Technological Development and Advances for Constructing and Analyzing Plant Pangenomes.

A pangenome captures the genomic diversity for a species, derived from a collection of genetic sequences of diverse populations. Advances in sequencing technologies have given rise to three primary methods for pangenome construction and analysis: de novo assembly and comparison, reference genome-based iterative assembly, and graph-based pangenome construction. Each method presents advantages and challenges in processing varying amounts and structures of DNA sequencing data. With the emergence of high-quality genome assemblies and advanced bioinformatic tools, the graph-based pangenome is emerging as an advanced reference for exploring the biological and functional implications of genetic variations.

Probabilistic Risk Assessment of Heavy Metals in Mining Soils Based on Fractions: A Case Study in Southern Shaanxi, China.

With rapid economic development, soil heavy metal (HM) pollution has emerged as a global environmental concern. Because the toxicity of HMs differs dramatically among various fractions, risk assessments based on these fractions are of great significance for environmental management. This study employed a modified Hakanson index approach to evaluate the possible ecological impacts of soil HMs in a gold mine tailings pond in Shaanxi Province, China. A modified Hakanson-Monte Carlo model was built to perform a probabilistic risk assessment. The results showed that: (1) the exceedance rates of chromium (Cr) and zinc (Zn) were 68.75% and 93.75%, respectively. Moreover, the overall concentrations of nickel (Ni), copper (Cu), arsenic (As), and lead (Pb) were higher than the background soil environmental values in China. (2) HMs with the lowest oxidizable fraction were mostly present in the residual fraction. The oxidizable portions of Cr, Cu, and Pb and the reducible and residual fractions of As were notably distinct. (3) The risk degrees of Cr, Ni, Cu, and Zn were low; those of As and Pb were very high and moderate; and the comprehensive ecological hazard index was very high. This study offers a solid scientific foundation for ecological risk notification and environmental management.

Characteristics of Soil Arsenic Contamination and the Potential of Pioneer Plants for Arsenic Remediation in Gold Mine Tailings.

Arsenic (As) contamination of gold mine tailings poses major threats to the natural environment and human health, necessitating adequate management measures. To investigate the soil As contamination level and the potential of pioneer plants for As remediation, the soil and plants of an abandoned gold mine tailings in the Qinling Mountains were analyzed. The level of As contamination was assessed using the single-factor pollution index and potential ecological risk index, and its bioeffectiveness was analyzed. The enrichment capability of plants was investigated using the bioaccumulation factor and translocation factor. Redundancy analysis and partial least squares regression were employed to investigate factors affecting the distribution of As in soil and plants. The results show that As in soil mainly existed in the difficult-available state, with serious contamination and extremely high ecological risk. Lythrum salicaria L. and Equisetum ramosissimum Desf. are the preferred plants for remediation of As contamination through screening pioneer plants. Soil total nitrogen (STN) and available phosphorus (SAP) are the main factors influencing the characteristics of As distribution in the soil. Soil available potassium (SAK), water content (SWC), and SAP promote the accumulation of As by plants. This study provides plant materials and new ideas for mine ecological remediation.

Adsorption of Toxic Tetracycline, Thiamphenicol and Sulfamethoxazole by a Granular Activated Carbon (GAC) under Different Conditions.

Activated carbon can be applied to the treatment of wastewater loading with different types of pollutants. In this paper, a kind of activated carbon in granular form (GAC) was utilized to eliminate antibiotics from an aqueous solution, in which Tetracycline (TC), Thiamphenicol (THI), and Sulfamethoxazole (SMZ) were selected as the testing pollutants. The specific surface area, total pore volume, and micropore volume of GAC were 1059.011 m2/g, 0.625 cm3/g, and 0.488 cm3/g, respectively. The sorption capacity of GAC towards TC, THI, and SMZ was evaluated based on the adsorption kinetics and isotherm. It was found that the pseudo-second-order kinetic model described the sorption of TC, THI, and SMZ on GAC better than the pseudo-first-order kinetic model. According to the Langmuir isotherm model, the maximum adsorption capacity of GAC towards TC, THI, and SMZ was calculated to be 17.02, 30.40, and 26.77 mg/g, respectively. Thermodynamic parameters of ΔG0, ΔS0, and ΔH0 were obtained, indicating that all the sorptions were spontaneous and exothermic in nature. These results provided a knowledge base on using activated carbon to remove TC, THI, and SMZ from water.

