Functional analysis of a down-regulated transcription factor-SoxNeuroA gene involved in the acaricidal mechanism of scopoletin against spider mites.

BACKGROUND: Insight into the mode of action of plant-derived acaricides will help in the development of sustainable control strategies for mite pests. Scopoletin, a promising plant-derived bioactive compound, displays prominent acaricidal activity against Tetranychus cinnabarinus. The transcription factor SoxNeuroA plays a vital role in maintaining calcium ion (Ca2+ ) homeostasis. Down-regulation of SoxNeuroA gene expression occurs in scopoletin-exposed mites, but the functional role of this gene remains unknown. RESULTS: A SoxNeuroA gene from T. cinnabarinus (TcSoxNeuroA) was first cloned and identified. Reverse transcription polymerase chain reaction (RT-PCR), quantitative real-time polymerase chain reaction (qPCR), and Western blotting assays all confirmed that the gene expression and protein levels of TcSoxNeuroA were significantly reduced under scopoletin exposure. Furthermore, RNA interference silencing of the weakly expressed SoxNeuroA gene significantly enhanced the susceptibility of mites to scopoletin, suggesting that the acaricidal mechanism of scopoletin was mediated by the weakly expressed SoxNeuroA gene. Additionally, yeast one-hybrid (Y1H) and dual-luciferase reporter assays revealed that TcSoxNeuroA was a repressor of Orai1 Ca2+ channel gene transcription, and the key binding sequence was ATCAAAG (positions -361 to -368 of the Orai1 promoter). Importantly, site-directed mutagenesis and microscale thermophoresis assays further indicated that ASP185, ARG189, and LYS217, which were key predicted hydrogen-bonding sites in the molecular docking model, may be the vital binding sites for scopoletin in TcSoxNeuroA. CONCLUSION: These results demonstrate that the acaricidal mechanism of scopoletin involves inhibition of the transcription factor SoxNeuroA, thus inducing the activation of the Orai1 Ca2+ channel, eventually leading to Ca2+ overload and lethality. Elucidation of the transcription factor-targeted mechanism for this potent plant-derived acaricide has vital implications for the design of next-generation green acaricides with novel targets. © 2023 Society of Chemical Industry.

TEFDTA: a transformer encoder and fingerprint representation combined prediction method for bonded and non-bonded drug-target affinities.

MOTIVATION: The prediction of binding affinity between drug and target is crucial in drug discovery. However, the accuracy of current methods still needs to be improved. On the other hand, most deep learning methods focus only on the prediction of non-covalent (non-bonded) binding molecular systems, but neglect the cases of covalent binding, which has gained increasing attention in the field of drug development. RESULTS: In this work, a new attention-based model, A Transformer Encoder and Fingerprint combined Prediction method for Drug-Target Affinity (TEFDTA) is proposed to predict the binding affinity for bonded and non-bonded drug-target interactions. To deal with such complicated problems, we used different representations for protein and drug molecules, respectively. In detail, an initial framework was built by training our model using the datasets of non-bonded protein-ligand interactions. For the widely used dataset Davis, an additional contribution of this study is that we provide a manually corrected Davis database. The model was subsequently fine-tuned on a smaller dataset of covalent interactions from the CovalentInDB database to optimize performance. The results demonstrate a significant improvement over existing approaches, with an average improvement of 7.6% in predicting non-covalent binding affinity and a remarkable average improvement of 62.9% in predicting covalent binding affinity compared to using BindingDB data alone. At the end, the potential ability of our model to identify activity cliffs was investigated through a case study. The prediction results indicate that our model is sensitive to discriminate the difference of binding affinities arising from small variances in the structures of compounds. AVAILABILITY AND IMPLEMENTATION: The codes and datasets of TEFDTA are available at https://github.com/lizongquan01/TEFDTA.

Development of Sustainable Insecticide Candidates for Protecting Pollinators: Insight into the Bioactivities, Selective Mechanism of Action and QSAR of Natural Coumarin Derivatives against Aphids.

