, rather than in a less organized pattern characteristic of most culture systems.

Alginates↗
PubMed1984

Addition of proteins to the cylindrical gel embedding medium for transverse molecular-weight markers in two-dimensional gel electrophoresis.

As an aid in the comparison of different complex mixtures of proteins resolved by two-dimensional electrophoresis, a simple method which results in the electrophoresis of molecular-weight standards as appropriately migrating, highly resolved bands extending across the entire second-dimension slab gel is described. The proteins to be used as markers are included in the molten agarose mixture used to affix the first-dimension cylindrical gel atop the second-dimension slab gel. As the proteins which are resolved in the first dimension migrate through the second-dimension slab gel, the marker proteins also migrate, experiencing the same electrophoretic conditions as the sample proteins in the immediate vicinity. If the same protein is resolved in the first dimension and also used as a marker, it electrophoreses in the second dimension as a spot intersected by a band traversing the entire gel. This sensitive method is applied to a comparison of soluble seed proteins of two cotton species, Gossypium hirsutum and G. arboreum, using G. hirsutum seed protein as the molecular-weight marker. Other applications are described.

Electrophoresis, Polyacrylamide Gel↗
PubMed2005

Solvent-induced lysozyme gels: rheology, fractal analysis, and sol-gel kinetics.

In this work, the gelation kinetics and fractal character of lysozyme gel matrices developed in tetramethylurea (TMU)-water media were investigated. Gelation times were determined from the temporal crossover point between the storage, G', and loss, G'', moduli, as a function of the binary solvent composition and of protein concentration. The inverse dependence of the upper limit of the linear viscoelastic region (gamma0) on protein concentration indicate that the lysozyme gels belong to the "strong link" kind, a gel category where interparticle links are stronger than intraparticle ones. Lysozyme gel fractal dimensions (Df) were determined from the analysis of rheological data according to a scaling theory by Shih et al. [Phys. Rev. A 42 (1990) 4772-4779] and were found to be compatible with a diffusion-limited cluster-aggregation kinetics (DLCA) for lysozyme gels formed at the TMU mass fraction in the binary organic-aqueous solvent, wTMU=0.9, and with a reaction-limited cluster aggregation kinetics (RLCA) for wTMU in the 0.6< or =wTMU< or =0.8 range.

Fractals↗
PubMed2006

Fluorescent tetraruthenated porphyrins embedded in monolithic SiO2 gels by the sol-gel process.

In this work silica gels have been prepared by a sol-gel method using tetraethylorthosilicate as gel precursor. The tetraruthenated porphyrins H2(3-TRPyP), Co(3-TRPyP), and H2(4-TRPyP) were incorporated into the systems during gel formation without problems commonly found in the process, such as aggregation. Spectroscopic studies of the resulting silica gels revealed the presence of absorption bands in the range 200-400 nm associated with the transitions of the groups ruthenium-bipyridine, along with the Soret band at the same wavelengths observed in solution. The porphyrins were found to preserve fluorescence emission properties in the range 650-700 nm even after the aging period. Study of the thermal behavior and decomposition kinetics evidenced that the porphyrin H2(4-TRPyP) is the least stable of the group and that all compounds decompose according to first-order kinetics.

Fluorescence↗
PubMed2002

Detection of serum proteins by native polyacrylamide gel electrophoresis using Blue Sepharose CL-6B-containing stacking gels.

Analysis of serum proteins by native polyacrylamide gel electrophoresis is difficult because albumin is abundant in serum and interferes with the resolution of other proteins, especially alpha-antitrypsin which has mobility that is very similar to that of albumin. We present here a method in which serum proteins are separated by polyacrylamide gel electrophoresis using stacking gels containing Blue Sepharose CL-6B, which has a high affinity for albumin, lipoproteins, kinases, and pyridine-nucleotide-dependent oxidoreductases. During electrophoresis, proteins that bind to Blue Sepharose CL-6B stay in the stacking gel and do not migrate into the separating gel. As a consequence, certain proteins, including alpha(1)-antitrypsin, can be detected as clear bands. This method overcomes the requirement for fractionation of serum samples prior to electrophoresis to remove albumin and allows the simultaneous analysis of many samples.

