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1.
BMC Bioinformatics ; 25(1): 206, 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38840038

ABSTRACT

BACKGROUND: Bisulfite sequencing (BS-Seq) is a fundamental technique for characterizing DNA methylation profiles. Genotype calling from bisulfite-converted BS-Seq data allows allele-specific methylation analysis and the concurrent exploration of genetic and epigenetic profiles. Despite various methods have been proposed, single nucleotide polymorphisms (SNPs) calling from BS-Seq data, particularly for SNPs on chromosome X and in the presence of contaminative data, poses ongoing challenges. RESULTS: We introduce bsgenova, a novel SNP caller tailored for bisulfite sequencing data, employing a Bayesian multinomial model. The performance of bsgenova is assessed by comparing SNPs called from real-world BS-Seq data with those from corresponding whole-genome sequencing (WGS) data across three human cell lines. bsgenova is both sensitive and precise, especially for chromosome X, compared with three existing methods. Moreover, in the presence of low-quality reads, bsgenova outperforms other methods notably. In addition, bsgenova is meticulously implemented, leveraging matrix imputation and multi-process parallelization. Compared to existing methods, bsgenova stands out for its speed and efficiency in memory and disk usage. Furthermore, bsgenova integrates bsextractor, a methylation extractor, enhancing its flexibility and expanding its utility. CONCLUSIONS: We introduce bsgenova for SNP calling from bisulfite-sequencing data. The source code is available at https://github.com/hippo-yf/bsgenova under license GPL-3.0.


Subject(s)
DNA Methylation , Polymorphism, Single Nucleotide , Sequence Analysis, DNA , Sulfites , Humans , DNA Methylation/genetics , Sulfites/chemistry , Sequence Analysis, DNA/methods , Genotype , Software , Whole Genome Sequencing/methods , Bayes Theorem
2.
Spectrochim Acta A Mol Biomol Spectrosc ; 319: 124540, 2024 Oct 15.
Article in English | MEDLINE | ID: mdl-38824754

ABSTRACT

In this work, a ratiometric and chromogenic fluorescent probe 1 was synthesized for the detection of SO32-. The probe 1 at PBS (10 mM, pH = 7.4) presented a marked emission band at 661 nm. Upon addition of SO32- ions, a highly emissive adduct with a marked fluorescence at 471 nm were obtained through a Michael addition. The probe 1 displayed a noticeable fluorescence ratiometric response with a large shift (190 nm) in emission wavelength. The probe can quantitatively detect SO32- with high specificity, fast response (within 130 s) as well as low detection limit (13 nM), and a large Stokes shift (139 nm). Fluorescence imaging of HeLa cells indicated that 1 could be used for monitoring the intrinsically generated intracellular SO32- in living cells by ratiometric fluorescence imaging. Furthermore, 1 could be application in real water and sugar samples with high sensitivity and good recoveries.


Subject(s)
Fluorescent Dyes , Spectrometry, Fluorescence , Sulfites , Humans , Sulfites/analysis , HeLa Cells , Fluorescent Dyes/chemistry , Fluorescent Dyes/chemical synthesis , Spectrometry, Fluorescence/methods , Limit of Detection , Food Analysis/methods , Optical Imaging/methods
3.
Genome Biol ; 25(1): 157, 2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38877540

ABSTRACT

Methylation-based liquid biopsies show promises in detecting cancer using circulating cell-free DNA; however, current limitations impede clinical application. Most assays necessitate substantial DNA inputs, posing challenges. Additionally, underrepresented tumor DNA fragments may go undetected during exponential amplification steps of traditional sequencing methods. Here, we report linear amplification-based bisulfite sequencing (LABS), enabling linear amplification of bisulfite-treated DNA fragments in a genome-wide, unbiased fashion, detecting cancer abnormalities with sub-nanogram inputs. Applying LABS to 100 patient samples revealed cancer-specific patterns, copy number alterations, and enhanced cancer detection accuracy by identifying tissue-of-origin and immune cell composition.


