Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions.

Nucleosomes drastically limit transcription factor (TF) occupancy, while pioneer transcription factors (PFs) somehow circumvent this nucleosome barrier. In this study, we compare nucleosome binding of two conserved S. cerevisiae basic helix-loop-helix (bHLH) TFs, Cbf1 and Pho4. A cryo-EM structure of Cbf1 in complex with the nucleosome reveals that the Cbf1 HLH region can electrostatically interact with exposed histone residues within a partially unwrapped nucleosome. Single-molecule fluorescence studies show that the Cbf1 HLH region facilitates efficient nucleosome invasion by slowing its dissociation rate relative to DNA through interactions with histones, whereas the Pho4 HLH region does not. In vivo studies show that this enhanced binding provided by the Cbf1 HLH region enables nucleosome invasion and ensuing repositioning. These structural, single-molecule, and in vivo studies reveal the mechanistic basis of dissociation rate compensation by PFs and how this translates to facilitating chromatin opening inside cells.

Systematic Study of Nucleosome-Displacing Factors in Budding Yeast.

Nucleosomes present a barrier for the binding of most transcription factors (TFs). However, special TFs known as nucleosome-displacing factors (NDFs) can access embedded sites and cause the depletion of the local nucleosomes as well as repositioning of the neighboring nucleosomes. Here, we developed a novel high-throughput method in yeast to identify NDFs among 104 TFs and systematically characterized the impact of orientation, affinity, location, and copy number of their binding motifs on the nucleosome occupancy. Using this assay, we identified 29 NDF motifs and divided the nuclear TFs into three groups with strong, weak, and no nucleosome-displacing activities. Further studies revealed that tight DNA binding is the key property that underlies NDF activity, and the NDFs may partially rely on the DNA replication to compete with nucleosome. Overall, our study presents a framework to functionally characterize NDFs and elucidate the mechanism of nucleosome invasion.

Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing.

Hemi-methylated cytosine dyads widely occur on mammalian genomic DNA, and can be stably inherited across cell divisions, serving as potential epigenetic marks. Previous identification of hemi-methylation relied on harsh bisulfite treatment, leading to extensive DNA degradation and loss of methylation information. Here we introduce Mhemi-seq, a bisulfite-free strategy, to efficiently resolve methylation status of cytosine dyads into unmethylation, strand-specific hemi-methylation, or full-methylation. Mhemi-seq reproduces methylomes from bisulfite-based sequencing (BS-seq & hpBS-seq), including the asymmetric hemi-methylation enrichment flanking CTCF motifs. By avoiding base conversion, Mhemi-seq resolves allele-specific methylation and associated imprinted gene expression more efficiently than BS-seq. Furthermore, we reveal an inhibitory role of hemi-methylation in gene expression and transcription factor (TF)-DNA binding, and some displays a similar extent of inhibition as full-methylation. Finally, we uncover new hemi-methylation patterns within Alu retrotransposon elements. Collectively, Mhemi-seq can accelerate the identification of DNA hemi-methylation and facilitate its integration into the chromatin environment for future studies.

Colorimetric assay based on peroxidase-like activity of dodecyl trimethylammonium bromide-tetramethyl zinc (4-pyridinyl) porphyrin for detection of organophosphorus pesticides.

A simple and sensitive colorimetric assay for detecting organophosphorus pesticides (OPs) was developed based on 3,3',5,5'-tetramethylbenzidine (TMB)/hydrogen peroxide (H2O2)/dodecyl trimethylammonium bromide (DTAB)-tetramethyl zinc (4-pyridinyl) porphyrin (ZnTPyP). In this system, based on the peroxidase-like activity of DTAB-ZnTPyP, H2O2 decomposes to produce hydroxyl radicals, which oxidize TMB, resulting in blue oxidation products. The OPs (trichlorfon, dichlorvos, and thimet) were first combined with DTAB-ZnTPyP through electrostatic interactions. The OPs caused a decrease in the peroxidase-like activity of DTAB-ZnTPyP due to spatial site blocking. At the same time, π-interactions occurred between them, and these interactions also inhibited the oxidation of TMB (652 nm), thus making the detection of OPs possible. The limits of detection for trichlorfon, dichlorvos, and thimet were 0.25, 1.02, and 0.66 µg/L, respectively, and the corresponding linear ranges were 1-35, 5-45, and 1-40 µg/L, respectively. Moreover, the assay was successfully used to determine OPs in cabbage, apple, soil, and traditional Chinese medicine samples (the recovery ratios were 91.8-109.8%), showing a great promising potential for detecting OPs also in other complex samples.

