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Molecular Cell Feb 2024Although DNA N-methyl-deoxyadenosine (6mA) is abundant in bacteria and protists, its presence and function in mammalian genomes have been less clear. We present...
Although DNA N-methyl-deoxyadenosine (6mA) is abundant in bacteria and protists, its presence and function in mammalian genomes have been less clear. We present Direct-Read 6mA sequencing (DR-6mA-seq), an antibody-independent method, to measure 6mA at base resolution. DR-6mA-seq employs a unique mutation-based strategy to reveal 6mA sites as misincorporation signatures without any chemical or enzymatic modulation of 6mA. We validated DR-6mA-seq through the successful mapping of the well-characterized G(6mA)TC motif in the E. coli DNA. As expected, when applying DR-6mA-seq to mammalian systems, we found that genomic DNA (gDNA) 6mA abundance is generally low in most mammalian tissues and cells; however, we did observe distinct gDNA 6mA sites in mouse testis and glioblastoma cells. DR-6mA-seq provides an enabling tool to detect 6mA at single-base resolution for a comprehensive understanding of DNA 6mA in eukaryotes.
Topics: Animals; Mice; Escherichia coli; DNA Methylation; Genome; DNA; Eukaryota; Deoxyadenosines; Mammals
PubMed: 38215754
DOI: 10.1016/j.molcel.2023.12.021 -
Acta Crystallographica. Section E,... Apr 2024The structure of the title compound, CHBrNO, contains two independent mol-ecules connected by hydrogen bonds of the type N-H⋯N≡C to form a dimer. The configuration...
The structure of the title compound, CHBrNO, contains two independent mol-ecules connected by hydrogen bonds of the type N-H⋯N≡C to form a dimer. The configuration at the exocyclic C=C double bond is . The mol-ecules are roughly planar except for the isopropyl groups. There are minor differences in the orientations of these groups and the phenyl rings at N1. The dimers are further linked by 'weak' hydrogen bonds, two each of the types H⋯O=C (H⋯O = 2.50, 2.51 Å) and H⋯Br (H⋯Br = 2.89, 2.91 Å), to form ribbons parallel to the and axes, respectively. The studied crystal was a non-merohedral twin.
PubMed: 38721424
DOI: 10.1107/S2056989024003086 -
PloS One 2023The current study is designed to synthesize gold nanoparticles using Ajuga bracteosa extract, which is a highly known medicinal herb found in the northern Himalayas. The...
The current study is designed to synthesize gold nanoparticles using Ajuga bracteosa extract, which is a highly known medicinal herb found in the northern Himalayas. The synthesized gold nanoparticles were initially characterized by UV-Vis spectrophotometer, SEM, FTIR, pXRD, and, GC-MS. Antibacterial efficacy of A. bracteosa extract, AuNps, and AuNps-free supernatant activity was checked against highly pathogenic clinical isolates of Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa via agar well diffusion method, assuming that supernatant might have active compounds. The Nps-free supernatant showed the maximum antibacterial activity against E. coli (20.8±0.3 mm), Staphylococcus aureus (16.5±0.5), and Pseudomonas aeruginosa (13±0.6). While green synthesized AuNps showed effective antibacterial activity (Escherichia coli (16.4±0.3mm), Staphylococcus aureus (15.05±0.5mm), and Pseudomonas aeruginosa (11.07±0.6mm)) which was high compared to A. bracteosa extract. Anticancer activity was assessed by MTT assay on U87 and HEK293 cell lines. Aj-AuNps have an antigrowth effect on both the cell lines however Aj-AuNps-free supernatant which was also evaluated along with the Aj-AuNps, showed high toxicity toward HEK293 cell line compared to U87. Further, the GC-MS analysis of supernatant showed the presence of resultant toxic compounds after the reduction of gold salt, which include Trichloromethane, Propanoic acid, 2-methyl-, methyl ester, Methyl isovalerate, Pentanoic acid, 2-hydroxy-4-methyl-, Benzene-propanoic acid, and alpha-hydroxy. Based on the observation small molecular weight ligands of Ajuga bracteosa were analyzed in-silico for their binding efficacy towards selected membrane proteins of our target pathogens. RMSD is also calculated for the best docked protein ligand pose. The results revealed that among all listed ligands, Ergosterol and Decacetylajugrin IV have high virtuous binding affinities towards the membrane proteins of targeted pathogens. The current findings revealed that the Aj-AuNps are good antibacterial as well as anticancerous agents while the Nps-free supernatant is also exceedingly effective against resistant pathogens and cancer cell lines.