Plants employ abundant toxic secondary metabolites to withstand insect attack, while pollinators can tolerate some natural defensive compounds. Coumarins, as promising green alternatives to chemical insecticides, possess wide application prospects in the crop protection field. Herein, the bioactivities of 30 natural coumarin derivatives against Aphis gossypii were assessed and revealed that 6-methylcoumarin exhibited potent aphicidal activity against aphids but displayed no toxicity to honeybees. Additionally, using biochemical, bioinformatic, and molecular assays, we confirmed that the action mode of 6-methylcoumarin against aphids was by inhibiting acetylcholinesterase (AChE). Meanwhile, functional assays revealed that the difference in action site, which located in Lys585 in aphid AChE (equivalent to Val548 in honeybee AChE), was the principal reason for 6-methylcoumarin being toxic to aphids but safe to pollinators. This action site was further validated by mutagenesis data, which uncovered how 6-methylcoumarin was unique selective to the aphid over honeybee or mammalian AChE. Furthermore, a 2D-QSAR model was established, revealing that the central structural feature was H3m, which offers guidance for the future design of more potent coumarin compounds. This work provides a sustainable strategy to take advantage of coumarin analogues for pest management while protecting nontarget pollinators.

Enhancement of lignin removal from pre-hydrolysis liquor for saccharide recovery via horseradish peroxidase treatment in the presence of Ca2.

The removal of lignin is important to the recovery of saccharides from the pre-hydrolysis liquor (PHL) in kraft-based dissolved pulp production. A one-step process for lignin removal from PHL via treatment with horseradish peroxidase (HRP) in the presence of Ca2+ was proposed, and its principle was studied. The results demonstrated synergy between HRP and Ca2+ in lignin removal from PHL, whereas NH4+ had little effect on lignin removal. HRP treatment in the presence of 60 mmol/L of Ca2+ resulted in a lignin removal of 64.8% accompanied by a saccharide loss of 14.2%. HRP catalyzed both the polymerization and depolymerization of the lignin in the PHL. The HRP-catalyzed lignin polymerization rendered some lignin insoluble enabling it to be directly removed. The HRP-catalyzed depolymerization of lignin decreased its molecular weight with an evident increase in its carboxyl content. The insoluble complexes formed between the lignin with carboxyl and the Ca2+ facilitated the removal of the depolymerized lignin.

Recycling of pre-hydrolysis liquor to improve the concentrations of hemicellulosic saccharides during water pre-hydrolysis of aspen woodchips.

In this study, the pre-hydrolysis liquor (PHL) was recycled during aspen chip water pre-hydrolysis, and the effects of PHL recycling on the extraction and accumulation of the hemicellulosic saccharides especially that with high molecular weight in the PHL were studied. The results showed that the concentration of hemicellulose saccharides in PHL depended on the pre-hydrolysis temperature and PHL recycling times. Compared to the unrecycled PHL, the concentration of hemicellulosic saccharides in PHL increased significantly when recycling PHL once or twice at 170°C. Furthermore, the amount of high-molecular-weight hemicelluloses (HMHs) in PHL recycled once at 170°C increased from 2.58g/L (unrecycled) to 6.18g/L, but the corresponding average molecular weight of HMHs decreased from 9.2kDa to 7.6kDa. The concentration of hemicellulosic saccharides in PHL decreased with PHL recycling time at 180°C, accompanied by the formation of a significant amount of furfural.

Limited adsorption selectivity of active carbon toward non-saccharide compounds in lignocellulose hydrolysate.

Prehydrolysis of lignocellulose produces abundant hemicellulose-derived saccharides (HDS). To obtain pure HDS for application in food or pharmaceutical industries, the prehydrolysis liquor (PHL) must be refined to remove non-saccharide compounds (NSC) derived from lignin depolymerization and carbohydrate degradation. In this work, activated carbon (AC) adsorption was employed to purify HDS from NSC with emphasis on adsorption selectivity. The adsorption isotherms showed the priority of NSC to be absorbed over HDS at low AC level. However, increase of AC over 90% of NSC removal made adsorption non-selective due to competitive adsorption between NSC and HDS. Size exclusion chromatography showed that the adsorption of oligomeric HDS was dominant while monomeric HDS was inappreciable. The limited selectivity suggested that AC adsorption is infeasibility for HDS purification, but applicable as a pretreatment method.

