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1.
Methods Mol Biol ; 2624: 1-6, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36723805

RESUMO

DNA methylation is a widespread epigenetic modification responsible for many biological regulation pathways. The development of various powerful biochemical assays, including conventional bisulfite treatment-based and emerging bisulfite-free techniques, has promised high-resolution DNA methylome profiling and significantly propelled the DNA methylation research field. However, the analysis of large-scale data generated from such assays is still complex and challenging. In this paper, we present a step-by-step protocol for using Msuite for whole-spectrum DNA methylation data analysis, from quality control, read alignment, to methylation call and data visualization. The Msuite package and a testing dataset are freely available at https://github.com/hellosunking/Msuite.


Assuntos
Metilação de DNA , Epigênese Genética , Análise de Dados , Análise de Sequência de DNA/métodos , Sulfitos , Ilhas de CpG , Software
2.
Methods Mol Biol ; 2624: 115-126, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36723812

RESUMO

DNA methylation is studied extensively for its relations with several biological processes such as transcriptional regulation. While methylation levels are usually estimated per cytosine or genomic region, additional information on methylation heterogeneity can be obtained when considering stretches of successive cytosines on the same reads; however, the majority of methylomes suffer from low coverage of genomic regions with sequencing depths enough for accurate estimation of methylation heterogeneity using existing methods. Here we describe a probabilistic-based imputation method that makes use of methylation information from neighboring sites to recover partially observed methylation patterns. Our method and software are proven to be faster and more accurate among all evaluated. Ultimately, our method allows for a more streamlined monitoring of epigenetic changes within cellular populations and their putative role in disease.


Assuntos
Epigenoma , Sulfitos , Metilação de DNA , Genômica/métodos , Epigênese Genética , Citosina , Análise de Sequência de DNA/métodos
3.
Bioinformatics ; 39(1)2023 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-36629453

RESUMO

MOTIVATION: Nowadays, epigenetic gene regulations are studied in each part of the biology, from embryonic development to diseases such as cancers and neurodegenerative disorders. Currently, to quantify and compare CpG methylation levels of a specific region of interest, the most accessible technique is the bisulfite sequencing PCR (BSP). However, no existing user-friendly tool is able to analyze data from all approaches of BSP. Therefore, the most convenient way to process results from the direct sequencing of PCR products (direct-BSP) is to manually analyze the chromatogram traces, which is a repetitive and prone to error task. RESULTS: Here, we implement a new R-based tool, called ABSP for analysis of bisulfite sequencing PCR, providing a complete analytic process of both direct-BSP and cloning-BSP data. It uses the raw sequencing trace files (.ab1) as input to compute and compare CpG methylation percentages. It is fully automated and includes a user-friendly interface as a built-in R shiny app, quality control steps and generates publication-ready graphics. AVAILABILITY AND IMPLEMENTATION: The ABSP tool and associated data are available on GitHub at https://github.com/ABSP-methylation-tool/ABSP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Metilação de DNA , Sulfitos , Análise de Sequência de DNA/métodos , Reação em Cadeia da Polimerase/métodos , Software
4.
Anal Chim Acta ; 1239: 340704, 2023 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-36628712

RESUMO

This work describes the analysis of formaldehyde using a 96-well microplate as multiple headspaces for the separation of sulfur dioxide gas generated from the sulfite remaining after its reaction with the formaldehyde in the sample. The quantitation of the gas is by colorimetric detection of an indicator paper placed over the microplate. The samples are aqueous extracts of various foods that are possibly adulterated with formaldehyde. A known excess amount of sulfite is added to the extract solution aliquoted in the well. The remaining sulfite is acidified with hydrochloric acid to generate sulfur dioxide gas which diffuses through the headspace above the solution to be absorbed at the moist strip of the indicator paper placed over the mouth of the wells. Anthocyanins extracted from the butterfly pea flower is used as the pH indicator giving a color change from the increase of hydrogen ions by hydrolysis of the absorbed sulfur dioxide gas. The exposed paper strip is scanned, and the digital images of the colored region analyzed using ImageJ software. The optimized method has a linear range of 200-1000 mg L-1 formaldehyde with limit of detection ((2.57*SD of intercept)/(slope of calibration line)) of the aqueous extract of 40 mg L-1 and coefficient of determination (r2) > 0.9979. Samples of fresh produce, such as seafood, meat, and vegetables, and various processed food were analyzed for their possible formaldehyde content. The results obtained from the headspace paper-based colorimetric detection are not statistically different from the values obtained from the titration method by paired t-tests.