Topics: Humans; Ajuga; Propionates; Gold; Escherichia coli; Ligands; HEK293 Cells; Metal Nanoparticles; Anti-Bacterial Agents; Staphylococcus aureus; Plant Extracts; Microbial Sensitivity Tests; Green Chemistry Technology
PubMed: 37549158
DOI: 10.1371/journal.pone.0282485 -
Molecules (Basel, Switzerland) Jan 2024In this paper, the green synthesis of isoeugenol methyl ether (IEME) from eugenol by -methylation and isomerization is completed using a one-step green process. In the...
In this paper, the green synthesis of isoeugenol methyl ether (IEME) from eugenol by -methylation and isomerization is completed using a one-step green process. In the methylation reaction, dimethyl carbonate (DMC) was used as a green chemistry reagent instead of the traditional harmful methylation reagents, in accordance with the current concept of green chemistry. The phase transfer catalyst (PTC) polyethylene glycol 800 (PEG-800) was introduced into the isomerization reaction to break the barrier of difficult contact between solid and liquid phases and drastically reduce the reaction conditions by shortening the reaction time and reducing the alkalinity of the reaction system. The catalytic systems for the one-step green synthesis of IEME were screened, and it was shown that the catalytic system "KCO + PEG-800" was the most effective. The effects of reaction temperature, n(DMC):n(eugenol) ratio, n(PEG-800):n(eugenol) ratio, and n(KCO):n(eugenol) ratio on eugenol conversion, IEME yield, and IEME selectivity were investigated. The results showed that the best reaction was achieved at a reaction temperature of 140 °C, a reaction time of 3 h, a DMC drip rate of 0.09 mL/min, and n(eugenol):n(DMC):n(KCO):n(PEG-800) = 1:3:0.09:0.08. As a result of the conversion of 93.1% of eugenol to IEME, a yield of 86.1% IEME as well as 91.6% IEME selectivity were obtained.
PubMed: 38276627
DOI: 10.3390/molecules29020551 -
Biomedical Chromatography : BMC Jul 2023The purpose of this review study was to sum up the main recent advances reported in the scientific literature about the detection of common drugs of abuse in biological... (Review)
Review
The purpose of this review study was to sum up the main recent advances reported in the scientific literature about the detection of common drugs of abuse in biological samples upon their collection by dried blood spot devices. The most recent, innovative and fully validated methods for the qualitative and/or quantitative detection of common drugs of abuse are reported, including alprazolam, clonazepam, diazepam, 3,4-methylenedioxymethamphetamine, 3,4-methylenedioxyamphetamine, 3,4-methyl-enedioxyethylamphetamine, amphetamine, methamphetamine, cocaine, tetrahydrocannabinol, 6-monoacetylmorphine, morphine, codeine, hydromorphone, hydrocodone, oxycodone, noroxycodone, tramadol, methadone, buprenorphine, fentanyl, ketamine and their respective metabolites and γ-hydroxybutyric acid. Dried blood spot proved to be extremely promising for routine analysis of forensic cases, although large-scale experiments on real samples need to be performed to confirm the emerging advantages of the technique and remove the potential limitations still affecting its widespread application.
Topics: Tandem Mass Spectrometry; Substance Abuse Detection; Codeine; Methamphetamine; Amphetamine
PubMed: 36417316
DOI: 10.1002/bmc.5555 -
Materials (Basel, Switzerland) Nov 2023The aim of this work was to biosynthesize SnO-decorated ZnO (ZT) nanocomposites (NCs) of different Sn content (10, 20, and 30 mol%), namely, ZT10, ZT20, and ZT30, using...
