A survey on computational strategies for genome-resolved gut metagenomics.

Recovering high-quality metagenome-assembled genomes (HQ-MAGs) is critical for exploring microbial compositions and microbe-phenotype associations. However, multiple sequencing platforms and computational tools for this purpose may confuse researchers and thus call for extensive evaluation. Here, we systematically evaluated a total of 40 combinations of popular computational tools and sequencing platforms (i.e. strategies), involving eight assemblers, eight metagenomic binners and four sequencing technologies, including short-, long-read and metaHiC sequencing. We identified the best tools for the individual tasks (e.g. the assembly and binning) and combinations (e.g. generating more HQ-MAGs) depending on the availability of the sequencing data. We found that the combination of the hybrid assemblies and metaHiC-based binning performed best, followed by the hybrid and long-read assemblies. More importantly, both long-read and metaHiC sequencings link more mobile elements and antibiotic resistance genes to bacterial hosts and improve the quality of public human gut reference genomes with 32% (34/105) HQ-MAGs that were either of better quality than those in the Unified Human Gastrointestinal Genome catalog version 2 or novel.

Phytochemical Profile of Alkaloid Extract from Dendrobium huoshanense and Inhibitory Effects against Oxidative Stress in H2 O2 -Induced PC12 Cells.

This study aimed to explore the alkaloid profile of Dendrobium huoshanense and determine the potential protective effect against oxidative damage. The crude D. huoshanense alkaloid extract (DHAE) was obtained by 70 % ethanol extraction and liquid-liquid partition. DHAE contained specific alkaloid components with abundant 6-hydroxynobiline (58.15 %) and trace dendrobine (3.23 %) in the preliminary HPLC fingerprint and GC-MS analysis, which was distinguished from D. officinale or D. nobile. Subsequently, six alkaloids including 6-hydroxynobiline, 2-hydroxy dendrobine, nobilonine, dendrobine, Findlayines D and trans-dendrochrysanine were identified in the purified DHAE (namely DHSAE-3, DHSAE-3') via further solid phase extraction coupled with UPLC-MS/MS analysis. Meanwhile, pretreatment with DHAE or DHSAE (0.5, 5 µg/mL) increased cell viability by 14.0-57.4 % compared to that of H2 O2 -induced PC12 Model cells. Among them, 5 µg/mL DHSAE-3-treated cells displayed a pronounced reversion than the positive vitamin E (p<0.01). Furthermore, a clear cellular morphological restoration and 38.4 % reduction in intracellular reactive oxidative species level were achieved. Our findings suggest that D. huoshanense has a characteristic alkaloid profile represented by abundant 6-hydroxynobiline, and DHAEs exhibit obvious protection against oxidative neuronal damage. Overall, this study indicates that DHAEs might be used to inhibit oxidative stress and provide a source to develop novel neuroprotective drugs.

Holistic quality evaluation method of Epimedii Folium based on NIR spectroscopy and chemometrics.

INTRODUCTION: There are some problems in the quality control of Epimedii Folium (leaves of Epimedium brevicornum Maxim.), such as the mixed use of Epimedii Folium from different harvesting periods and regions, incomplete quality evaluation, and time-consuming analysis methods. OBJECTIVE: Near-infrared (NIR) spectroscopy was conducted to establish a rapid overall quality evaluation method for Epimedii Folium. MATERIALS AND METHODS: Quantitative models of the total solid, moisture, total flavonoid, and flavonol glycoside (Epimedin A, Epimedin B, Epimedin C, Icariin) contents of Epimedii Folium were established by partial least squares regression (PLSR). The root mean square error (RMSE) and correlation coefficient (R) were used to evaluate the performance of models. The qualitative models of Epimedii Folium from different geographic origins and harvest periods were established based on K-nearest neighbor (KNN), back-propagation neural network (BPNN), and random forest (RF). Accuracy and Kappa values were used to evaluate the performance of models. A new multivariable signal conversion strategy was proposed, which combines NIR spectroscopy with the PLSR model to predict the absorbance values of retention time points in the high-performance liquid chromatography (HPLC) fingerprint to obtain the predicted HPLC fingerprint. The Pearson correlation coefficient and cosine coefficient were used to evaluate the similarity between real and predicted HPLC fingerprints. RESULTS: Qualitative models, quantitative models, and the similarity between real and predicted HPLC fingerprints are satisfactory. CONCLUSION: The method serves as a fast and green analytical quality evaluation method of Epimedii Folium and can replace traditional methods to achieve the overall quality evaluation of Epimedii Folium.