Dynamic Analysis of Physicochemical Properties and Polysaccharide Composition during the Pile-Fermentation of Post-Fermented Tea.

Ultra-high performance liquid chromatography-quadrupole-time of flight tandem mass spectrometry (UHPLC-Q-TOF-MS/MS) was used to study the diversity of tea polysaccharides and the dynamic changes in the physicochemical indexes of tea samples. FT-IR spectra and the free radical scavenging ability of tea polysaccharides, during pile-fermentation of post-fermented tea, were analyzed. The results showed that 23 saccharide co mponents in tea polysaccharides were identified: these belonged to 11 monosaccharides, 5 oligosaccharides, and 6 derivatives of monosaccharides and oligosaccharides. The abundance of oligosaccharides decreased gradually, while monosaccharides, and derivatives of monosaccharides and oligosaccharides increased gradually with the development of pile-fermentation. According to the differences in polysaccharide composition and their abundance, the tea polysaccharide samples extracted from different pile-fermentation stages could be clearly classed into three groups, W-0, W-1~W-4 and W-5~C-1. The pile-fermentation process affected the yield, the content of each component, FT-IR spectra, and the DPPH free radical scavenging ability of tea polysaccharides. Correlation analysis showed that microorganisms were directly related to the changes in composition and the abundance of polysaccharides extracted from different pile-fermentation stages. The study will further help to reveal the function of tea polysaccharides and promote their practical application as a functional food.

In situ formic acid dehydrogenation observation using a UV-vis-diffuse-reflectance spectroscopy system.

By applying a simple method on the generated gas concentration in the center of a round cell through high-speed stirring, we succeeded in continuously monitoring catalytic formic acid dehydrogenation using a newly developed in situ/operando UV-vis-diffuse-reflectance spectroscopy system, which can exhibit a high S/N ratio and reliable spectra without any mechanical errors from gas meters.

Distribution characteristics and ecological risk assessment of heavy metals in sediments of Shahe reservoir.

Shahe Reservoir of Northern Canal Basin was selected as the study area. Nineteen surface (0~20 cm) sediment samples and three sediment core samples were collected to analyze the spatial distribution characteristics of As, Cd, Cu, Mn, Pb and Zn in the sediments. The geo-accumulation index, potential ecological risk index and risk assessment code were used to evaluate heavy metal pollution, as well as its potential risk was analyzed according to the speciation of heavy metals. Results showed that the average enrichment factors of heavy metals compared to the background value in soil of Beijing were ranked at the order as the point source pollution area > the central area of the reservoir > the downstream area of the reservoir > the Nansha River > the upstream area of the reservoir > the Beisha River, namely, 2.57 times, 2.06 times, 1.97 times, 1.95 times, 1.87 times and 1.85 times, respectively. The sediment core samples in the central area of the reservoir and the inlet of the Beisha River showed a trend of increasing firstly and then decreasing with the change of depth. Pollution assessment results showed that sediment was moderately contaminated or moderately to strongly contaminated by As, but the other heavy metals were not polluted or lightly polluted. The potential ecological risk index of all sampling sites was less than 150, showing a low ecological risk. As Cr and Cu were mainly in the speciation of residues, with low bioavailability. Although the content of Mn and Zn were low, they showed high bioavailability. Based on correlation analysis and principal component analysis, it was speculated that the sources of various heavy metal pollution in the sediment were similar, which were possibly input from the external wastewater. The heavy metals in sediment were positively related to nutrients and organic matter, indicating that all of them were mostly from the same point polluted sources.

