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Oxidation-Reduction

Oxidation-Reduction is a fundamental biomedical process involving the transfer of electrons between molecules, resulting in changes in their oxidation states.
This process is crucial for various biological functions, such as energy production, signaling pathways, and cellular homeostasis.
Researchers studying Oxidation-Reduction can leverage the power of PubCompare.ai, an AI-driven platform that enhances research workflows by providing easy access to relevant protocols from literature, pre-prints, and patents.
The platform's advanced AI comparisons help identify the most reproducible and accurate protocols, optimizing research and elevating results.
With PubCompare.ai's intuitive tools, scientists can streamline their Oxidation-Reduction studies, saving time and improving the quality of their findings.

Most cited protocols related to «Oxidation-Reduction»

A stoichiometric matrix, S (m × n), is constructed where m is the number of metabolites and n the number of reactions. Each column of S specifies the stoichiometry of the metabolites in a given reaction from the metabolic network. Mass balance equations can be written for each metabolite by taking the dot product of a row in S, corresponding to a particular metabolite, and a vector, v, containing the values of the fluxes through all reactions in the network. A system of mass balance equations for all the metabolites can be represented as follows:
where X is a concentration vector of length m, and v is a flux vector of length n. At steady-state, the time derivatives of metabolite concentrations are zero, and equation (1) can be simplified to:
Sv = 0
It follows that in order for a flux vector v to satisfy this relationship, the rate of production must equal the rate of consumption for each metabolite. Application of additional constraints further reduces the number of allowable flux distributions, v.
Limits on the range of individual flux values can further reduce the number of allowable solutions. These constraints have the form:
α ≤ vi≤ β
where α and β are the lower and upper limits, respectively. Maximum flux values (β) can be estimated based on enzymatic capacity limitations or, for the case of exchange reactions, measured maximal uptake rates can be used. Thermodynamic constraints, regarding the reversibility or irreversibility of a reaction, can be applied by setting the α for the corresponding flux to zero if the reaction is irreversible.
These constraints are not sufficient to shrink the original solution space to a single solution. Instead a number of solutions remain which make up the allowable solution space. Linear optimization can be used to find the solution that maximizes a particular objective function. Some examples of objective functions include the production of ATP, NADH, NADPH or a particular metabolite. An objective function with a combination of the metabolic precursors, energy and redox potential required for the production of biomass has proven useful in predicting in vivo cellular behavior [9 (link),10 (link),25 (link),26 ].
Publication 2003
Cells Cloning Vectors derivatives Enzymes Metabolic Networks NADH NADP Oxidation-Reduction
Patch to patch variations in the half-activation voltage (Vh) of GK-V and Q-V relationships are observed for mSlo1 (Horrigan and Aldrich, 1999 (link); Horrigan et al., 1999 (link)) and hSlo1 (Stefani et al., 1997 (link)), possibly due to differences in the redox state of channels (DiChiara and Reinhart, 1997 (link); Tang et al., 2001 (link)). Such shifts do not appreciably alter the shape of voltage-dependent relationships but make comparison of data between different experiments difficult and cause broadening in averaged voltage-dependent relationships. To compensate for this effect, Vh was determined for each patch and compared with the mean for all experiments (h>) at the same [Ca2+]. Data from individual experiments were then shifted along the voltage-axis by ΔVh = (h> − Vh) before averaging. This procedure yields average relationships that accurately represent the shape of individual GK-V and Q-V relationships.
Publication 2002
Epistropheus Oxidation-Reduction
Super-resolution imaging experiments were performed on live samples (Fig. 2j, Supplementary Fig. 2c, Supplementary Fig. 4d, Supplementary Fig. 4g) and fixed cells (Fig. 1i, Fig. 2b, Supplementary Fig. 2a, Supplementary Fig. 4a). For live-cell dSTORM imaging the cells were labeled, washed, and imaged directly in DMEM–FBS. For fixed cell preparations, cells were labeled, washed, and fixed in 4% paraformaldehyde (Electron Microscopy Sciences) in PBS buffer (pH = 7.5). The cells were imaged in a sealed cell chamber (Life Technologies) containing nitrogen-degassed redox buffer consisting of PBS supplemented with 50 mM mercaptoethylamine (Sigma–Aldrich), 10% w/v glucose, 0.5 mg/mL glucose oxidase (Sigma–Aldrich), and 28400 U/mL catalase (Sigma–Aldrich). Before imaging, JF549 could be efficiently “shelved” in a dark state upon illumination with 2 kW·cm−2 of excitation light (561 nm), and then activated back to a fluorescent state by blue light (405 nm) with low intensity (~20·W cm−2). JF646 fluorophores were converted into a predominately dark state using continuous illumination of 637 nm excitation light at 14 kW·cm−2, after which individual rapidly blinking molecules of JF646 fluorophores were observed. These experiments were conducted on the two wide-field microscope systems described above: the Nikon Eclipse Ti epifluorescence microscope (Fig. 1i, Fig. 2j, Supplementary Fig. 2a, Supplementary Fig. 2c, Supplementary Fig. 4g), and the custom-built three-camera microscope with an ASI RAMM frame (Fig. 2b, Supplementary Fig. 4a, Supplementary Fig. 4d).