Research on the Algorithm of Position Correction for High-Speed Moving Express Packages Based on Traditional Vision and AI Vision.

The rapid development of the logistics industry poses significant challenges to the sorting work within this sector. The fast and precise identification of moving express parcels holds immense significance for the performance of logistics sorting systems. This paper proposes a motion express parcel positioning algorithm that combines traditional vision and AI-based vision. In the traditional vision aspect, we employ a brightness-based traditional visual parcel detection algorithm. In the AI vision aspect, we introduce a Convolutional Block Attention Module (CBAM) and Focal-EIoU to enhance YOLOv5, improving the model's recall rate and robustness. Additionally, we adopt an Optimal Transport Assignment (OTA) label assignment strategy to provide a training dataset based on global optimality for the model training phase. Our experimental results demonstrate that our modified AI model surpasses traditional algorithms in both parcel recognition accuracy and inference speed. The combined approach of traditional vision and AI vision in the motion express parcel positioning algorithm proves applicable for practical logistics sorting systems.

Target gene mutations endowed cross-resistance to acetolactate synthase-inhibiting herbicides in wild Brassica juncea.

Wild Brassica juncea is a troublesome weed that infests wheat fields in China. Two suspected wild B. juncea populations (19-5 and 19-6) resistant to acetolactate synthase (ALS) inhibitors were collected from wheat fields in China. To clarify their resistance profiles and resistance mechanism, the resistance levels of populations 19-5 and 19-6 to ALS-inhibiting herbicides and their underlying target-site resistance mechanism were investigated. The results showed that the 19-5 population exhibited resistance to tribenuron-methyl, pyrithiobac­sodium and florasulam, while the 19-6 population was resistant to tribenuron-methyl, pyrithiobac­sodium, imazethapyr and florasulam. Using the homologous cloning method, two ALS genes were identified in wild B. juncea, with one gene (ALS1) encoding 652 amino acids and the other (ALS2) encoding 655 amino acids. Pro-197-Arg mutation on ALS2 and Trp-574-Leu mutation on ALS1, together with the combination of these two mutations in a single plant, were observed in both 19-5 and 19-6 populations. ALS2 enzymes carrying the Pro-197-Arg mutation were cross-resistant to tribenuron-methyl, pyrithiobac­sodium, imazerthapyr and florasulam, with resistance index (RI) values of 6.23, 32.81, 7.97 and 1162.50, respectively. Similarly, ALS1 enzymes with Trp-574-leu substitutions also displayed high resistance to these four herbicides (RI values ranging from 132.61 to 3375.00). In addition, the combination of Pro-197-Arg (ALS2) and Trp-574-Leu (ALS1) mutations increased the resistance level of the ALS enzyme to ALS inhibitors, with its RI values 3.83-214.19, 6.88-37.34, 1.91-31.82 and 2.03-5.90-fold higher than a single mutation for tribenuron-methyl, pyrithiobac­sodium, imazerthapyr and florasulam, respectively. Collectively, Pro-197-Arg mutation on ALS2, Trp-574-Leu mutation on ALS1 and the combination of Pro-197-Arg (ALS2) and Trp-574-Leu (ALS1) mutations in wild B. juncea could endow broad-spectrum resistance to ALS inhibitors, which might provide guides for establishing effective strategies to prevent or delay such resistance evolution in this weed.

Enhanced metabolic resistance mechanism endows resistance to metamifop in Echinochloa crus-galli (L.) P. Beauv.