Assuntos
Colorimetria , Dióxido de Enxofre , Dióxido de Enxofre/análise , Colorimetria/métodos , Antocianinas , Sulfitos/análise , Água , Formaldeído
5.
Bioresour Technol ; 371: 128589, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-36627086

RESUMO

Anaerobic fermentation is a promising method for waste activated sludge (WAS) treatment, but ineffective solubilization and hydrolysis limit its application. The current study examined the function of sodium sulfite (SDS) in potassium permanganate (PP)-conditioned WAS fermentation for short-chain fatty acids (SCFAs) biosynthesis. The presence of SDS in the PP system (PP/SDS) reduced the positive effects of PP on total SCFAs yield (2755 versus 3471 mg COD/L), while effectively increasing the proportion of acetate (from 41 to 81 %). Not only did SDS decrease the promoting effects of PP on WAS solubilization and hydrolysis efficiency by 5-42 %, it also shifted microbial metabolic pathways to favor acetate production. In addition, the amino acid metabolism with acetate as end product was enhanced. Moreover, PP/SDS inhibited methanogenesis, resulting in an accumulation of acetate in high quantities. Thus, the current study a provided insight and direction for effective WAS treatment with acetate-enriched SCFAs production.


Assuntos
Ácidos Graxos Voláteis , Esgotos , Fermentação , Esgotos/química , Anaerobiose , Acetatos/farmacologia , Sulfitos/farmacologia , Concentração de Íons de Hidrogênio
6.
Org Lett ; 25(1): 304-308, 2023 01 13.
Artigo em Inglês | MEDLINE | ID: mdl-36583507

RESUMO

A three-component reaction of alkenyl-tethered oxime ethers, sodium metabisulfite, and aryldiazonium tetrafluoroborates under mild conditions is developed. This reaction proceeds at room temperature without any oxidants or additives, affording ß-amino sulfones with good functional group tolerance through aminosulfonylation of unactivated alkene. Mechanistic studies show that this transformation undergoes a radical process, including radical trapping with sulfur dioxide and radical 1,4-amino migration.


Assuntos
Sulfitos , Sulfonas , Éteres , Dióxido de Enxofre
7.
J Environ Sci (China) ; 126: 81-94, 2023 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-36503806

RESUMO

Sulfite (S(IV)) is a promising substitute for sulfate radical-based advanced oxidation processes. Here, a composite of in-situ anchoring NiCo2O4 nanosheets on biochar (BC) was firstly employed as a heterogeneous activator for sulfite (NiCo2O4@BC-sulfite) to degrade atrazine (ATZ) in the neutral environment. The synergistic coupling of BC and NiCo2O4 endows the resulting composite excellent catalytic activity. 82% of the degradation ratio of ATZ (1 mg/L) could be achieved within 10 min at initial concentrations of 0.6 g/L NiCo2O4@BC, 3.0 mmol/L sulfite in neutral environment. When further supplementing sulfite into the system at 20 min (considering the depletion of sulfite), outstanding degradation efficiency (∼ 100%) were achieved in the next 10 min without any other energy input by the NiCo2O4@BC-sulfite system. The features of the prepared catalysts and the effects of some key parameters on ATZ degradation were systematically examined. A strong inner-sphere complexation (Co2+/Ni2+-SO32-) was explored between sulfite and the metal sites on the NiCo2O4@BC surface. The redox cycle of the surface metal efficiently mediated sulfite activation and triggered the series radical chain reactions. The generated radicals, in particular the surface-bound radicals were involved in ATZ degradation. High performance liquid chromatography-tandem mass spectrometry (LC-MS) technique was used to detect the degradation intermediates. Density functional theory (DFT) calculations were performed to illustrate the possible degradation pathways of ATZ. Finally, an underlying mechanism for ATZ removal was proposed. The present study offered a low-cost and sustainable catalyst for sulfite activation to remove ATZ in an environmentally friendly manner from wastewater.