Publication 2014
Buffers Catalase Cells Cysteamine Electron Microscopy Glucose Light Microscopy Nitrogen Oxidase, Glucose Oxidation-Reduction paraform Reading Frames
Super-resolution imaging experiments were performed on live samples (Fig. 2j, Supplementary Fig. 2c, Supplementary Fig. 4d, Supplementary Fig. 4g) and fixed cells (Fig. 1i, Fig. 2b, Supplementary Fig. 2a, Supplementary Fig. 4a). For live-cell dSTORM imaging the cells were labeled, washed, and imaged directly in DMEM–FBS. For fixed cell preparations, cells were labeled, washed, and fixed in 4% paraformaldehyde (Electron Microscopy Sciences) in PBS buffer (pH = 7.5). The cells were imaged in a sealed cell chamber (Life Technologies) containing nitrogen-degassed redox buffer consisting of PBS supplemented with 50 mM mercaptoethylamine (Sigma–Aldrich), 10% w/v glucose, 0.5 mg/mL glucose oxidase (Sigma–Aldrich), and 28400 U/mL catalase (Sigma–Aldrich). Before imaging, JF549 could be efficiently “shelved” in a dark state upon illumination with 2 kW·cm−2 of excitation light (561 nm), and then activated back to a fluorescent state by blue light (405 nm) with low intensity (~20·W cm−2). JF646 fluorophores were converted into a predominately dark state using continuous illumination of 637 nm excitation light at 14 kW·cm−2, after which individual rapidly blinking molecules of JF646 fluorophores were observed. These experiments were conducted on the two wide-field microscope systems described above: the Nikon Eclipse Ti epifluorescence microscope (Fig. 1i, Fig. 2j, Supplementary Fig. 2a, Supplementary Fig. 2c, Supplementary Fig. 4g), and the custom-built three-camera microscope with an ASI RAMM frame (Fig. 2b, Supplementary Fig. 4a, Supplementary Fig. 4d).
Publication 2014
Buffers Catalase Cells Cysteamine Electron Microscopy Glucose Light Microscopy Nitrogen Oxidase, Glucose Oxidation-Reduction paraform Reading Frames
The RoGFP protein contains two engineered cysteine thiols, as first described by Remington et al. (RoGFP2) 11 (link). The cDNA encoding the protein was created by introducing four mutations in the mammalian GFP expression vector (pEGFP-N1) (C48S, Q80R, S147C, and Q204C) using a QuikChange Multi Site-directed mutagenesis kit (Strategene). The RoGFP construct was ligated into the VQ Ad5CMV K-NpA adenoviral shuttle vector between the KpnI and NotI sites; after sequencing and amplification this plasmid was used to generate a recombinant adenovirus to permit widespread expression in our cells (ViraQuest Inc., North Liberty, IA). The resulting redox-sensitive protein has excitation maxima at 400 and 484 nm, with emission at 525 nm. In response to changes in redox conditions, RoGFP exhibits reciprocal changes in intensity at the two excitation maxima 12 (link), and its ratiometric characteristics render it insensitive to expression levels 13 (link)-15 (link). Although RoGFP’s fluorescence behavior is relatively independent of pH and it does not respond to authentic nitric oxide (NO), reduced NADH, or the antioxidant N-acetyl-L-cysteine (NAC), its spectrum is slightly affected by reduced glutathione (GSH) possibly due to thiol-disulfide exchange (Online Figures I and II).
RoGFP was expressed in the mitochondrial matrix (Mito-RoGFP) by appending a 48 bp region encoding the mitochondrial targeting sequence from cytochrome oxidase subunit IV, at the 5′ end of the coding sequence. This construct was then ligated into the VQ Ad5CMV K-NpA plasmid between the KpnI and NotI sites, and used to generate an adenoviral vector. RoGFP was targeted to the mitochondrial inter-membrane space (IMS-RoGFP) by appending it to glycerol phosphate dehydrogenase (GPD). A cDNA construct encoding GPD, an integral protein of the inner mitochondrial membrane whose C-terminus protrudes into the inter-membrane space 17 (link), was ligated in-frame with cDNA encoding RoGFP 17 (link). The corresponding polypeptide includes amino acids 1–626 of GPD, with RoGFP at the carboxy terminus. This method has been used previously to express YFP in the inter-membrane space 18 (link). (See Online Supplemental Material for characterization of the RoGFP sensors and experimental protocols).
Publication 2009
Acetylcysteine Adenoviruses Adenovirus Vaccine Amino Acids Antioxidants Cells Cloning Vectors Cysteine Cytochrome-c Oxidase Subunit IV Disulfides DNA, Complementary Fluorescence glycerol-1-phosphate dehydrogenase Glycerol-3-Phosphate Dehydrogenase Integral Membrane Proteins Mammals Mitochondria Mitochondrial Membrane, Inner Mitochondrial Membranes Mitomycin Mutagenesis, Site-Directed Mutation NADH Open Reading Frames Oxidation-Reduction Oxide, Nitric Plasmids Polypeptides Proteins Reading Frames Reduced Glutathione Shuttle Vectors Sulfhydryl Compounds Tissue, Membrane