Barnyardgrass (Echinochloa crus-galli (L.) P. Beauv.), one of the worst weeds in paddy fields in China, has been frequently reported evolving resistance to acetyl-CoA carboxylase (ACCase) inhibiting herbicides. However, in the previous research, more attention was paid to target-site resistance (TSR) mechanisms, the non-target-site resistance (NTSR) mechanisms have not been well-established. In this study, the potential mechanism of resistance in a metamifop-resistant E. crus-galli collected from Kunshan city, Jiangsu Province, China was investigated. Dose-response assays showed that the phenotypic resistant population (JS-R) has evolved 4.3-fold resistance to metamifop compared with the phenotypic susceptible population (YN-S). The ACCase CT gene sequencing and relative ACCase gene expression levels studies showed that no mutations were detected in the ACCase CT gene in both YN-S and JS-R, and there was no significant difference in the relative ACCase gene expression between YN-S and JS-R. After the pre-processing of glutathione-S-transferase (GSTs) inhibitor NBD-Cl, the resistance level of JS-R to metamifop was reversed 18.73%. Furthermore, the GSTs activity of JS-R plants was significantly enhanced compared to that of YN-S plants. UPLC-MS/MS revealed that JS-R plants had faster metabolic rates to metamifop than YN-S plants. Meanwhile, the JS-R popultion exhibited resistant to cyhalofop-butyl and penoxsulam. In summary, this study presented a novel discovery regarding the global emergence of metabolic resistance to metamifop in E. crus-galli. The low-level resistance observed in the JS-R population was not found to be related to TSR but rather appeared to be primarily associated with the overexpression of genes in the GSTs metabolic enzyme superfamily.

Potential Role of EPSPS Mutations in the Resistance of Eleusine indica to Glyphosate.

Gene mutation is a basic evolutionary mechanism in plants under selection pressure of herbicides. Such mutation has pleiotropic effects on plant growth. We systemically investigated the effects of Pro106Leu (P106L), Pro106Ser (P106S), and Thr102Ile + Pro106Ser (TIPS) mutations on EPSPS functionality and fitness traits in Eleusine indica at the biochemical and physiological levels. The affinity of natural EPSPS for glyphosate was 53.8 times higher than that for phosphoenolpyruvate (PEP), as revealed by the dissociation constant; the constant decreased in both the P106L (39.9-fold) and P106S (46.9-fold) mutants but increased in the TIPS (87.5-fold) mutant. The Km (PEP) values of the P106L, P106S, and TIPS mutants were 2.4-, 0.7-, and 4.1-fold higher than that of natural EPSPS, corresponding to resistance levels of 2.5, 1.9, and 11.4, respectively. The catalytic efficiency values (maximum reaction rates) were 0.89-, 0.94-, and 0.26-fold higher than that of natural EPSPS. The levels of metabolites related to amino acids and nucleotides were significantly reduced in the mutated plants. The fitness costs were substantial for the biomass, total leaf area, seed number, and seedling emergence throughout the growth period in the plants with P106L and TIPS mutations. These results provide insights into EPSPS kinetics and their effect on plant growth.

EST-SSR Markers' Development Based on RNA-Sequencing and Their Application in Population Genetic Structure and Diversity Analysis of Eleusine indica in China.

Goosegrass (Eleusine indica) is one of the worst agricultural weeds in China. Molecular markers were developed for genetic diversity and population structure analyses. In this study, we identified 8391 expressed sequence tag-simple sequence repeat (EST-SSR) markers from the de novo assembled unigenes of E. indica. Mononucleotides were the most abundant type of repeats (3591, 42.79%), followed by trinucleotides (3162, 37.68%). The most dominant mononucleotide and trinucleotide repeat motifs were A/T (3406, 40.59%) and AAT/ATT (103, 1.5%), respectively. Fourteen pairs of EST-SSR primers were verified and used to analyze the genetic diversity and population structure of 59 goosegrass populations. A total of 49 alleles were amplified, with the number of alleles (Na) ranging from two to eleven per locus, and the effective number of alleles (Ne) ranged from 1.07 to 4.53. The average polymorphic information content (PIC) was 0.36. Genetic structure analysis (K = 2) and principal coordinate analysis divided 59 E. indica populations into two groups in a manner similar to the unweighted pair-group method (Dice genetic similarity coefficient = 0.700). This study developed a set of EST-SSR markers in E. indica and successfully analyzed the diversity and population genetic structures of 59 E. indica populations in China.

Umpolung Reactivity of Imine Ester: Visible-Light Mediated Transfer Hydrogenation of α-Aryl Imino Esters by Phenylsilane and Water.