Subject(s)
DNA Methylation , Neoplasms , Sequence Analysis, DNA , Sulfites , Humans , Neoplasms/genetics , Sequence Analysis, DNA/methods , Cell-Free Nucleic Acids , Nucleic Acid Amplification Techniques/methods , DNA Copy Number Variations , DNA, Neoplasm/genetics , Circulating Tumor DNA/genetics
4.
Bioorg Chem ; 148: 107423, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38733751

ABSTRACT

Viscosity and sulfur dioxide derivatives were significant indicators for the assessment of health threat and even cancers, therefore, on-site and real time detection of viscosity and sulfur dioxide derivatives has obtained considerable attentions. An FRET-based fluorescence probe JZX was designed and synthesized based on a novel energy donor of N,N-diethyl-4-(1H-phenanthro[9,10-d]imidazol-2-yl)benzamide fluorophore. JZX exhibited a large Stokes shift (230 nm), high energy transfer efficiency, wide emission channel gap (135 nm) and excellent stability and biocompatibility. JZX detected sulfur dioxide with low detection limit (55 nM), fast responding (16 min), high selectivity and sensitivity. Additionally, JZX tend to target endoplasmic reticulum of which normal metabolism will be disturbed by the abnormal levels of viscosity and sulfur dioxide derivatives. Prominently, JZX could concurrently detect viscosity and sulfur dioxide derivatives depending on different fluorescence signals in living cells for the screening of cancer cells. Hence, probe JZX will be a promising candidate for the detection of viscosity and sulfur dioxide derivatives, and even for the diagnosis of liver cancers.


Subject(s)
Fluorescence Resonance Energy Transfer , Fluorescent Dyes , Sulfites , Fluorescent Dyes/chemistry , Fluorescent Dyes/chemical synthesis , Humans , Viscosity , Sulfites/analysis , Molecular Structure , Sulfur Dioxide/analysis , Optical Imaging , HeLa Cells
5.
Ecotoxicol Environ Saf ; 279: 116474, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38772144

ABSTRACT

Rhubarb is widely used in health care, but causing a great amount of rhein-containing herbal residue. Rhein with several toxicities might pollute environment, damage ecology and even hazard human health if left untreated. In this study, the degradation effects of bisulfite- (BS) and peroxymonosulfate- (PMS) based oxidation systems on rhein in rhubarb residue were compared and investigated. The effects of BS and PMS with two valence states of ferric ion (Fe) on the degradation of rhein in rhubarb residue were optimized for the selection of optimal oxidation system. The influences of reaction temperature, reaction time and initial pH on the removal of rhein under the optimal oxidation system were evaluated. The chemical profiles of rhubarb residue with and without oxidation process were compared by UPLC-QTOF-MS/MS, and the degradation effects were investigated by PLS-DA and S plot/OPLS-DA analysis. The results manifested that PMS showed relative higher efficiency than BS on the degradation of rhein. Moreover, Fe(III) promoted the degradation effect of PMS, demonstrated that Fe(III)/PMS is the optimal oxidation system to degrade rhein in rhubarb residue. Further studies indicated that the degradation of rhein by the Fe(III)/PMS oxidation system was accelerated with the prolong of reaction time and the elevation of reaction temperature, and also affected by the initial pH. More importantly, Fe(III)/PMS oxidation system could degrade rhein in rhubarb residue completely under the optimal conditions. In conclusion, Fe(III)/PMS oxidation system is a feasible method to treat rhein in rhubarb residue.


Subject(s)
Anthraquinones , Oxidation-Reduction , Peroxides , Rheum , Anthraquinones/chemistry , Rheum/chemistry , Peroxides/chemistry , Tandem Mass Spectrometry , Sulfites/chemistry , Hydrogen-Ion Concentration , Ferric Compounds/chemistry , Temperature
6.
Analyst ; 149(12): 3356-3362, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38712511

ABSTRACT

Many diseases in the human body are related to the overexpression of viscosity and sulfur dioxide. Therefore, it is essential to develop rapid and sensitive fluorescent probes to detect viscosity and sulfur dioxide. In the present work, we developed a dual-response fluorescent probe (ES) for efficient detection of viscosity and sulfur dioxide while targeting mitochondria well. The probe generates intramolecular charge transfer by pushing and pulling the electron-electron system, and the ICT effect is destroyed and the fluorescence quenched upon reaction with sulfite. The rotation of the molecule is inhibited in the high-viscosity system, producing a bright red light. In addition, the probe has good biocompatibility and can be used to detect sulfite in cells, zebrafish and mice, as well as upregulation of viscosity in LPS-induced inflammation models. We expect that the dual response fluorescent probe ES will be able to detect viscosity and sulfite efficiently, providing an effective means of detecting viscosity and sulfite-related diseases.


