Computational Insights into the Dynamic Structural Features and Binding Characteristics of Recombinase UvsX Compared with RecA.

RecA family recombinases are the core enzymes in the process of homologous recombination, and their normal operation ensures the stability of the genome and the healthy development of organisms. The UvsX protein from bacteriophage T4 is a member of the RecA family recombinases and plays a central role in T4 phage DNA repair and replication, which provides an important model for the biochemistry and genetics of DNA metabolism. UvsX shares a high degree of structural similarity and function with RecA, which is the most deeply studied member of the RecA family. However, the detailed molecular mechanism of UvsX has not been resolved. In this study, a comprehensive all-atom molecular dynamics simulation of the UvsX protein dimer complex was carried out in order to investigate the conformational and binding properties of UvsX in combination with ATP and DNA, and the simulation of RecA was synchronized with the property comparison learning for UvsX. This study confirmed the highly conserved molecular structure characteristics and catalytic centers of RecA and UvsX, and also discovered differences in regional conformation, volatility and the ability to bind DNA between the two proteins at different temperatures, which would be helpful for the subsequent understanding and application of related recombinases.

Development and critical evaluation of a novel fluorescent nanosensor based on a molecularly imprinted polymer for the rapid detection of procymidone in ginseng.

Effective methods are required to quantify the organochlorine pesticide procymidone due to its potentially harmful effects toward human health and the environment. Here, hydrophilic hollow imprinted microspheres were prepared via a simple method as fluorescent sensors (@MIH-prm) for the sensitive and selective detection of PRM in ginseng. A new method of adsorption efficiency evaluation for @MIH-prm was subsequently introduced (EBS%), the effective binding site, which provided a comprehensive evaluation of the performance compared with conventional methods. The results showed that @MIH-prm could detect PRM in filtered and diluted ginseng juice with high sensitivity (LOD, 0.569 nM) and a rapid detection rate (quantitative detection of PRM within 18 min). Good selectivity was observed in the presence of combinations of different pesticides, and the adsorption of PRM could be described by the pseudo-second-order kinetic model. PRM concentrations exhibited good linearity over 1-40 nM, and the accuracy (recovery rates, 99.2 to 103.1%) and precision (RSD at 1.0 × 10-9 M, 3.14%) indicated that @MIH-prm could be used for the quantitative analysis of PRM in complex matrices. Hence, @MIH-prm has good application potential in pollution control monitoring and enforcement.

Study on a 65-mer peptide mimetic enzyme with GPx and SOD dual function.

Excessive reactive oxygen species (ROS) levels are harmful to the body. The peroxidase, GPx, and the superoxide dismutase, SOD, are important antioxidant enzymes for preventing ROS-induced damage. Se-CuZn-65P is an enzyme mimetic with dual GPx and SOD antioxidant function. However, currently, its production is mainly based on the cysteine auxotrophic expression technique, which is inefficient, expensive, and time consuming. In this study, we combined protein engineering and the chemical mutation method to synthesize Se-CuZn-65P. The DNA sequence encoding the 65 amino acid peptide with the desired sequence transformations to incorporate the SOD and the GPx catalytic sites was cloned and expressed in a soluble protein expression vector. The protein yield increased up to 152 mg/L, which is 10 times higher than in previous studies. The SOD and GPx activity of Se-CuZn-65P was high (1181 U/mg and 753 U/µmol, respectively). The binding constant of glutathione was 5.6 × 104  L·mol-1 , which shows that Se-CuZn-65P efficiently catalyzed hydrogen peroxide reduction by glutathione. Mitochondrial damage experiments confirmed the double protective role of the Se-CuZn-65P peptide and demonstrated functional synergy between the SOD and the GPx domains, which indicates its potential to be used in the treatment of ROS-related diseases. Our research may give a new thought to increase the yield of mimic.

Study of Fluorescent Imaging of Se (IV) in Living Cells Using a Turn-on Fluorescent Probe Based on a Rhodamine Spirolactame Derivative.

