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Gels

Gels are semi-solid, gelatinous substances that can be used in a variety of applications, such as in cosmetics, pharmaceuticals, and biotechnology.
They are typically composed of cross-linked polymers that trap liquid within their three-dimensional network, resulting in a substance that is more viscous than a liquid but less rigid than a solid.
Gels can be classified based on their composition, such as hydorgels, organogels, and aerogels.
Researchers can use PubCompare.ai to locate the best gel protocols from literature, preprints, and patents, enhancing their research accuracy and reproducibility.
This AI-powered platform can help optimize experiments and unlock new insigths related to gels and their applications.

Most cited protocols related to «Gels»

(See Supplementary Protocol 1 for detailed Standard Operating Procedures for ENCODE-style eCLIP experiments, including oligonucleotide sequences, catalog numbers for all reagents, and specific details for eCLIP experiments). RNA binding protein (RBP)-RNA interactions were stabilized with UV crosslinking (254 nm, 400 mJ/cm2), followed by lysis in iCLIP lysis buffer, limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific primary antibody of interest using magnetic beads with pre-coupled secondary antibody (typically M-280 Sheep Anti-Rabbit IgG Dynabeads, ThermoFisher Scientific 11204D), and stringent washes. After dephosphorylation with FastAP (ThermoFisher) and T4 PNK (NEB), a barcoded RNA adapter was ligated to the 3′ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2a). Ligations were performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples were then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size was isolated and proteinase K (NEB) treated to isolate RNA. RNA was reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5′ end) was then ligated to the cDNA fragment 3′ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample was first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder was PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis. Samples were sequenced on the Illumina HiSeq 2500 or 4000 platform as two Paired End 50bp (for N5) or 55bp (for N10) reads. All analyses were performed using identical antibody lots for RBFOX2 (A300-864A lot 002, Bethyl), SLBP (RN045P lot 001, MBL International), and IgG Isotype Control (02-6102 lot 32013, Thermo Fisher Scientific). SLBP experiments were performed with 20×106 cells and 10 ug of primary antibody; RBFOX2 experiments were performed with 20×106 cells and 10 ug (eCLIP Rep1 and Rep2) or 10×106 cells and 5 ug (RNase I variation experiments). All experiments in K562 and HepG2 cells were performed with 20×106 cells and 10 ug of indicated primary antibody (Supplementary Table 2). Antibody validation documentation (including Western images of immunoprecipitation and shRNA knockdown19 (link)) are available at http://www.encodeproject.org/. Additional experiments performed in K562 and HepG2 cells in which the antibody failed to successfully immunoprecipitate the targeted RBP were excluded from analysis. 293T cells were obtained from Clontech (Lenti-X 293T cell line). K562 and HepG2 cells were purchased from ATCC, and were not independently verified. Cells were routinely tested for mycoplasma using MycoAlert PLUS (Lonza).
Publication 2016
anti-IgG Buffers Cell Lines Cells Digestion DNA, Complementary Domestic Sheep Electrophoresis, Agar Gel Endopeptidase K Gels HEK293 Cells Hep G2 Cells Immunoglobulin Isotypes Immunoglobulins Immunoprecipitation Ligation M 280 Mycoplasma Nitrocellulose Oligonucleotides polyethylene glycol 8000 Proteins Psychological Inhibition Rabbits Ribonuclease, Pancreatic RNA-Binding Proteins RNA Ligase (ATP) Short Hairpin RNA Silanes Sulfoxide, Dimethyl Tissue, Membrane
Genomic DNA was extracted with various standard procedures, and specimens were identified to species and molecular forms by PCR-RFLP [38 (link),39 (link)]. SINE200 elements were located in silico by BLASTN searches on the genome sequence of the A. gambiae PEST genome using the obtained SINE200 consensus sequence as a query. Thirteen SINE200 insertions lying within the A. gambiae molecular form speciation islands (sensu Turner [11 (link)]) on X, 2L and 2R chromosomes, and characterized by the presence of 500 bp flanking regions showing a single hit in the genome, were selected. Primers were designed to amplify across the element using Primer 3 software [40 (link)]. The selected loci were named 'S200' followed by the abbreviation of the chromosomal arm (2L, 2R, X), by a number/letter corresponding to the chromosomal location on the cytogenetic map [4 (link)] and by an additional number aimed to distinguish primer sets positioned on the same chromosome division. Genes annotated within a 20 Kb genome sequence including SINE200 insertions for each locus were retrieved from the PEST genome ver. Agam P3 Feb. 2006 (Table 2).