Subject(s)
Fluorescent Dyes , Inflammation , Mitochondria , Sulfites , Zebrafish , Fluorescent Dyes/chemistry , Fluorescent Dyes/chemical synthesis , Fluorescent Dyes/toxicity , Animals , Sulfites/chemistry , Sulfites/analysis , Viscosity , Mitochondria/metabolism , Mitochondria/chemistry , Mice , Humans , Inflammation/chemically induced , Sulfur Dioxide/analysis , Sulfur Dioxide/chemistry , Lipopolysaccharides , RAW 264.7 Cells , Optical Imaging/methods
7.
Nucleic Acids Res ; 52(10): e49, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38709875

ABSTRACT

Over 150 types of chemical modifications have been identified in RNA to date, with pseudouridine (Ψ) being one of the most prevalent modifications in RNA. Ψ plays vital roles in various biological processes, and precise, base-resolution detection methods are fundamental for deep analysis of its distribution and function. In this study, we introduced a novel base-resolution Ψ detection method named pseU-TRACE. pseU-TRACE relied on the fact that RNA containing Ψ underwent a base deletion after treatment of bisulfite (BS) during reverse transcription, which enabled efficient ligation of two probes complementary to the cDNA sequence on either side of the Ψ site and successful amplification in subsequent real-time quantitative PCR (qPCR), thereby achieving selective and accurate Ψ detection. Our method accurately and sensitively detected several known Ψ sites in 28S, 18S, 5.8S, and even mRNA. Moreover, pseU-TRACE could be employed to measure the Ψ fraction in RNA and explore the Ψ metabolism of different pseudouridine synthases (PUSs), providing valuable insights into the function of Ψ. Overall, pseU-TRACE represents a reliable, time-efficient and sensitive Ψ detection method.


Subject(s)
Pseudouridine , Real-Time Polymerase Chain Reaction , Sulfites , Humans , Pseudouridine/chemistry , Pseudouridine/genetics , Pseudouridine/isolation & purification , Real-Time Polymerase Chain Reaction/methods , RNA/chemistry , RNA/genetics , RNA, Messenger/genetics , RNA, Messenger/chemistry , RNA, Messenger/metabolism , Sulfites/chemistry
8.
Environ Pollut ; 355: 124182, 2024 Aug 15.
Article in English | MEDLINE | ID: mdl-38776997

ABSTRACT

The treatment of textile wastewater containing harmful metal ions poses a significant challenge in industrial applications due to its environmental impact. In this study, the use of sulfite for treating simulated dye wastewater containing New Coccine (NC) and Cr(VI) was investigated. The removal of NC was influenced by the redox reaction between Cr(VI) and sulfite, demonstrating a strong self-boosting effect of Cr(VI) on NC removal. Remarkable NC decoloration (95%) and Cr(VI) reduction (90%) were achieved within 1 min, highlighting the effectiveness of the treatment. Quenching experiments and electron paramagnetic resonance (EPR) technology confirmed that singlet oxygen (1O2) was the main oxidative agent for organic dye removal and SO4•-, •OH and Cr(V) were also identified as key contributors to NC degradation. The Cr(VI)/sulfite system exhibited higher efficiency in degrading azo dyes, such as NC and Congo Red (CR), compared to non-azo dyes like Methylene Blue (MB). This superiority may be attributed to the action of Cr(V) on azo groups. Additionally, the COD removal experiments were conducted on the actual dye wastewater, showing the excellent performance of the Cr(VI)/Sulfite system in treating industrial textile wastewater. This approach presents a promising strategy for effective "waste control by waste", offering great potential for addressing challenges related to dye wastewater treatment and environmental pollution control in practical industrial scenarios.


