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Abstract Advances in deep learning have significantly aided protein engineering in addressing challenges in industrial production, healthcare, and environmental sustainability. This review frames frequently researched problems in protein understanding and engineering from the perspective of deep learning. It provides a thorough discussion of representation methods for protein sequences and structures, along with general encoding pipelines that support both pre‐training and supervised learning tasks. We summarize state‐of‐the‐art protein language models, geometric deep learning techniques, and the combination of distinct approaches to learning from multi‐modal biological data. Additionally, we outline common downstream tasks and relevant benchmark datasets for training and evaluating deep learning models, focusing on satisfying the particular needs of protein engineering applications, such as identifying mutation sites and predicting properties for candidates' virtual screening. This review offers biologists the latest tools for assisting their engineering projects while providing a clear and comprehensive guide for computer scientists to develop more powerful solutions by standardizing problem formulation and consolidating data resources. Future research can foresee a deeper integration of the communities of biology and computer science, unleashing the full potential of deep learning in protein engineering and driving new scientific breakthroughs.

This study investigates the Chinese market’s physicochemical properties and sensory attributes of 14 original-cut potato chip brands. Color characteristics, compositional analysis, sugar content, acrylamide levels, and textural properties were examined alongside sensory evaluations. Significant variations were observed across all the parameters. Color analysis revealed diverse L*, a*, and b* values, with total color difference (ΔE) strongly correlating with sensory scores (r = 0.73, p < 0.01). A compositional analysis showed substantial differences in protein (5.19–8.51%), fat (27.91–40.16%), and moisture (0.67–3.78%) contents. Acrylamide levels varied widely (166.7–1101.78 mg/kg), positively correlating with the sucrose content (r = 0.57, p < 0.05). A textural analysis demonstrated significant variations in hardness (379.38–1103.6 gf) and fracturability (167.5–857.77 gf), with fracturability negatively correlating with sensory scores (r = −0.75, p < 0.01). A sensory evaluation revealed distinct brand preferences, with the total scores ranging from 65 to 85. This comprehensive analysis provides valuable insights into the complex interplay between the physicochemical properties and consumer perception of potato chips in the Chinese market and offers potential directions for product optimization and quality control in the snack food industry, inspiring hope and innovation among industry professionals.

Carotenoids are essential components in tea quality, contributing to leaf color and aroma. However, little information about carotenoids in different tea cultivars and their biosynthesis regulation mechanism during leaf development is known. Here we analyzed carotenoids by HPLC in the buds and leaves of 113 tea cultivars harvested on the same day. By profile clustering, carotenoids were divided into five groups. Same group cultivars displayed divergence in the total content of carotenoids but a similar molar ratio. To figure out the molecular mechanisms of this phenomenon, we further characterized all functional lycopene cyclases, which are the branch point of the carotenoid biosynthesis pathway. Two β-lycopene cyclases (CsLCYB1 and CsLCYB2) and one ε-lycopene cyclase (CsLCYE1) were cloned. Subcellular localization analysis showed that all cloned CsLCYs were localized in plastids. Enzyme activity assays in E. coli indicated both CsLCYBs catalyzed lycopene into β-carotene, and CsLCYE1 produced δ-carotene and ε-carotene. We found CsLCYB1 and CsLCYE1 predominantly expressed in leaf, while CsLCYB2 was mainly expressed during flowering stages. Suppression by antisense oligonucleotides reduced CsLCYB1 and CsLCYE1 transcripts and led to reduction of both β,β-branch and β,ε-branch carotenoids in leaf. The expression levels of CsLCYB1 showed a significant positive correlation with β,β-branch carotenoids in leaf. Our study provides carotenoid profiles of different tea cultivars, which can assist tea producers in selecting cultivars of interest. Meanwhile, we proposed the molecular mechanism of carotenoids reflecting the tenderness of tea plant leaf from a metabolic flux perspective, and suggested lycopene cyclase that could be applied to the breeding of tea varieties with different branch carotenoids.

IntroductionUnderstanding the response of cross-domain co-occurrence networks of soil microorganisms to phosphorus stability and the resulting impacts is critical in ecosystems, but the underlying mechanism is unclear in artificial grassland ecosystems.MethodsIn this study, the effects of four phosphorus concentrations, P0 (0 kg P ha−1), P1 (15.3 kg P ha−1), P2 (30.6 kg P ha−1), and P3 (45.9 kg P ha−1), on the cross-domain co-occurrence network of bacteria and fungi were investigated in an artificial Leymus chinensis grassland in an arid region.Results and discussionThe results of the present study showed that phosphorus addition significantly altered the stem number, biomass and plant height of the Leymus chinensis but had no significant effect on the soil bacterial or fungal alpha (ACE) diversity or beta diversity. The phosphorus treatments all increased the cross-domain co-occurrence network edge, node, proportion of positively correlated edges, edge density, average degree, proximity to centrality, and robustness and increased the complexity and stability of the bacterial-fungal cross-domain co-occurrence network after 3 years of continuous phosphorus addition. Among them, fungi (Ascomycota, Basidiomycota, Mortierellomycota and Glomeromycota) play important roles as keystone species in the co-occurrence network, and they are significantly associated with soil AN, AK and EC. Finally, the growth of Leymus chinensis was mainly due to the influence of the soil phosphorus content and AN. This study revealed the factors affecting the growth of Leymus chinense in artificial grasslands in arid areas and provided a theoretical basis for the construction of artificial grasslands.