An inner filter effect-based nitrogen-doped carbon dots-CoOOH nanoflakes fluorescence probe for detection of ascorbic acid by chemical redox modulation.

BACKGROUND: Ascorbic acid (AA) is an essential nutrient for humans, which must be obtained from vegetables, fruits, and other foods. The content of AA has become an important standard to evaluate the quality and nutritional value of food. The fluorescence sensing method based on nanomaterials is a good alternative for the rapid detection of AA. In this study, we developed an inner filter effect-based fluorescent probe that hybridized nitrogen-doped carbon dots (NCDs) with cobalt oxyhydroxide nanoflakes (CoOOH NFs). RESULTS: An optimal NCDs was successfully selected because it has a strong fluorescence at 430 nm and the most significant quenching phenomenon with CoOOH NFs due to the inner filter effect. When adding AA into the NCDs-CoOOH NFs probe solution, a specific redox reaction will occur between the enediol group of AA and the CoOOH NFs to interfere with the quenching ability of CoOOH NFs and recover the fluorescence of NCDs. The recovered fluorescence intensities demonstrated a linear relationship with the concentrations of AA. The assay based on the NCDs-CoOOH NFs probe allows AA to be tested in a wide range of 5-200 µmol L-1 with a detection limit of 2.31 nmol L-1 . Furthermore, to evaluate its practical application, the NCDs-CoOOH NFs fluorescence probe was utilized to analyze AA in vegetable, fruit, and serum matrixes with satisfactory results. CONCLUSION: An inner filter effect-based fluorescence probe for the rapid detection of AA was developed, and it has a good potential to be applied in both food and clinical testing. © 2022 Society of Chemical Industry.

Maillard reaction products and guaiacol as production process and raw material markers for the authentication of sesame oil.

BACKGROUND: Sesame oil has an excellent flavor and is widely appreciated. It has a higher price than other vegetable oils because of the high price of its raw materials, and different processing techniques also result in products of different quality levels, which can command different prices. In the market, there is a persistent problem of adulteration of sesame oil, driven by economic interests. The screening of volatile markers used to distinguish the authenticity of sesame oil raw materials and production processes is therefore very important. RESULTS: In this work, six markers related to the production processes and raw materials of sesame oil were screened by gas chromatography-tandem mass spectrometry (GC-MS/MS) combined with chemometric analysis. They were 3-methyl-2-butanone, 2-ethyl-5-methyl-pyrazine, guaiacol, 2,6-dimethyl-pyrazine, 5-methyl furfural, and ethyl-pyrazine. The concentration of these markers in sesame oil is between 10 and1000 times that found in other vegetable oils. However, only 3-methyl-2-butanone and 2-ethyl-5-methyl-pyrazine differed significantly as the result of the use of different production processes. Except for guaiacol, which was mainly derived from raw materials, the other five compounds mentioned above all result from the Maillard reaction during thermal processing. The six compounds mentioned above are sufficient to distinguish fraud involving sesame oil raw materials and production processes, and can identify accurately adulteration levels of 30% concentration. CONCLUSION: In this study, the classification markers can identify the adulteration of sesame oil accurately. These six compounds are therefore important for the authenticity of sesame oil and provide a theoretical basis for the rapid and accurate identification of the authenticity of sesame oil. © 2021 Society of Chemical Industry.

[Research progress on common pesticide residues in Chinese medicinal materials].

