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 91 records · Page 5Linked to original sources
PubMed2003

Optimization of in-gel protein digestion system in combination with thin-gel separation and negative staining in 96-well plate format.

Improvement of in-gel digestion efficiency is highly desirable for one- or two-dimensional gel electrophoretic separation and mass spectrometric (MS) analysis in proteomics, because the resultant increases in sequence coverage and MS signal intensity lead to higher confidence in protein identification. Here an optimized in-gel digestion system, in combination with thin-gel separation and negative staining in a high-throughput format using 96-well plates, is described. The combination of negative staining and protein separation on a 0.9 mm thick gel showed a clear improvement in in-gel digestion efficiency in comparison with the more typical protocols such as the combination of silver staining and a 1.0 mm gel. In addition, the use of 96-well plates to increase throughput did not decrease the efficiency of this strategy when the stirring of the gel pieces in processes such as destaining, washing, gel-shrinking and peptide extraction was performed by sonication instead of shaking the plates. This procedure was optimized and applied to identify proteins of the postsynaptic density fraction; 105 proteins were identified after SDS-PAGE separation.

Animals↗
PubMed2006

Disease proteomics of high-molecular-mass proteins by two-dimensional gel electrophoresis with agarose gels in the first dimension (Agarose 2-DE).

Agarose gel is the preferred electrophoretic medium currently used for separating high molecular mass (HMM) proteins (MW>100 kDa). Agarose gels are widely used for both SDS-agarose gel electrophoresis and agarose isoelectric focusing (IEF). A two-dimensional gel electrophoresis method employing agarose gels in the first dimension (agarose 2-DE) that is sufficiently good at separating up to 1.5mg of HMM proteins with molecular masses as large as 500 kDa has been used to separate proteins from various diseased tissues and cells. Although resolution of the agarose 2-DE pattern always depends on the tissue being analyzed, sample preparation procedures including (i) protein extraction with an SDS sample buffer; (ii) ultracentrifugation of a tissue homogenate; and (iii) 1% SDS in both stacking and separation gels of the second-dimension SDS-PAGE gel, are generally effective for HMM protein detection. In a comprehensive prostate cancer proteome study using agarose 2-DE, the HMM region of the gel was rich in proteins of particular gene/protein expression groups (39.1% of the HMM proteins but only 28.4% of the LMM ones were classified as transcription/translation-related proteins). Examples include transcription factors, DNA or RNA binding proteins, and ribosomal proteins. To understand oxidative stress-induced cellular damage at the protein level, a novel proteomic method, in which protein carbonyls were derivatized with biotin hydrazide followed by agarose 2-DE, was useful for detecting HMM protein carbonyls in tissues of both a diabetes model Ostuka Long-Evans Tokushima Fatty (OLETF) rat and a control Long-Evans Tokushima Otsuka (LETO) rat. In this paper, we review the use of agarose gels for separation of HMM proteins and disease proteomics of HMM proteins in general, with particular attention paid to our proteome analyzes based on the use of agarose 2-DE for protein separation followed by the use of mass spectrometry for protein identification.

Animals↗
PubMed2000

A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling.

Proteomic projects are often focused on the discovery of differentially expressed proteins between control and experimental samples. Most laboratories choose the approach of running two-dimensional (2-D) gels, analyzing them and identifying the differentially expressed proteins by in-gel digestion and mass spectrometry. To date, the available stains for visualizing proteins on 2-D gels have been less than ideal for these projects because of poor detection sensitivity (Coomassie blue stain) or poor peptide recovery from in-gel digests and mass spectrometry (silver stain), unless extra destaining and washing steps are included in the protocol. In addition, the limited dynamic range of these stains has made it difficult to rigorously and reliably determine subtle differences in protein quantities. SYPRO Ruby Protein Gel Stain is a novel, ruthenium-based fluorescent dye for the detection of proteins in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels that has properties making it well suited to high-throughput proteomics projects. The advantages of SYPRO Ruby Protein Gel Stain relative to silver stain demonstrated in this study include a broad linear dynamic range and enhanced recovery of peptides from in-gel digests for matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry.