Subject(s)
Chromium , Coloring Agents , Oxidation-Reduction , Sulfites , Waste Disposal, Fluid , Wastewater , Water Pollutants, Chemical , Wastewater/chemistry , Coloring Agents/chemistry , Water Pollutants, Chemical/chemistry , Chromium/chemistry , Sulfites/chemistry , Waste Disposal, Fluid/methods , Textiles , Textile Industry , Industrial Waste
9.
Sci Total Environ ; 931: 172898, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38697543

ABSTRACT

The production of short-chain fatty acids (SCFAs) is constrained by substrate availability and the increased fractional pressure of H2 emitted by acidogenic/fermentative bacteria during anaerobic fermentation of waste activated sludge (WAS). This study introduced a novel approach employing zero-valent iron (ZVI)-activated sulfite pretreatment combined with H2-consuming sulfate-reducing bacteria (SRB) mediation to improve SCFAs, especially acetate production from WAS fermentation. Experimental results showed that the combined ZVI-activated sulfite and incomplete-oxidative SRB (io-SRB) process achieved a peak SCFAs production of 868.11 mg COD/L, with acetate accounting for 80.55 %, which was 7.90- and 2.18-fold higher than that obtained from raw WAS fermentation, respectively. This could be firstly attributed to the SO4- and OH generated by ZVI-activated sulfite, which significantly promoted WAS decomposition, e.g., soluble proteins and carbohydrates increased 14.3- and 10.8-fold, respectively, over those in raw WAS. The biodegradation of dissolved organic matter was subsequently enhanced by the synergistic interaction and H2 transfer between anaerobic fermentation bacteria (AFB) and io-SRB. The positive and negative correlations among AFB, nitrate-reducing bacteria (NRB) and the io-SRB consortia were revealed by molecular ecological network (MEN) and Mantel test. Moreover, the expression of functional genes was also improved, for instance, in relation to acetate formation, the relative abundances of phosphate acetyltransferase and acetate kinase was 0.002 % and 0.005 % higher than that in the control test, respectively. These findings emphasized the importance of sulfate radicals-based oxidation pretreatment and the collaborative relationships of multifunctional microbes on the value-added chemicals and energy recovery from sludge fermentation.


Subject(s)
Fatty Acids, Volatile , Fermentation , Sewage , Sulfites , Waste Disposal, Fluid , Sewage/microbiology , Sulfites/metabolism , Fatty Acids, Volatile/metabolism , Waste Disposal, Fluid/methods , Sulfates/metabolism , Hydrogen/metabolism , Bacteria/metabolism , Iron/metabolism
10.
Water Res ; 258: 121773, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38796910

ABSTRACT

Sulfite (S(IV)), as an alternative to persulfate, has demonstrated its cost-effectiveness and environmentally friendly nature, garnering increasing attention in Advanced Oxidation Processes (AOPs). Dissolved organic matter (DOM) commonly occurred in diverse environments and was often regarded as an interfering factor in sulfite-based AOPs. However, less attention has been paid to the promotion of the activation of sulfite by excited DOM, which could produce various reactive intermediates. The study focused on the activation of sulfite using visible light (VL) - excited humic acid (HA) to efficiently degrade many common organic pollutants, which was better than peroxydisulfate (PDS) and peroxymonosulfate (PMS) systems. Quenching experiments and electron paramagnetic resonance (EPR) analysis revealed that the triplet states of HA (3HA*) activated sulfite through energy transfer, resulting in the production of SO4·-, O2·-, and 1O2. The most significant active species found in the degradation of roxarsone (ROX) was 1O2, which was a non-radical pathway and exhibits high selectivity for pollutant degradation. This non-radical pathway was not commonly observed in traditional sulfite-based AOPs. Additionally, the coexistence of various inorganic anions, such as NO3-, Cl-, SO42-, CO32-, and PO43-, had little effect on the degradation of ROX. Furthermore, DOM from different natural water demonstrated efficient activation of S(IV) under light conditions, opening up new possibilities for applying sulfite-based advanced oxidation to the remediation of organic pollution in diverse sites and water bodies. In summary, this research offered promising insights into the potential application of sulfite-based AOPs, facilitated by photo-excited HA, as a new strategy for efficiently degrading organic pollutants in various environmental settings.