Assessment of Soil-Heavy Metal Pollution and the Health Risks in a Mining Area from Southern Shaanxi Province, China.

Soil-heavy metal pollution in mining areas is one of the problems in the comprehensive treatment of soil environmental pollution. To explore the degree of soil-heavy metal pollution and the human health risk in mining areas, the contents of soil As, Cd, Cu, Cr, Hg, Ni, Pb, and Cr(VI) in an abandoned gold mining area were determined. The geoaccumulation index (Igeo), single-factor pollution index (SPI), Nemerow comprehensive pollution index (NCPI), potential ecological risk index (PERI), and the human health risk assessment model were used to assess the pollution degree and the risk of soil-heavy metal pollution. Finally, the assessment results were used to provide remediation guidance. The results showed that (1) the average contents of As, Cd, Cr, Cu, Hg, and Ni in the mining area exceeded the background values of the soil elements. (2) The mining area was polluted by heavy metals to different degrees and had strong potential ecological hazards. (3) The total carcinogenic risk of heavy metals exceeded the health risk standard. The main components of pollution in the mining area were As, Cd, Cr, and Hg. Results from this study are expected to play a positive role in pollution treatment and the balance between humans and ecology.

Improved stability of liposome-stabilized emulsions as a co-encapsulation delivery system for vitamin B2, vitamin E and ß-carotene.

To realize the co-encapsulation of multiple nutraceuticals with different solubilities, Pickering emulsions stabilized by freshly-prepared liposome suspension stabilized emulsion (Fre-Lip-Sus-E) and hydrated lyophilized liposome stabilized emulsion (Hyd-Lyo-Lip-E) were prepared, in comparison with the phospholipid stabilized emulsion (Pho-E). The particle size, zeta-potential, emulsification activity (EAI), emulsion stability (ESI), morphology, environmental stability and rheological properties of the three emulsions were compared. In addition, the in vitro digestive stability and bioaccessibility of three emulsions loaded with vitamin B2, vitamin E and ß-carotene were assessed. The results showed that the Fre-Lip-Sus-E and Hyd-Lyo-Lip-E were characterized by smaller particles and higher environmental stability than the Pho-E. The slight difference between the Hyd-Lyo-Lip-E and Fre-Lip-Sus-E might be due to the partial destruction of the phospholipid bilayer during the lyophilization of lyophilized liposomes. Rheological analysis demonstrated that all emulsions had high interfacial viscosity and significant shear thinning characteristics of pseudoplastic fluids. Compared with the Pho-E, the liposome-stabilized emulsions demonstrated good environmental stability and antioxidant properties, and the Fre-Lip-Sus-E and Hyd-Lyo-Lip-E exhibited comparable stabilising effects. Higher bioaccessibility of vitamin B2 and vitamin E in the Fre-Lip-Sus-E and Hyd-Lyo-Lip-E was observed, while ß-carotene had higher bioaccessibility in Pho-E. These results provide valuable insight into the potential for designing emulsion co-encapsulation delivery systems using liposomes as stabilizers.

Fabrication and characterization of walnut peptides-loaded proliposomes with three lyoprotectants: Environmental stabilities and antioxidant/antibacterial activities.

To protect walnut peptides from harsh external environments during their storage and digestion, proliposomes loaded with walnut peptides were fabricated using sucrose, trehalose, and mannitol as carriers and lyoprotectants. The physicochemical properties, environmental stability, antioxidant/antibacterial activities, and digestion in vitro of the proliposomes were evaluated. The freshly prepared liposomes were uniform in size, but the hydrated proliposomes showed a more uneven size distribution. The lyoprotectants helped maintain favorable liposome shape during lyophilization. Alongside the lyoprotectants, the walnut peptides further stabilized the lipid bilayer. Proliposomes encapsulation didn't impact the peptides' antioxidant activity. Furthermore, walnut peptides-loaded proliposomes exhibited antibacterial activity against Escherichia coli and Staphylococcus aureus. The proliposomes were stable during gastric-phase digestion. The lyoprotectants changed the free fatty acid release behaviors of the proliposomes. These characteristics suggest potential applications for proliposomes as effective delivery systems for biopeptides in food stuffs, thereby protecting bioactivities during storage and passage through the gastrointestinal tract.