Assuntos
Atrazina , Sulfitos , Cromatografia Líquida de Alta Pressão , Espectrometria de Massas
8.
Anal Chem ; 95(2): 1556-1565, 2023 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-36563112

RESUMO

DNA methylation (5-methylcytosine, 5mC) is the most important epigenetic modification in mammals. Deciphering the roles of 5mC relies on the quantitative detection of 5mC at the single-base resolution. Bisulfite sequencing (BS-seq) is the most often employed technique for mapping 5mC in DNA. However, bisulfite treatment may cause serious degradation of input DNA due to the harsh reaction conditions. Here, we engineered the human apolipoprotein B mRNA-editing catalytic polypeptide-like 3C (A3C) protein to endow the engineered A3C (eA3C) protein with differential deamination activity toward cytosine and 5mC. By the virtue of the unique property of eA3C, we proposed an engineered A3C sequencing (EAC-seq) method for the bisulfite-free and quantitative mapping of 5mC in DNA at the single-base resolution. In EAC-seq, the eA3C protein can deaminate C but not 5mC, which is employed to differentiate C and 5mC in sequencing. Using the EAC-seq method, we quantitatively detected 5mC in genomic DNA of lung cancer tissue. In contrast to the harsh reaction conditions of BS-seq, which could lead to significant degradation of DNA, the whole procedure of EAC-seq is carried out under mild conditions, thereby preventing DNA damage. Taken together, the EAC-seq approach is bisulfite-free and straightforward, making it an invaluable tool for the quantitative detection of 5mC in limited DNA at the single-base resolution.


Assuntos
5-Metilcitosina , Citidina Desaminase , Metilação de DNA , Humanos , 5-Metilcitosina/metabolismo , Citidina Desaminase/genética , Citidina Desaminase/metabolismo , Citosina , DNA/genética , DNA/metabolismo , Epigênese Genética , Análise de Sequência de DNA/métodos , Sulfitos/metabolismo
9.
Food Chem ; 407: 135146, 2023 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-36502733

RESUMO

Bisulfite (HSO3-) has the functions of bleaching, antiseptic, antioxidant, inhibiting bacterial growth, and controlling enzymatic reactions in food. However, long-term consumption of foods containing excessive amounts of bisulfite can be harmful to health. In addition, large doses of sulfur dioxide (SO2) can cause diarrhea, hypotension, allergic and asthmatic reactions in susceptible individuals. Therefore, it is urgent and essential to explore some rapid, reliable, and convenient tools to detect HSO3- in food and SO2 gas. Herein, we exploited a fluorescent probe, NPO, to detect HSO3- in 100 % aqueous solution. The probe has the advantages of easy synthesis, excellent water solubility, significant colorimetric change, good selectivity, high sensitivity, and fast response (within 1 min). Probe NPO was successfully applied for testing strips to visualize the behavior of HSO3- and SO2 gas. Moreover, the probe has been used to monitor the behavior of HSO3- in real food samples and animal serum samples.


Assuntos
Colorimetria , Água , Animais , Corantes Fluorescentes , Sulfitos , Dióxido de Enxofre
10.
Sci Total Environ ; 806(Pt 2): 150612, 2022 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-34597579