Blood Proteins↗
PubMed2001

Neuronal contact guidance in magnetically aligned fibrin gels: effect of variation in gel mechano-structural properties.

Neurite outgrowth from chick dorsal root ganglia entrapped in isotropic and magnetically aligned fibrin gels was studied, and the dependence on the diameter of the fibrin fibrils was characterized. The fibrin fibril diameter was varied, as inferred from turbidity measurements, by using different Ca2+ concentrations in the fibrin-forming solution, but this variation was accomplished without affecting the degree of magnetic-induced alignment, as directly visualized in fluorescently spiked gels. Magnetically aligned fibrin gels possessing different fibril diameters but similar alignment resulted in drastic changes in the contact guidance response of neurites, with no response in gels formed in 1.2 mM Ca2+ (having smaller fibril diameter, ca. 150 nm), but a strong response in gels formed in 12 and 30 mM Ca2+ (having larger fibril diameter, ca. 510 nm) with an attendant two-fold increase in neurite length. These changes are attributed to variation of the mechano-structural properties of the network of aligned fibrils as the fibril diameter is varied.

Animals↗
PubMed2000

Gel-sol transition can describe the proteolysis of extracellular matrix gels.

We monitored the cell-free solubilization of extracellular matrix and fibronectin gels, catalyzed by exogenous proteinases. The corresponding measurements could not be interpreted according to usual proteinase kinetics. The observation that this experimental system did not consist in surface but in bulk degradation and appeared specific to gel substrates, incited us to use gelation-related approaches to describe these kinetics. We show that the gel-sol transition theory adequately describes the enzyme reactions. This allowed formulation and experimental confirmation of a power law relating macroscopic changes of the gel to enzyme kinetics. This approach could also be used for other power laws predicted by the gel-sol transition theory, allowing a better understanding of macroscopic modification of the extracellular matrix during proteolysis, which is implied in many biological situations, especially tumor dissemination.

Cell-Free System↗
PubMed2006

High-throughput three-dimensional gel electrophoresis for versatile utilities: a stacked slice-gel system for separation and reactions (4SR).

A novel high-throughput system, called the stacked slice-gel system for separation and reactions (4SR), was developed for the analysis of DNA/RNA and protein/peptide. The system provides a novel three-dimensional gel electrophoresis approach that exploits the property of stacked slice gels. It allows multiple samples simultaneously to react as well as to be separated, offering a two-dimensional (mxn) sample loading system. For this purpose, high-throughput multi-micro vessels (MMVs) containing variable numbers of wells (100 wells in this paper) have been used, which are made of 25 mm square-size polyacrylamide gels. Furthermore, after electrophoretic separation, a slice gel containing a desired sample can be easily removed and proceeded to the next step. Different biological reactions as well as successive separation of products were effectively carried out dealing with DNA/RNA and protein/peptide. It shows that this system has a diversity of potentials to be developed.

DNA↗
PubMed1998

A comparison of the efficacy and tolerability of adapalene 0.1% gel versus tretinoin 0.025% gel in patients with acne vulgaris: a meta-analysis of five randomized trials.

The purpose of this meta-analysis was to determine if adapalene 0.1% gel (Differin) provided superior efficacy and better tolerability than tretinoin 0.025% gel in the treatment of acne vulgaris. All comparative studies, both published and unpublished, from the United States and Europe, that fulfilled rigorous protocol criteria (multicentre, randomized, investigator-blind) were used. Five comparative studies met these criteria. In total, the meta-analysis evaluated 900 patients (450 treated with adapalene 0.1% gel, 450 treated with tretinoin 0.025% gel) with mild-to-moderate acne from the combined clinical trials. To avoid study bias, the meta-analysis used an intention-to-treat analysis. Statistical methodology for the meta-analysis included analysis of covariance, analysis of variance and Cochran-Mantel-Haenszel test. All statistical tests were two-sided, with the 0.05 probability level used to establish statistical significance, and 95% confidence intervals used to assess equivalence. Adapalene demonstrated equivalent efficacy to tretinoin in terms of reducing total lesion count. Adapalene demonstrated more rapid efficacy, as evidenced by a significant difference in the reduction of inflammatory and total lesions at week 1. Adapalene also demonstrated considerably greater local tolerability at all evaluation periods. The findings from this meta-analysis suggest that adapalene 0.1% gel constitutes a pharmacologic advance over such classic retinoids as tretinoin for the treatment of acne vulgaris.

