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At least 145 records · Page 8Linked to original sources
PubMed2003

Diffusion of redox probes in hydrated sol-gel-derived glasses. Effect of gel structure.

The diffusion coefficients of redox probes entrapped in a silica matrix prepared by the sol-gel process were measured using a combination of cyclic voltammetry and chronoamperometry at an ultramicroelectrode. In this study, the porosities of the gels were varied to assess the importance of constrained environments vs intermolecular interactions on the translational mobility of guests entrapped in this solid host matrix. The average pore diameter of the gels was varied from 40 to 400 A by utilizing different catalysts (HCl, NH3, NaF) or different silicon precursors (tetramethoxysilane or Ludox colloidal silica). The diffusion coefficients of cobalt(II) tris(bipyridine), ferrocenemethyltrimethylammonium ion, and dicyanobis(phenanthroline)iron(II) and their rate of change as the gel dried were found to be nearly identical for gels prepared from TMOS and catalyzed with either HCl, NH3, or NaF. When trapped in gels prepared from Ludox, ferrocenemethanol and potassium ferricyanide diffused at rates identical to that measured in solution. In contrast, Dapp for ferrocenemethyl(trimethylammonium) dropped 1 order of magnitude over a 30-day drying period. These results attest to the importance of intermolecular interactions in governing diffusion in sol-gel-derived materials.

Journal Article↗
PubMed1977

A 13C nuclear magnetic resonance study of gel-forming (1 goes to 3)-beta-d-glucans. Evidence of the presence of single-helical conformation in a resilient gel of a curdlan-type polysaccharide 13140 from Alcaligenes faecalis var. myxogenes IFO 13140.

A 13C nuclear magnetic resonance (NMR) study of a resilient gel of a curdlan-type polysaccharide 13140, a (1 goes to 3)-beta-D-glucan, from Alcaligenes faecalis var. myxogenes IFO 13140, was performed in an effort to understand the gel structure. It was found that very broad 13C resonance peaks of line widths ca. 150 (C-1-C-5) and 50 HZ (C-6) are able to be seen in the gel state. Because of a fivefold increase of the peak intensities with respect to those in an aqueous suspension by gelation, these peaks are unequivocally ascribed to certain regions relevant to the gel structure. Those 13 C NMR peaks, however, account for only 20-30 (as viewed from C-1-C-5) and 60% (from C-6) of the total gel, the peak areas of the rest being lost. With respect to those of the disordered low molecular weight acid degraded fraction, fraction II, and laminaran, downfield displacements of C-1, C-3, and C-4 signals are found to take place by amounts of 2.8, 3.2, and 0.9 ppm, respectively, while the remaining peaks (C-2, C-5, and C-6) are unchanged. In view of similar differences of chemical shifts between cyclodextrins and linear (1 goes to 4)-alpha-D-glucans (Colson, P., Jennings, H.J., and Smith, I.C.P. (1974), J. Am. Chem. Soc. 96, 8081-8087), the observed downfield 13C shifts of the glucosidic bonds in the gel are explained by the presence of the fixed conformation of the preferred dihedral angles, in which internal rotations around the glucosidic bonds are not allowed. Combined with the results of theoretical prediction and the downfield shift of C-4 signals, which is consistent with the presence of an O-4'...O-5 intramolecular hydrogen bond, the observed 13C peaks are ascribed to a region of single helical conformation, whereas the peak-loss portion of 13C NMR signals (70-80 and 40% from C-1 and C-6, respectively) is presumably ascribed to the multiple-helical junction zones for the gel structure and their vicinities. The variation of the line widths as well as the peak positions is also found to take place by stepwise addition of NaOH (greater than 0.22 M). The onset of the conformational transition, helix to random coil, is in good agreement with the change of viscosity, specific rotation, optical rotatory dispersion, and absorption maximum shift by complex formation with Congo Red reported by Ogawa et al. (Ogawa, K., Watanabe, T., Tsurugi, J., and Ono, S. (1972), Carbohydr. Res. 23, 399-405).

Alcaligenes↗
PubMed2005

Porphyrin gels reinforced by sol-gel reaction via the organogel phase.