Subject(s)
Humic Substances , Light , Sulfites , Wastewater , Water Pollutants, Chemical , Sulfites/chemistry , Wastewater/chemistry , Water Pollutants, Chemical/chemistry , Water Purification/methods , Waste Disposal, Fluid/methods , Oxidation-Reduction
11.
Molecules ; 29(10)2024 May 08.
Article in English | MEDLINE | ID: mdl-38792053

ABSTRACT

Sulfite, a widely used food additive, is subject to regulated labeling. The extraction of sulfite as the stable hydroxymethylsulfonate (HMS) form and its quantitative analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been recognized for their good sensitivity, selectivity, and versatility across various food materials. This study aimed to develop a cost-effective and simpler method for sulfite quantitation, while maintaining the superior sensitivity and selectivity of mass spectrometry (MS). To achieve this, we introduced paper spray ionization (PSI), an ambient desorption ionization technique that could achieve the direct measurement of analytes without employing separation. We also employed a novel internal standard (IS) structurally similar to the analyte, replacing the more expensive isotopically labeled IS. Although the PSI-MS/MS method developed in this study exhibited slightly lower analytical performance compared to the conventional LC-MS/MS, it remained effective for sulfite analysis in dried fruits.


Subject(s)
Fruit , Sulfites , Tandem Mass Spectrometry , Sulfites/analysis , Sulfites/chemistry , Tandem Mass Spectrometry/methods , Fruit/chemistry , Chromatography, Liquid/methods , Paper , Food Analysis/methods
12.
Environ Sci Technol ; 58(21): 9427-9435, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38747404

ABSTRACT

Photoexcitation of sulfite (SO32-) is often used to generate hydrated electrons (eaq-) in processes to degrade perfluoroalkyl and polyfluoroalkyl substances (PFASs). Conventional consensus discourages the utilization of SO32- concentrations exceeding 10 mM for effective defluorination. This has hindered our understanding of SO32- chemistry beyond its electron photogeneration properties. In contrast, the radiation-chemical study presented here, directly producing eaq- through water radiolysis, suggests that SO32- plays a previously overlooked activation role in the defluorination. Quantitative 60Co gamma irradiation experiments indicate that the increased SO32- concentration from 0.1 to 1 M enhances the defluorination rate by a remarkable 15-fold, especially for short-chain perfluoroalkyl sulfonate (PFSA). Furthermore, during the treatment of long-chain PFSA (C8F17-SO3-) with a higher concentration of SO32-, the intermediates of C8H17-SO3- and C3F7-COO- were observed, which are absent without SO32-. These observations highlight that a higher concentration of SO32- facilitates both reaction pathways: chain shortening and H/F exchange. Pulse radiolysis measurements show that elevated SO32- concentrations accelerate the bimolecular reaction between eaq- and PFSA by 2 orders of magnitude. 19F NMR measurements and theoretical simulations reveal the noncovalent interactions between SO32- and F atoms, which exceptionally reduce the C-F bond dissociation energy by nearly 40%. As a result, our study offers a more effective strategy for degrading highly persistent PFSA contaminants.


Subject(s)
Electrons , Fluorocarbons , Sulfites , Sulfites/chemistry , Fluorocarbons/chemistry , Water/chemistry
13.
PLoS One ; 19(5): e0297006, 2024.
Article in English | MEDLINE | ID: mdl-38743704

ABSTRACT

Epigenetic ageing in a human context, has been used to better understand the relationship between age and factors such as lifestyle and genetics. In an ecological setting, it has been used to predict the age of individual animals for wildlife management. Despite the importance of epigenetic ageing in a range of research fields, the assays to measure epigenetic ageing are either expensive on a large scale or complex. In this study, we aimed to improve the efficiency and sequencing quality of an existing epigenetic ageing assay for the Australian Lungfish (Neoceratodus forsteri). We used an enzyme-based alternative to bisulfite conversion to reduce DNA fragmentation and evaluated its performance relative to bisulfite conversion. We found the sequencing quality to be 12% higher with the enzymatic alternative compared to bisulfite treatment (p-value < 0.01). This new enzymatic based approach, although currently double the cost of bisulfite treatment can increases the throughput and sequencing quality. We envisage this assay setup being adopted increasingly as the scope and scale of epigenetic ageing research continues to grow.