RESUMO

The formation of haloacetonitriles (HANs) during chlorination after sulfite/ultraviolet (UV) treatment of bromate (BrO3-) in the presence of amino acids (AAs) was investigated. During sulfite/UV treatment, the primary species hydrated electrons (eaq-) and hydrogen atom radicals (H) dominated the reduction of BrO3- to bromide (Br-), whereas the sulfite anion radicals (SO3-) and H degraded AAs to produce the intermediates HN=C(CH3)-COOH, CH3-CH=NH, and CH3-C≡N via α­hydrogen abstraction and NH2-hydrogen abstraction mechanisms. During post-chlorination, Br- was converted to HBrO/BrO-, and the HN=C(CH3)-COOH, CH3-CH=NH, and CH3-C≡N groups featured higher bromine utilization factor (BUF) and chlorine utilization factor (CUF) values than AAs, enhancing the formation of dibromoacetonitrile (DBAN) and dichloroacetonitrile (DCAN). The energetic feasibility of the transformation pathway, that is, HN=C(CH3)-COOH, CH3-CH=NH, and CH3-C ≡ N formation via hydrogen abstraction by SO3- and H and their further conversion to HANs, was proved by density functional theory calculations, which showed stepwise negative Gibbs free energy changes (ΔG < 0). The effects of pH and water matrices (e.g., HCO3-, Cl-, Fe3+, and natural organic matter) were comprehensively evaluated. Although 72% of BrO3- was removed by sulfite/UV treatment in the presence of AAs, the cytotoxicity index (CTI) and genotoxicity index (GTI) during post-chlorination increased by 213% and 125%, respectively, due to the formation of 24 CX3R-type disinfection by-products (DBPs), especially brominated DBPs. Accordingly, more attention should be given to the formation of brominated DBPs during post-chlorination when using sulfite/UV processes to remove BrO3- in the presence of AAs. As a solution, using monochloramine instead of chlorine as a disinfectant after the sulfite/UV process could significantly lower the CTI and GTI values by alleviating the formation of brominated DBPs.


Assuntos
Desinfetantes , Poluentes Químicos da Água , Purificação da Água , Bromatos , Cloro , Desinfecção , Halogenação , Sulfitos , Tecnologia , Poluentes Químicos da Água/análise
11.
Extremophiles ; 26(3): 33, 2022 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-36352059

RESUMO

In hydrothermal ecosystems, the dissolution of sulfur dioxide in water results in the formation of sulfite, which can be used in microbial metabolism. A limited number of thermophiles have been isolated using sulfite as an electron acceptor. From a terrestrial thermal spring, Sakhalin Island, Russia, we isolated a thermophilic anaerobic bacterium (strain SLA38T). Cells of strain SLA38T were spore-forming straight rods. Growth was observed at temperatures 45-65 °C (optimum at 60 °C) and pH 5.5-9.0 (optimum at pH 6.5-7.0). The novel isolate was capable of anaerobic respiration with sulfite, thiosulfate, fumarate and perchlorate or fermentative growth. Strain SLA38T utilized glycerol, lactate, pyruvate and yeast extract. It grew lithoautotrophically on carbon monoxide with thiosulfate as electron acceptor, producing acetate. The genome size of the isolate was 2.9 Mbp and genomic DNA G + C content was 53.6 mol%. Analysis of the 16S rRNA gene sequences revealed that strain SLA38T belongs to the genus Moorella. Based on the physiological features and phylogenetic analysis, we propose to assign strain SLA38T to a new species of the genus Moorella, as Moorella sulfitireducens sp. nov. The type strain is SLA38T (= DSM 111068T = VKM B-3584T).


Assuntos
Fontes Termais , Moorella , Moorella/genética , RNA Ribossômico 16S/genética , Filogenia , Fontes Termais/microbiologia , Composição de Bases , Anaerobiose , Tiossulfatos , DNA Bacteriano/química , Técnicas de Tipagem Bacteriana , Ecossistema , Análise de Sequência de DNA , Bactérias Anaeróbias/genética , Sulfitos
12.
Trop Anim Health Prod ; 54(6): 391, 2022 Nov 22.
Artigo em Inglês | MEDLINE | ID: mdl-36414743