Improving the hydrogen peroxide bleaching efficiency of aspen chemithermomechanical pulp by using chitosan.

The presence of transition metals during the hydrogen peroxide bleaching of pulp results in the decomposition of hydrogen peroxide, which decreases the bleaching efficiency. In this study, chitosans were used as peroxide stabilizer in the alkaline hydrogen peroxide bleaching of aspen chemithermomechanical pulp (CTMP). The results showed that the brightness of the bleached CTMP increased 1.5% ISO by addition of 0.1% chitosan with 95% degree of deacetylation during peroxide bleaching. Transition metals in the form of ions or metal colloid particles, such as iron, copper and manganese, could be adsorbed by chitosans. Chitosans could inhibit the decomposition of hydrogen peroxide catalyzed by different transition metals under alkaline conditions. The ability of chitosans to inhibit peroxide decomposition depended on the type of transition metals, chitosan concentration and degree of deacetylation applied. The addition of chitosan slightly reduced the concentration of the hydroxyl radical formed during the hydrogen peroxide bleaching of aspen CTMP.

Selective removal of phenolic lignin derivatives enables sugars recovery from wood prehydrolysis liquor with remarkable yield.

The specific elimination of lignin derivatives from wood hydrolysate without sugar loss has great practical significance to biorefinery and bioenergy. In the present study, a process consisting of calcium hydroxide and anion exchange resin treatments was developed for the purpose of selective removal of lignin from wood prehydrolysis liquor (PHL). Particular emphasis was made on the ionization of phenolic lignin, and the subsequent binding to metallic salts. It was observed that phenolic hydroxyl groups (PhOH) in lignin played an important role in lignin removal. The results showed that up to 95.2% lignin was removed from PHL with 78.8% sugar recovery. This suggested that the proposed process is highly specific to lignin, and therefore can be envisaged as a great contribution to wood-sugar production or bioenergy conversion.

Specific lignin precipitation for oligosaccharides recovery from hot water wood extract.

Hot water extraction is an important strategy of wood fractionation, by which the hemicelluloses can be separated for value-added products, while the residual solid can still be processed into traditional wood products. In this study, a combined process consisting of specific lignin precipitation and dialysis was proposed to recover hemicellulosic oligosaccharides (OS) from hot water extract (HWE). The results showed that polyaluminium chloride (PAC) precipitation was highly specific to large molecular lignin, leading to 25.1% lignin removal with negligible OS loss through charge neutralization mechanism. The separation was further enhanced by dialysis, reaching 37.6% OS recovery from HWE with remarkable purity of 94.1%. By the proposed process, 56.36 g OS, mainly xylooligosaccharides with two fractions of 5.2 and 0.51 kDa was recovered from one kg dried wood. This process can be envisaged as a great contribution to wood biorefinery.

Evaluation energy efficiency of bioconversion knot rejects to ethanol in comparison to other thermochemically pretreated biomass.

Rejects from sulfite pulp mill that otherwise would be disposed of by incineration were converted to ethanol by a combined physical-biological process that was comprised of physical refining and simultaneous saccharification and fermentation (SSF). The energy efficiency was evaluated with comparison to thermochemically pretreated biomass, such as those pretreated by dilute acid (DA) and sulfite pretreatment to overcome recalcitrance of lignocelluloses (SPORL). It was observed that the structure deconstruction of rejects by physical refining was indispensable to effective bioconversion but more energy intensive than that of thermochemically pretreated biomass. Fortunately, the energy consumption was compensated by the reduced enzyme dosage and the elevated ethanol yield. Furthermore, adjustment of disk-plates gap led to reduction in energy consumption with negligible influence on ethanol yield. In this context, energy efficiency up to 717.7% was achieved for rejects, much higher than that of SPORL sample (283.7%) and DA sample (152.8%).