Subject(s)
Aging , Epigenesis, Genetic , Sulfites , Animals , Aging/genetics , Sulfites/chemistry , Fishes/genetics , Sequence Analysis, DNA/methods , DNA Methylation , DNA Fragmentation
14.
Sci Rep ; 14(1): 10124, 2024 05 02.
Article in English | MEDLINE | ID: mdl-38698114

ABSTRACT

Despite the high energetic cost of the reduction of sulfate to H2S, required for the synthesis of sulfur-containing amino acids, some wine Saccharomyces cerevisiae strains have been reported to produce excessive amounts of H2S during alcoholic fermentation, which is detrimental to wine quality. Surprisingly, in the presence of sulfite, used as a preservative, wine strains produce more H2S than wild (oak) or wine velum (flor) isolates during fermentation. Since copper resistance caused by the amplification of the sulfur rich protein Cup1p is a specific adaptation trait of wine strains, we analyzed the link between copper resistance mechanism, sulfur metabolism and H2S production. We show that a higher content of copper in the must increases the production of H2S, and that SO2 increases the resistance to copper. Using a set of 51 strains we observed a positive and then negative relation between the number of copies of CUP1 and H2S production during fermentation. This complex pattern could be mimicked using a multicopy plasmid carrying CUP1, confirming the relation between copper resistance and H2S production. The massive use of copper for vine sanitary management has led to the selection of resistant strains at the cost of a metabolic tradeoff: the overproduction of H2S, resulting in a decrease in wine quality.


Subject(s)
Copper , Fermentation , Hydrogen Sulfide , Metallothionein , Odorants , Saccharomyces cerevisiae , Vitis , Wine , Wine/analysis , Copper/metabolism , Vitis/microbiology , Saccharomyces cerevisiae/metabolism , Hydrogen Sulfide/metabolism , Odorants/analysis , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Sulfites/pharmacology , Pest Control/methods
15.
Spectrochim Acta A Mol Biomol Spectrosc ; 317: 124463, 2024 Sep 05.
Article in English | MEDLINE | ID: mdl-38749205

ABSTRACT

In this work, a triphenylamine-benzofuran-derived fluorescent probe TBSF was developed for monitoring the sulfite level in Chinese medicinal materials and imaging in living cells. In the testing system, under 445 nm excitation, TBSF responded to sulfite steadily with a 540 nm fluorescence reporting signal. The testing system showed advantages including high sensitivity, rapid response, and high selectivity. In particular, TBSF achieved the sulfite detection in the water decoction of Chinese medicinal materials from both addition and excessive fumigation. It also realized the intracellular imaging of both exogenous and endogenous sulfite in living HepG2 cells. The imaging in water decoction-treated cells inferred the potential for the interdisciplinary detection.


Subject(s)
Benzofurans , Fluorescent Dyes , Spectrometry, Fluorescence , Sulfites , Sulfites/analysis , Fluorescent Dyes/chemistry , Humans , Benzofurans/chemistry , Benzofurans/analysis , Hep G2 Cells , Drugs, Chinese Herbal/chemistry , Drugs, Chinese Herbal/analysis , Aniline Compounds/chemistry , Optical Imaging
16.
Oncol Res ; 32(4): 737-752, 2024.
Article in English | MEDLINE | ID: mdl-38560573