RESUMO

The milk quality and characteristics of the local Gharbi sheep and autochthonous goat population were studied and compared to those of the local Maghrebi camel. Milk samples from 378 lactating animals raised in the Tunisian oasis region were obtained and processed for various physicochemical compositions (pH, density, acidity, dry matter, fat, protein, lactose, casein, ash, and casein-protein ratio), mineral concentrations (Ca, P, Na, and K), and bacteriological properties (total mesophilic aerobic bacteria (TMAB), total coliform count (TCC), lactic acid bacteria (LAB), sulfite-reducing Clostridium (CSR), yeast and molds (Y/M), Staphylococcus aureus (S. aureus), Escherichia coli (E. coli), and Salmonella) using standard methods. Milk from sheep breeds had a higher average of all physical parameters (pH, density, and dornic acidity) than milk from goat species. The sheep population produced milk with a similar pH to the camel population, but with a higher density and acidity content. The pH and acidity were higher in Neggas than in goat species, while density was similar in both. For chemical composition, the results showed significant heterogeneity in milk content across all species. Except for the casein-protein ratio, which favors goat species, the analysis indicates that sheep species were superior to populations of goats and camels in all chemical compositions. The present results showed considerable variation in the mineral content of milk from different species. The levels of calcium and phosphorus are higher in sheep than in goat and camel milk. Compared to small ruminants, milk from camels is the richest in Na and K. Additionally, more calcium is present in the milk of camels than that of goats. Goat milk, the lowest in Ca and Na, contains more P than camel milk and more K than sheep's milk on average. The poorest microbial quality was that of camel milk for all bacterial counts. Based on TMAB, TCC, and E. coli counts, the microbiological quality of goat milk was higher than that of ovine milk, while ovine milk had better quality based on LAB, Y/M, and S. aureus values. For Escherichia coli and Staphylococcus aureus, there were no significant variations between the species studied. Results showed that all milk samples studied were completely free of two dangerous pathogens, Salmonella and sulfite-reducing Clostridium. The bacteriological quality of small ruminant's milk was acceptable and met the regulatory limits set by Tunisian dairy legislation. Regarding camel milk, the microbial analysis revealed poor quality that exceeds standard criteria.


Assuntos
Camelus , Lactobacillales , Feminino , Ovinos , Animais , Leite/química , Caseínas , Staphylococcus aureus , Escherichia coli , Cálcio/análise , Tunísia , Lactação , Cabras , Sulfitos/análise
13.
Anal Chim Acta ; 1236: 340596, 2022 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-36396227

RESUMO

The increasing consumption of processed foods demands the usage of chemical preservatives to ensure freshness and extended shelf life. For this purpose, sodium sulfite and its derivatives have been widely used in a variety of food products to inhibit microbial spoilage and for mitigating oxidative decay. However, the excessive consumption of sulfite may cause health problems, thus requiring rapid and accurate analytical methods for the rapid identification of threshold levels. Conventionally, sulfite is volatilized from food samples by acidification followed by trapping of the gaseous SO2 and determination using a suitable analytical technique. Herein, we propose a yet unprecedented reagent-less approach via direct absorbance measurements of gaseous SO2 at 280 nm after sample acidification. The detection system combines a deep-UV LED and a SiC photodiode with a substrate-integrated hollow waveguide (iHWG) gas cell. Absorbance measurements were performed using a log-ratio amplifier circuitry, resulting in noise levels <0.7 mAU. This innovative concept enabled the determination of sulfite in beverages in the range of 25-1000 mg L-1 with suitable linearity (r2 > 0.99) and an analysis time <30 s. The limit of detection (LOD) was calculated at 14.3 mg L-1 (3σ) with an iHWG providing an optical path length of 75 mm. As a proof of concept, this innovative analytical platform was employed for sulfite quantification in concentrated grape juice, coconut water and beer, with suitable accuracy in terms of recovery (83-117%) and favorable comparison with the official Monier-Williams method. Given the inherent modularity and adaptability of the device concept, we anticipate the application of the proposed analytical platform for the in-situ studies addressing sulfite and other volatilized preservatives in a wide variety of food products with tailorable detectability.


Assuntos
Análise de Alimentos , Sulfitos , Indicadores e Reagentes , Sulfitos/análise , Fenômenos Químicos , Bebidas/análise
14.
BMC Plant Biol ; 22(1): 491, 2022 Oct 18.
Artigo em Inglês | MEDLINE | ID: mdl-36253724

