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Nature Protocols Oct 20125-Hydroxymethylcytosine (5hmC) is a newly discovered DNA base present at detectable levels in most mammalian cell types and tissues. It is generated by...
5-Hydroxymethylcytosine (5hmC) is a newly discovered DNA base present at detectable levels in most mammalian cell types and tissues. It is generated by Tet-enzyme-mediated oxidation of 5-methylcytosine (5mC). 5hmC is important both because of its potential role in regulating gene expression and because it may be an intermediate in DNA demethylation. Here we describe a technique termed GLIB (glucosylation, periodate oxidation and biotinylation), which combines several enzymatic and chemical modification steps to attach biotin to 5hmC. Biotin-containing genomic DNA fragments are then enriched using streptavidin beads, eluted and sequenced. GLIB is capable of quantitatively tagging and precipitating fragments containing a single 5hmC molecule. Sample preparation and GLIB can be conducted in 2-3 d.
Topics: 5-Methylcytosine; Base Sequence; Biotinylation; Cytosine; Genomics; Glucose; Molecular Sequence Data; Oxidation-Reduction; Periodic Acid
PubMed: 23018194
DOI: 10.1038/nprot.2012.104 -
Toxins Dec 2019Amatoxins (AMAs) are lethal toxins found in a variety of mushroom species. Detection methods are needed to determine the occurrence of AMAs in mushroom species suspected...
Amatoxins (AMAs) are lethal toxins found in a variety of mushroom species. Detection methods are needed to determine the occurrence of AMAs in mushroom species suspected in mushroom poisonings. In this manuscript, we report the generation of novel monoclonal antibodies (mAbs, AMA9G3 and AMA9C12) and the development of a competitive, enzyme-linked immunosorbent assay (cELISA) that is sensitive at 1 ng mL and shows selectivity for α-amanitin (α-AMA) and γ-amanitin (γ-AMA), and less for β-amanitin (β-AMA). In order to decrease the overall time needed for analysis, the extraction procedure for mushrooms was also simplified. A rapid (1 min) extraction procedure of AMAs using solvents as simple as water alone was successfully demonstrated using mushrooms. Together, the extraction method and the mAb-based ELISA represent a simple and rapid method that readily detects AMAs extracted from mushroom samples.
Topics: Amanita; Amanitins; Animals; Antibodies, Monoclonal; Enzyme-Linked Immunosorbent Assay; Female; Hemocyanins; Mice, Inbred BALB C; Periodic Acid
PubMed: 31835792
DOI: 10.3390/toxins11120724 -
Water Research May 2024The periodate (PI)-based advanced oxidation process is valued for environmental remediation, but current activation methods involve high costs, secondary contamination...
The periodate (PI)-based advanced oxidation process is valued for environmental remediation, but current activation methods involve high costs, secondary contamination risks, and limited applicability due to external energy inputs (e.g., UV), catalyst incorporation (e.g., Fe), or environmental modifications (e.g., freezing). In this work, novel bioelectric activation of PI using the electrons generated by electroactive bacteria was developed and investigated for rapid removal of carbamazepine (CBZ), achieving 100 %, 100 %, and 76 % removal efficiency for 4.22 µM of CBZ in 20 min at pH 2, 120 min at pH 6.4, and HRT of 30 min at pH 8.5, respectively, with a 1 mM PI dose and without an input voltage. It was deduced that electrons derived from bacteria could directly activate PI using Ti mesh electrodes and generate •IO via single electron transfer under strongly acidic conditions (e.g., pH 2). Nevertheless, under weak alkaline conditions (e.g., pH 8.5), biogenic electrons indirectly activated PI by generating OHvia 4ereduction at the Ti mesh cathode, resulting in the formation of •O and O. In addition to the metal cathode, a carbon-based cathode finely modulates the 2ereduction, yielding HO and activating PI to mainly form •OH. Moreover, primarily non-toxic IO was produced during treatment, while no detectable reactive iodine species (HOI, I, and I) were observed. Furthermore, the bioelectric activation of PI demonstrated its capability to remove various micropollutants present in secondary-treated municipal wastewater, showcasing its broad-spectrum degradation ability. This study introduces a novel, cost-effective, and environmentally friendly PI activation technique with promising applicability for micropollutant elimination in water treatment.