The aim of this work was to biosynthesize SnO-decorated ZnO (ZT) nanocomposites (NCs) of different Sn content (10, 20, and 30 mol%), namely, ZT10, ZT20, and ZT30, using leaf aqueous extract-based phytocompounds as nanoparticle facilitating agents for application as effective photocatalyst in the removal of dyes from polluted water. The obtained ZT NCs were characterized using various techniques, including FTIR, XRD, TGA, TEM, EDS, UV-Vis, PL, and BET surface area. X-ray diffraction patterns show that rutile SnO and hexagonal ZnO coexist in the composites, and their crystallite size (D) is affected by the SnO ratio; the obtained D-values were 17.24, 19.07, 13.99, 6.45, and 12.30 nm for ZnO, SnO, ZT10, ZT20, and ZT30, respectively. The direct band gaps of the ZT heterostructure increase with increasing SnO ratio (band gap = 3.10, 3.45, 3.14, 3.17, and 3.21 eV, respectively). TEM spectroscopy revealed nanorod and spherical grain morphologies of the composites, while EDS confirmed the elemental composition, the element ratio, and the composite's purity. All catalysts exhibit type III isotherm with macropore structure. The photocatalytic efficiency against cationic (methylene blue (MB), rhodamine B (RB)), and anionic (methyl orange (MO)) dyes, under sunlight, was optimal with ZT20. The results revealed almost complete degradation at 55, 65, and 55 min, respectively. Hence, it is evident that incorporating SnO improves the photocatalyst's performance, with an apparent optimal enhancement at 20 mol% Sn decorating ZT NCs. More interestingly, the catalyst stability and activity remained unaffected even after four activating cycles.
PubMed: 38068143
DOI: 10.3390/ma16237398 -
BMC Chemistry Nov 2023Recently, green analytical chemistry (GAC) is a key issue towards the idea of sustainability, the analytical community is focused on developing analytical methods that...
Green chromatographic methods for determination of co-formulated lidocaine hydrochloride and miconazole nitrate along with an endocrine disruptor preservative and potential impurity.
Recently, green analytical chemistry (GAC) is a key issue towards the idea of sustainability, the analytical community is focused on developing analytical methods that incorporate green chemistry principles to minimize adverse impacts on the environment and humans. Herein, we present 2 sustainable, selective, and validated chromatographic methods. Initially, lidocaine hydrochloride (LDC) and miconazole nitrate (MIC) with two preservatives; methyl paraben (MTP) and saccharin sodium (SAC) were chromatographed via TLC-densitometric method which employed ethyl acetate: methanol: formic acid (9:1:0.1, by volume) as the mobile phase with UV detection at 220.0 nm, good correlation was obtained in the range of 0.3-3.0 µg/band for MIC and LDC. Following that, RP-HPLC was successfully applied for separating quinary mixture of LDC, MIC, MTP, SAC along with LDC impurity; dimethyl aniline (DMA) using C18 column, and a gradient green mobile phase composed of methanol and phosphate buffer (pH 6.0) in different ratios with a flow rate 1.5 mL/min and UV detection at 210.0 nm, linearity ranges from 1.00 to 100.00 µg/mL for MIC, 2.00-100.00 µg/mL for LDC and 1.00--20.00 µg/mL for MTP and DMA. No records to date regarding the determination of the two drugs, besides MTP and DMA. The proposed methods were validated according to the ICH guidelines and applied successfully to the analysis of the compounds. The methods' results were statistically compared to those obtained by applying the reported one, indicating no significant difference regarding both accuracy and precision. The methods' greenness profiles have been assessed and compared with those of the reported method using different assessment tools.
PubMed: 37941018
DOI: 10.1186/s13065-023-01065-3 -
Molecules (Basel, Switzerland) Jul 2023In this study, pristine kiwi peel (KP) and nitric acid modified kiwi peel (NA-KP) based adsorbents were prepared and evaluated for selective removal of cationic dye. The...