RESUMO

BACKGROUND: ATP sulfurylase (ATPS) is a crucial enzyme for the selenate assimilation pathway in plants. RESULTS: In this study, genome-wide and comparative analyses of ATPS in Cardamine hupingshanensis, including sequence and structural analyses, were performed. The expression of ChATPS gene family members in C. hupingshanensis under selenium (Se) stress was also investigated, and our results suggest that ChATPS1-2 play key roles in the response to Se stress. Nine ATPS genes were found from C. hupingshanensis, which share highly conserved sequences with ATPS from Arabidopsis thaliana. In addition, we performed molecular docking of ATP sulfurylase in complex with compounds ATP, selenate, selenite, sulfate, and sulfite. ChAPS3-1 was found to have stronger binding energies with all compounds tested. Among these complexes, amino acid residues Arg, Gly, Ser, Glu, and Asn were commonly present. CONCLUSION: Our study reveals the molecular mechanism of C. hupingshanensis ATP sulfurylase interacting with selenate, which is essential for understanding selenium assimilation. This information will guide further studies on the function of the ChATPS gene family in the selenium stress response and lay the foundation for the selenium metabolic pathway in higher plants.


Assuntos
Arabidopsis , Cardamine , Selênio , Trifosfato de Adenosina , Aminoácidos/metabolismo , Arabidopsis/metabolismo , Cardamine/metabolismo , Simulação de Acoplamento Molecular , Ácido Selênico , Ácido Selenioso/metabolismo , Selênio/metabolismo , Sulfato Adenililtransferase/química , Sulfato Adenililtransferase/genética , Sulfato Adenililtransferase/metabolismo , Sulfatos/metabolismo , Sulfitos/metabolismo
15.
Pol J Microbiol ; 71(3): 453-461, 2022 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-36185029

RESUMO

In the present study, a comparative genome analysis of the novel alkaliphilic actinobacterial Nesterenkonia haasae with other members of the genus Nesterenkonia was performed. The genome size of Nesterenkonia members ranged from 2,188,008 to 3,676,111 bp. N. haasae and Nesterenkonia members of the present study encode the essential glycolysis and pentose phosphate pathway genes. In addition, some Nesterenkonia members encode the crucial genes for Entner-Doudoroff pathways. Some Nesterenkonia members possess the genes responsible for sulfate/thiosulfate transport system permease protein/ ATP-binding protein and conversion of sulfate to sulfite. Nesterenkonia members also encode the genes for assimilatory nitrate reduction, nitrite reductase, and the urea cycle. All Nesterenkonia members have the genes to overcome environmental stress and produce secondary metabolites. The present study helps to understand N. haasae and Nesterenkonia members' environmental adaptation and niches specificity based on their specific metabolic properties. Further, based on genome analysis, we propose reclassifying Nesterenkonia jeotgali as a later heterotypic synonym of Nesterenkonia sandarakina.


Assuntos
Nitratos , Tiossulfatos , Trifosfato de Adenosina , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos , Proteínas de Membrana Transportadoras/genética , Nitrito Redutases/genética , Hibridização de Ácido Nucleico , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sulfitos , Ureia
16.
PLoS One ; 17(10): e0273392, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36206251

RESUMO

Herein we report the use of an environmental multimetal(loid)-resistant strain, MF05, to biosynthesize single- or multi-element nanostructures under anaerobic conditions. Inorganic nanostructure synthesis typically requires methodologies and conditions that are harsh and environmentally hazardous. Thus, green/eco-friendly procedures are desirable, where the use of microorganisms and their extracts as bionanofactories is a reliable strategy. First, MF05 was entirely sequenced and identified as an Escherichia coli-related strain with some genetic differences from the traditional BW25113. Secondly, we compared the CdS nanostructure biosynthesis by whole-cell in a design defined minimal culture medium containing sulfite as the only sulfur source to obtain sulfide reduction from a low-cost chalcogen reactant. Under anaerobic conditions, this process was greatly favored, and irregular CdS (ex. 370 nm; em. 520-530 nm) was obtained. When other chalcogenites were tested (selenite and tellurite), only spherical Se0 and elongated Te0 nanostructures were observed by TEM and analyzed by SEM-EDX. In addition, enzymatic-mediated chalcogenite (sulfite, selenite, and tellurite) reduction was assessed by using MF05 crude extracts in anaerobiosis; similar results for nanostructures were obtained; however Se0 and Te0 formation were more regular in shape and cleaner (with less background). Finally, the in vitro nanostructure biosynthesis was assessed with salts of Ag, Au, Cd, and Li alone or in combination with chalcogenites. Several single or binary nanostructures were detected. Our results showed that MF05 is a versatile anaerobic bionanofactory for different types of inorganic NS. synthesis.