Most recents protocols related to «Oxidation-Reduction»

Example 7

Synthetic urine is prepared by dissolving 14.1 g of NaCl, 2.8 g KCl, 17.3 g of urea, 19 ml ammonia water (25%), 0.60 g CaCl2 and 0.43 g MgSO4 in 0.02 mole/L of HCl. The final pH of synthetic urine is adjusted to 6.04 by using HCl and ammonia water.

40 mg Sigma creatinine is dissolved in 10 ml of synthetic urine solution. 3 mg of human albumin is dissolved in 10 ml of synthetic urine solution to prepare the micro albumin solution.

4 mg Sigma hemin is dissolved in 20 ml of synthetic urine, 20 μL Hemin solution is used as a receptor for urine albumin detection at different creatinine concentration.

A desired volume of the biological sample (synthetic urine) is taken and dispensed on the electrode of the biosensor device and the corresponding cyclic voltammogram is obtained by the CHI-Electrochemical workstation using the potential window, that varies from 0 V to −1 V with scan rate of 0.1 V/sec.

The albumin content in the urine sample binds hemin thereby demonstrates a linear decrease in peak redox current with urine albumin concentration as shown in FIG. 15(a) for different creatinine concentrations. If the concentration of albumin in urine sample is increased, then the albumin increasingly binds with hemin thereby reducing the free hemin concentration on the electrode resulting in the decrease in peak redox current of free hemin. FIG. 16 shows the urine albumin concentrations, urine creatinine concentrations and calculated ACR for different samples.

The values of concentrations of the urine albumin (mg/L) and creatinine for different samples is shown in Table 4.

TABLE 4
SampleUrine albuminUrine CreatinineACR
Number(mg/L)(mg/dL)(mg/g)
1526.719
22026.775
35026.7187
410026.7375
515026.7562
65133.34
720133.315
850133.338
9100133.375
10150133.3113

Patent 2024
Albumins Ammonium Hydroxide Biopharmaceuticals Biosensors Creatinine Hemin Moles Oxidation-Reduction Radionuclide Imaging Receptors, Albumin Serum Albumin, Human Sodium Chloride Sulfate, Magnesium Urea Urine
Not available on PMC !

Example 12

Different thin-film electrodes were tested using the Type 1 Linear Sweep Voltammetry Test. In more detail, thin-film electrodes formed with a stainless steel 304 (SS304) conductive layer, including an electrode with an amorphous carbon layer deposited thereon in a pure Ar atmosphere, an electrode with an amorphous carbon-containing layer deposited thereon in a 20% nitrogen atmosphere, and an electrode with an amorphous carbon-containing layer deposited thereon in a 50% nitrogen atmosphere were tested. The electrodes were all produced in a roll-to-roll sputter coater.