A highly selective fluorescent probe 2-(2-(2-aminoethylamino)ethyl)-3',6'-bis(ethylamino)-2',7'-dimethylspiro[isoindoline-1,9'-xanthen]-3-one (ABDO) for Se (IV) had been synthesized in our earlier report. In this study, this fluorescent sensor is applied on analysis fluorescent imaging of Se (IV) in Hela cells. The experiment conditions, such as the MTT assay, different concentration of saline, incubated time of Hela cells with ABDO and Se (IV), and intracellular action position of Se (IV), are investigated. Through a series of experiments, the fluorescent image of Se (IV) in Hela cells can be observed when the cells cultured by 2 µM ABDO and 2 µM Se (IV) for 210 min. And the intracellular action position of Se (IV) is verified after the co-localization experiments are done. It is mitochondria. These experimental results show that ABDO will be an eagerly anticipated sensor for fluorescent imaging analysis of selenium ion in living cells. Besides, we also can use the complexes of ABDO-Se to observe morphology and distribution of mitochondria in cells like JG-B.

Study on the Correlation between Gene Expression and Enzyme Activity of Seven Key Enzymes and Ginsenoside Content in Ginseng in Over Time in Ji'an, China.

Panax ginseng is a traditional medicine. Fresh ginseng is one of the most important industries related to ginseng development, and fresh ginseng of varying ages has different medicinal properties. Previous research has not systematically reported the correlation between changes in key enzyme activity with changes in ginsenoside content in fresh ginseng over time. In this study, for the first time, we use ginseng samples of varying ages in Ji'an and systematically reported the changes in the activity of seven key enzymes (HMGR, FPS, SS, SE, DS, CYP450, and GT). We investigated the content of ginsenoside and gene expression of these key enzymes. Ginsenoside content was measured using HPLC. HPLC, GC-MS, and LC-MS were combined to measure the enzyme activity of the key enzymes. Quantitative PCR was used in the investigation of gene expression. By analyzing the correlation between the enzyme activity and the transcription level of the key enzymes with ginsenoside content, we found that DS and GT enzyme activities are significantly correlated with the ginsenoside content in different ages of ginseng. Our findings might provide a new strategy to discriminate between ginseng of different years. Meanwhile, this research provides important information for the in-depth study of ginsenoside biosynthesis.

The Small Glutathione Peroxidase Mimic 5P May Represent a New Strategy for the Treatment of Liver Cancer.

Glutathione peroxidase (GPx) is an antioxidant protein containing selenium. Owing to the limitations of native GPx, considerable efforts have been made to develop GPx mimics. Here, a short 5-mer peptides (5P) was synthesized and characterized using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Enzyme coupled assays were used to evaluate GPx activity. The cell viability and apoptosis of H22 cells were tested, and mice bearing H22 cell-derived tumors were used to determine the effects of 5P on tumor inhibition. In comparison with other enzyme models, 5P provided a suitable substrate with proper catalytic site positions, resulting in enhanced catalytic activity. In our mouse model, 5P showed excellent inhibition of tumor growth and improved immunity. In summary, our findings demonstrated the design and synthesis of the small 5P molecule, which inhibited tumor growth and improved immunity. Notably, 5P could inhibit tumor growth without affecting normal growth. Based on these advantages, the novel mimic may have several clinical applications.

Comparative analysis of structural dynamics and allosteric mechanisms of RecA/Rad51 family proteins: Integrated atomistic MD simulation and network-based analysis.

Homologous recombination plays a key role in double-strand break repair, stalled replication fork repair, and meiosis. The RecA/Rad51 family recombinases catalyze the DNA strand invasion reaction that occurs during homologous recombination. However, the high sequence differences between homologous groups have hindered the thoroughly studies of this ancient protein family. The dynamic mechanisms of the family, particularly at the residual level, remain poorly understood. In this work, five representative RecA/Rad51 recombinase family members from all major kingdoms of living organisms: prokaryotes, eukaryotes, archaea, and viruses, were selected to explore the molecular mechanisms behind their conserved biological significance. A variety of techniques, including all-atom molecular dynamics simulation, perturbation response scanning, and protein structure network analysis, were used to examine the flexibility and correlation of protein domains, distribution of sensors and effectors and conserved hub residues. Furthermore, the potential communication routes between the ATP-binding region and the DNA-binding region of each recombinase were identified. Our results demonstrate the conserved molecular dynamics of these recombinases in the early stage of homologous recombination, including cooperative motions between regions, conserved sensing and effecting functional residue distribution, and conserved hub residues. Meanwhile, the unique ATP-DNA communication routes of each recombinase was also revealed. These results provide new insights into the mechanism of RecA/Rad51 family proteins, and provide new theoretical guidance for the development of allosteric inhibitors and the application of RecA/Rad51 family proteins.

