miRNA expression was measured as described previously [10 (link)]. Briefly, 20 ng of total RNA was reverse transcribed using the Megaplex RT stem-loop primer pool (Applied Biosystems, Foster City, CA, USA), enabling miRNA specific cDNA synthesis for 430 different human miRNAs and 18 small RNA controls. Subsequently, Megaplex RT product was pre-amplified by means of a 14-cycle PCR reaction with a miRNA specific forward primer and universal reverse primer to increase detection sensitivity. Finally, a 1,600-fold dilution of pre-amplified miRNA cDNA was used as input for a 40-cycle qPCR reaction with miRNA specific hydrolysis probes and primers (Applied Biosystems). All reactions were performed on the 7900 HT (Applied Biosystems) using the gene maximization strategy [41 (link)]. Raw Cq values were calculated using the SDS software version 2.1 applying automatic baseline settings and a threshold of 0.05. For further data analysis, only those miRNAs with a Cq value equal to or below 35 (representing single molecule template detection [10 (link)]) were taken into account. For NB tumor samples all 448 miRNAs and small RNA controls were profiled. RT-qPCR assays were spread across two 384-well plates. Inter-run variation was accounted for by equalizing the mean Cq-value of the 18 small RNA controls that were profiled in both plates. For the remaining samples 366 miRNAs and 18 small RNA controls were profiled in a single 384-well plate.
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Phenomena
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Natural Phenomenon or Process
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Hydrolysis
Hydrolysis
Hydrolysis is a chemical process in which a molecule is cleaved into two or more smaller molecules by the addition of water.
This process is fundamental to many biological and industrial applications, including the breakdown of complex carbohydrates, proteins, and other macromolecules.
Optimizing hydrolysis protocols through AI-driven platforms like PubCompare.ai can enhance reproducibility, accuracy, and exploration of kits for enhanced hydrlysis research.
By comparing hydrolysis methods across literature, preprints, and patents, researchers can identify the most effective approaches and improve the reliability of their findings.
This process is fundamental to many biological and industrial applications, including the breakdown of complex carbohydrates, proteins, and other macromolecules.
Optimizing hydrolysis protocols through AI-driven platforms like PubCompare.ai can enhance reproducibility, accuracy, and exploration of kits for enhanced hydrlysis research.
By comparing hydrolysis methods across literature, preprints, and patents, researchers can identify the most effective approaches and improve the reliability of their findings.
Most cited protocols related to «Hydrolysis»
Anabolism
Biological Assay
DNA, Complementary
Genes
Hydrolysis
Hypersensitivity
MicroRNAs
MIRN430 microRNA, human
Neoplasms
Oligonucleotide Primers
Stem, Plant
Technique, Dilution
Preparation of cDNA followed the procedure described in Mortazavi et al.2 (link), with minor modifications as described below. Prior to fragmentation, a 7 uL aliquot (∼ 500 pgs total mass) containing known concentrations of 7 “spiked in” control transcripts from A. thaliana and the lambda phage genome were added to a 100 ng aliquot of mRNA from each time point. This mixture was then fragmented to an average length of 200 nts by metal ion/heat catalyzed hydrolysis. The hydrolysis was performed in a 25 uL volume at 94°C for 90 seconds. The 5X hydrolyis buffer components are: 200 mM Tris acetate, pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate. After removal of hydrolysis ions by G50 Sephadex filtration (USA Scientific catalog # 1415-1602), the fragmented mRNA was random primed with hexamers and reverse-transcribed using the Super Script II cDNA synthesis kit (Invitrogen catalog # 11917010). After second strand synthesis, the cDNA went through end-repair and ligation reactions according to the Illumina ChIP-Seq genomic DNA preparation kit protocol (Illumina catalog # IP102-1001), using the paired end adapters and amplification primers (Illumina Catalog # PE102-1004). Ligation of the adapters adds 94 bases to the length of the cDNA molecules.