Anodic polarization scans in PBS, with 1 mM K4[FeII(CN)6] redox mediator added, at 25 mV/s using a saturated calomel (SCE) reference electrode and each of the SS304 electrodes as the working electrode. The results are illustrated graphically in FIG. 11. A review of FIG. 11 reveals that the electron transfer kinetics between the mediator and electrode are slightly faster when the carbon layer is sputtered in a pure Ar atmosphere, compared to a N2 containing atmosphere. However, even the films sputtered in a 1:1 Ar:N2 gas mixture is still useful in a biosensor and has an increase in deposition rate of ˜164% compared to carbon sputtered in pure Ar.

Patent 2024
Atmosphere Biosensors calomel Carbon Electric Conductivity Electron Transport Kinetics Nitrogen Oxidation-Reduction Radionuclide Imaging Stainless Steel

Example 13

Different thin-film electrodes were tested using the Type 1 Cyclic Voltammetry Test. In more detail, thin-film electrodes formed with a stainless steel 304 (SS304) conductive layer and capped with a carbon containing layer sputtered in an atmosphere of N2 that ranged from 0, 5, 10, 15, 20, 40, and 50% N2 by partial pressure, respectively. The electrodes were all produced in a roll-to-roll sputter coater.

Cyclic voltammograms in PBS, with 2 mM [RuIII(NH3)6]Cl3 mediator added, at 25 mV/s using a saturated calomel (SCE) reference electrode and each of the SS304 electrodes as the working electrode. The results are illustrated graphically in FIG. 12. A review of FIG. 12 reveals that the electron transfer kinetics between the mediator and electrode are not affected by the introduction of N2 into the sputtering chamber when [RuIII(NH3)6]Cl3 is used as the redox mediator. This is unexpected because the electron transfer kinetics with a K4[FeII(CN)6] redox mediator are slightly negatively affected by the introduction of N2 into the sputtering chamber during carbon deposition.

Patent 2024
Atmosphere calomel Carbon Electric Conductivity Electron Transport Kinetics Oxidation-Reduction Partial Pressure Stainless Steel

Example 1

To generate an attenuated strain of P. aeruginosa for production of alginate, the following virulence factor genes were sequentially deleted from the chromosome of the wild-type strain PAO1: toxA, plcH, phzM, wapR, and aroA. toxA encodes the secreted toxin Exotoxin A, which inhibits protein synthesis in the host by deactivating elongation factor 2 (EF-2). plcH encodes the secreted toxin hemolytic phospholipase C, which acts as a surfactant and damages host cell membranes. phzM encodes phenazine-specific methyltransferase, an enzyme required for the production of the redox active, pro-inflammatory, blue-green secreted pigment, pyocyanin. wapR encodes a rhamnosyltransferase involved in synthesizing O-antigen, a component of lipopolysaccharide (LPS) of the outer membrane of the organism. aroA encodes 3-phosphoshikimate 1-carboxyvinyltransferase, which is required intracellularly for aromatic amino acid synthesis. Deletion of aroA from the P. aeruginosa genome has previously been shown to attenuate the pathogen. Each gene was successfully deleted using a homologous recombination strategy with the pEX100T-Not1 plasmid. The in-frame, marker-less deletion of these five gene sequences was verified by Sanger sequencing and by whole genome resequencing (FIG. 1 and FIG. 8). This engineered strain was designated as PGN5. The whole genome sequence of PGN5 has been deposited to NCBI Genbank with an accession number of CP032541. All five in-frame gene deletions were detected and validated to be the deletion as designed using PCR (FIG. 7).