PCR reactions were carried out in a 25 μl reaction which contained 1 pmol of each primer, 0.2 mM of each dNTP, 1.5 mM MgCl2, 2.5 U Taq polymerase, and 0.5 μl of template DNA extracted from a single mosquito. Thermocycler conditions were 94°C for 10 min followed by thirty-five cycles of 94°C for 30 s, 54°C for 30 s and 72°C for 1 min., with a final elongation at 72°C for 10 min, and a 4°C hold. The resulting products were analysed on 1.5% agarose gels stained with ethidium bromide, with low and high molecular weight bands corresponding to fragments containing or lacking the targeted SINE200, respectively.
PCR products representing 'filled' and 'empty' sites of S200 X6.1 locus on X chromosome were sequenced on both strands using ABI Big Dye Terminator v.2 chemistry and an ABI Prism 3700 DNA Analyser. Multiple alignments were performed using ClustalX [37 (link)]. All sequences were deposited in GenBank under accession numbers EU881868EU881887.
Indices of polymorphism (i.e. SINE200 insertion frequency and heterozygosity) and differentiation (Fst) at polymorphic loci were computed using Fstat 2.9.3.2 [41 ]. Significance was tested with Bonferroni-adjusted P-values, using the randomization approach implemented in Fstat.
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Publication 2008
2-(2-(2-chloro-3-(2-(3,3-dimethyl-5-sulfo-1-(4-sulfo-butyl)-3H-indol-2-yl)-vinyl)-cyclohex-2-enylidene)-ethylidene)-3,3-dimethyl-1-(4-sulfo-butyl)-2,3-dihydro-1H-indole-5-carboxylic acid Chromosomes Chromosome Segregation Consensus Sequence Culicidae Ethidium Bromide Gels Genes Genetic Polymorphism Genome Heterozygote Magnesium Chloride Neutrophil Oligonucleotide Primers Plague prisma Restriction Fragment Length Polymorphism Sepharose Taq Polymerase X Chromosome
Each sample was prepared by combining 20 nM scaffold (p7560 or p8064, derived from M13mp18), 100 nM of each staple oligonucleotide, buffer and salts including 5 mM Tris, 1 mM EDTA (pH 7.9 at 20°C), and 22 mM MgCl2, except for the 30-helix-per-x-raster block, which was folded with 15 mM MgCl2. Folding was carried out by rapid heat denaturation followed by slow cooling from 80 to 61°C over 80 min, then 60 to 24°C over 173 h. Samples were electrophoresed on 2% agarose gels (0.5× TBE, 11 mM MgCl2, 0.5 μg/ml ethidium bromide) at 70 V for 4 h in an ice-water bath. Leading monomer bands were visualized with ultraviolet light, physically excised, crushed with a pestle (17 (link)) and filtered through a cellulose-acetate spin column for 3 min at 15 000 × g, 4°C.
Publication 2009
acetylcellulose Bath Buffers Edetic Acid Ethidium Bromide Gels Helix (Snails) Magnesium Chloride Oligonucleotides Salts Sepharose Staple, Surgical Strains Tromethamine Ultraviolet Rays
For miRNA sequencing, 5 µg of total RNA form each sample was ligated with both a 5′ adapter and 3′ adapter for reverse transcription using Superscript II at 42°C for 1 h and 70°C for 15 min. Subsequently, the reverse transcribed products were amplified using the following PCR program: a 15-cycle reaction at 98°C for 30 sec, followed by 15 cycles of 98°C for 10 sec, 72°C for 15 sec, and then 72°C for 10 min. After obtaining a ∼92-bp DNA band on 6% PAGE gels, the PCR products were ethanol precipitated and purified using Spin-X filter columns. Finally, miRNA libraries were sequenced on the Illumina Cluster Station and Genome Analyzer II following the manufacturer's protocol.
Low quality reads were trimmed and adapter sequences were accurately clipped with the aid of a dynamic programming algorithm before subsequent statistical analysis. After elimination of the duplicate reads, the remaining reads of at least 18 nt were mapped to a human reference genome (hg19) using SOAP V2.0. To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, we also mapped the short read tags to UCSC RefGene, RepeatMasker and NCBI Refseq, as well as our in-house ncRNA annotation datasets compiled from the NCBI GenBank database (http://www.ncbi.nih.gov). The same pipeline used for DGE mRNA differential expression analysis was also used for miRNA expression analysis.
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Publication 2010
DNA, A-Form Ethanol Gels Gene Products, Protein Genome Genome, Human Homo sapiens MicroRNAs Repetitive Region Reverse Transcription Ribosomal RNA RNA, Messenger RNA, Untranslated Small Nuclear RNA Small Nucleolar RNA Transfer RNA
Total RNAs were extracted using standard hot phenol RNA preparation method (51 (link)). For RT-PCR analysis, 1.5 µg of total RNAs were subjected to reverse transcription (RT) using gene-specific primers, and then the resulting cDNAs were analysed by standard PCR method or qPCR. Primers used are listed in Supplementary Table S3. The half-life of pre-mRNAs was determined as described previously (52 (link),53 (link)). For northern blotting, the procedures were as previously described (50 (link)) except that total RNAs (10 µg) were separated by 6% acrylamide gels. Sequences of oligonucleotide probes are listed in Supplementary Table S3. Band intensities were quantified using ImageJ densitometry software.
Publication 2013
Acrylamide Densitometry DNA, Complementary Gels Genes mRNA Precursor Oligonucleotide Primers Oligonucleotide Probes Phenol Reverse Transcription RNA Standard Preparations