Acrylic Resins↗
PubMed1990

Anomalously slow electrophoretic mobilities of DNA restriction fragments in polyacrylamide gels are not eliminated by increasing the gel pore size.

The effect of gel pore size on the anomalous mobility of certain curved DNA restriction fragments in polyacrylamide gels was studied by comparing the electrophoretic mobilities of normal and anomalous fragments in gels of varying composition but constant acrylamide concentration. Molecular weight ladders were prepared from two 147 base pair G-C rich restriction fragments, called 12A (anomalous) and 12B (normal), obtained from the MspI digestion of plasmid pBR322. The electrophoretic mobilities of multimers of the two fragments increasingly diverged with increasing molecular weight. The anomalous mobility of fragment 12A was essentially independent of gel pore size, regardless of whether the pore size was varied by increasing the acrylamide concentration at constant cross-linker concentration or by increasing the cross-linker concentration at constant acrylamide concentration. The anomalous mobility of higher multimers of fragment 12A decreased with increasing gel pore size when the pore size was varied by changing the gel concentration. However, when the gel pore size was changed by varying the cross-linker concentration at constant acrylamide concentration, the anomalous mobility of higher multimers of fragment 12A went through a maximum and then decreased as the pore size was increased. Copolymerizing acrylamide with high molecular weight linear polyacrylamides had no effect on the anomalous mobility of the 12A multimer ladder, even though the apparent absolute mobilities of all fragments increased markedly. Only by incorporating charged residues into the gel matrix or by copolymerizing acrylamide with the intercalator ethidium bromide could the difference in mobility between the 12A and 12B multimer ladders be substantially reduced or eliminated. Similar results were observed with a molecular weight ladder containing 78 base pair repeats of the bending locus of kinetoplast DNA. These results suggest that pore size alone is not responsible for the anomalously slow migration of curved DNA molecules in polyacrylamide gels.

Base Sequence↗
PubMed1991

Analysis of one-dimensional gels and two-dimensional Serwer-type gels on the basis of the extended Ogston model using personal computers.

This report presents the stand-alone computer application ELPHOFIT, a software package for the analysis of gel electrophoretic data based on Ferguson plots. Either conventional one-dimensional gels or two-dimensional agarose gels (Serwer-type) can be evaluated. Special emphasis is on the latter gel type, which has been applied previously for the separation of DNA, intact viruses and polydisperse meningitis vaccines. ELPHOFIT is designed for Macintosh PCs and for the IBM XT, AT, PS/2 and compatibles. The program operates interactively with the user, who determines the course of evaluation. Data input is in the format of files providing values of gel electrophoretic migration distances or particle mobility (absolute or relative). Data processing involves a simultaneous least-square curve fitting algorithm (Newton-Gauss, Marquardt-Levenberg) which uses equations derived from the extended Ogston model. Functions are fit to the database by adjusting their variables, representing physical parameters of the gel and the electrophoresed particle. The program output consists of tables and graphics accompanied by an explanatory text providing the following information: (i) radius and free mobility of the electrophoresed particle, (ii) fiber radius, length and volume, mean or median pore radius of the gel, (iii) linear Ferguson plots, (iv) iso-free-mobility/iso-size nomogram for two-dimensional gels, (v) confidence ellipses, (vi) required parameters for image processing program GELFIT and (vii) goodness-of-fit and other statistical parameters, such as standard errors, dependency values, root-mean-square (RMS) error and determination coefficient. Other features of the program are (i) simulation of Serwer-type two-dimensional electrophoresis, (ii) standardization according to size, or size and free mobility, (iii) the conversion of particle radii to molecular (or particle) weight and vice versa, (iv) interconversion of DNA size specifications, i.e. the number of base pairs and the geometric mean radii, (v) computation of gel concentration for optimal resolution of two components, (vi) option to obtain a session record, (viii) option to establish a data output file containing the information of generated graphics (IBM only) and (ix) a text editing facility, e.g., for creating data files. Graphics (Macintosh version, PICT format) and text output files (both IBM and Macintosh versions, standard ASCII format) generated by ELPHOFIT are compatible with commercially available software.