A visible-light mediated chemoselective transfer hydrogenation of α-aryl imino esters was demonstrated. The methodology allowed the efficient and practical preparation of α-amino acid esters. The mechanism of the reaction was probed by DFT calculations, and deuteration experiments indicated deuterium was introduced into amino acid esters efficiently (up to 99 % D ratio), enabling a feasible way to obtain deuterated amino acids using D2 O as a cheap deuterium source.

Chiral Phosphoric Acid-Catalyzed Enantioselective Aza-Friedel-Crafts Addition of Naphthols with Isatin-Derived Ketimines.

The enantioselective Friedel-Crafts addition of naphthols with isatin-derived ketimines was developed with H8-BINOL-derived chiral biaryl phosphoric acid. A wide range of isatin-derived ketimines and naphthols were successfully applied and gave a series of chiral 3-amino-2-oxindoles in excellent yields with high optical purities.

Tetrabutylammonium Bromide-Catalyzed Transfer Hydrogenation of Quinoxaline with HBpin as a Hydrogen Source.

A metal-free environmentally benign, simple, and efficient transfer hydrogenation process of quinoxaline has been developed using the HBpin reagent as a hydrogen source. This reaction is compatible with a variety of quinoxalines offering the desired tetrahydroquinoxalines in moderate-to-excellent yields with Bu4NBr as a noncorrosive and low-cost catalyst.

PsbA gene over-expression and enhanced metabolism conferring resistance to atrazine in Commelina communis.

Commelina communis L. is a troublesome weed in agronomic fields and increasingly threatens the yield security of corn in north-eastern China. Previously, we found that a C. communis population (JL-1) has evolved resistance to atrazine. Although the potential genetic and enzymic differences contributing to atrazine resistance in this population have been investigated, the specific molecular mechanisms underlying C. communis resistance are still poorly understood. Here, the expression level of the target gene PsbA and the non-target-site resistance (NTSR) mechanism for this population were studied. The results showed that the decline in chlorophyll content in JL-1 leaves was less than in the susceptible JS-10 population following atrazine treatment. JL-1 exhibited an enhanced expression of the PsbA gene compared with JS-10 of 7.28- and 14.28-fold higher at 0 and 24 h after treatment with atrazine, respectively. The cytochrome P450 monooxygenase (P450) inhibitor piperonyl butoxide (PBO) increased the phytotoxicity of atrazine in both populations of C. communis. Seven candidate genes associated with NTSR of Jl-1 were identified through RNA-seq and validated by quantitative real-time PCR, including 5 upregulated genes involved in herbicide metabolism. In addition, the activities of glutathione S-transferases and P450s in JL-1 were increased compared with JS-10. Collectively, PsbA gene overexpression and enhanced metabolism are likely to be responsible for JL-1 resistance to atrazine.

Progress in Visible Light-Induced Difluroalkylation of Olefins.

The incorporation of difluoromethylated (CF2 ) moiety into potentially useful parent molecules lead to significant changes in metabolic stability, lipophilicity, and solubility of the molecules. Over the past several years, with the advent of new difluoromethylating reagents, great progress has been made in the development of a protocol for the direct incorporation of the CF2 H group into organic molecules. Among them, difluroalkylation induced by visible light has emerged as an efficient strategy over the past few years. In particular, this protocol provides a more sustainable alternative to other traditional radical-triggered reactions in terms of environment, energy, step-economy, health, and safety. The present review mainly focuses on the development of the photocatalytic difluoroalkylation to olefinic moiety using transition-metal complexes, organic dyes as the photocatalyst; and some organic compounds as a medium of photocatalysis.

Asymmetric Reduction of Aromatic α-Dehydroamino Acid Esters with Water as Hydrogen Source.

The asymmetric reduction of aromatic α-dehydroamino acid esters with water as the hydrogen source was developed by a Rh/Cu co-catalytic system. The reaction tolerates various functional groups, providing a valuable synthetic tool to access chiral α-amino acid esters readily. Moreover, the present methodology also was applied in the cost-effective and easy to handle preparation of chiral deuterated α-amino esters by using D2O.

Zinc salt-catalyzed reduction of α-aryl imino esters, diketones and phenylacetylenes with water as hydrogen source.