Abstract Phosphorus (P) deficiencies are widespread in calcareous soils. The poor availability of nitrogen (N) and P in soils often restricts crop growth. However, the effects of P addition on plant growth and plant nutrient transport changes during the establishment of Leymus chinensis fields in Xinjiang are not clear. We investigated the responses of Leymus chinensis biomass and nutrient absorption and utilization to changes in soil N and P by adding P (0, 15.3, 30.6, and 45.9 kg P ha−1 year−1) with basally applied N fertilizer (150 kg N ha−1 year−1). The results showed that (a) Principal component analysis (PCA) of biomass, nutrient accumulation, soil available P, and soil available N during the different periods of Leymus chinensis growth showed that their cumulative contributions during the jointing and harvest periods reached 95.4% and 88%, respectively. (b) Phosphorus use efficiency (PUE) increased with the increase of P fertilizer gradient and then decreased and the maximum PUE was 13.14% under moderate P addition. The accumulation of biomass and nutrients in Leymus chinensis can be effectively improved by the addition of P fertilizer at 30.6 kg ha−1. Different P additions either moderately promoted or excessively inhibited Leymus chinensis growth and nutrient utilization.

Salvianolic acid B (Sal B) is the primary water-soluble bioactive constituent derived from the roots of Salvia miltiorrhiza Bunge. This research was designed to reveal the potential mechanism of Sal B anti-liver injury from the perspective of macrophages. In our lipopolysaccharide-induced M1 macrophage model, Sal B showed a clear dose-dependent gradient of inhibition of the macrophage trend of the M1 type. Moreover, Sal B downregulated the expression of lactate dehydrogenase A (LDHA), while the overexpression of LDHA impaired Sal B’s effect of inhibiting the trend of macrophage M1 polarization. Additionally, this study revealed that Sal B exhibited inhibitory effects on the lactylation process of histone H3 lysine 18 (H3K18la). In a ChIP-qPCR analysis, Sal B was observed to drive a reduction in H3K18la levels in the promoter region of the LDHA, NLRP3, and IL-1β genes. Furthermore, our in vivo experiments showed that Sal B has a good effect on alleviating CCl4-induced liver injury. An examination of liver tissues and the Kupffer cells isolated from those tissues proved that Sal B affects the M1 polarization of macrophages and the level of histone lactylation. Together, our data reveal that Sal B has a potential mechanism of inhibiting the histone lactylation of macrophages by downregulating the level of LDHA in the treatment of liver injury.

ObjectiveTo investigate the clinical efficacy and imaging outcomes of unilateral biportal endoscopy (UBE) with unilateral laminotomy for bilateral decompression (ULBD) in the treatment of severe lumbar spinal stenosis (SLSS).MethodsWe retrospectively analyzed 50 patients with SLSS treated with UBE-ULBD from October 2018 to March 2021. Visual analog scale (VAS) for back and legs pain, Oswestry disability index (ODI), modified Macnab criteria, complications, hospital stay, preoperative and postoperative dural sac cross-sectional area (DSCA) and Schizas grade, mean angle of facetectomy and osseous lateral recess decompression rate were examined.ResultsThe mean follow-up period was 10.7 months. The mean hospital stay was 2.76 ± 1.02 days. At the final follow-up, VAS for back pain and legs pain decreased from 7.22 ± 0.95 to 1.26 ± 0.44 and from 7.88 ± 0.69 to 1.18 ± 0.39, respectively; ODI decreased from 69.88 ± 6.32% to 14.96 ± 2.75%. According to the modified Macnab criteria, the results were excellent in 24 (48%), good in 22 (44%), and fair in 4 (8%). Excellent or good results (a satisfactory outcome) were obtained in 92% of the patients. There were 2 cases of complications of dural sac tear. The postoperative DSCA was significantly enlarged compared with that before surgery, from 44.74 ± 9.85 to 126.86 ± 14.81 mm2. According to Schizas grade, the stenosis grade changes from preoperative grade C in 16 cases, grade D in 34 cases, to postoperative grade A in 40 cases, and grade B in 10 cases. The mean angle of facetectomy of the ipsilateral facet joint was 70.87 ± 5.68∘, contralateral was 65.07 ± 4.98∘. The decompression rate was 70.81 ± 4.43% (ipsilateral side) and 71.22 ± 3.68% (contralateral).ConclusionsUBE-ULBD has a good clinical effect in the treatment of SLSS, and has achieved satisfactory results in spinal canal enlargement, undercutting of facet joints, and decompression effect. It is a safe and effective surgical for SLSS.