Chinese medicinal materials are the precious resources of China and favored by patients at home and abroad because of their natural sources and curative effects. Pesticides are often used to prevent and control diseases and insect pests and regulate the growth of Chinese medicinal plants, so as to improve the yield and quality of Chinese medicinal materials. Most of the pesticides can play a role in pest control through systemic action, stomach toxicity, contact, fumigation and other ways, especially the systemic pesticides can kill hidden pests by entering the Chinese medicinal plants. Despite the good pest control effect, it is difficult to remove the systemic pesticides by simple cleaning, which poses a great risk to the safety of Chinese medicinal materials. At the same time, excessive or non-standard use of pesticides leads to serious pesticide residues in Chinese medicinal materials, which affects not only the quality and efficacy of the materials and harm human health but also the international development of Chinese medicinal materials industry. Pesticide residues have become a bottleneck affecting the industry development and hindering the export of Chinese medicinal materials. Therefore, it is of great significance to study how to quickly, sensitively, and accurately detect and remove pesticide residues in Chinese medicinal materials. We reviewed the common pesticide residues in Chinese medicinal materials in recent years in terms of characteristics, harm, and detection and removal techniques, and discussed the future development of the detection and removal deve-lopment. With this review, we aimed to provide a reference for the quality control of Chinese medicinal materials and promote the healthy development of Chinese medicine industry.

Visual paper-based sensor for the highly sensitive detection of caffeine in food and biological matrix based on CdTe-nano ZnTPyP combined with chemometrics.

Caffeine naturally occurs in tea and cocoa, which is also used as an additive in beverages and has pharmacological effects such as refreshing, antidepressant, and digestion promotion, but excessive caffeine can cause harm to the human body. In this work, based on the specific response between nano zinc 5, 10, 15, 20-tetra(4-pyridyl)-21H-23H-porphine (nano ZnTPyP)-CdTe quantum dots (QDs) and caffeine, combined with chemometrics, a visual paper-based sensor was constructed for rapid and on-site detection of caffeine. The fluorescence of QDs can be quenched by nano ZnTPyP. When caffeine is added to the system, it can pull nano ZnTPyP off the surface of the QDs to achieve fluorescence recovery through electrostatic attraction and nitrogen/zinc coordination. The detection range is 5 × 10-11~3 × 10-9 mol L-1, and the detection limit is 1.53 × 10-11 mol L-1 (R2 = 0.9990) (S/N = 3). The paper-based sensor constructed exhibits good results in real samples, such as tea water, cell culture fluid, newborn bovine serum, and human plasma. Therefore, the sensor is expected to be applied to the rapid instrument-free detection of caffeine in food and biological samples.Graphical abstract.

Capsulactone: a new 4-hydroxy-α-pyrone derivative from an endophytic fungus Penicillium capsulatum and its antimicrobial activity.

A new 4-hydroxy-α-pyrone, namely capsulactone (1), was isolated from an endophytic fungus Penicillium capsulatum XL027 obtained from the leaves of Panax notoginseng. The structure and absolute configuration of 1 were elucidated through a combination of spectroscopic data and computed methods, as well as by comparison with literature data. Compound 1 exhibited weak activity against methicinllin-resistant Staphylococcus aureus with an MIC value of 100 µg/ml.

Fluorescent sensor based on quantum dots and nano-porphyrin for highly sensitive and specific determination of ethyl carbamate in fermented food.

BACKGROUND: Ethyl carbamate (EC) is a potentially toxic carcinogen produced during fermentation and storage of fermented foods, and many countries have set thresholds for its content in food. Therefore, sensitive, rapid and accurate detection of EC is meaningful to ensure the quality of fermented food. RESULTS: This study introduces a CdTe quantum dots/nano-5,10,15,20-tetrakis (4-methoxyphenyl)-porphyrin (nano TPP-OCH3 ) fluorescence sensor system detection of EC. The specificity of this sensing mainly relies on a photo-induced electron transfer and electrostatic force interaction between EC and nano TPP-OCH3 . This sensor presented a linear range of 10 to 1000 µg L-1 (R2  = 0.9903) with a low detection limit of 7.14 µg L-1 . Meanwhile, the recovery (91.19-101.09%) and precision [relative standard deviation (RSD) = 0.64-3.05%] of the sensor for the analysis of fermented food (yellow rice wine, soy sauce, Chinese spirits, Pu-erh tea) samples were good and could meet the requirements of practical detection. Moreover, the detection results of fermented food (yellow rice wine, soy sauce, Chinese spirits, Pu-erh tea) samples by this sensor are basically consistent with those of high-performance liquid chromatography with fluorescence detector (HPLC-FLD). CONCLUSION: This method was expected to provide a potential platform for sensitive and accurate detection of EC in food safety monitoring, which would provide knowledge of the flavor and quality related to fermented food. © 2021 Society of Chemical Industry.