Most recents protocols related to «Gels»

Example 2

PAO1, the parent strain of PGN5, is a wild-type P. aeruginosa strain that produces relatively small amounts of alginate and exhibits a non-mucoid phenotype; thus, PGN5 is also non-mucoid when cultured (FIG. 3A). In PAO1, the alginate biosynthetic operon, which contains genes required for alginate production, is negatively regulated. Activation of this operon leads to alginate production and a mucoid phenotype. For example, over-expression of mucE, an activator of the alginate biosynthetic pathway, induces a strong mucoid phenotype in the PAO1 strain (e.g., P. aeruginosa strain VE2; FIG. 3B). The plasmid pUCP20-pGm-mucE, which constitutively over-expresses MucE, was used to test whether the genetically-modified PGN5 strain could produce alginate. Indeed, the presence of this plasmid in PGN5 (PGN5+mucE) induced a mucoid phenotype (FIG. 3B). To measure the amount of alginate produced by PGN5+mucE on a cellular level, a standard carbazole assay was performed, which showed that the PGN5+mucE and VE2 (i.e., PAO1+mucE) strains produce comparable amounts of alginate (FIG. 3C; 80-120 g/L wet weight).

To examine whether the alginate produced by PGN5+mucE was similar in composition to alginate produced by VE2, HPLC was performed to compare the M and G content of alginate produced by each strain. The chromatograms obtained from alginate prepared from VE2 and PGN5+mucE were identical (FIG. 3D), and the M:G ratios were comparable to a commercial alginate control (data not shown). To confirm that the physical properties of VE2 and PGN5+mucE alginates were also similar, alginate gels were prepared from alginate produced by each strain and the viscosity and yield stress was measured. The viscosities of VE2 and PGN5+mucE alginate gels were comparable at 73.58 and 72.12 mPa, respectively (FIG. 3E). Similarly, the yield stress of VE2 and PGN5+mucE alginate gels were comparable at 47.34 and 47.16 Pa, respectively (FIG. 3G).