Acetate
Anabolism
Bacteriophage lambda
Buffers
Chromatin Immunoprecipitation Sequencing
DNA, Complementary
DNA Chips
Filtration
Genome
Hydrolysis
Ions
Ligation
magnesium acetate
Metals
Oligonucleotide Primers
Potassium Acetate
RNA, Messenger
sephadex
Tromethamine
Cells
Culture Media
Cycloheximide
Gene Expression
Genome
Granulocyte Colony-Stimulating Factor
HeLa Cells
Hematopoietic System
Hydrolysis
Males
Mice, Knockout
MicroRNAs
mRNA, Polyadenylated
RNA, Messenger
Stem Cell Factor
The use of a two-stage sulfuric acid hydrolysis for the analysis of lignin dates to the turn of the 20th century, although the use of concentrated acid to release sugars from wood dates to the early 19th century (7 ). Klason, in 1906, is often credited as the first to use sulfuric acid to isolate lignin from wood (7 −9 ). The method became named after Klason, and the insoluble residue from the test is known as “Klason lignin.” An English translation of a Klason paper, from this period (10 ), describes his attempt to determine the structure of spruce wood lignin. According to Brauns (7 ), Klason’s method originally used 72 wt % sulfuric acid; he later reduced this to 66 wt % to gelatinize the wood. He filtered the solids and subjected them to a second hydrolysis in 0.5 wt % hydrochloric acid.
Although Klason is generally credited as being the first to use sulfuric acid for lignin analysis, Sherrard and Harris (11 ) credit the use of sulfuric acid to Fleschsig in 1883, Ost and Wilkening in 1912, and König and Rump in 1913. According to Harris (12 ), Fleschsig, in 1883, dissolved cotton cellulose and converted it nearly quantitatively into sugars using strong sulfuric acid followed by dilution and heating. According to Browning (13 ), Ost and Wilkening introduced the use of 72 wt % sulfuric acid for lignin determinations in 1910. A translated paper by Heuser (14 ) credited König and Ost and Wilkening for the sulfuric acid lignin method. Dore (15 ) described several improved analytical methods (cellulose, lignin, soluble pentosans, mannan, and galactan) for the summative analysis of coniferous woods. The discrepancies in attribution may be due to differing definitions for the method cited (e.g., first to use acid to determine lignin, first to use sulfuric acid, first to use 72 wt % sulfuric acid, etc.) and to missed citations across continental distances in the early 20th century.
Although Klason is generally credited as being the first to use sulfuric acid for lignin analysis, Sherrard and Harris (11 ) credit the use of sulfuric acid to Fleschsig in 1883, Ost and Wilkening in 1912, and König and Rump in 1913. According to Harris (12 ), Fleschsig, in 1883, dissolved cotton cellulose and converted it nearly quantitatively into sugars using strong sulfuric acid followed by dilution and heating. According to Browning (13 ), Ost and Wilkening introduced the use of 72 wt % sulfuric acid for lignin determinations in 1910. A translated paper by Heuser (14 ) credited König and Ost and Wilkening for the sulfuric acid lignin method. Dore (15 ) described several improved analytical methods (cellulose, lignin, soluble pentosans, mannan, and galactan) for the summative analysis of coniferous woods. The discrepancies in attribution may be due to differing definitions for the method cited (e.g., first to use acid to determine lignin, first to use sulfuric acid, first to use 72 wt % sulfuric acid, etc.) and to missed citations across continental distances in the early 20th century.
Acids
Cellulose
Galactans
Gossypium
Hydrochloric acid
Hydrolysis
Lignin
Mannans
Pentosan Sulfuric Polyester
Picea
Sugars
sulfuric acid
Technique, Dilution
Tracheophyta
Xylose
For our analysis, we employed publicly available read data (Supplementary Methods ) from: Saccharomyces cerevisiae (9 (link)), Arabidopsis thaliana (28 (link)), Mus musculus (11 (link)), the same Homo sapiens sample sequenced with two different RNA-Seq protocols, i.e. flowcell RT-Seq (FRT) and standard hydrolysis (STD) protocol (17), and RNA control sequences spiked-in in high concentrations (29 (link)). In a first step, we mapped and split-mapped non-redundantly all the reads to the respective reference genome sequence using the GEM library (http://sourceforge.net/projects/gemlibrary ); in the case of the cress data set, which is comparatively small, we also considered additional read mappings with long indels obtained with BLAT (30 (link)).