Assuntos
Nanoestruturas , Sais , Anaerobiose , Cádmio , Misturas Complexas , Nanoestruturas/química , Ácido Selenioso , Sulfetos , Sulfitos , Enxofre , Telúrio
17.
Food Res Int ; 161: 111780, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-36192876

RESUMO

Sulfite is widely used to prevent enzymatic browning in shrimp and lobster processing. However, sulfite may cause allergy in sensitive consumers. Thus, regulatory agencies set limits for its use. Sulfite is usually controlled by the normalized Monier-Williams (MW) titrimetric method that allows a limited number of samples to be analyzed. This manuscript consolidates an innovative method for sulfite inspection in seafood by capillary zone electrophoresis with diode array detector (CZE-DAD). A simple, fast, and simultaneous extraction and derivatization method was developed to provide high throughput for analytical routine. The high instability of the sulfite was suppressed by its derivatization with formaldehyde producing hydroxymethylsulfonate. The evaluation of its analytical performance yielded excellent results in compliance with the strict parameters required for metrological accreditation. The CZE-DAD method was selective and specific when submitted to confirmatory evaluations by liquid chromatography coupled to mass spectrometry. The limit of detection (3.50 mg kg-1), limit of quantitation (11.7 mg kg-1) and recoveries (99-103%) were adequate for sample analysis. The measurement uncertainty was estimated by the propagation of errors and experimental standard uncertainties (precision, accuracy, and analytical curves) and type B uncertainties from traceable measurement instruments. The low relative uncertainty (10%) and the adequate reproducibility demonstrated method suitability. The CZE-DAD results were compared to the MW method through the respective expanded standard uncertainties and normalized error. This new method is promising to be used in seafood inspection and continuous laboratory evaluations using instrumentation not very expensive to acquire and maintain.


Assuntos
Eletroforese Capilar , Sulfitos , Eletroforese Capilar/métodos , Formaldeído , Reprodutibilidade dos Testes , Alimentos Marinhos/análise
18.
Anal Chem ; 94(44): 15489-15498, 2022 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-36280344

RESUMO

DNA methylation (5-methylcytosine, 5mC) is the most prevalent epigenetic modification that is predominantly found in CG dinucleotides in mammalian genomes. In-depth investigation of the functions of 5mC heavily relies on the quantitative measurement of 5mC at single-base resolution in genomes. Here, we proposed a methyltransferase-directed labeling with APOBEC3A (A3A) deamination sequencing (MLAD-seq) method for the single-base resolution and quantitative detection of 5mC in DNA. In MLAD-seq, a mutant of DNA methyltransferase, M.MpeI-N374K, is utilized to selectively transfer a carboxymethyl group to the 5 position of cytosine in the CG dinucleotide to form 5-carboxymethylcytosine (5camC) using carboxy-S-adenosyl-l-methionine (caSAM) as the cofactor. After A3A treatment, 5camC is resistant to the deamination and base pairs with guanine. Thus, the cytosines in CG sites are read as C in sequencing. On the contrary, the methyl group in 5mC inhibits its carboxymethylcytosine by M.MpeI-N374K and therefore is readily deaminated by A3A to produce thymine that pairs with adenine and is read as T in sequencing. The differential readouts from C and 5mC in the MLAD-seq enable the single-base resolution mapping of 5mC in CG sites in DNA. With the developed MLAD-seq method, we observed the hypermethylation in the promoter region of retinoic acid receptor ß (RARB) gene from human nonsmall cell lung tumor tissue. Compared to harsh reaction conditions in bisulfite sequencing that could lead to significant degradation of DNA, the whole procedure of MLAD-seq is carried out under mild conditions, which will avoid DNA damage. Thus, MLAD-seq is more suitable in the scenario where only limited input DNA is available. Taken together, the MLAD-seq offers a valuable tool for bisulfite-free, single-base resolution and quantitative detection of 5mC in limited DNA.