Computers↗
PubMed2003

Spot volume vs. amount of protein loaded onto a gel: a detailed, statistical comparison of two gel electrophoresis systems.

The long-term goal of this research program is to clarify the molecular mechanisms that participate in the formation of human pituitary macroadenomas. One approach to that goal is to characterize the differentially expressed proteins that are found by a comparison of the proteomes of control pituitary vs. macroadenoma tissues. In order to accurately perform a comparative proteomics study, based on the combination of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and PDQuest 2-D analysis software, a reproducible 2-DE separation system with a wide linear dynamic measure range is needed. A typical horizontal system is the Multiphor II system that analyzes one gel at a time, using a precast gradient gel (180 x 245 x 0.5 mm); a typical vertical system is the Dodeca system that analyzes up to 12 gels at a time on a single-concentration gel (190 x 205 x 1.0 mm). We have evaluated (Zhan and Desiderio, Electrophoresis 2003, 24, 1834-1846) the spatial and quantitative reproducibility of the two second-dimensional gel systems to separate a human pituitary proteome; that study showed a higher reproducibility for the Dodeca gel system. This present study investigated the relationship between the spot volume and the amount of protein loaded onto the gel for those two 2-D systems. The results demonstrated that the Dodeca gel system provides a wider linear dynamic range to measure the changes in the protein abundance in pituitary proteome.

Electronic Data Processing↗
PubMed1996

A comparison of the efficacy and safety of adapalene gel 0.1% and tretinoin gel 0.025% in the treatment of acne vulgaris: a multicenter trial.

BACKGROUND: Adapalene is a new synthetic retinoid analogue developed for the topical treatment of acne vulgaris. OBJECTIVE: The study was designed to compare the efficacy and safety and adapalene gel 0.1% with tretinoin gel 0.025% in the treatment of grade II to II facial acne vulgaris. METHODS: Three hundred twenty-three patients were enrolled in this investigator-masked, randomized, parallel group, multicenter trial. Patients applied the test materials to the entire facial area daily, for a period of 12 weeks. Efficacy and cutaneous tolerance were assessed at baseline and weeks 2,4,8, and 12. Efficacy was determined by investigator counts of noninflammatory open and closed comedones, and inflammatory papules and pustules, as well as global improvement. Cutaneous tolerance was evaluated by erythema, scaling, and dryness, along with burning and pruritus. RESULTS: Staring at weeks 2 and 4, adapalene gel produced numerically greater lesion reductions than did tretinoin gel for all lesion types. At week 12, the mean percent reduction in the different lesion counts was as follow: 49% versus 37% for total lesions (p<0.01); 46% versus 33% for noninflammatory lesions (p=0.02); 48% versus 38% for inflammatory lesions (p=0.06) in adapalene and tretinoin gel treatment groups, respectively. Cutaneous side effects were limited to a mild "retinoid dermatitis" occurring in both treatment groups; however, patients treated with adapalene gel tolerated this therapy significantly better than those treated with tretinoin gel. Laboratory test evaluations (hematology, blood chemistries, urinalysis) were performed in 54 patients before and after 3 months of treatment. No clinically significant changes were observed. CONCLUSION: Adapalene gel 0.1% applied once daily was significantly more effective in reducing acne lesions and was better tolerated than tretinoin gel 0.025% in the treatment of acne vulgaris.

Acne Vulgaris↗
PubMed1999

Comparison of a silicone gel-filled cushion and silicon gel sheeting for the treatment of hypertrophic or keloid scars.