Acne Vulgaris↗
PubMed2004

Comparison in fractal dimension between those obtained from structure factor and viscoelasticity of gel networks of 1,3:2,4-bis-O-(p-methylbenzylidene)-D-sorbitol in polystyrene melt at gel point.

We investigated time evolution of shear moduli in the physical gelation process of 1,3:2,4-bis-O-(p-methylbenzylidene)-D-sorbitol in polystyrene melt. At the gel point, storage and loss shear moduli, G' and G", were described by the power law of frequency omega, G' approximately G" approximately omegan, with the critical exponent n being nearly equal to 2/3, in agreement with the value predicted by the percolation theory. We also investigated the structure factor over two decades in length scale at gel point by using ultra-small-angle X-ray scattering, and small-angle X-ray scattering. We found the power-law behavior in low-q region, indicating that the gel network forms the self-similar structure with mass-fractal dimension. Comparison between the exponent of mass-fractal dimension from structure factor and that from viscoelasticity indicates that hydrodynamic interactions are completely screened out and the excluded volume effects are dominant in the gel. The gel strength was found to increase with the decrease in the lower limit length scale of fractality.

Benzylidene Compounds↗
PubMed2002

Structure of fibrin gels studied by elastic light scattering techniques: dependence of fractal dimension, gel crossover length, fiber diameter, and fiber density on monomer concentration.

The concentration dependence of the structure of fibrin gels, formed following fibrinogen activation by thrombin at a constant molar ratio, was investigated by means of elastic light scattering techniques. The scattered intensity distributions were measured in absolute units over a wave-vector range q of about three decades ( approximately 3x10(2)-3x10(5) cm(-1)). A set of gel-characterizing parameters were recovered by accurately fitting the data with a single function recently developed by us [F. Ferri et al., Phys. Rev. E 63, 031401 (2001)], based on a simple structural model. Accordingly, the gels can be described as random networks of fibers of average diameter d and density rho, entangled together to form densely packed and spatially correlated blobs of mass fractal dimension D(m) and average size (or crossover length) xi. As previously done for d, we show here that the recovered xi is also a good approximation of a weight average, namely, d approximately sqrt[ (w)] and xi approximately (w). By varying the fibrinogen concentration c(F) between 0.034-0.81 mg/ml, gels with 100> or =xi> or =10 microm, 100< or =d< or =200 nm, 1.2< or =D(m)< or =1.4, and constant rho approximately 0.4 mg/ml were obtained. The power-law c(F) dependencies that we found for both xi and d are consistent with the model, provided that the blobs are allowed to partially overlap by a factor eta likewise scaling with c(F) (2> or =eta> or =1). Recasting the whole dataset on a single master curve provided further evidence of the similarity between the structures of all the gels, and confirmed the self-consistency of the model.

Fibrin↗
PubMed1995

An agarose-based gel-concentration system for microsequence and mass spectrometric characterization of proteins previously purified in polyacrylamide gels starting at low picomole levels.

An agarose-based concentration gel system is described for eluting and concentrating proteins previously purified either in one-dimensional or two-dimensional gels. Using the technique, proteins can be concentrated from about 1 ml into volumes as small as 10 microliters. After the proteins have been melted out of the agarose gels, they can be digested with proteases, producing peptide patterns similar to those observed with in-solution digestions. The overall peptide recovery, calculated from the amount of protein loaded on the primary separating gel to the collection of fragments after HPLC, is at least 70% of the peptide yields obtained with digests of the same amount of protein in free solution. These results are routinely obtained with 50 pmol amounts (referring to amounts of protein initially loaded on the primary gel). Proteins can also be analysed by a combination of microsequencing and on-line electrospray mass spectrometry, allowing their identification by peptide mass fingerprinting.

Amino Acid Sequence↗