Assuntos
5-Metilcitosina , Metiltransferases , Animais , Humanos , Desaminação , Análise de Sequência de DNA/métodos , Sulfitos , Epigênese Genética , DNA/genética , Citosina , Metilação de DNA , Mamíferos
19.
Int J Mol Sci ; 23(19)2022 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-36232908

RESUMO

Long interspersed nuclear element 1 (LINE-1) bisulfite pyrosequencing is a widely used technique for genome-wide methylation analyses. We aimed to investigate the effects of experimental and biological factors on its results to improve the comparability. LINE-1 bisulfite pyrosequencing was performed on colorectal tissue (n = 222), buffy coat (n = 39), and plasma samples (n = 9) of healthy individuals and patients with colorectal tumors. Significantly altered methylation was observed between investigated LINE-1 CpG positions of non-tumorous tissues (p ≤ 0.01). Formalin-fixed, paraffin-embedded biopsies (73.0 ± 5.3%) resulted in lower methylation than fresh frozen samples (76.1 ± 2.8%) (p ≤ 0.01). DNA specimens after long-term storage showed higher methylation levels (+3.2%, p ≤ 0.01). In blood collection tubes with preservatives, cfDNA and buffy coat methylation significantly changed compared to K3EDTA tubes (p ≤ 0.05). Lower methylation was detected in older (>40 years, 76.8 ± 1.7%) vs. younger (78.1 ± 1.0%) female patients (p ≤ 0.05), and also in adenomatous tissues with MTHFR 677CT, or 1298AC mutations vs. wild-type (p ≤ 0.05) comparisons. Based on our findings, it is highly recommended to consider the application of standard DNA samples in the case of a possible clinical screening approach, as well as in experimental research studies.


Assuntos
Ácidos Nucleicos Livres , Neoplasias Colorretais , Idoso , Fatores Biológicos , Biópsia , Ácidos Nucleicos Livres/genética , Neoplasias Colorretais/genética , Neoplasias Colorretais/patologia , DNA/genética , Metilação de DNA , Feminino , Formaldeído , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Biópsia Líquida , Elementos Nucleotídeos Longos e Dispersos/genética , Masculino , Sulfitos
20.
Water Res ; 225: 119207, 2022 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-36215832

RESUMO

The integration of UV/sulfite autoxidation process (USAP, i.e., UV activation of sulfite in the presence of 5 ∼ 10 mg/L O2) into conventional water to degrade micropollutants rises extensive attention, but its impact on water quality, and especially the formation of disinfection byproducts is still unclear. Herein, the formation of dibromoacetonitrile (DBAN) from bromate (BrO3-) upon treatment with USAP followed by chlorination was evaluated, in the presence of amino acids (AAs) selected as representative organic matter in drinking water. Results revealed that hydrated electrons (eaq-) produced during USAP contribute to the reduction of BrO3- to Br-, which is then converted into HBrO/BrO- during post-chlorination. At the same time, sulfate radicals (SO4•-) and hydroxyl radicals (•OH) generated in USAP mediated AAs' conversion via α-hydrogen abstraction and NH2-hydrogen abstraction reactions to produce HN=C(CH3)‒COOH, CH3‒CH=NH, and CH3‒CN, which are released into the post-chlorination stage and therefore, enhance the bromine utilization factor (BUF) value and DBAN formation. The effects of the USAP treatment time, BrO3- concentration, AA concentration, pH, and real waters were also evaluated. Although 63.5% of BrO3- was eliminated by USAP followed by chlorination, the toxicity index (TI) was increased by 1.5-fold due to the formation of the all brominated CX3R-type nitrogenous disinfection byproducts (N-DBPs), demonstrating the potential risk of applying USAP as a treatment process in BrO3- containing waters.


Assuntos
Desinfetantes , Água Potável , Poluentes Químicos da Água , Purificação da Água , Bromatos/química , Halogenação , Purificação da Água/métodos , Bromo , Poluentes Químicos da Água/química , Desinfecção/métodos , Sulfitos , Sulfatos , Hidrogênio , Aminoácidos , Desinfetantes/química
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