BACKGROUND: The exact mechanisms of action responsible for the effectiveness of silicone gel dressings are unknown, although it has been proposed that static electricity generated by friction could be the reason for their anti-scarring effects. OBJECTIVE: We compared the efficacy of a cushion of silicone filled with liquid silicone gel reported to induce greater negative static-electric charge with silicone gel sheeting in the treatment of hypertrophic and keloid scars. METHODS: The size, volume, symptoms (tenderness and itching), and signs (color and induration) of hypertrophic (10 patients) or keloid scars (22 patients) were measured at baseline at 16 weeks following use of either the silicone gel cushion or silicone gel sheeting, as determined by random assignment. RESULTS: Both the silicone gel cushion and the silicone gel sheeting treatments were effective in decreasing scar volume, 53.0% and 36.3%, respectively. The percentages of keloids and hypertrophic scars benefiting from the silicone cushion and the silicone sheeting were similar with respect to reduction in tenderness (36.3% vs 33.3%), itching (45.5% vs 33.3%), and redness (0.1% vs 0.1%), and in the degree of softening (45.5 vs 25.0%). CONCLUSIONS: Both the silicone gel cushion and the silicone gel sheeting treatments were effective in the treatment of keloids and hypertrophic scars, although no statistically significant differences were found between the two treatment modalities.

Adult↗
PubMed1990

A comparative study of naproxen gel and flufenamic acid gel in the treatment of soft tissue injuries.

One hundred patients were enrolled in a single-blind, randomized, parallel group study to compare naproxen gel (10%) with flufenamic acid gel (3%) for the treatment of soft tissue injuries. Demographic variables, the distribution of diagnoses (tendinitis, bursitis/synovitis, synovitis, periarthritis, epicondylitis) and initial severity of the complaint were similar between the two groups. The gels were applied 2 to 6 times per day, as required, and conventional clinical indices were evaluated at Day 1 (on entry to the study), Day 3 and Day 7. Global assessments of efficacy were made by both physicians and patients at the end of the study. By Day 7 both treatments had produced a highly significant improvement in symptoms (p less than 0.001). The patients using naproxen gel, however, improved more rapidly. At Day 3 the number of patients rating 'swelling', 'tenderness to firm palpation' or 'limitation of use' as 'severe' or 'moderate' was significantly less (p less than 0.05) than for patients using flufenamic acid gel. At the end of the study the physician's global efficacy rating showed no significant differences between the two gels; patients, in contrast, showed a significant preference for naproxen gel (p less than 0.05). Both gels were well tolerated. The more rapid onset of effect and patient preference for naproxen gel may be important factors in the choice of medication.

Adolescent↗
PubMed2004

Patient evaluation of a novel non-injectable anesthetic gel: a multicenter crossover study comparing the gel to infiltration anesthesia during scaling and root planing.

BACKGROUND: Periodontal scaling procedures commonly require some kind of anesthesia. From the patient's perspective, the choice of anesthetic method is a trade-off between the degree of anesthesia and accepting the side effects. The present study evaluates the preferences for a novel non-injection anesthetic product (a gel, containing lidocaine 25 mg/g plus prilocaine 25 mg/g and thermosetting agents) versus injection anesthesia (lidocaine 2% adrenaline) in conjunction with scaling and/or root planing (SRP). METHODS: In a multicenter, crossover, randomized, open study patients were asked, after they had experienced both products, if they preferred anesthetic gel or injection anesthesia. In addition, the adequacy of anesthesia and occurrence of post-procedure problems were assessed. The patients were also asked about their willingness to return if they were offered anesthetic gel at their next visit and their maximum willingness to pay (WTP) for this option. RESULTS: One-hundred seventy (170) patients at eight centers in Belgium were included in the study. There were 157 per protocol (PP) patients. A vast majority of the PP patients (70%) preferred the anesthetic gel to injection anesthesia (22%). The most common reason was less post-procedure numbness. Eighty percent (80%) of the patients expressed satisfactory anesthesia with the gel and 96% with injection anesthesia (P <0.001). Post-procedure problems were significantly less with the gel than with injection (P <0.001): numbness 15% versus 66%, unpleasant sensations such as soreness and pain 44% versus 63%, and problems connected with daily activities 19% versus 69%. The majority of patients (60%) who preferred gel were also willing to pay for it. A conservative estimate of the median WTP was $10.00. Furthermore, anesthetic gel would make almost every second patient (45%) more or much more willing to return for the next treatment. CONCLUSIONS: The data suggest that a somewhat less profound anesthesia with gel is clearly preferred by the patients because of the low incidence of post-procedure problems as compared to conventional injection anesthesia. The median WTP is likely in excess of the acquisition cost of the product, which indicates a favorable cost-benefit ratio for the individual patient.