The spatial distribution characteristics of typical pathogens and nitrogen and phosphorus in the sediments of Shahe Reservoir and their relationships.

Using samples collected in Shahe Reservoir in the upper North Canal in China, this research analyzes the structure of a microorganism group in sediment and the absolute abundance of two typical pathogenic bacteria (Escherichia coli and Enterococcus), and their relationship with environmental factors including total nitrogen (TN) and total phosphorus (TP). The study of samples collected from the surface (0-20 cm) and sediment cores shows that the absolute abundance of E. coli in horizontal distribution in the sediment is highest in downstream of the reservoir and point source pollution area. In vertical distribution, the absolute gene expression level of the two pathogenic bacteria in the sediment tends to decrease with increasing depth, although its highest value at 10-30 cm depth. The relative abundance the two pathogenic bacteria is much greater in the sediment of Shahe Reservoir with the structure of horizontal groups including Clortridium sensu stricto, unclassified Anaeroineaceae, and Povalibacter, while Anaeroineaceae is much more abundant in the group structure of the vertical distribution. Pearson correlation analysis suggests positive correlation in horizontal distribution for E. coli and TN and TP (P < 0.05) and for Enterococcus and TP (P < 0.05). The results clearly show that the amount of pathogenic bacteria in the sediment in Shahe Reservoir is most likely due to water eutrophication.

Synthesis of efficient Y-Bi2WO6/G visible light photocatalysts with high stability for pollutant degradation.

For effective photocatalytic pollutant degradation on bismuth tungstate (Bi2WO6), it is vital to enhance the photogenerated charge separation and the photochemical stability. Herein, we successfully fabricated yttrium (Y)-Bi2WO6/graphene (G) nanocomposites with a significantly enhanced visible light-driven photocatalytic ability to degrade Rhodamine B compared with the bare Bi2WO6. This is attributed to the remarkably improved visible light absorption capability and photogenerated charge separation after doping yttrium and subsequent coupling with graphene, as revealed by photoluminescence and electrochemical impedance spectroscopies. Moreover, trapping experiments were carried out to clarify that photogenerated ·O2- and holes were the dominant oxidative species in the photocatalytic reaction. In addition, it was confirmed that the resulting composites maintained good photostability and chemical stability during recycling tests. Graphical abstract.

Influence of sulfamethazine (SMT) on the adsorption of antimony by the black soil: Implication for the complexation between SMT and antimony.

This paper reported when sulfamethazine (SMT) and antimony (Sb(V)) coexisted in aqueous solution at pH of 3.0, 5.0 and 7.0, the complexation between SMT and Sb(V) occurred. Such a complexation impeded the adsorption of Sb(V) on the black soil. The higher the solution pH value was, the more the amount of Sb(V) was prevented from adsorbing on the black soil. The maximum adsorption capacity (qm) of Sb(V) at the presence of SMT under pH of 3.0, 5.0 and 7.0 was 5.28, 3.45 and 1.95 mg/g, respectively. -NH2, NH, SO and CN of pyrimidine ring carried by SMT acted as the complexation sites with Sb(V). The complexation constant K were - 3.15, -3.26 and - 3.48 at pH of 7.0, 5.0 and 3.0, respectively, indicating that the complexation strength between SMT and Sb(V) followed the order of pH 7.0 > pH 5.0 > pH 3.0. The binding energy between Sb(V) and the CN group of pyrimidine ring was the highest (1.42 eV), and then followed by the groups of -NH (1.37 eV), SO (0.66 eV) and -NH2 (0.39 eV). Besides SO and CN, Sb(V) tends to complex with NH via coordination bond at pH of 7.0 while -NH2 via cation-π interaction at pH 3.0 and 5.0. Compared to pH of 5.0, the strength of cation-π interaction at pH of 3.0 weakened according to the molecular electrostatic potential map. These results demonstrated that different from the situation where Sb(V) exists in aqueous solution alone, the coexistence of SMT with Sb(V) affected the adsorption behavior of Sb(V) in soil and solution pH was also an influence factor. These findings in this paper would be helpful for further understanding the mobility, bioavailability and other environmental behavior of Sb(V) in soil when Sb(V) coexists with antibiotics even other organic compounds.