Determination of l-theanine in tea water using fluorescence-visualized paper-based sensors based on CdTe quantum dots/corn carbon dots and nano-porphyrin with chemometrics.

BACKGROUND: The quality of tea is influenced by numerous factors, especially l-theanine, which is one of the important markers used to evaluate the sweetness and freshness of tea. Sensitive, rapid, and accurate detection of l-theanine is therefore useful to identify the grade and quality of tea. RESULTS: A high-sensitivity, paper-based fluorescent sensor combined with chemometrics was established to detect l-theanine in tea water based on CdTe quantum dots / corn carbon dots and nano tetra pyridel-porphine zinc (ZnTPyP). To verify the reliability of this method, fluorescence spectra and fluorescence-visualized paper-based sensors were compared. The fluorescence spectrum method demonstrated a linear range of 1 to 10 000 nmol L-1 and a limit of detection (LOD) of 0.19 nmol L-1 . In the fluorescence-visualized paper-based sensors there was a linear range of 10-1000 nmol L-1 , and the LOD was 10 nmol L-1 . Partial least squares discriminant analysis (PLSDA) and partial least squares regression analysis (PLSR) were used successfully to determine l-theanine accurately in tea water with this approach. The accuracy of the PLSDA model was 100% both in the training set and the predicting set, and the correlation coefficient between the actual concentration and the predicted concentration was greater than 0.9997 in the PLSR model. CONCLUSION: This fluorescence-visualized paper-based sensor, combined with chemometrics, could be applied efficiently to the practical analysis of tea water samples, which provides a new idea to ensure the flavor and quality of tea. © 2020 Society of Chemical Industry.

A novel fluorescence sensing strategy based on nanoparticles combined with spectral splicing and chemometrics for the recognition of Citrus reticulata 'Chachi' and its storage year.

BACKGROUND: The fluorescence sensing method has been increasingly applied in food quality control because it is fast and sensitive. However, its application in quality evaluation is challenging. Using Citri Reticulatae Pericarpium (CRP; dried mandarin orange peel) as an example, we developed a simple and low-cost fluorescence sensing strategy based on nanoparticles combined with spectral splicing and chemometrics for quality evaluation. This method can recognize Citrus reticulata 'Chachi' (CRC) from other CRP cultivars and further identify the storage year. RESULTS: Nanogold particles and cadmium telluride quantum dots were selected as nanosensors and mixed with aqueous extracts of CRP separately to produce fluorescence quenching spectra. Then, a simple spectral splicing procedure was applied to obtain spliced spectra comprising different combinations of the self-fluorescence and fluorescence quenching spectra of CRP samples. With the aid of partial least-squares discriminant analysis, the new strategy achieved recognition rates of 100% in distinguishing CRC samples from other CRP samples, as well as recognition rates of 100% for the training set and 98.04% for the prediction set in the discrimination of the storage year of CRC. The recognition mechanism is dominated by interactions between the nanoparticles and the fluorescent components in the CRP samples, but other components also have concurrent effects. CONCLUSIONS: This novel fluorescence sensing strategy not only provides a new tool for the quality evaluation of CRC but also has good prospects for the authentication and traceability of other foods and herbs. Crucially, the developed method is convenient, simple and effective. © 2020 Society of Chemical Industry.

Rapid detection of five pesticide residues using complexes of gold nanoparticle and porphyrin combined with ultraviolet visible spectrum.