In this study, pristine kiwi peel (KP) and nitric acid modified kiwi peel (NA-KP) based adsorbents were prepared and evaluated for selective removal of cationic dye. The morphology and chemical structure of KP and NA-KP were fully characterized and compared, and results showed nitric acid modification introduced more functional groups. Moreover, the adsorption kinetics and isotherms of malachite green (MG) by KP and NA-KP were investigated and discussed. The results showed that the adsorption process of MG onto KP followed a pseudo-second-order kinetic model and the Langmuir isotherm model, while the adsorption process of MG onto NA-KP followed a pseudo-first-order kinetic model and the Freundlich isotherm model. Notably, the Langmuir maximum adsorption capacity of NA-KP was 580.61 mg g, which was superior to that of KP (297.15 mg g). Furthermore, thermodynamic studies demonstrated the feasible, spontaneous, and endothermic nature of the adsorption process of MG by NA-KP. Importantly, NA-KP showed superior selectivity to KP towards cationic dye MG against anionic dye methyl orange (MO). When the molar ratio of MG/MO was 1:1, the separation factor (α) of NA-KP was 698.10, which was 5.93 times of KP. In addition, hydrogen bonding, π-π interactions, and electrostatic interaction played important roles during the MG adsorption process by NA-KP. This work provided a low-cost, eco-friendly, and efficient option for the selective removal of cationic dye from dyeing wastewater.
Topics: Coloring Agents; Adsorption; Nitric Acid; Rosaniline Dyes; Thermodynamics; Kinetics; Water Pollutants, Chemical; Hydrogen-Ion Concentration
PubMed: 37513184
DOI: 10.3390/molecules28145310 -
Journal of Fluorescence Jan 2024Three rhodamine 6G derivatives (REHA, RETA and REDA) were designed and synthesized by connecting rhodamine 6G and 3-methyl-2-thiophenal with hydrazine hydrate,...
Three rhodamine 6G derivatives (REHA, RETA and REDA) were designed and synthesized by connecting rhodamine 6G and 3-methyl-2-thiophenal with hydrazine hydrate, ethylenediamine and diethylenetriamine, respectively. In CHCN/HO (50/50, v/v), the absorbance of REHA, RETA and REDA at 528 nm was suddenly enhanced by 3.2, 3.8 and 7.2 times within the pH range of 3.03-2.31, 3.05-2.32 and 3.06-2.34, respectively, and the solution changed from colorless to pink. Meanwhile, the maximal fluorescence intensity sharply increased by 53.9, 26.6 and 24.9 times in the pH range of 3.86-3.46, 3.88-3.47 and 3.89-3.48, respectively, and the solution changed from dark to bright yellow-green fluorescence. REHA, RETA and REDA can act as highly selective and sensitive colorimetric and fluorescent pH switches with good recyclability and anti-interference ability. The response mechanism of REHA, RETA and REDA to pH was studied by H NMR spectroscopy, and their application in indicating small pH changes in dyeing wastewater was investigated.
PubMed: 38252215
DOI: 10.1007/s10895-023-03574-9 -
Frontiers in Plant Science 2023Bacterial wilt caused by ranks the second top important bacterial plant disease worldwide. It is also the most important bacterial disease threatening the healthy...
Bacterial wilt caused by ranks the second top important bacterial plant disease worldwide. It is also the most important bacterial disease threatening the healthy development of protection forest. 3-hydroxypalmitic acid methyl ester (3-OH PAME) functions as an important quorum sensing (QS) signal regulating the expression of virulence genes in , and has been regarded as an ideal target for disease prevention and control. To screen native microorganisms capable of degrading 3-OH PAME, samples of branches and forest soil were collected and cultured in the medium containing 3-OH PAME as the sole carbon source. Bacteria with over 85% degradation rates of 3-OH PAME after 7-day incubation were further separated and purified. As a result, strain Q1-7 isolated from forest soil and strain Q4-3 isolated from branches were obtained and identified as novel species sp. nov. and , respectively, according to whole genome sequencing results. The degradation efficiencies of 3-OH PAME of strains Q1-7 and Q4-3 were 95.80% and 100.00% at 48 h, respectively. Both strains showed high esterase activities and inhibited exopolysaccharide (EPS) and cellulase production. Application of strains Q1-7 and Q4-3 effectively protects , peanut and tomato plants from infection by . Findings in this study provide potential resources for the prevention and control of bacterial wilt caused by , as well as valuable materials for the identification of downstream quenching genes and the research and development of quenching enzymes for disease control.
PubMed: 37457350
DOI: 10.3389/fpls.2023.1193297