The protective effects of 6-CySeCD with GPx activity against UVB-induced injury in HaCaT cells.

BACKGROUND: The generation of harmful reactive oxygen species (ROS) induced by UVB irradiation could induce cell apoptosis and change the cell cycle. 6A,6A'-dicyclohexylamine-6B,6B'-diselenide-bis-ß-cyclodextrin (6-CySeCD) is a novel glutathione peroxidase (GPx; EC 1.11.1.9) mimic. The aim of this study was to investigate the anti-oxidative effects of 6-CySeCD in cultured immortalised human keratinocyte cells (HaCaT). METHODS: HaCaT cells were treated with 30 mJ/cm(2) UVB to establish a damage model. The cultured HaCaT cells were randomly assigned to the control, UVB and treatment groups. The treatment group was incubated with 20 µmol/L of GPx mimics before UVB irradiation. Cell viability was detected by (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, the level of lipid peroxidation was determined by the formation of malondialdehyde (MDA), DNA fragmentation was observed using agarose gel electrophoresis and the levels of intracellular ROS and cell cycle progression were measured by flow cytometry. RESULTS: The levels of cytotoxicity, intracellular ROS, lipid peroxidation and oxidative DNA damage significantly increased after UVB irradiation in the HaCaT cells. UVB irradiation caused pre-G1 -phase arrest in HaCaT cells and significantly reduced the number of HaCaT cells in the S phase. The GPx mimics 6-CySeCD and 2-phenyl-l,2-benzisoselenazol-3(2H)-one (ebselen) significantly blocked UVB-induced apoptosis and changed the cell cycle of the HaCaT cells. The blocked effect of pretreatment 6-CySeCD in UVB-irradiated HaCaT cells was better than that of pretreatment with ebselen. CONCLUSION: 6-CySeCD can relieve the damage induced by UVB irradiation in HaCaT cells.

Ginseng of different ages is affected by the accumulation of heavy metals in ginseng soil.

Heavy-metal pollution has been established to affect ginseng quality. However, this effect is still unknown in ginseng of different ages, emphasizing the need to investigate the effects of heavy metals in soils on ginseng growth. Herein, we determined the content of heavy metals (Cu, Cd, Pb, Hg, and As) in ginseng of different ages (2 to 6-year-old) and the corresponding soil samples. Then, the total ginsenosides content of ginseng and rate-limiting enzyme (HMGR, SQE, CYP450) activity in the synthesis of ginsenosides were assessed. Results from 200 differently-aged Chinese ginseng showed that increased ginsenoside content in 3 to 5-year-old ginseng was paralleled by increased heavy metal element content in ginseng and its soil. The activity of rate-limiting enzymes increased in the first four years of ginseng growth and then exhibited a steady or downward trend. Further analysis suggested that heavy metal elements in soils could directly affect ginsenoside content. Moreover, we found that Cu significantly affected the rate-limiting enzyme CYP450 activity. Further principal component analysis and correlation analysis found that heavy metals could obviously inhibit ginseng growth during the 5th and 6th years. Heavy metal content in soils has huge prospects for predicting ginsenoside, Cu and As content in ginseng. This study provided support for ginseng cultivation, quality research and quality assessment.

Detection of Sodium Formaldehyde Sulfoxylate, Aluminum, and Borate Compounds in Bread and Pasta Products Consumed by Residents in Jilin Province, China.