BACKGROUD: Pesticides are widely used to control insect infestation and weeds in agriculture. However, concerns about the pesticide residues in agricultural products have been raised in recent years because of public interest in health and food quality and safety. Thus, rapid, convenient, and accurate analytical methods for the detection and quantification of pesticides are urgently required. RESULTS: A nanohybrid system composed of gold nanoparticles (AuNPs) and tetrakis(N-methyl-4-pyridiniumyl) porphyrin (TMPyP) was used as an optical probe for the detection and quantification of five pesticides (Paraquat, Dipterex, Dursban, methyl thiophanate and Cartap). The method is based on the aggregation effect of pesticides on the carboxyl group modified by AuNPs. Subsequently, with the help of particle swarm optimization-optimized sample weighted least squares-support vector machine (PSO-OSWLS-SVM), all the pesticides could be successfully quantified. In addition, partial least squares discriminant analysis (PLS-DA) was applied and the five pesticides were satisfactorily recognized based on data array obtained from the ultraviolet visible (UV-visible) spectra of AuNP-TMPyP complex. Furthermore, the quantitative and qualitative analysis of the five pesticides could be also achieved in the complex real samples, in which all the relative standard deviations (RSDs) were less than 0.3‰ and all the linear absolute correlation coefficients were more than 0.9990. Furthermore, recognition rate of the training set and the prediction set based on multiplicative scatter correction (MSC), or second-order derivative (2nd derivative) UV-visible spectra in PLS-DA model could reach 100%. CONCLUSION: This method was successfully applied for the rapid and accurate determination of multicomponent pesticide residues in real food samples. © 2020 Society of Chemical Industry.

Emerones A-C: three novel merosesquiterpenoids with unprecedented skeletons from Emericella sp. XL029.

Three novel highly oxygenated α-pyrone merosesquiterpenoids, emerones A-C (1-3), have been obtained from the fungus, Emericella sp. XL029, which was isolated from the leaves of the traditional Chinese medicinal plant, Panax notoginseng. The structures and absolute configurations of 1-3 were determined by NMR experiments, X-ray diffraction analysis, and computational methods. Structurally, compound 1 possessed an unprecedented 5/7 bicyclic ring architecture, compound 2 had an unusual substituted 10-membered ring, and compound 3 had an undescribed norsesquiterpene skeleton. In addition, compounds 1 and 2 showed moderate activity towards several types of bacteria and fungi, exhibiting MIC values ranging from 12.5 to 50 µg mL-1, whereas compound 3 showed no antimicrobial activity.

Aureonitols A and B, Two New C13 -Polyketides from Chaetomium globosum, an Endophytic Fungus in Salvia miltiorrhiza.

Two new C13 -polyketides, aureonitols A and B (1 and 2), along with five known compounds (3-7), were isolated from the solid fermentation culture of the plant endophytic fungus Chaetomium globosum from the aerial parts of Salvia miltiorrhiza. The structures and absolute configurations of 1 and 2 were determined by comprehensive spectroscopic data analysis and computed methods. Compound 5 was found to display the remarkable antimicrobial activities against four multidrug-resistant bacteria (Enterococcus faecalis, Enterococcus faecium, Staphylococcus aureus, and Staphylococcus epidermidis) with MIC values of 3.13-6.25 µg/mL (ciprofloxacin: 0.78-1.56 µg/mL), and also against all tested fungal strains with MIC values of 3.13-25 µg/mL (ketoconazole: 0.78-12.50 µg/mL).

The AAA ATPase Vps4 Plays Important Roles in Candida albicans Hyphal Formation and is Inhibited by DBeQ.

Candida albicans is an opportunistic human pathogen, and its pathogenicity is associated with hyphal formation. Previous studies have shown that at neutral-to-alkaline pH, hyphal growth is dependent on the Rim101 pathway whose activation requires Snf7, a member of the ESCRT system. In this work, we described the purification and characterization of the C. albicans Vps4, an AAA ATPase required for recycling of the ESCRTs. Its role on hyphal growth has been investigated. Our data suggest deletion of Vps4 decreases overall hyphal growth at pH 7 and increases the growth of multiple hyphae induced by serum, which indicates that the ESCRTs may make a Rim101-independent contribution to hyphal growth. Furthermore, DBeQ, an inhibitor of the AAA ATPase p97, was shown to inhibit the ATPase activity of Vps4 with an IC50 of about 11.5 µM. To a less degree, it also inhibits hyphal growth. Our work may provide a new strategy to control C. albicans infection.

Phenolic acids inhibit the formation of advanced glycation end products in food simulation systems depending on their reducing powers and structures.