Topics: Hydrogen Peroxide; Water Pollutants, Chemical; Wastewater; Periodic Acid; Oxidation-Reduction; Carbamazepine
PubMed: 38430759
DOI: 10.1016/j.watres.2024.121388 -
Experimental Parasitology Jul 2016Glycoconjugates play a crucial role in the host-parasite relationships of helminthic infections, including angiostrongyliasis. It has previously been shown that the...
Glycoconjugates play a crucial role in the host-parasite relationships of helminthic infections, including angiostrongyliasis. It has previously been shown that the antigenicity of proteins from female Angiostrongylus cantonensis worms may depend on their associated glycan moieties. Here, an N-glycan profile of A. cantonensis is reported. A total soluble extract (TE) was prepared from female A. cantonensis worms and was tested by western blot before and after glycan oxidation or N- and O-glycosidase treatment. The importance of N-glycans for the immunogenicity of A. cantonensis was demonstrated when deglycosylation of the TE with PNGase F completely abrogated IgG recognition. The TE was also fractionated using various lectin columns [Ulex europaeus (UEA), concanavalin A (Con A), Arachis hypogaea (PNA), Triticum vulgaris (WGA) and Lycopersicon esculentum (LEA)], and then each fraction was digested with PNGase F. Released N-glycans were analyzed with matrix-assisted laser desorption ionization (MALDI)-time-of-flight (TOF)-mass spectrometry (MS) and MALDI-TOF/TOF-MS/MS. Complex-type, high mannose, and truncated glycan structures were identified in all five fractions. Sequential MALDI-TOF-TOF analysis of the major MS peaks identified complex-type structures, with a α1-6 fucosylated core and truncated antennas. Glycoproteins in the TE were labeled with BodipyAF558-SE dye for a lectin microarray analysis. Fluorescent images were analyzed with ProScanArray imaging software followed by statistical analysis. A total of 29 lectins showed positive binding to the TE. Of these, Bandeiraea simplicifolia (BS-I), PNA, and Wisteria floribunda (WFA), which recognize galactose (Gal) and N-acetylgalactosamine (GalNAc), exhibited high affinity binding. Taken together, our findings demonstrate that female A. cantonensis worms have characteristic helminth N-glycans.
Topics: Angiostrongylus cantonensis; Animals; Female; Glycoside Hydrolases; Lectins; Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase; Periodic Acid; Polysaccharides; Rats; Rats, Wistar; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 27107931
DOI: 10.1016/j.exppara.2016.04.012 -
European Journal of Biochemistry May 1980Three heparan sulphate fractions were subjected to degradation by periodate oxidation and alkaline elimination. The starting materials were one low-sulphated fraction...
Three heparan sulphate fractions were subjected to degradation by periodate oxidation and alkaline elimination. The starting materials were one low-sulphated fraction rich in glucuronic acid and N-acetylglucosamine (I), one fraction (IV) that was medium-sulphated, contained similar proportions of N-acetyl and N-sulphate as well as of glucuronic and iduronic acid and one fraction (V) that was oversulphated, contained an excess of N-sulphate and was rich in iduronic acid. Selective periodate oxidation of glucuronic acid residues within N-acetylated regions followed by scission in alkali yielded three categories of fragments that were isolated by gel and ion-exchange chromatography. (a) N-Acetylglucosamine-R compounds where R is the remnant of an oxidised and degraded glucuronic acid residue. (b) Medium-sized oligosaccharides, of the general structure glucosamine-(glycuronic acid-glucosamine)n-R where n = 1--4, contained largely glucuronic acid associated with glucosamines that were N-sulphated, N-acetylated or unsubstituted. In saccharides where n = 4 indications of an alternating arrangement of N-sulphate and N-acetyl groups as well as of iduronic and glucuronic acid residues were obtained. The glucuronic acid residues of the oligosaccharide fragments were susceptible to reoxidation with periodate. The smaller saccharides were not depolymerised by HNO2 despite the presence of N-sulphate groups. (c) Longer oligosaccharide fragments (n greater than or equal to 5) that were highly sulphated and contained heparin-like repeating units, i.e. iduronic acid--glucosamine-N-sulphate with ester-sulphate on both sugars. These oligosaccharides were susceptible to deaminative cleavage.
Topics: Animals; Cattle; Chemical Phenomena; Chemistry; Chromatography, Gel; Chromatography, Ion Exchange; Glycosaminoglycans; Heparitin Sulfate; Hydrogen-Ion Concentration; Oligosaccharides; Oxidation-Reduction; Periodic Acid; Swine
PubMed: 6280999
DOI: No ID Found -
ChemSusChem Aug 2022Periodate, a platform oxidizer, can be electrochemically recycled in a self-cleaning process. Electrosynthesis of periodate is well established at boron-doped diamond...