ABSTRACT

Kidney Renal Clear Cell Carcinoma (KIRC) is a malignant tumor that carries a substantial risk of morbidity and mortality. The MMP family assumes a crucial role in tumor invasion and metastasis. This study aimed to uncover the mechanistic relevance of the MMP gene family as a therapeutic target and diagnostic biomarker in Kidney Renal Clear Cell Carcinoma (KIRC) through a comprehensive approach encompassing both computational and molecular analyses. STRING, Cytoscape, UALCAN, GEPIA, OncoDB, HPA, cBioPortal, GSEA, TIMER, ENCORI, DrugBank, targeted bisulfite sequencing (bisulfite-seq), conventional PCR, Sanger sequencing, and RT-qPCR based analyses were used in the present study to analyze MMP gene family members to accurately determine a few hub genes that can be utilized as both therapeutic targets and diagnostic biomarkers for KIRC. By performing STRING and Cytohubba analyses of the 24 MMP gene family members, MMP2 (matrix metallopeptidase 2), MMP9 (matrix metallopeptidase 9), MMP12 (matrix metallopeptidase 12), and MMP16 (matrix metallopeptidase 16) genes were denoted as hub genes having highest degree scores. After analyzing MMP2, MMP9, MMP12, and MMP16 via various TCGA databases and RT-qPCR technique across clinical samples and KIRC cell lines, interestingly, all these hub genes were found significantly overexpressed at mRNA and protein levels in KIRC samples relative to controls. The notable effect of the up-regulated MMP2, MMP9, MMP12, and MMP16 was also documented on the overall survival (OS) of the KIRC patients. Moreover, targeted bisulfite-sequencing (bisulfite-seq) analysis revealed that promoter hypomethylation pattern was associated with up-regulation of hub genes (MMP2, MMP9, MMP12, and MMP16). In addition to this, hub genes were involved in various diverse oncogenic pathways. The MMP gene family members (MMP2, MMP9, MMP12, and MMP16) may serve as therapeutic targets and prognostic biomarkers in KIRC.


Subject(s)
Carcinoma, Renal Cell , Kidney Neoplasms , Sulfites , Humans , Kidney Neoplasms/genetics , Kidney Neoplasms/pathology , Matrix Metalloproteinase 12 , Matrix Metalloproteinase 9/genetics , Matrix Metalloproteinase 9/metabolism , Matrix Metalloproteinase 2/genetics , Matrix Metalloproteinase 16 , Prognosis , Biomarkers, Tumor/genetics , Carcinoma, Renal Cell/pathology , Kidney/metabolism , Kidney/pathology
17.
Biomed Environ Sci ; 37(2): 228-232, 2024 Feb 20.
Article in English | MEDLINE | ID: mdl-38582987

ABSTRACT

As a reducing salt, sodium sulfite could deprive oxygen in solution, which could mimic hypoxic stress in Caenorhabditis elegans. In this study, the wild-type Escherichia coli strain MG1655 was used to examine the inhibition of sodium sulfite-induced hypoxia by observing the bacterial growth curves. We also analyzed the growth curves of mutant strains (for arcA/B, soxR/S, fnr, and oxyR) related to E. coli hypoxic pathways to reveal roles of the related genes during hypoxia. The ultrastructure of hypoxia-inhibited bacteria were also observed using transmission electron microscopy. Sodium sulfite could maintain hypoxic condition of bacterial culture for 8 h with concentrations over 40 mmol/L. Complete ultrastructure of the bacteria indicated sodium sulfite did inhibit bacterial growth and division. Among the hypoxia genes, fnr and arcB played key roles in sodium sulfite-induced hypoxia. This study showed that sodium sulfite could be used as a novel hypoxia revulsant for bacterial cultures.


Subject(s)
Escherichia coli Proteins , Escherichia coli , Sulfites , Humans , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Repressor Proteins/genetics , Repressor Proteins/metabolism , Bacterial Outer Membrane Proteins/genetics , Hypoxia , Gene Expression Regulation, Bacterial
18.
J Colloid Interface Sci ; 666: 512-528, 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-38613974

ABSTRACT

Metronidazole (MNZ), a commonly used antibiotic, poses risks to water bodies and human health due to its potential carcinogenic, mutagenic, and genotoxic effects. In this study, mesoporous cobalt-manganese layered double hydroxides (CoxMny-LDH) with abundant oxygen vacancies (Ov) were successfully synthesized using the co-precipitation method and used to activate calcium sulfite (CaSO3) with slight soluble in water for MNZ degradation. The characterization results revealed that Co2Mn-LDH had higher specific areas and exhibited good crystallinity. Co2Mn-LDH/CaSO3 exhibited the best catalytic performance under optimal conditions, achieving a remarkable MNZ degradation efficiency of up to 98.1 % in only 8 min. Quenching experiments and electron paramagnetic resonance (EPR) tests showed that SO4•- and 1O2 played pivotal roles in the MNZ degradation process by activated CaSO3, while the redox cycles of Co2+/Co3+ and Mn3+/Mn4+ on the catalyst surface accelerated electron transfer, promoting radical generation. Three MNZ degradation routes were put forward based on the density functional theory (DFT) and liquid chromatography-mass spectrometer (LC-MS) analysis. Meanwhile, the toxicity analysis result demonstrated that the toxicity of intermediates post-catalytic reaction was decreased. Furthermore, the Co2Mn-LDH/CaSO3 system displayed excellent stability, reusability, and anti-interference capability, and achieved a comparably high removal efficiency across various organic pollutant water bodies. This study provides valuable insights into the development and optimization of effective heterogeneous catalysts for treating antibiotic-contaminated wastewater.