Subsequently, we focused on the distribution of reads that map to transcripts without alternatively processed forms. To define such transcripts, we considered a standard reference annotation of the transcriptome, i.e. the SGD annotation for yeast (31 (link)), the TAIR annotation for cress (32 (link)) and the murine as well as the human RefSeq annotation (33 (link)). This procedure provided us with mappings for 6 606 768 reads (47%) from yeast, 351 336 reads (65%) from cress and for 21 359 481 reads (68%) from mouse, and with 530 996 reads that map in proper pairs to the spike-in control sequences. Due to substantially different data set sizes (90 million versus 13 million reads), in the case of the human FRT- and the STD-Seq experiments, we extracted subsets of reads of suitable size before mapping to ensure comparability (Supplementary Table S1 ).
Subsequently, we focused on the distribution of reads that map to transcripts without alternatively processed forms. To define such transcripts, we considered a standard reference annotation of the transcriptome, i.e. the SGD annotation for yeast (31 (link)), the TAIR annotation for cress (32 (link)) and the murine as well as the human RefSeq annotation (33 (link)). This procedure provided us with mappings for 6 606 768 reads (47%) from yeast, 351 336 reads (65%) from cress and for 21 359 481 reads (68%) from mouse, and with 530 996 reads that map in proper pairs to the spike-in control sequences. Due to substantially different data set sizes (90 million versus 13 million reads), in the case of the human FRT- and the STD-Seq experiments, we extracted subsets of reads of suitable size before mapping to ensure comparability (
Arabidopsis thalianas
Brassicaceae
DNA Library
Genome
Homo sapiens
Hydrolysis
INDEL Mutation
Mice, House
Mus
RNA-Seq
Saccharomyces cerevisiae
Transcriptome
Most recents protocols related to «Hydrolysis»
Example 8
Characterization of Absorption, Distribution, Metabolism, and Excretion of Oral [14C]Vorasidenib with Concomitant Intravenous Microdose Administration of [13C315N3]Vorasidenib in Humans
Metabolite profiling and identification of vorasidenib (AG-881) was performed in plasma, urine, and fecal samples collected from five healthy subjects after a single 50-mg (100 μCi) oral dose of [14C]AG-881 and concomitant intravenous microdose of [13C3 15N3]AG-881.
Plasma samples collected at selected time points from 0 through 336 hour postdose were pooled across subjects to generate 0—to 72 and 96-336-hour area under the concentration-time curve (AUC)-representative samples. Urine and feces samples were pooled by subject to generate individual urine and fecal pools. Plasma, urine, and feces samples were extracted, as appropriate, the extracts were profiled using high performance liquid chromatography (HPLC), and metabolites were identified by liquid chromatography-mass spectrometry (LC-MS and/or LC-MS/MS) analysis and by comparison of retention time with reference standards, when available.
Due to low radioactivity in samples, plasma metabolite profiling was performed by using accelerator mass spectrometry (AMS). In plasma, AG-881 was accounted for 66.24 and 29.47% of the total radioactivity in the pooled AUC0-72 h and AUC96-336 h plasma, respectively. The most abundant radioactive peak (P7; M458) represented 0.10 and 43.92% of total radioactivity for pooled AUC0-72 and AUC96-336 h plasma, respectively. All other radioactive peaks accounted for less than 6% of the total plasma radioactivity and were not identified.
The majority of the radioactivity recovered in feces was associated with unchanged AG-881 (55.5% of the dose), while no AG-881 was detected in urine. In comparison, metabolites in excreta accounted for approximately 18% of dose in feces and for approximately 4% of dose in urine. M515, M460-1, M499, M516/M460-2, and M472/M476 were the most abundant metabolites in feces, and each accounted for approximately 2 to 5% of the radioactive dose, while M266 was the most abundant metabolite identified in urine and accounted for a mean of 2.54% of the dose. The remaining radioactive components in urine and feces each accounted for <1% of the dose.
Overall, the data presented indicate [14C]AG-881 underwent moderate metabolism after a single oral dose of 50-mg (100 μCi) and was eliminated in humans via a combination of metabolism and excretion of unchanged parent. AG-881 metabolism involved the oxidation and conjugation with glutathione (GSH) by displacement of the chlorine at the chloropyridine moiety. Subsequent biotransformation of GSH intermediates resulted in elimination of both glutamic acid and glycine to form the cysteinyl conjugates (M515 and M499). The cysteinyl conjugates were further converted by a series of biotransformation reactions such as oxidation, S-dealkylation, S-methylation, S-oxidation, S-acetylation and N-dealkylation resulting in the formation multiple metabolites.