Porphyrins bearing four urea-linked dodecyl groups (3a) or four urea-linked triethoxysilylpropyl groups (3TEOS) at their peripheral positions were synthesized. 3a tends to assemble into a sheetlike two-dimensional structure due to the predominant hydrogen-bonding interaction among the urea groups and acts as a moderate gelator of organic solvents. On the other hand, its Cu(II) compelx (3a.Cu) tends to assemble into a fibrous one-dimensional structure due to the predominant porphyrin-porphyrin pi-pi stacking interaction and acts as an excellent gelator of many organic solvents. 3TEOS and 3TEOS.Cu, which also act as gelators, afforded similar superstructures as those of 3a and 3a.Cu, respectively, and as evidenced by SEM and TEM observations and XRD measurements, the original superstructures could be precisely immobilized by in situ sol-gel polycondensation of the triethoxysilyl groups. The TEM images of 3a gels and 3TEOS gels after sol-gel polycondensation showed a fine striped structure, the periodical distance of which was either 2 or 4 nm. X-ray crystallographic analysis of a single crystal obtained from a reference porphyrin bearing four urea-linked butyl groups revealed that there are two different porphyrin-stacked columns in the crystal and both the 2 nm distance and the 4 nm distance can appear, depending on the observation tilting angle. The hybrid gel prepared from 3TEOS.Cu by sol-gel polycondensation showed unique physicochemical properties such as a high sol-gel phase-transition temperature (>160 degrees C), sufficient elasticity, high mechanical strength, etc. Thus, the present study has established new concepts for molecular design of porphyrin-based gelators on the basis of cooperative and/or competitive actions of hydrogen-bonding and pi-pi stacking interactions and for immobilization of their superstructures leading to development of new functional organic/inorganic hybrid materials.

Journal Article↗
PubMed1995

Lidocaine adrenaline tetracaine gel versus tetracaine adrenaline cocaine gel for topical anesthesia in linear scalp and facial lacerations in children aged 5 to 17 years.

STUDY OBJECTIVE: The purpose of the present study is to compare LAT gel (4% lidocaine, 1:2000 adrenaline, 0.5% tetracaine) to TAC gel (0.5% tetracaine, 1:2000 adrenaline, 11.8% cocaine) for efficacy, side effects, and costs in children aged 5 to 17 years with facial or scalp lacerations. DESIGN: Randomized, prospective, double-blinded clinical trial. SETTING: Inner-city Emergency Department with an Emergency Medicine residency program. PATIENTS OR OTHER PARTICIPANTS: Children aged 5 to 17 years with linear lacerations of the face or scalp. INTERVENTION: After informed consent was obtained patients had lacerations anesthetized with topical TAC or LAT gel according to a random numbers table. MEASUREMENTS AND MAIN RESULTS: A total of 95 patients were included in the statistical analysis with 47 receiving TAC and 48 receiving LAT. Physicians and patients/parents separately rated the overall pain of suturing using a modified multidimensional scale for pain assessment specifically for children. Patients/parents also stated the number of sutures causing pain. The power of the study to determine a ranked sum difference of 15 was 0.8. Multidimensional rating scale results and number and percentage of sutures causing pain were compared using Wilcoxon's rank sum test. According to patients no difference could be detected in percent of sutures causing pain in the LAT versus TAC group (P = .51). Using the multidimensional scale, physicians and patients/parents found LAT statistically the same as TAC in effectiveness (P = .80 for physicians and P = .71 for patients). Cost per application was $3.00 for LAT compared to $35.00 for TAC. Follow-up was accomplished in 85 of 95 participants in the study with no reported complications for either medication. CONCLUSION: LAT gel worked as well as TAC gel for topical anesthesia in facial and scalp lacerations. Considering the advantages of a noncontrolled substance and less expense, LAT gel appears to be better suited than TAC gel for topical anesthesia in laceration repair in children.

Adolescent↗
PubMed2002

Modeling the gel electrophoresis of short duplex DNA by Brownian dynamics: cubic gel lattice with direct interaction.

The technique of Brownian dynamics is used to model the electrophoretic mobility of spherical and rod-like particles in a three-dimensional cubic gel lattice. In addition to excluded volume interactions between the migrating particle and the gel, direct interactions are also included. The methodology is first applied to spherical particles in the absence of direct interactions and the resulting mobilities are shown to agree with independent studies. The methodology is then applied to rod-like models of short duplex DNA fragments 10-50 base pairs in length. In the absence of direct interactions between gel and DNA, calculated mobilities show a much weaker dependence on gel concentration than observed in experiments of DNA in Tris-acetate buffer and polyacrylamide gels. When an attractive interaction between gel and DNA of approximately -0.3 k(B)T per base pair at contact is included, good agreement between calculated and experimental mobilities is achieved.