ABSTRACT: Food additives are widespread in the human diet; however, their excessive intake can have an impact on the quality of health. This study evaluated food additives in bread and pasta products consumed by residents in various regions of Jilin Province, People's Republic of China, from 2019 to 2021. We collected samples of bread and six types of pasta products from farmers' markets and morning markets and used high-performance liquid chromatography, UV-visible spectrophotometry, and graphite furnace atomic absorption spectrometry to detect the content of the following food additives: sodium formaldehyde sulfoxylate, aluminum, and borate compounds. For 836 samples in total, we detected the presence of sodium formaldehyde sulfoxylate, aluminum, and borate compounds in excess rates reaching 3.5, 10, and 4.7%, respectively. Aluminum in fried breadsticks exceeded the standard by 40%. The results of this study can be used to assess the overall pass rate of bread and pasta products sold in Jilin Province and support the detection of possible food safety problems.

Evaluation of Microbial Contamination in Cold Dishes and Prevalence of Foodborne Pathogens in Jilin Province.

ABSTRACT: This study evaluated the microbial contamination status of cold dishes consumed by residents of Jilin Province and investigated to determine the incidence of four pathogenic bacteria in cold dishes. A total of 300 samples of cold dishes, including meat, vegetable, and mixed products, were collected from three purchasing places: supermarkets, farmers' markets, and mobile vendors. Viable bacteria were isolated using conventional culture methods. After separation, a quick and easy PCR was used to detect Listeria monocytogenes, Staphylococcus aureus, enterotoxigenic Escherichia coli, and Salmonella. The results showed that the total number of microbial colonies in the vegetable samples exceeded the standard rate of 8% and the total number of microbial colonies in the meat and mixed samples did not exceed the standard. The total microbial colony count exceeded the standard in all three procurement sites, with the highest exceedance of 7.4% in the mobile vendor sites. The detection rates of enterotoxigenic E. coli, S. aureus, L. monocytogenes, and Salmonella, among the four pathogenic bacteria detected in all samples, were 4.3, 3.3, 3.0, and 1.0%, respectively. This study can be used to qualitatively assess the microbiological quality associated with cold dishes. It provides data to support the detection of possible food safety problems.

Detection of Pesticide Residues in Vegetables Sold in Changchun City, China.

ABSTRACT: We evaluated fresh vegetables for residues of 18 pesticides with different chemical structures, including organochlorine pesticides, organophosphorus pesticides, carbamate pesticides, and pyrethroid pesticides and estimated that the potential health risks for consumers. A total of 313 samples were collected from 12 kinds of vegetables in Changchun, the capital of Jilin Province, People's Republic of China. Pesticide residues were analyzed by gas chromatography and mass spectrometry, and the curves were highly linear at 0.01 to 1.00 µg/mL (R2 ≥ 0.99). The mean recovery rate of the pesticides was 62 to 110% (relative standard deviation of <5%). The limit of detection was 0.0001 to 0.0167 mg/kg, the limit of quantification was 0.0002 to 0.0556 mg/kg, and the overall detection rate was 28.43%. The prevalence of pesticides and of samples above the standard limit were highest in celery, the prevalence of pesticides was lowest in potatoes, and the prevalence of samples above the standard limit was lowest in cucumber. Three of the 18 pesticides were not detected: omethoate, chlorpyrifos, and fenvalerate. Among the 15 pesticides detected, the maximum risk factor of six (carbofuran, omethoate, phorate, dicofol, dimethoate, and dichlorvos) is >1, indicating possible harm to human health. Residues of a single pesticide may not adversely affect a person's health, but multiple pesticide residues could present a health risk.

A new human catalytic antibody Se-scFv-2D8 and its selenium-containing single domains with high GPX activity.

Glutathione peroxidase (GPX) is a well-known antioxidant selenoenzyme, which can catalyze the reduction of a variety of hydroperoxides and consequently protect cells and other biological tissues against oxidative damage. Many attempts have been made to mimic its function, and a human catalytic antibody Se-scFv-B3 with GPX activity has been prepared in our previous study. This time, a new clone 2D8 that bound specifically to the glutathione analog GSH-S-DNPBu was selected again by using the technology of phage display antibody library, and then scFv-2D8 was successfully expressed in soluble form and purified using Ni(2+)-immobilized metal affinity chromatography. After being converted into selenium-containing scFv by chemically modification, it showed higher GPX activity than previous abzyme Se-scFv-B3. The heavy chain variable fragment of scFv-2D8 was also prepared and converted into selenium-containing protein using the same method. This selenium-containing single-domain antibody showed some GPX activity and, to the best of our knowledge, is the first human single-domain abzyme with GPX activity, which lays a foundation for preparing GPX abzyme with human origin, lower molecular weight and higher activity.