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Patent 2024
Alginate Alginates Anabolism Biological Assay Biosynthetic Pathways carbazole Cells Gels Genes High-Performance Liquid Chromatographies Operon Parent Phenotype Physical Processes Plasmids Pseudomonas aeruginosa Strains Viscosity
Not available on PMC !

Example 10

Steps:
Green Tea PrepHeat 250 mL water to boil
Steep tea bag 2-3 minutes
with occasional stir
remove tea bag and let cool
Gel SolutionUse TFF-10-0047 (3.71% silk)
Prepdilute to 3% silk with water
dilute to 2% with green tea
add L-ascorbic acid
GelGelation occurred like standard
gel at room temperature
Green/yellow color
Green Tea scent
Solution Spec:2% silk solution
65 mL (35 ml of 3.71% silk, 8.3
mL water, 21.66 mL green tea)
0.43 gL-ascorbic acid

FIG. 92 is a table summarizing an embodiment of a caffeine gel of the present disclosure. A silk gel with 2% silk and 100 mg L-ascorbic acid/15 mL solution was created with the addition of 50 mg caffeine/15 mL solution. The gel has the exact appearance of standard L-ascorbic acid gels.

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Patent 2024
Ascorbic Acid Caffeine Fast Green FCF Furuncles Gels Green Tea Pheromone Silk STEEP1 protein, human Technique, Dilution

Example 14

[Figure (not displayed)]

Polymer 13 (0.250 g, 1.396 mmol) was placed in a RB flask under a nitrogen atmosphere. Compound 14-a (90 mg, 0.679 mmol) was dissolved in dry DMF (5 mL) under nitrogen atmosphere and added to polymer 13 with stirring. The reaction mixture was stirred for 90 min at RT under a nitrogen atmosphere before being filtered and washed with DMF (5×5 mL) and methanol (5×5 mL). The product was concentrated in vacuo to yield polymer 14 as off-white powdery solid. Weight=0.1852 g (52% yield). A Kaiser test was used to confirm presence of terminal amines (a reading at 570 nm equating to 1.86 nmol amine). FTIR: 3251 (N—H/O—H), 2915/2874 (C—H), 1649 (C═O, amide of coupled product), 1583 (C═O of CMC), 1405/1316/1262/1020. Elemental analysis: Expected of product if DoS of raw material were 0.7: Mass 519 g mol−1: C 48%, H 5.8%, N 5.6%. Actual: C 42.8%, H 6.95%, N 4.25%. Therefore of all monomers, approximately 53% contain the linker group.

Solubility of Polymer 14 was determined in a similar manner as for compound 1-c. Data is shown below: x indicates insoluble material.

AfterAfter
SolventInitialheatingsonicationOvernight
pH 9 bufferxNot testedNot testedSlight swelling/gelling
over time; particles
well dispersed

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Patent 2024
Amides Amines Atmosphere Buffers Gels Methanol Nitrogen Polymers Powder Solvents Spectroscopy, Fourier Transform Infrared
Not available on PMC !

Example 10

Steps:

    • Green Tea Prep Heat 250 mL water to boil
      • Steep tea bag 2-3 minutes with occasional
      • stir
      • remove tea bag and let cool
    • Gel Solution
    • Prep Use TFF-10-0047 (3.71% silk)
      • dilute to 3% silk with water
      • dilute to 2% with green tea
      • add L-ascorbic acid
      • Gelation occurred like standard gel at room
    • Gel temperature
      • Green/yellow color
      • Green Tea scent
    • Solution Spec: 2% silk solution
      • 65 mL (35 ml of 3.71% silk, 8.3 mL water,
      • 21.66 mL green tea)
      • 0.43 g L-ascorbic acid

FIG. 92 is a table summarizing an embodiment of a caffeine gel of the present disclosure. A silk gel with 2% silk and 100 mg L-ascorbic acid/15 mL solution was created with the addition of 50 mg caffeine/15 mL solution. The gel has the exact appearance of standard L-ascorbic acid gels.