Administration, Topical↗
PubMed1998

Efficacy of the fixed 1.2% clindamycin phosphate, 0.025% tretinoin gel formulation (Velac) and a proprietary 0.025% tretinoin gel formulation (Aberela) in the topical control of facial acne.

BACKGROUND: A formulation containing agents affecting the non-inflammatory as well as the inflammatory lesions of acne vulgaris at the same time would be efficient, probably showing a high efficacy and possibly a considerable shortening of the duration of treatment. One single formulation would simplify drug administration thereby enhancing patient compliance and possibly leading to improved therapeutic results. In two studies this seems to have been corroborated for the fixed clindamycin phosphate-tretinoin gel formulation. OBJECTIVE: This study was designed to assess whether the recently developed fixed formulation of 1.2% clindamycin phosphate and 0.025% tretinoin in a gel base (Velac), further referred to as Clindamycin phosphate Tretinoin Gel is at least as effective as a proprietary 0.025% tretinoin gel formulation (Aberela, Janssen Cilag Ab, Sollentuna, Sweden; further defined as tretinoin) showing an additional anti-inflammatory effect in the treatment of moderate to severe acne vulgaris. METHODS: In a double-blind, randomised study 72 patients were treated with CTG and 73 with tretinoin gel in a once daily regimen for 12 weeks. Responses, irritation as well as possible systemic and other adverse effects were recorded after 4, 8 and 12 weeks of treatment and the improvement, compared to baseline, assessed in all included patients. An additional assessment of the safety parameters was carried out at week 2. Parameters of efficacy were the various acne lesion counts, the overall acne severity grade and the calculated totals of acne lesion counts. RESULTS: CTG was statistically significantly more effective than tretinoin at the P = 0.05 level in the papular and the total mean inflammatory lesion counts as well as in the estimated or calculated mean overall acne severity scores. CTG and tretinoin gel were equally effective in the remaining parameters: open and closed comedones, the calculated total mean comedone, the pustule as well as the nodule lesion counts. The onset of action was faster for CTG than for tretinoin gel and evident in all assessed parameters except in open comedone lesion counts. In the calculated total mean acne lesion counts, half of all acne lesions had disappeared by week 6 of treatment with CTG, whereas this was recorded at week 9 for tretinoin gel. No clinically relevant changes in the parameters of safety as a consequence of treatment were observed, although the burning component of irritation was shown to be significantly less for CTG than for tretinoin gel. The observed adverse effects were considered minor. Treatment had to be discontinued in five patients on CTG and three on tretinoin. CONCLUSION: The addition of clindamycin to tretinoin, as in CTG, enhances the comedolytic efficacy of tretinoin in moderate to severe acne of the face, maintaining at the same time its anti-inflammatory efficacy thus accelerating resolution of all types of acne lesions without affecting the safety of response to both components.

Acne Vulgaris↗
PubMed1994

Electrophoresis for genotyping: microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose.