DNA↗
PubMed1992

Formamide modified polyacrylamide gels for DNA sequencing by capillary gel electrophoresis.

Compressions are occasionally found during the separation of DNA sequencing fragments, particularly in G/C-rich regions and in gels operated at room temperature. Addition of at least 10% formamide to urea/polyacrylamide sequencing gels improves the denaturing capacity of the gel, minimizing compressions. Addition of 20% or more formamide decreases the separation rate, theoretical plate count, and resolution for normally migrating fragments. An optimum concentration of 10% formamide improves resolution of compressed regions without degrading the other characteristics of the gel. Operation of gels at room temperature simplifies the engineering associated with automated sequencers based on capillary gel electrophoresis.

Base Sequence↗
PubMedDate not supplied

Rapid mass spectrometric identification of proteins from two-dimensional polyacrylamide gels after in gel proteolytic digestion.

We report a rapid method for identifying proteins resolved by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) using matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS). In-gel digestion was performed in a way such that the volume ratio of trypsin solution to gel plug was quantitatively controlled to promote reproducible digestion and to maximize the digestion yield. To make the digestion samples more compatible with MALDI-MS, the volatile salt ammonium bicarbonate in the digestion buffer was largely removed prior to peptide extraction. Samples of mixed tryptic peptides from in-gel digestion were used without purification to obtain molecular weights by MALDI-MS with alpha-cyano, 4-hydroxy-cinnamic acid as the matrix. Modifications of MALDI sample loading procedures improved the detection sensitivity by one half to one order of magnitude. The peptide mass peaks in MALDI-MS spectra were distinguished from those of impurities by using several types of controls, and masses were corrected by using trypsin autodigestion fragments as internal calibration standards. Two different peptide-matching computer programs were used to interrogate sequence databases and identify proteins. Identification was enhanced by generation of orthogonal data sets (by using different proteases) and by including experimental values of isoelectric point (pI) and molecular weight to exclude false entries in the candidate lists. Approximately 1% of the material from a spot was used in each sample loading, and nine protein spots from rat liver 2-D PAGE gels were identified correctly, as judged by comparison with identification results previously obtained from Edman sequencing. A previously identified low-abundance spot was not identified by MALDI-MS, presumably because there was insufficient material in a single gel. The sample handling procedure reported here should permit us to identify many 2-D PAGE protein spots of medium abundance.

Acrylic Resins↗
PubMed1998

Ultrathin-layer zone electrophoresis of alcohol dehydrogenase in partly rehydrated polyacrylamide gels: an alternative to starch gel electrophoresis.

A highly sensitive electrophoretic technique for the separation of alcohol dehydrogenase isoenzymes by zone electrophoresis in partly rehydrated polyacrylamide gels is described. Five hundred microm thin polyacrylamide gels are polymerized under standardized conditions. After polymerization the gels are washed thoroughly with distilled water to remove any unreacted monomers, catalysts or still soluble polymers. The washed gels are then impregnated with 0.5% Tween 20 and dried. Before electrophoresis the dry gels are rehydrated to a thickness of 250 microm, which makes up 50% of the original gel volume. Rehydration is carried out by use of a degassed buffer solution. This method permits the demonstration of the isoenzymes of alcohol-dehydrogenase class I and II in man and allows quantitative determination.

Acrylic Resins↗
PubMed1987

Electrophoretic separation of proteins on agarose gel--application for direct immunization with a gel piece containing an antigen.

An efficient method of separating proteins by electrophoresis with agarose gels containing sodium dodecyl sulfate is described. The separated proteins were then used to make antibodies. The separation of proteins in the molecular weight range 25K to 94K on 4 to 5% agarose gels showed good resolution which was comparable to that obtained by electrophoresis with polyacrylamide gels containing sodium dodecyl sulfate. The subunits of human chorionic gonadotropin were separated by the preparative agarose gel electrophoresis and the gel bands containing the subunits were used directly to raise antibodies against these proteins. The degree of solubilization of the proteins from the gel slices was found to be complete.

Antibody Formation↗
PubMed1984

Counterimmunoblotting: detection of non-denatured or denatured antigens in antibody-containing agarose gels following polyacrylamide gel electrophoresis.