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Patent 2024
Ascorbic Acid Caffeine Fast Green FCF Furuncles Gels Green Tea Pheromone Silk STEEP1 protein, human Technique, Dilution
Not available on PMC !

Example 6

A gel mass can be prepared in order to encapsulate the pharmaceutical compositions of the various Examples herein.

Gel mass compositions were formulated and produced according to the following steps. Purified water (22.2 kg) and glycerin (10.8 kg) were charged into a stainless steel tank with mixing and heated to a temperature of 80±5° C. Hydrolyzed gelatin (1.8 kg) and gelatin 200 bloom limed bone, NF (24.0 kg) were then added to the water/glycerin mixture and were mixed until all solids were completely dissolved. This resulted in the formation of a gel mass. The resulting gel mass was de-gassed under vacuum. Coloring agents OPATINT® white (0.6 kg) and OPATINT® red (0.6 kg) were then added to the gel mass and the resultant was mixed for about 5 minutes. The resultant was then de-gassed under vacuum for a sufficient period of time and ultimately passed to an encapsulation device for preparation of gel capsules of the types disclosed herein.

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Patent 2024
Bones Capsule Coloring Agents Gelatins Gels Glycerin Medical Devices Pharmaceutical Preparations Progesterone Stainless Steel Vacuum

Top products related to «Gels»

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Protease inhibitor cocktail is a laboratory reagent used to inhibit the activity of proteases, which are enzymes that break down proteins. It is commonly used in protein extraction and purification procedures to prevent protein degradation.
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PVDF membranes are a type of laboratory equipment used for protein transfer and detection in Western blot analysis. They provide a stable and durable surface for the immobilization of proteins, enabling effective identification and quantification of target proteins in complex biological samples.
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Image Lab software is a data analysis tool designed for use with Bio-Rad's gel and blot imaging systems. The software provides a user-friendly interface for capturing, analyzing, and processing images of gels, blots, and other samples.
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The Pierce BCA Protein Assay Kit is a colorimetric-based method for the quantification of total protein in a sample. It utilizes the bicinchoninic acid (BCA) reaction, where proteins reduce Cu2+ to Cu+ in an alkaline environment, and the resulting purple-colored reaction is measured spectrophotometrically.
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The BCA Protein Assay Kit is a colorimetric detection and quantification method for total protein concentration. It utilizes bicinchoninic acid (BCA) for the colorimetric detection and quantification of total protein. The assay is based on the reduction of Cu2+ to Cu1+ by protein in an alkaline medium, with the chelation of BCA with the Cu1+ ion resulting in a purple-colored reaction product that exhibits a strong absorbance at 562 nm, which is proportional to the amount of protein present in the sample.

More about "Gels"

Gels are a versatile class of semi-solid, gelatinous substances used in a wide range of applications, from cosmetics and pharmaceuticals to biotechnology.
These materials are typically composed of cross-linked polymers that trap liquid within their three-dimensional network, resulting in a substance that is more viscous than a liquid but less rigid than a solid.
Gels can be classified based on their composition, such as hydrogels, organogels, and aerogels.
Researchers can utilize the power of AI-driven platforms like PubCompare.ai to locate the best gel protocols from the literature, preprints, and patents, enhancing their research accuracy and reproducibility.
This platform can help optimize experiments and unlock new insights related to gels and their applications.
In addition to gels, researchers may also encounter other important materials in their work, such as PVDF (polyvinylidene fluoride) membranes, which are commonly used for protein transfer and detection in Western blotting; TRIzol reagent, a popular solution for RNA extraction; nitrocellulose membranes, which are widely used for protein immobilization; and protease inhibitor cocktails, which help preserve protein integrity during sample preparation.
To analyze and visualize their experimental data, researchers may rely on software tools like Image Lab and the Odyssey Infrared Imaging System.
Additionally, the Pierce BCA Protein Assay Kit and the BCA protein assay kit are widely used for the quantification of protein concentrations.
By leveraging these resources and technologies, researchers can enhance their ability to work with gels and other important materials, ultimately driving advancements in their fields of study.