A novel selenium and copper-containing peptide with both superoxide dismutase and glutathione peroxidase activities.

Superoxide dismutase (SOD), glutathione peroxidase (GPX) and catalase (CAT) play crucial roles in balancing the production and decomposition of reactive oxygen species (ROS) in living organisms. These enzymes act cooperatively and synergistically to scavenge ROS. In order to imitate the synergism of these enzymes, we designed and synthesized a novel 32-mer peptide (32P) on the basis of the previous 15-mer peptide with GPX activity and a 17-mer peptide with SOD activity. Upon the selenation and chelation of copper, the 32-mer peptide is converted to a new Se- and Cu-containing 32-mer peptide (Se-Cu-32P) and displays both SOD and GPX activities and its kinetics was studied. Moreover, the novel peptide was demonstrated to be able to better protect vero cells from the injury induced by xanthine oxidase (XOD)/xanthine/Fe2+ damage system than its parents. Thus, this bifunctional enzyme imitated the synergism of SOD and GPX and could be a better candidate of therapeutic medicine.

Advanced "lab-on-a-chip" to detect viruses - Current challenges and future perspectives.

Massive viral outbreaks draw attention to viruses that have not been thoroughly studied or understood. In recent decades, microfluidic chips, known as "lab-on-a-chip", appears as a promising tool for the detection of viruses. Here, we review the development of microfluidic chips that could be used in response to viral detection, specifically for viruses involved in more recent outbreaks. The advantages as well as the disadvantages of microfluidic systems are discussed and analyzed. We also propose ideas for future development of these microfluidic chips and we expect this advanced technology to be used in the future for viral outbreaks.

A "sample-in-multiplex-digital-answer-out" chip for fast detection of pathogens.

Point-of-care (POC) testing offers rapid diagnostic results. However, the quantification of current methods is performed using standard curves and external references, and not direct and absolute quantification. This paper describes an integrated multiplex digital recombinase polymerase amplification (ImdRPA) microfluidic chip which combines DNA extraction, multiplex digital RPA and fluorescence detection together in one chip, creating a "sample-in-multiplex-digital-answer-out" system. Multi-layer soft lithography technology was used, with polydimethylsiloxane (PDMS) as the chip material and a glass slide as the substrate. This microfluidic chip has a six-layer structure and screw microvalve control function. The sample preparation for the chip involved magnetic bead-based nucleic acid extraction, which was completed within 15 min without any instrument dependence. The dRPA region was divided into 4 regions (3 positive detection areas and 1 negative control area) and included a total of 12 800 chambers, with each chamber being able to contain a volume of 2.7 nL. The screw valve allowed for the reaction components of each specific goal to be pre-embedded in different regions of the chambers. The reagents were passively driven into the dRPA region using vacuum-based self-priming introduction. Furthermore, we successfully demonstrated that the chip can simultaneously detect three species of pathogenic bacteria within 45 min and give digital quantitative results without the need to establish a standard curve in contaminated milk. Moreover, the detection limit of this ImdRPA microfluidic chip was found to be 10 bacterial cells for each kind of pathogen. These characteristics enhance its applicability for rapid detection of foodborne bacteria at the point-of-care (POC). We envision that the further development of this integrated chip will lead to rapid, multiplex and accurate detection of foodborne bacteria in a feasible manner.

A Self-Priming Digital Polymerase Chain Reaction Chip for Multiplex Genetic Analysis.

Digital PCR (polymerase chain reaction) is a powerful and attractive tool for the quantification of nucleic acids. However, the multiplex detection capabilities of this system are limited or require expensive instrumentation and reagents, all of which can hinder multiplex detection goals. Here, we propose strategies toward solving these issues regarding digital PCR. We designed and tested a self-priming digital PCR chip containing 6-plex detection capabilities using monochrome fluorescence, which has six detection areas and four-layer structures. This strategy achieved multiplex digital detection by the use of self-priming to preintroduce the specific reaction mix to a certain detection area. This avoids competition when multiple primer pairs coexist, allowing for multiplexing in a shorter time while using less reagents and low-cost instruments. This also prevents the digital PCR chip from experiencing long sample introduction time and evaporation. For further validation, this multiplex digital PCR chip was used to detect five types of EGFR (epidermal growth factor receptor) gene mutations in 15 blood samples from lung cancer patients. We conclude that this technique can precisely quantify EGFR mutations in high-performance diagnostics. This multiplex digital detection chip is a simple and inexpensive test intended for liquid biopsies. It can be applied and used in prenatal diagnostics, the monitoring of residual disease, rapid pathogen detection, and many other procedures.