The zinc salt-catalyzed reduction of α-aryl imino esters, diketones and phenylacetylenes with water as hydrogen source and zinc as reductant was successfully conducted. The presented method provides a low-cost, environmentally friendly and practical preparation of α-aryl amino esters, α-hydroxyketones and phenylethylenes. By using D2O as deuterium source, the corresponding products were obtained in high efficiency with excellent deuterium incorporation rate, which gives a cheap and safe tool for access to valuable deuterium-labelled compounds.

RNA-Seq transcriptome analysis to identify candidate genes involved in non-target site-based mesosulfuron-methyl resistance in Beckmannia syzigachne.

American sloughgrass (Beckmannia syzigachne Steud.) has become a dominant weed in fields with rice-wheat rotation. Moreover, herbicide resistance has rendered weed control difficult. We identified a biotype showing resistance to ALS inhibitor mesosulfuron-methyl with a resistant index 3.3, but without any ALS mutation. This study aims to identify and confirm the factors associated with non-target site resistance of this biotype to mesosulfuron-methyl using RNA-Seq. 118,111 unigenes were assembled, and 50.9% of these were annotated across seven databases. Eleven contigs related to metabolic resistance were identified based on differential expression via RNA-Seq which include a novel resistance-related transcription factor (MYC3) and two disease resistance proteins were also identified (At1g58602 and At1g15890). Fold changes in expression of these genes in comparison M-R vs. M-S ranged from 3.9 to 11.6, as confirmed by qPCR. The expression of a contig annotated as cytochrome P450 (CYP86B1) in resistant individuals was over 3 times higher than that in sensitive individuals at 0-72 h after mesosulfuron-methyl treatment. A similar trend was noted for three other genes annotated as glutathione S-transferase (GST), namely GST-T3, GST-U6, and GST-U14; the expression of GST-U6 in resistant individuals was up to 142.3 times higher than that in sensitive individuals at 24 h after mesosulfuron-methyl treatment. In addition, GST activity in resistant individuals was 2.1 to 5.3 times higher than that in sensitive individuals. The GR50 of resistant biotype decreased from 24.4 to 11.3 g a.i. ha-1 after P450 inhibitor malathion treatment. This study identified a cytochrome P450 gene CYP86B1 and three GST genes GST-T3, GST-U6, and GST-U14 that have higher expression in mesosulfuron-methyl resistant B. syzigachne, suggesting that both P450- and GST-based activities could be involved in resistance.

Characterization of glyphosate and quizalofop-p-ethyl multiple resistance in Eleusine indica.

Glyphosate and Acetyl-coenzyme A Carboxylase (ACCase) inhibitors are popular herbicides that control goosegrass. However, some populations are difficult to control due to resistance resulting from the increasing selection pressure. The objectives of this research were to detect the multiple resistance levels, resistance mechanisms, and fitness costs of two goosegrass populations collected in China. The resistance indices of two resistant populations (denominated as R1 and R2) to glyphosate were 3.8 and 2.3, respectively; and it was 18.0 and 14.2 to quizalofop-p-ethyl, respectively. Shikimate accumulation in R1 and R2 populations was only 8% of that of the susceptible population after glyphosate treatment. A Pro-106-Ala mutation in EPSPS and an Asp-2078-Gly mutation in ACCase were present in both resistant populations. Both the expression level of EPSPS and ACCase in resistant populations were similar to that of susceptible populations. The leaf area of the individuals in wild-type populations was more than three times of the leaf area in the resistant populations. Similarly, resistant plants were 45-49% shorter, had 70-76% less fresh shoot weight, and 67-69% fewer seeds than wild-type plants. Goosegrass populations have evolved multiple resistance to glyphosate and the ACCase inhibitor quizalofop-p-ethyl in China. The Pro-106-Ala mutation in the EPSPS and the Asp-2078-Gly mutation in the ACCase were responsible for this resistance. In addition, a fitness cost exists in the resistant populations, and more work should conduct to clear which mutation is responsible for the fitness penalty.

Different leaf-mediated deposition, absorbed and metabolism behaviors of 2,4-D isooctyl ester between Triticum aestivum and Aegilops tauschii Coss.