The concentration of advanced glycation end products (AGEs) in foods, which are formed by Maillard reaction, has demonstrated as risk factors associated with many chronic diseases. The AGEs inhibitory activities of five common phenolic acids (protocatechuic acid, dihydroferulic acid, p-coumaric acid, p-hydroxybenzoic acid and salicylic acid) with different chemical properties had been investigated in two food simulation systems (glucose-bovine serum albumin (BSA) and oleic acid-BSA). The results substantiated that the AGEs inhibitory abilities of phenolic acids in the oleic acid BSA system were much better than the glucose-BSA system for their strong reducing powers and structures. Among them, dihydrogenferulic acid showed strong inhibition of AGEs formation in oleic acid-BSA system at 0.01 mg/mL compared to nonsignificant AGEs inhibitory effect in oleic acid-BSA system at 10-fold higher concentration (0.1 mg/mL). This study suggests that edible plants rich in phenolic acids may be used as AGEs inhibitor during high-fat cooking.

Vinegar Functions on Health: Constituents, Sources, and Formation Mechanisms.

Vinegars are one of only a few acidic condiments throughout the world. Vinegars can mainly be considered grain vinegars and fruit vinegars, according to the raw materials used. Both grain vinegars and fruit vinegars, which are fermented by traditional methods, possess a variety of physiological functions, such as antibacteria, anti-infection, antioxidation, blood glucose control, lipid metabolism regulation, weight loss, and anticancer activities. The antibacteria and anti-infection abilities of vinegars are mainly due to the presence of organic acids, polyphenols, and melanoidins. The polyphenols and melanoidins also provide the antioxidant abilities of vinegars, which are produced from the raw materials and fermentation processes, respectively. The blood glucose control, lipid metabolism regulation, and weight loss capabilities from vinegars are mainly due to acetic acid. Besides caffeoylsophorose (inhibits disaccharidase) and ligustrazine (improves blood circulation), other functional ingredients present in vinegars provide certain health benefits as well. Regarding anticancer activities, several grain vinegars strongly inhibit the growth of some cancer cells in vivo or in vitro, but related functional ingredients remain largely unknown, except tryptophol in Japanese black soybean vinegar. Considering the discovering of various functional ingredients and clarifying their mechanisms, some vinegars could be functional foods or even medicines, depending on a number of proofs that demonstrate these constituents can cure chronic diseases such as diabetes or cardiovascular problems.

A novel organic acids-targeted colorimetric sensor array for the rapid discrimination of origins of Baijiu with three main aroma types.

Given the severe problem of Baijiu authenticity, it is essential to discriminate Baijiu from different origins quickly and effectively. As organic acids (OAs) are the most dominant taste-imparting substances in Baijiu, we proposed a simple, fast, and effective OAs-targeted colorimetric sensor array based on the colorimetric reaction of 4-aminophenol (AP)/4-amino-3-chlorophenol (ACP) under oxidation of Cu(NO3)2 for the rapid discrimination of origins of Baijiu with three main aroma types. Hydrogen ions ionized from OAs induced the protonation of the amino group, which blocked the colorimetric reaction, and the different levels of OAs in Baijiu enabled the array to discriminate different origins of Baijiu. The array was implemented to analyze 10 simple OAs and 16 mixed OAs and further for the discrimination of 42 Baijius with an accuracy of 98%. This method provided an efficient research strategy for a basis for rapid quality analysis of Baijiu.

Esters-targeted colorimetric sensor array for the authenticity discrimination of strong-aroma baijiu with different origins.

Baijiu authenticity has been a frequent problem driven by economic interests in recent years, so it is important to discriminate against baijiu with different origins. Herein, we proposed a simple and efficient esters-targeted colorimetric sensor array mediated by hydroxylamine hydrochloride. Esters undergo a nucleophilic addition reaction with hydroxylamine hydrochloride to form hydroxamic acid, which rapidly forms a purplish red ferric hydroxamate under FeCl3·6H2O. Bromophenol blue and rhodamine B enrich the color effects. The array detected 12 esters with a detection limit on the order of 10-5 of most esters and 16 mixed esters with R2 > 0.999 and recoveries close to 100%. Otherwise, for discriminating 34 strong-aroma baijius (SABs), the array has an accuracy of 98% according to the origin, and 95% according to the grades, with a response time of 1 min. This study provides a new strategy for authenticity determination and quality control of baijiu.