A summary of the metabolites observed is included in Table 2
Acetylation
AG 30
Biotransformation
Chlorine
Dealkylation
Deamination
Elements, Radioactive
Feces
Glutamic Acid
Glutathione
Glycine
Healthy Volunteers
High-Performance Liquid Chromatographies
Homo sapiens
Hydrolysis
Intravenous Infusion
Ions
Liquid Chromatography
Mass Spectrometry
Metabolism
Methylation
Parent
Plasma
Radioactivity
Retention (Psychology)
Tandem Mass Spectrometry
Urinalysis
Urine
vorasidenib
EXAMPLE 8
Rhizopus oryzae (RO) lipase was covalently bound to acrylic beads and contained in a device resembling a teabag. Enfalac infant formula (25 g) was combined with tap water (88 mL) at 37° C. Reactions were carried out in a glass bottle with 100 mL of infant formula and a tea bag containing either 100, 500, 1000, or 2000 mg of immobilized RO lipase. Each reaction was incubated at 37° C. for 30 minutes with inversion. Samples were taken at the following timepoints: 0, 1, 2, 3, 4, 5, 10, 20, and 30 minutes. Samples were analyzed for DHA and ARA by reverse phase high performance liquid chromatography (RP-HPLC).
At each concentration of immobilized RO lipase, the percent hydrolysis of DHA and ARA increased as the amount of immobilized RO lipase increased (FIGS. 27A-27D). These data demonstrate the feasibility of the tea bag device for pre-hydrolyzing formula with lipase.
Figs
High-Performance Liquid Chromatographies
Hydrolysis
Infant Formula
Inversion, Chromosome
Lipase
Medical Devices
Rhizopus oryzae
Example 4
Experiments were performed in 100 ml Kautex bottles. Model waste was mixed with water to a volume at 50 ml and at TS concentration of 7.5%. CBC and the selected blend (B.a protease:T.I pholip:A.a BG:CBC in ratio of 10:5:15:70) were added in amounts corresponding to 0%, 25%, 50%, 75%, 100% and 200% of the concentration that has been used as default during the previous experiments (2.4% enzymes protein/TS). Bottles were incubated on a Stuart Rotator SB3 and placed in a 50° C. oven for 24 hours.
A significant improvement in TS-solubilization was seen at all applied enzyme concentrations, when comparing the blend with CBC. The TS-solubilization at default settings (2.4% CBC/TS) was around 25%. This was obtained with only approximately 0.9% of the blend, which corresponds to a lowering in enzyme dosage of approximately 2.5 to 2.7 times (See
Cellulase
Enzymes
Fermentation
Glucose
Hydrolysis
Lactic Acid
Lipase
Peptide Hydrolases
Proteins
Xylose
EXAMPLE 9
Rhizopus oryzae (RO) lipase and Chromobacterium viscosum (CV) lipase were immobilized onto macroporous acrylic polymer beads (Immobeads™ ChiralVision). Approximately 200 mg of RO lipase were used per gram of beads. A sample of CV lipase-coated beads was irradiated (CVI) to determine the effect of irradiation on potency of immobilized lipase. Approximately 1.7 g of each bead preparation (RO, CV, and CVI) were packed into columns with bed volumes of approximately 5 mL. Infant formula containing DHA and ARA triglycerides was passed over the column at a flow rate of 75 mL/hr. The column eluate was analyzed for DHA and ARA hydrolysis by HPLC. The percent hydrolysis of DHA and ARA triglycerides by CV, CVI, and RO lipases is shown in Table 6.
Chromobacterium viscosum
High-Performance Liquid Chromatographies
Hydrolysis
Infant Formula
Lipase
lipase, Chromobacterium viscosum
Polymers
Radiotherapy
Rhizopus oryzae
Triglycerides
EXAMPLE 7
Efflux pumps draw energy from hydrolysis of ATP, ions, or protons. Therefore, disruption of these processes could lead to inhibition of efflux pumps. Ethidium bromide (EtBr), a fluorescent dye, is an efflux pumps' substrate and damages on the membrane directly or indirectly lead to the accumulation of EtBr. As shown in
Biological Assay
Cells
Ethidium
Ethidium Bromide
Fluorescence
Fluorescent Dyes
Hydrolysis
Ions
lead bromide
Physical Examination
Protons
Psychological Inhibition
Tissue, Membrane
Top products related to «Hydrolysis»
Whatman is a brand of laboratory filtration products and equipment manufactured by Cytiva. Whatman products are designed for a variety of laboratory applications, including sample preparation, purification, and analysis. The product line includes filter papers, membranes, and related accessories.