To verify gene deletion and attenuation of the PGN5 strain, the presence of the products of the deleted genes was measured and was either undetectable, or significantly reduced in the PGN5 strain. To test for the toxA gene deletion in PGN5, a Western blot analysis was performed for the presence of Exotoxin A in the culture medium. Exotoxin A secretion was detected in wild-type PAO1 control, but not in the PGN5 strain (FIG. 2A). To confirm the loss of plcH, hemolysis was assessed on blood agar. The hemolytic assay was carried out by streaking PAO1, PGN5, P. aeruginosa mucoid strain VE2, and a negative control, Escherichia coli strain BL21 on blood agar plates. A clear zone was observed surrounding PAO1 and VE2 cell growth, indicating complete (β-) hemolysis (FIG. 2B). In contrast, the blood agar remained red and opaque surrounding PGN5 and BL21 growth, indicating negligible or no hemolytic activity in these strains (FIG. 2B). To assess for deletion of phzM, the amount of pyocyanin secreted by PAO1 and PGN5 was extracted and measured. The amount of pyocyanin detected was significantly reduced in PGN5 (FIG. 2C). In fact, the difference in pigment production between PAO1 and PGN5 was immediately apparent on agar plates (FIG. 3A-3B). To test for wapR gene deletion, an LPS extraction was performed, followed by silver-stained SDS-PAGE and Western blot on the following strains: PAO1, PGN4 (PGN5 without aroA deletion), VE2, and PAO1wbpL, which serves as a negative control due to a deletion in the O-antigen ligase gene, and thus produces no O-antigen. The presence of O-antigen was detected in PGN4, but the level of LPS banding was significantly reduced compared to the LPS banding profile observed in PAO1 and VE2 (FIG. 2D). Lastly, to test for aroA deletion, ELISA was performed to detect the presence of 3-phosphoshikimate 1-carboxyvinyltransferase in cell lysates prepared from PAO1 and PGN5. The ELISA results showed that the amount of 3-phosphoshikimate 1-carboxyvinyltransferase was significantly reduced in PGN5, compared to that in PAO1 (FIG. 2E). Additionally, the deletion of aroA resulted in slower growth in the PGN5 strain, a growth defect that was restored with the addition of 1 mg/mL of aromatic amino acids (W, Y, F) to the culture medium (data not shown).

Patent 2024
1-Carboxyvinyltransferase, 3-Phosphoshikimate Agar Alginate Anabolism Aromatic Amino Acids Biological Assay BLOOD Cardiac Arrest Chromosomes Culture Media Deletion Mutation Enzyme-Linked Immunosorbent Assay Enzymes Escherichia coli Exotoxins Gene Deletion Genes Genetic Markers Genome Hemolysis Homologous Recombination Inflammation Ligase Lipopolysaccharides Methyltransferase O Antigens Oxidation-Reduction Pathogenicity Peptide Elongation Factor 2 Phenazines Phospholipase C Pigmentation Plasma Membrane Plasmids Protein Biosynthesis Pseudomonas aeruginosa Pyocyanine Reading Frames SDS-PAGE secretion SERPINA3 protein, human Silver Strains Surface-Active Agents Tissue, Membrane Toxins, Biological Virulence Factors Western Blot Western Blotting
Not available on PMC !

Example 5

Electrode material used: The electrode material was indium tin oxide. The fluorescent protein used is GFP immobilized on a glass substrate which includes an array of electrodes. The GFP is applied as spots, each spot covers an area that overlaps with one electrode and an area that is not overlapping with an electrode.

The pH change at the surface of ITO working electrode is generated via current-driven oxidation of a redox active molecule, 2-methyl-1,4-dihydroquinone, in diluted phosphate buffer (pH=7.4) containing 0.1M Na2SO4. After 10 seconds of induction, current (50 microamps) was applied for 30 second, which resulted in a drop of solution pH to 5.5, as was observed by a change in GFP fluorescence intensity. FIG. 10 is used as calibration curve to assess the pH values. After current was turned off, the pH recovered to neutral value within 50 seconds (as shown in FIGS. 11 and 12B).

Patent 2024
Buffers dihydroquinone Exanthema Figs Fluorescence Green Fluorescent Proteins indium tin oxide Neoplasm Metastasis Oxidation-Reduction Phosphates Proteins

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More about "Oxidation-Reduction"

Oxidation-Reduction (Redox) is a fundamental biomedical process that involves the transfer of electrons between molecules, resulting in changes in their oxidation states.
This process is crucial for various biological functions, such as energy production, signaling pathways, and cellular homeostasis.
Researchers studying Redox can leverage the power of PubCompare.ai, an AI-driven platform that enhances research workflows by providing easy access to relevant protocols from literature, pre-prints, and patents.
The platform's advanced AI comparisons help identify the most reproducible and accurate protocols, optimizing research and elevating results.
With PubCompare.ai's intuitive tools, scientists can streamline their Redox studies, saving time and improving the quality of their findings.
Oxidative stress, a state of imbalance between Redox reactions, can be measured using fluorescent probes like CM-H2DCFDA, Resazurin, and MitoSOX Red.
These probes can be analyzed using flow cytometry (FACSCalibur) or plate readers (Synergy HT, Alamar Blue).
Computational tools like MATLAB can be utilized to analyze Redox-related data and optimize experimental design.
By incorporating the insights from PubCompare.ai and leveraging the power of advanced Redox measurement techniques and analytical tools, researchers can enhance their understanding of this fundamental biomedical process and drive breakthroughs in fields such as energy metabolism, cell signaling, and oxidative stress management.