Subject(s)
Cobalt , Hydroxides , Manganese , Metronidazole , Cobalt/chemistry , Metronidazole/chemistry , Hydroxides/chemistry , Manganese/chemistry , Porosity , Surface Properties , Sulfites/chemistry , Catalysis , Particle Size , Density Functional Theory , Water Pollutants, Chemical/chemistry
19.
Food Chem ; 448: 139112, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38569404

ABSTRACT

Ginseng is a most popular health-promoting food with ginsenosides as its main bioactive ingredients. Illegal sulfur-fumigation causes ginsenosides convert to toxic sulfur-containing derivatives, and reduced the efficacy/safety of ginseng. 24-sulfo-25-ene ginsenoside Rg1 (25-ene SRg1), one of the sulfur-containing derivatives, is a potential quality control marker of fumigated ginseng, but with low accessibility owing to its unknown generation mechanism. In this study, metals/bisulfite system involved generation mechanism was investigated and verified. The generation of 25-ene SRg1 in sulfur-fumigated ginseng is that SO2, formed during sulfur-fumigation, reacted with water and ionized into HSO3-. On the one hand, under the metals/bisulfite system, HSO3- generates HSO5- and free radicals which converted ginsenoside Rg1 to 24,25-epoxide Rg1; on the other hand, as a nucleophilic group, HSO3- reacted with 24,25-epoxide Rg1 and further dehydrated to 25-ene SRg1. This study provided a technical support for the promotion of 25-ene SRg1 as the characteristic quality control marker of sulfur-fumigated ginseng.


Subject(s)
Fumigation , Ginsenosides , Panax , Quality Control , Sulfur , Ginsenosides/chemistry , Ginsenosides/analysis , Panax/chemistry , Sulfur/chemistry , Sulfites/chemistry , Sulfites/analysis , Metals/chemistry , Metals/analysis , Plant Extracts/chemistry
20.
Food Chem ; 449: 138944, 2024 Aug 15.
Article in English | MEDLINE | ID: mdl-38613993

ABSTRACT

Sulfite addition is a common tool for ensuring wines' oxidative stability via the activity of its free and weakly bound molecular fraction. As a nucleophile, bisulfite forms covalent adducts with wine's most relevant electrophiles, such as carbonyls, polyphenols, and thiols. The equilibrium in these reactions is often represented as dissociation rather than formation. Recent studies from our laboratory demonstrate, first, the acetaldehyde sulfonate dissociation, and second, the chemical stability of cysteine and epicatechin sulfonates under wine aging conditions. Thus, the objective of this study was to monitor by 1H NMR the binding specificity of known carbonyl-derived SO2 binders (acetaldehyde and pyruvic acid) in the presence of S-containing compounds (cysteine and glutathione). We report that during simulated wine aging, the sulfur dioxide that is rapidly bound to carbonyl compounds will be released and will bind to cysteine and glutathione, demonstrating the long-term sulfur dioxide binding potential of S-containing compounds. These results are meant to serve as a complement to existing literature reviews focused on molecular markers related to wines' oxidative stability and emphasize once more the importance of S-containing compounds in wine aging chemical mechanisms.


Subject(s)
Sulfhydryl Compounds , Wine , Wine/analysis , Kinetics , Sulfhydryl Compounds/chemistry , Oxidation-Reduction , Sulfur Dioxide/chemistry , Cysteine/chemistry , Cysteine/metabolism , Acetaldehyde/chemistry , Sulfites/chemistry , Proton Magnetic Resonance Spectroscopy , Magnetic Resonance Spectroscopy , Glutathione/chemistry , Glutathione/metabolism
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