Periodate, a platform oxidizer, can be electrochemically recycled in a self-cleaning process. Electrosynthesis of periodate is well established at boron-doped diamond (BDD) anodes. However, recovered iodate and other iodo species for recycling can contain traces of organic impurities from previous applications. For the first time, it was shown that the organic impurities do not hamper the electrochemical re-oxidation of used periodate. In a hydroxyl-mediated environment, the organic compounds form CO and H O during the degradation process. This process is often referred to as "cold combustion" and provides orthogonal conditions to periodate synthesis. To demonstrate the strategy, different dyes, pharmaceutically active ingredients, and iodine compounds were added as model contaminations into the process of electrochemical periodate production. UV/Vis spectroscopy, NMR spectroscopy, and mass spectrometry (MS) were used to monitor the degradation of organic molecules, and liquid chromatography-MS was used to control the purity of periodate. As a representative example, dimethyl 5-iodoisophthalate (2 mm), was degraded in 90, 95, and 99 % while generating 0.042, 0.054, and 0.082 kilo equiv. of periodate, respectively. In addition, various organic iodo compounds could be fed into the periodate generation for upcycling such iodo-containing waste, for example, contrast media.
Topics: Boron; Diamond; Electrodes; Organic Chemicals; Oxidation-Reduction; Periodic Acid; Water Pollutants, Chemical
PubMed: 35670517
DOI: 10.1002/cssc.202200874 -
Journal of the American Society For... Jun 2014The gas-phase oxidation of methionine residues is demonstrated here using ion/ion reactions with periodate anions. Periodate anions are observed to attach in varying...
The gas-phase oxidation of methionine residues is demonstrated here using ion/ion reactions with periodate anions. Periodate anions are observed to attach in varying degrees to all polypeptide ions irrespective of amino acid composition. Direct proton transfer yielding a charge-reduced peptide ion is also observed. In the case of methionine and, to a much lesser degree, tryptophan-containing peptide ions, collisional activation of the complex ion generated by periodate attachment yields an oxidized peptide product (i.e., [M + H + O](+)), in addition to periodic acid detachment. Detachment of periodic acid takes place exclusively for peptides that do not contain either a methionine or tryptophan side chain. In the case of methionine-containing peptides, the [M + H + O](+) product is observed at a much greater abundance than the proton transfer product (viz., [M + H](+)). Collisional activation of oxidized Met-containing peptides yields a signature loss of 64 Da from the precursor and/or product ions. This unique loss corresponds to the ejection of methanesulfenic acid from the oxidized methionine side chain and is commonly used in solution-phase proteomics studies to determine the presence of oxidized methionine residues. The present work shows that periodate anions can be used to 'label' methionine residues in polypeptides in the gas phase. The selectivity of the periodate anion for the methionine side chain suggests several applications including identification and location of methionine residues in sequencing applications.
Topics: Amino Acid Sequence; Gases; Ions; Mass Spectrometry; Methionine; Oligopeptides; Oxidation-Reduction; Periodic Acid; Protons
PubMed: 24671696
DOI: 10.1007/s13361-014-0861-8 -
Journal of Virology Jun 1968Deoxyribonucleic acid (DNA) extracted from phage SPP1 is highly infectious on Bacillus subtilis competent cells; the efficiency of infection is 5 x 10(3) to 6 x 10(3)...
Deoxyribonucleic acid (DNA) extracted from phage SPP1 is highly infectious on Bacillus subtilis competent cells; the efficiency of infection is 5 x 10(3) to 6 x 10(3) phage equivalents per plaque-forming unit. This DNA was used to study the relationship between competence for transfection and for transformation. The experiments were concerned with the frequency of infection and transformation in mutants exhibiting different levels of competence, the effect of periodate on competence for infection and for transformation, the competition between phage and bacterial DNA, the transformation of cells preinfected with phage DNA, and the infection of cells pretreated with bacterial DNA. The data show that B. subtilis cells competent for transformation are also competent for transfection and vice versa; transfection with phage DNA represents, therefore, a simple way to measure the total number of competent cells in a culture. The fraction of competent cells, determined by SPP1 DNA infection, varied from 10(-2) to 7 x 10(-2).