Heavy Metals in Grains from Jilin Province, China, and Human Health Risk.

ABSTRACT: Heavy metals are an indispensable part of industrial and agricultural development. As the cradle of China's industry and an important province for agricultural production, Jilin Province has been an area of concern about heavy metal pollution in the local environment and grains. In this study, we focused on four heavy metals that are harmful to humans: arsenic (As), cadmium (Cd), methylmercury (MeHg), and inorganic arsenic (iAs). We determined the contents of these metals in 341 grain samples by using graphite furnace atomic absorption spectrometry and liquid chromatography-atomic fluorescence spectrometry and compared our results with the limit value of national standards. To evaluate the potential risk to human health, we determined the target hazard quotient and hazard index. Heavy metals were detected at these rates, from high to low: Cd (48%) > iAs (20.8%) > MeHg (4.6%) > Pb (3%). Most of these values are far below the limit of national standards. The target hazard quotient and hazard index were both smaller than 1; thus, we conclude that heavy metal pollution in grains in Jilin Province is not serious and that people are not at high risk from heavy metals in grains.

A trifunctional enzyme with glutathione S-transferase, glutathione peroxidase and superoxide dismutase activity.

Superoxide dismutase (SOD), glutathione peroxidase (GPX), glutathione S-transferase (GST) and glutathione reductase (GR) play crucial roles in balancing the production and decomposition of reactive oxygen species (ROS) in living organisms. These enzymes act cooperatively and synergistically to scavenge ROS, as not one of them can singlehandedly clear all forms of ROS. In order to imitate the synergy of the enzymes, we designed and generated a recombinant protein, which comprises of a Schistosoma japonicum GST (SjGST) and a bifunctional 35-mer peptide with SOD and GPX activities. The engineered protein demonstrated SOD, GPX and GST activities simultaneously. This trifunctional enzyme with SOD, GPX and GST activities is expected to be the best ROS scavenger.

Diverse autophagy and apoptosis in myeloid leukemia cells induced by 20(s)-GRh2 and blue LED irradiation.

Autophagy is an important mechanism for cell death regulation. To improve the anticancer effect during the treatment of leukemia and promote the apoptosis of leukemic cells, it is important to define the relationship between autophagy and apoptosis. A key bioactive compound in traditional Chinese medicine, 20(s)-Ginsenoside (GRh2), demonstrated an advancement in leukemia treatment. Blue LED therapy (BL) is a physical treatment method that can induce leukemic cell death. In this study, we tested the effect of 20(s)-GRh2, BL, and their combination (BL-GRh2) on the activation of leukemic cell apoptosis and autophagy. Both treatments, whether used individually or simultaneously, induce apoptosis through the induction of reactive oxygen species (ROS), disrupted mitochondrial membrane potential (MMP) and regulated the expression of apoptosis-related genes and proteins. Furthermore, using western blotting to analyze the autophagy markers LC3B and P62, we detected the activation of autophagy. In cells treated with autophagy inhibitor 3-MA, both autophagy and apoptosis were inhibited, either by BL alone or by BL-GRh2. However, apoptosis in 20(s)-GRh2-treated cells was enhanced. In cells treated with apoptosis suppressor Z-VAD-FMK, autophagy was inhibited in the BL and BL-GRh2-treated cells, although it was enhanced in cells treated with 20(s)-GRh2 alone. Moreover, we observed a stronger induction of apoptosis by BL-GRh2 in myeloid leukemia cells. Our data indicate that autophagy induced by different factors can play diverse roles on the same cells. Our results also indicate that the combination of traditional Chinese medicine with physical therapy may be a new strategy for anti-cancer therapy.