Non-enzymatic sensor for determination of glucose based on PtNi nanoparticles decorated graphene.

Diabetes has become a universal epidemic in recent years. Herein, the monitoring of glucose in blood is of importance in clinical applications. In this work, PtNi alloy nanoparticles homogeneously dispersed on graphene (PtNi alloy-graphene) was synthesized as a highly effective electrode material for glucose detection. Based on the modified PtNi alloy-graphene/glass carbon (PtNi alloy-graphene/GC) electrode, it is found that the PtNi alloy-graphene/GC electrode exhibited excellent electrocatalytic performance on glucose oxidation. Furthermore, the results from amperometric current-time curve show a good linear range of 0.5-15 mM with the limit of detection of 16 uM (S/N = 3) and a high sensitivity of 24.03 uAmM-1 cm-2. On account of the good selectivity and durability, the modified electrode was successfully applied on glucose detection in blood serum samples.

Determination of the Total Content of Arsenic, Antimony, Selenium and Mercury in Chinese Herbal Food by Chemical Vapor Generation-Four-Channel Non-dispersive Atomic Fluorescence Spectrometry.

Food security is related to safe and nutritious food which meets people's dietary needs and food preferences for an active and healthy life. A simple and feasible method was proposed for the simultaneous analysis of trace arsenic (As), antimony (Sb), selenium (Se) and mercury (Hg) in Chinese herbal food by chemical vapor generation coupled non-dispersive atomic fluorescence spectrometry (CVG-NDAFS) in this paper. The operating parameters, such as observation height, carrier and shield gas flow rate, were optimized. The detection limits were obtained under optimal conditions, which were 0.051, 0.034, 0.050 and 0.0058 ng mL-1, respectively for As, Sb, Se and Hg. The relative standard deviations were 0.42%, 0.74%, 0.97% and 1.0% (n = 7), respectively (10 ng mL-1of As, Sb, Se and 1 ng ml-1of Hg). The proposed method is verified to simultaneously determine As, Sb, Se and Hg for Chinese herbal food.

Influence of design probe and sequence mismatches on the efficiency of fluorescent RPA.

Recombinase polymerase amplification (RPA) is an isothermal amplification technique. Because of its short detection cycle and high specificity, it has been applied in various fields. However, the design of probe on the efficiency of RPA is not well understood and the effect of sequence mismatches of oligonucleotides on the performance of RPA is rarely discussed. In this study, we found that different primers with the same probe have a slight effect on the efficiency of fluorescent RPA, and different probes with the same amplified region have a great influence on the efficiency of fluorescent RPA. We summarized the design rules of probes suitable for fluorescent RPA by analyzing the experimental data. The rule is that the best distance between fluorescent groups in the probe is 1-2 bases, and the G content should be reduced as far as possible. In addition, we verified this rule by designing a series of probes. Furthermore, we found the base mismatches of the probe had a significant effect on RPA, which can lead to false positives and can change the amplification efficiency. However, 1-3 mismatches covering the center of the primer sequence only affect the amplification efficiency of RPA, not its specificity. And with an increase in the number of primer mismatches, the efficiency of RPA will decrease accordingly. This study suggests that the efficiency of fluorescent RPA is closely related to the probe. We recommend that when designing a fluorescent probe, one must consider the presence of closely related non-targets and specific bases.