Tausch's goatgrass (Aegilops tauschii Coss.), is a major weed species, infesting wheat (Triticum aestivum) fields in China. 2,4-D isooctyl ester is widely used for broadleaf weed control and selected as a tool to study the differences between, A. tauschii and T. aestivum. In this study, we measured the growth responses of these species to 2,4-D isooctyl ester and found that T. aestivum was more sensitive to the herbicide than A. tauschii. To clarify the reasons for this difference, we measured the leaf-mediated deposition, absorption and metabolism of 2,4-D isooctyl ester and the expression of auxin receptor transport inhibitor response (TIR1) gene in T. aestivum and A. tauschii. The results indicated that the deposition of 2,4-D isooctyl ester droplets may be lower on A. tauschii than on T. aestivum, because of the increased contact angle and greater density of trichomes on the leaves of the former. A distinct increase in 2,4-D isooctyl ester uptake was detected in T. aestivum during the entire experimental period, and the rate was 2.2-fold greater than that in A. tauschii at 6 h after treatment. Compared with A. tauschii, T. aestivum exhibited a greater accumulation of primary metabolite 2,4-D in plants, which may be responsible for the different responses of the two species. Additionally, the absolute expression level of TIR1 was clearly greater in T. aestivum than that in A. tauschii. These data will be helpful to further understand the differences between T. aestivum and A. tauschii, which may provide a unique perspective for the development and identification of new target compounds that are effective against this weed species.

Selection and Validation of Reference Genes for RT-qPCR Analysis in Aegilops tauschii (Coss.) under Different Abiotic Stresses.

Aegilops tauschii (Coss.) is an aggressive and serious annual grass weed in China. Its DD genome is a rich source of genetic material and performs better under different abiotic stress conditions (salinity, drought, temperature, etc.). Reverse-transcribed quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for reference gene selection and validation. This work aimed to evaluate the stability of reference gene expression in Ae. tauschii under different abiotic stresses (salinity, drought, hot, and cold) and developmental stages (seedling and development). The results show that the ubiquitin-conjugating enzyme E2 36-like (UBC36) and protein microrchidia 2-like (HSP) are the most stable genes under control and salinity conditions, respectively. Under drought stress conditions, UBC36 is more stable as compared with others. Glyceraldehyde-3-phosphate dehydrogenase (GADPH) is the most stable reference gene during heat stress conditions and thioredoxin-like protein (YLS) under cold stress condition. Phosphate2A serine/threonine-protein phosphatase 2A (PP2A) and eukaryotic translation initiation factor 3 (ETIF3) are the most stable genes at seedling and developmental stages. Intracellular transport protein (CAC) is recommended as the most stable gene under different abiotic stresses and at developmental stages. Furthermore, the relative expression levels of NHX1 and DREB under different levels of salinity and drought stress conditions varied with the most (HSP and UBC36) and least (YLS and ACT) stable genes. This study provides reliable reference genes for understanding the tolerance mechanisms in Ae. tauschii under different abiotic stress conditions.

Dynamic metabolomic analysis of intestinal ischemia-reperfusion injury in rats.

Intestinal ischemia-reperfusion injury (IIR) is a life-threatening abdominal emergency. Compared to traditional steady-state works, we profiled the blood of rats over 72 hr (15 time points) and examined dynamic changes in molecular pathways during IIR. Using a series of methods designed for dynamic datasets analysis (batch effects corrections, metabolomics data reduction, and different features selection), we identified 39 significant different metabolites and discovered the trends of these molecules. Four main patterns were uncovered by a longitudinal pattern recognition method. Furthermore, pathway networks were explored to uncover the possible mechanisms of IIR. We found that IIR is a complex physiological process involved in multiple pathways, such as biosynthesis of amino acids, 2-oxocarboxylic acid metabolism, arginine-related metabolism, and glutathione metabolism. Among which, metabolites related with phenylalanine tyrosine and tryptophan metabolism reached a peak during the early stage of reperfusion, while molecules in biosynthesis of unsaturated fatty acids metabolism declined. Our work provides a feasible scheme to understand dynamic molecule variation and will provide new explications about the effect of intestinal ischemia reperfusion from a dynamic perspective.