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The RNeasy Mini Kit is a laboratory equipment designed for the purification of total RNA from a variety of sample types, including animal cells, tissues, and other biological materials. The kit utilizes a silica-based membrane technology to selectively bind and isolate RNA molecules, allowing for efficient extraction and recovery of high-quality RNA.
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GraphPad Prism 5 is a data analysis and graphing software. It provides tools for data organization, statistical analysis, and visual representation of results.
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Cellic CTec2 is a commercial enzyme product developed by Novozymes. It is a cellulase enzyme complex designed to hydrolyze cellulose, a key component of plant cell walls, into fermentable sugars. The core function of Cellic CTec2 is to facilitate the breakdown of cellulosic biomass to enable its conversion into biofuels and other bio-based products.
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TRIzol is a monophasic solution of phenol and guanidine isothiocyanate that is used for the isolation of total RNA from various biological samples. It is a reagent designed to facilitate the disruption of cells and the subsequent isolation of RNA.
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TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
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The L-8900 is a laboratory equipment product manufactured by Hitachi. It is designed for analytical purposes, providing users with the necessary tools to conduct various scientific experiments and analyses. The core function of the L-8900 is to facilitate the accurate measurement and evaluation of samples within a controlled laboratory environment.
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Polyvinyl alcohol is a synthetic, water-soluble polymer. It is commonly used as a raw material in the production of various laboratory equipment and supplies.
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Sodium hydroxide is a chemical compound with the formula NaOH. It is a white, odorless, crystalline solid that is highly soluble in water and is a strong base. It is commonly used in various laboratory applications as a reagent.
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The High-Capacity cDNA Reverse Transcription Kit is a laboratory tool used to convert RNA into complementary DNA (cDNA) molecules. It provides a reliable and efficient method for performing reverse transcription, a fundamental step in various molecular biology applications.
More about "Hydrolysis"
Hydrolysis is a fundamental chemical process where molecules are broken down into smaller components by the addition of water.
This process is crucial in many biological and industrial applications, including the breakdown of complex carbohydrates, proteins, and other macromolecules.
Synonymous terms include enzymatic cleavage, solvolysis, and aqueous lysis.
Researchers can leverage hydrolysis protocols from trusted sources like Whatman filter papers, RNeasy Mini Kits, and Cellic CTec2 enzymes.
Quantitative analysis can be performed using software like GraphPad Prism 5.
Reagents such as TRIzol, L-8900 polyvinyl alcohol, and sodium hydroxide are commonly used to facilitate hydrolysis.
PubCompare.ai's AI-driven platform empowers researchers to optimize their hydrolysis methods by comparing protocols across literature, preprints, and patents.
This enhances reproducibility, accuracy, and exploration of the most effective kits and approaches.
By leveraging this innovative tool, scientists can improve the reliability of their hydrolysis-based findings.
Try PubCompare.ai today to take your research to new heights.
This process is crucial in many biological and industrial applications, including the breakdown of complex carbohydrates, proteins, and other macromolecules.
Synonymous terms include enzymatic cleavage, solvolysis, and aqueous lysis.
Researchers can leverage hydrolysis protocols from trusted sources like Whatman filter papers, RNeasy Mini Kits, and Cellic CTec2 enzymes.
Quantitative analysis can be performed using software like GraphPad Prism 5.
Reagents such as TRIzol, L-8900 polyvinyl alcohol, and sodium hydroxide are commonly used to facilitate hydrolysis.
PubCompare.ai's AI-driven platform empowers researchers to optimize their hydrolysis methods by comparing protocols across literature, preprints, and patents.
This enhances reproducibility, accuracy, and exploration of the most effective kits and approaches.
By leveraging this innovative tool, scientists can improve the reliability of their hydrolysis-based findings.
Try PubCompare.ai today to take your research to new heights.