Topics: Bacillus subtilis; Bacteriophages; Centrifugation, Density Gradient; DNA, Bacterial; DNA, Viral; Dactinomycin; Drug Resistance, Microbial; Genetics, Microbial; Kinetics; Periodic Acid; Transformation, Genetic
PubMed: 4177104
DOI: 10.1128/JVI.2.6.587-593.1968 -
Analytical and Bioanalytical Chemistry Jan 2014Periodate oxidation followed by borohydride reduction converts the well-known antithrombotics heparin and low-molecular-weight heparins (LMWHs) into their "glycol-split"...
Periodate oxidation followed by borohydride reduction converts the well-known antithrombotics heparin and low-molecular-weight heparins (LMWHs) into their "glycol-split" (gs) derivatives of the "reduced oxyheparin" (RO) type, some of which are currently being developed as potential anti-cancer and anti-inflammatory drugs. Whereas the structure of gs-heparins has been recently studied, details of the more complex and more bioavailable gs-LMWHs have not been yet reported. We obtained RO derivatives of the three most common LMWHs (tinzaparin, enoxaparin, and dalteparin) and studied their structures by two-dimensional nuclear magnetic resonance spectroscopy and ion-pair reversed-phase high-performance liquid chromatography coupled with electrospray ionization mass spectrometry. The liquid chromatography-mass spectrometry (LC-MS) analysis was extended to their heparinase-generated oligosaccharides. The combined NMR/LC-MS analysis of RO-LMWHs provided evidence for glycol-splitting-induced transformations mainly involving internal nonsulfated glucuronic and iduronic acid residues (including partial hydrolysis with formation of "remnants") and for the hydrolysis of the gs uronic acid residues when formed at the non-reducing ends (mainly, in RO-dalteparin). Evidence for minor modifications, such as ring contraction of some dalteparin internal aminosugar residues, was also obtained. Unexpectedly, the N-sulfated 1,6-anhydromannosamine residues at the enoxaparin reducing end were found to be susceptible to the periodate oxidation. In addition, in tinzaparin and enoxaparin, the borohydride reduction converts the hemiacetalic aminosugars at the reducing end to alditols. Typical LC-MS signatures of RO-derivatives of individual LMWH both before and after digestion with heparinases included oligosaccharides generated from the original antithrombin-binding and "linkage" regions.
Topics: Borohydrides; Chromatography, Reverse-Phase; Dalteparin; Enoxaparin; Glucuronic Acid; Heparin Lyase; Heparin, Low-Molecular-Weight; Hydrolysis; Iduronic Acid; Magnetic Resonance Spectroscopy; Oxidation-Reduction; Periodic Acid; Tinzaparin
PubMed: 24253408
DOI: 10.1007/s00216-013-7446-4 -
Molecules (Basel, Switzerland) Jul 2022A sustainable downscaled procedure using smartphone-based colorimetric determination of manganese (Mn(II)) was developed. This novel Mn(II) determination procedure is...
Sustainable Downscaled Catalytic Colorimetric Determination of Manganese in Freshwater Using Smartphone-Based Monitoring Oxidation of 3,3',5,5'-Tetramethylbenzidine by Periodate.
A sustainable downscaled procedure using smartphone-based colorimetric determination of manganese (Mn(II)) was developed. This novel Mn(II) determination procedure is proposed using a simple, available microwell-plate platform and a smartphone as a detector. This approach is based on the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) by periodate using Mn(II) as a catalyst. The catalytic kinetics of Mn(II) under different conditions was investigated to determine the optimum condition where the different catalytic activities of various concentrations of Mn(II) evince. Under the optimum condition, the bluish-green product of oxidized TMB, proportioned to the concentration of Mn(II), was monitored using a smartphone camera, and the color signals were processed using ImageJ Software. The developed procedure showed great selectivity and sensitivity as linearity ranged from 1.8 × 10 to 4.6 × 10 M (0.1 to 2.5 μg/mL). The limits of detection and quantitation were 3.6 × 10 and 1.1 × 10 M (0.2 and 0.6 μg/mL), respectively. The determination of Mn(II) in freshwater samples was demonstrated to assess environmental water quality as an initial model to more easily promote water management according to the United Nations Sustainable Development Goals (UN-SDGs). The intensity of the red could be successfully applied to evaluate Mn(II) in canals and river water with no significant differences compared with the reference method of Inductively Coupled Plasma Optical Emission Spectrometry at a confidence level of 95%.
Topics: Benzidines; Colorimetry; Fresh Water; Manganese; Periodic Acid; Smartphone
PubMed: 35956794
DOI: 10.3390/molecules27154841