Electrophoresis of DNA has been performed traditionally in either an agarose or acrylamide gel matrix. Considerable effort has been directed to improved quality agaroses capable of high resolution, but for small fragments, such as those from polymerase chain reaction (PCR) and post-PCR digests, acrylamide still offers the highest resolution. Although agarose gels can easily be prepared in an open-faced format to gain the conveniences of horizontal electrophoresis, acrylamide does not polymerize in the presence of air and the usual configurations for gel preparation lead to electrophoresis in the vertical dimension. We describe here a very simple device and method to prepare and manipulate horizontal polyacrylamide gels (H-PAGE). In addition, the open-faced horizontal arrangement enables loading of arrays of wells. Since many procedures are undertaken in standard 96-well microtiter plates, we have also designed a device which preserves the exact configuration of the 8 x 12 array and enables electrophoresis in tracks following a 71.6 degrees diagonal between wells (MADGE, microtiter array diagonal gel electrophoresis), using either acrylamide or agarose. This eliminates almost all of the staff time taken in setup, loading, and recordkeeping and offers high resolution for genotyping pattern recognition. The nature and size of the gels allow direct stacking of gels in one tank, so that a tank used typically to analyze 30-60 samples can readily be used to analyze 1000-2000 samples. The gels would also enable robotic loading. Electrophoresis allows analysis of size and charge, parameters inaccessible to liquid-phase methods: thus, genotyping size patterns, variable length repeats, and haplotypes is possible, as well as adaptability to typing of point variations using protocols which create a difference detectable by electrophoresis.

DNA↗
PubMed2001

Randomized controlled trial of the tolerability, safety, and efficacy of adapalene gel 0.1% and tretinoin microsphere gel 0.1% for the treatment of acne vulgaris.

A prior meta-analysis of 5 randomized controlled trials indicates that adapalene gel 0.1% is as effective as tretinoin gel 0.025% against acne and has greater tolerability. To determine the tolerability and efficacy of adapalene gel 0.1% versus tretinoin microsphere gel 0.1% in 168 patients with acne vulgaris, we conducted a 12-week, multicenter, randomized, controlled, investigator-masked, parallel-group design study. Efficacy variables included noninflammatory, inflammatory, and total lesion counts; global grade; and global assessment of improvement in acne severity. Skin tolerability variables included erythema, desquamation (scaling), dryness, pruritus, and stinging/burning. Our results showed that the efficacy of adapalene gel 0.1% was comparable to that of tretinoin microsphere gel, and both treatments had similar onset of action. Cutaneous tolerability was noted in both groups, with scores significantly better with adapalene gel 0.1% than with tretinoin microsphere gel 0.1%, and significantly fewer treatment-related adverse events were reported with adapalene gel 0.1%.

Acne Vulgaris↗
PubMed2000

Preparative two-dimensional gel electrophoresis with agarose gels in the first dimension for high molecular mass proteins.

A two-dimensional gel electrophoresis (2-DE) method that uses an agarose isoelectric focusing (IEF) gel in the first dimension (agarose 2-DE) was compared with an immobilized pH gradient 2-DE method (IPG-Dalt). The former method was shown to produce significant improvements in the 2-D electrophoretic separation of high molecular mass proteins larger than 150 kDa, up to 500 kDa, and to have a higher loading capacity, as much as 1.5 mg proteins in total for micropreparative runs. The extraction medium found best in this study for agarose 2-DE of mammal tissues was 6 M urea, 1 M thiourea, 0.5% 2-mercaptoethanol, protease inhibitor cocktail (Complete Mini EDTA-free), 1% Triton X-100 and 3% 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS). Trichloroacetic acid (TCA) treatment of the agarose gel after IEF is to be carefully weighed beforehand, because some high molecular mass proteins were less likely to enter the second-dimensional polyacrylamide gel after TCA fixation, and proteins such as mouse skeletal muscle actin gave pseudospots in the agarose 2-DE patterns without TCA fixation. As a good compromise we suggest fixation of proteins in the agarose gel with TCA for one hour or less. The first-dimensional agarose IEF gel containing Pharmalyte as a carrier ampholyte was 180 mm in length and 2.5-4.8 mm in diameter. The gel diameter was shown to determine the loading capacity of the agarose 2-DE, and 1.5 mg liver proteins in total were successfully separated by the use of a 4.8 mm diameter agarose gel.

Animals↗