Avian pathogenic Escherichia coli (APEC) is one of the common extraintestinal infectious disease pathogens in chickens, geese, and other birds. It can cause a variety of infections, and even the death of poultry, causing enormous economic losses. However, the misuse and abuse of antibiotics in the poultry industry have led to the development of drug resistance in the gut microbes, posing a challenge for the treatment of APEC infections. It has been reported that the CpxRA two-component system has an effect on bacterial drug resistance, but the specific regulatory mechanism remains unclear. In this study, the regulatory mechanism of CpxRA on APEC biofilm formation and EmrKY efflux pump was investigated. The cpxRA knockout strain of E. coli APEC40 was constructed, and the molecular regulatory mechanism of CpxR on biofilms and efflux pump-coding genes were identified by biofilm formation assays, drug susceptibility test, real-time reverse transcription quantitative PCR, and electrophoretic mobility shift assay (EMSA). The results indicated that CpxR can directly bind to the promoter region of emrKY and negatively regulate the sensitivity of bacteria to ofloxacin and erythromycin. These results confirm the important regulatory role of the CpxRA two-component system under antibiotic stress in APEC.

In recent years, the chaos-based cryptographic algorithms have attracted a lot of attention. Specially, chaotic tent map (CTM)-based schemes show some good performances in randomness properties and security level. However, several shortcomings still can be found from them. In this paper, based on the security analysis of the pure CTM-based scheme, we propose a novel image encryption algorithm by using the combination of the rectangular transform and the CTM principle. It encrypts the three channels of the plain image at the same time, and these channel encryptions associate with each other. In addition, by generating the key streams related to both the secret keys and the plain image, its key-sensitivity has been further improved. The security of the proposed scheme has been verified by security analysis and experimental evaluations, and our results show that many drawbacks of pure CTM-based schemes have been overcome.

Abstract The low-potential aldehyde oxidation reaction can occur at low potential (~0 VRHE) and release H2 at the anode, enabling hydrogen production with less than one-tenth of the energy consumption required for water splitting. Nevertheless, the activity and stability of Cu catalysts remain inadequate due to the oxidative deactivation of Cu-based materials. Herein, we elucidate the deactivation and reactivation cycle of Cu electrocatalyst and develop a self-reactivating PdCu catalyst that exhibits significantly enhanced stability. Initially, in-situ Raman spectroscopy confirm the cycle involved in electrochemical oxidation and non-electrochemical reduction. Subsequently, in-situ Raman spectroscopy and X-ray absorption fine structure reveal that the Pd component accelerates the rate of the non-electrochemical reduction, thereby enhancing the stability of the Cu-based electrocatalyst. Finally, a bipolar hydrogen production device is assembled utilizing the PdCu electrocatalyst, which can deliver a current of 400 mA cm−2 at 0.42 V and operate continuously for 120 h. This work offers guidance to enhance the stability of the Cu-based electrocatalyst in a bipolar hydrogen production system.

Introduction: Peptide drugs are highly regarded for their therapeutic versatility, safety, and efficacy in treating conditions like cancer, hepatitis, and diabetes. Animal-derived Traditional Chinese Medicines (TCMs) are promising peptide sources, often outperforming plant-based alternatives. The therapeutic effects of leeches, earthworms, and Eupolyphaga sinensis Walkers in thrombosis and blood stasis have been clinically validated, with anticoagulant peptides as key components; however, their pharmacological mechanisms remain unclear. This review categorizes and summarizes anticoagulant peptides from animal-derived TCMs by species. Methods: This study explores the important role of anticoagulant peptides from animal-sourced medicine in treating thrombosis-related diseases. A literature search using keywords like “anticoagulant peptides,” “leech peptides,” and “earthworm peptides” yielded over 120 articles, of which 85 were selected. Priority was given to studies from the past 20 years, while significant historical research was also noted. Articles lacking specific information on the animal sources of these peptides were excluded. Data were obtained from a diverse range of references, including both ancient and modern texts, the Chinese Pharmacopoeia, Web of Science, PubMed, ScienceDirect, Google Scholar, Springer, and CNKI. Conclusion: This study reviews six promising animal-derived anticoagulant drugs currently in clinical use: leeches, earthworms, scorpions, Eupolyphaga sinensis Walkers, and centipedes. Key peptides under development include hirudin (Hirudo nipponica), WP-30 (Whitmania pigra), Lomburkinase (Eisenia foetida). These peptides exhibit potent anticoagulant, antiplatelet, and anti-inflammatory effects, rendering them valuable in the treatment of cardiovascular diseases, stroke, amenorrhea, cerebral thrombosis, and atherosclerosis. Discussion: This study critically evaluates the therapeutic mechanisms of anticoagulant peptides in animal-sourced medicines, emphasizing the potential of peptide-based therapies across different strains of the same species for traditional Chinese medicine and modern clinical use. Despite promising potential, challenges such as low bioavailability, difficulties in peptide identification, pharmacological evaluation, and toxicity assessment persist. Addressing these issues will facilitate deeper exploration and development of peptide-based therapies.