Utilizing the principles of counterimmunoelectrophoresis, a technique was devised to immunologically identify non-denatured protein antigens resolved by polyacrylamide gel electrophoresis. Proteins were electrophoretically transferred from polyacrylamide gel to antibody-containing agarose gel in a commercially available blotting apparatus. Detection of the antigen/antibody complex by Coomassie blue staining (in the ng range for unlabeled antigen) or autoradiography (in the pg range for radiolabeled antigen) established the sensitivity and specificity of this method. Similar sensitivity could be obtained following conventional sodium dodecyl sulfate polyacrylamide gel electrophoresis after partial removal of the detergent and possible renaturation of proteins. Placement of a nitrocellulose sheet on the anodal side of the agarose gel produced a 'negative replica' (proteins/polypeptides not reacting with specific antibodies in the agarose gel). Counterimmunoblotting provides an additional method for molecular weight determination of protein antigens with sensitivity and specificity comparable to established nitrocellulose blotting (unlabeled proteins) or immunoprecipitation (labeled proteins) procedures.

Antigen-Antibody Complex↗
PubMed2006

Gel-free and gel-based proteomics in Bacillus subtilis: a comparative study.

The proteome of exponentially growing Bacillus subtilis cells was dissected by the implementation of shotgun proteomics and a semigel-based approach for a particular exploration of membrane proteins. The current number of 745 protein identifications that was gained by the use of two-dimensional gel electrophoresis could be increased by 473 additional proteins. Therefore, almost 50% of the 2500 genes expressed in growing B. subtilis cells have been demonstrated at the protein level. In terms of exploring cellular physiology and adaptation to environmental changes or stress, proteins showing an alteration in expression level are of primary interest. The large number of vegetative proteins identified by gel-based and gel-free approaches is a good starting point for comparative physiological investigations. For this reason a gel-free quantitation with the recently introduced iTRAQ (isobaric tagging for relative and absolute quantitation) reagent technique was performed to investigate the heat shock response in B. subtilis. A comparison with gel-based data showed that both techniques revealed a similar level of up-regulation for proteins belonging to well studied heat hock regulons (SigB, HrcA, and CtsR). However, additional datasets have been obtained by the gel-free approach indicating a strong heat sensitivity of specific enzymes involved in amino acid synthesis.

Bacillus subtilis↗
PubMed1999

Effect of gelation conditions on the gel structure and resolving power of agarose-based DNA sequencing gels.

The effect of gelation conditions on the structure and resolving properties of agarose-based DNA sequencing gels were studied. Gels that were formed by rapid cooling gave separation patterns with sharp, well-defined bands, and resolved base repeats that were not separated on gels which were allowed to cool slowly. Analyses by electron microscopy indicated that the rapidly cooled gels have a homogeneous pore structure with a smaller average pore size than gels that were cooled slowly. The two types of gels also differ in optical clarity, and have significant differences in their melting characteristics as measured by differential scanning calorimetry.

Bacteriophage M13↗
PubMed1989

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis without a stacking gel: use for high sample throughput.

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis without a stacking gel minimizes lateral spreading of protein when samples are applied in agarose wells and allows high sample throughput (6 samples/cm gel width). The method is simple and convenient to use and gives comparable resolution to the standard method with 4-20% or 6-30% polyacrylamide gradient gels. Best results are obtained when the upper zone of the separating gel is of low polyacrylamide concentration. This indicates a need for the molten agarose to penetrate and anneal with the separating gel.

Electrophoresis, Polyacrylamide Gel↗
PubMed1997

Difference gel electrophoresis: a single gel method for detecting changes in protein extracts.

We describe a modification of two-dimensional (2-D) polyacrylamide gel electrophoresis that requires only a single gel to reproducibly detect differences between two protein samples. This was accomplished by fluorescently tagging the two samples with two different dyes, running them on the same 2-D gel, post-run fluorescence imaging of the gel into two images, and superimposing the images. The amine reactive dyes were designed to insure that proteins common to both samples have the same relative mobility regardless of the dye used to tag them. Thus, this technique, called difference gel electrophoresis (DIGE), circumvents the need to compare several 2-D gels. DIGE is reproducible, sensitive, and can detect an exogenous difference between two Drosophila embryo extracts at nanogram levels. Moreover, an inducible protein from E. coli was detected after 15 min of induction and identified using DIGE preparatively.

Animals↗
PubMed1998

An exactly solvable Ogston model of gel electrophoresis IV: sieving through periodic three-dimensional gels.

In this article, we extend our recently developed lattice model of gel electrophoresis to periodic three-dimensional gels made of either isolated obstacles or infinitely long fibers. Exact mobilities are calculated using a much improved numerical method that allows us to treat very large systems. A comparison of the exact mobilities and free available volumes indicates that the main assumption of the Ogston-Morris-Rodbard-Chrambach model (OMRCM), which postulates that the mobility (mu) of charged particles is directly related to the fractional gel volume available to them, is not valid. However, a study of the gel concentration and analyte size dependence of the zero-field mobility indicates that the OMRCM and the Ferguson plots can indeed be used to obtain useful, semi-quantitative information about the gel properties. A procedure to study more realistic three-dimensional gel systems is discussed.

Algorithms↗
PubMed2006

Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of proteins in dry-cured hams: data registration and multivariate analysis across multiple gels.

This study investigates whether dry-cured hams from two European countries can be distinguished using SDS-PAGE. Thirty-seven commercial hams (19 Spanish, 18 French) were used in the study. Four protein fractions were extracted from each sample, with sufficient material prepared to allow each fraction to be analysed in triplicate lanes. The complete extraction process was carried out in duplicate. The 24 specimens originating from each ham sample were randomly allocated to different lane positions and gels, as were at least two reference lanes (for reference proteins). In total, 118 gels were prepared. Mathematical routines were developed using a matrix language to process the gel image files. Procedures were written to carry out 'within-gel' image correction, lane extraction and normalization, 'between-gel' data registration and linear discriminant analysis (LDA) of each fraction's data to establish whether the provenance could be systematically distinguished. The between-gel registration was carried out using a genetic algorithm (GA). Feature selection was also performed using a GA, to pass subsets of features to the LDA routine. Cross-validated classification success rates were 84, 91, 81 and 85%, respectively, for the four fractions. We conclude that SDS-PAGE can be conducted in a sufficiently quantitative manner and can potentially verify the provenance of regional speciality dry-cured hams.

Electrophoresis, Polyacrylamide Gel↗
PubMed2006

Automated protein analysis by online detection of laser-induced fluorescence in slab gels and 3-D geometry gels.

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) still remains the most reliable and comprehensive analytical method for the evaluation of protein extracts. However, conventional SDS-PAGE is time-consuming and, thus, unpractical if several tens or hundreds of samples must be examined. We show that SDS-PAGE protein analysis can be automated using slab gel DNA sequencers and compare the instrument's performance with conventional SDS-PAGE in terms of resolution, sensitivity and sample capacity. Labeled protein bands are detected online by laser-induced fluorescence (LIF) and the acquired signals are electronically stored for further processing, avoiding gel staining and scanning. Appropriate software allows immediate display of recorded data and convenient evaluation. The method provides a higher sensitivity and dynamic range than conventional Coomassie-stained gels and the resolution of proteins with different masses is independent of the polyacrylamide concentration. Internal markers can also be used for direct quantification and assignment of the molecular masses. Additionally, we present a novel electrophoresis instrument for the simultaneous separation and online LIF detection of all samples of a microtiterplate in parallel lanes in a 3-D geometry gel cylinder. The specific gel thermostatting concept prevents irregular sample migration (smiling) and improves the reproducibility and comparability of individual separation patterns. In combination with the expected large capacity of 384 or 1,536 samples, this makes the instrument a valuable tool for high-throughput comparative screening applications.

Automation↗
PubMed1982

The use of three-dimensional collagen gels for the study of tumour cell invasion in vitro: experimental parameters influencing cell migration into the gel matrix.

We have been using three-dimensional gels of native collagen fibres as a substratum for the study of cell migratory behaviour. The objective of this work has been to develop an experimental model system for the study of tumour cell invasion. Data are presented in this communication concerning the effects of a number of experimental parameters on the migration of human foreskin fibroblasts (normal) and a Syrian hamster melanoma cell line (tumour) into three-dimensional gels of native collagen fibres. We find that the migration of both these cell types into the gel matrix is affected by the concentration of collagen in the gel, as well as by the initial density of cells plated onto the gel and the density of cells in the stock culture dishes. These results are discussed in terms of the control of cell migration into the gel and also demonstrate the potential utility of this model system for the study of tumour cell invasion.

Animals↗