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Abstract Hepatitis B virus (HBV) causes hepatitis B (HB) and distinct HBV genotypes can lead to different prognoses. However, HBV genotyping is rarely done in clinics, because the traditional method by PCR-based DNA sequencing is impractical for clinical diagnosis with tedious process and low success rate. Herein, we have established an ELISA-based genotyping method to quickly determine the HBV genotypes of HB patients in China. First, two commercial antibodies, 16D12 and 6H3 specific for HBV genotypes B and C respectively, are chosen as capture antibodies, since these two genotypes dominate in China. Then two home-made genotype-specific antibodies, B19 and C04, are used as the detection antibodies for genotypes B and C in sandwiched ELISA. The ELISA kit shows high sensitivity (> 95%) and specificity (> 95%) in detecting genotypes B and C of Chinese HB patients. Moreover, the ELISA kit has demonstrated higher success rate (98.7%) than PCR-based DNA sequencing (93.5%) and a commercial PCR-based genotyping kit (92.2%) for sera with HBV DNA ≥ 1000 IU/mL and HBsAg ≥ 250 IU/mL. Such an advantage is more obvious for the sera with HBV DNA

NLRP3 inflammasome activation in macrophages is involved in paraquat-induced acute lung injury (ALI). MANF exerts an inhibitory effect against inflammation and cell death. The aim of this study was to investigate the role of MANF in paraquat-stimulated alveolar macrophages and the potential mechanism. Paraquat-induced ALI mouse model was established by intraperitoneally injection of 30 mg/kg of paraquat. The lung pathological changes were observed by hematoxylin and eosin staining. The expression of MANF/DDX3X/NLRP3/Caspase-1 in mice lung macrophages was evaluated by double immunofluorescence staining and western blot. NLRP3 inflammasome activation and pro-inflammatory cytokines (IL-1β and IL-18) in paraquat-stimulated macrophage transfected with MANF overexpression plasmid (pcDNA3.1-MANF) or siRNA-MANF were measured by Western blot. The protein–protein interaction of MANF/DDX3X/NLRP3 was verified by Co-immunoprecipitation. As a result, MANF/DDX3X/NLRP3/Caspase-1 were upregulated in alveolar macrophages of paraquat-induced ALI in mice. In paraquat-stimulated alveolar macrophages, upregulation of MANF and DDX3X were also observed, accompanied by NLRP3 inflammasome activation. In addition, overexpression of MANF inhibited NLRP3 inflammasome activation in paraquat-stimulated alveolar macrophages. In contrast, knockdown of MANF aggravated NLRP3 inflammasome activation. Co-immunoprecipitation results revealed that DDX3X could bind to MANF and NLRP3, but MANF could not bind to NLRP3 in paraquat-stimulated alveolar macrophages. Furthermore, Co-immunoprecipitation of truncated three fragments of DDX3X confirmed MANF can interact with the helicase core of DDX3X which is the binding site for NLRP3. Taken together, MANF exerted a protective effect against paraquat-induced cytotoxicity by inhibiting the NLRP3 inflammasome activation in macrophages via competitive binding to the helicase core of DDX3X.

Phosphorus (P) is essential for living plants, and P deficiency is one of the key factors limiting the yield in rapeseed production worldwide. As the most important organ for plants, root morphology traits (RMTs) play a key role in P absorption. To investigate the genetic variability of RMT under low P availability, we dissected the genetic structure of RMTs by genome-wide association studies (GWAS), linkage mapping and candidate gene association studies (CGAS). A total of 52 suggestive loci were associated with RMTs under P stress conditions in 405 oilseed rape accessions. The purple acid phosphatase gene BnPAP17 was found to control the lateral root number (LRN) and root dry weight (RDW) under low P stress. The expression of BnPAP17 was increased in shoot tissue in P-efficient cultivars compared to root tissue and P-inefficient cultivars in response to low P stress. Moreover, the haplotype of BnPAP17Hap3 was detected for the selective breeding of P efficiency in oilseed rape. Over-expression of the BnPAP17Hap3 could promote the shoot and root growth with enhanced tolerance to low P stress and organic phosphorus (Po) utilization in oilseed rape. Collectively, these findings increase our understanding of the mechanisms underlying BnPAP17-mediated low P stress tolerance in oilseed rape.

Abstract The inflammatory response is a key factor affecting tissue regeneration. Inspired by the immunomodulatory role of spermidine, an injectable double network hydrogel functionalized with spermidine (DN‐SPD) is developed, where the first and second networks are formed by dynamic imine bonds and non‐dynamic photo‐crosslinked bonds respectively. The single network hydrogel before photo‐crosslinking exhibits excellent injectability and thus can be printed and photo‐crosslinked in situ to form double network hydrogels. DN‐SPD hydrogel has demonstrated desirable mechanical properties and tissue adhesion. More importantly, an “operando” comparison of hydrogels loaded with spermidine or diethylenetriamine (DETA), a sham molecule resembling spermidine, has shown similar physical properties, but quite different biological functions. Specifically, the outcomes of 3 sets of in vivo animal experiments demonstrate that DN‐SPD hydrogel can not only reduce inflammation caused by implanted exogenous biomaterials and reactive oxygen species but also promote the polarization of macrophages toward regenerative M2 phenotype, in comparison with DN‐DETA hydrogel. Moreover, the immunoregulation by spermidine can also translate into faster and more natural healing of both acute wounds and diabetic wounds. Hence, the local administration of spermidine affords a simple but elegant approach to attenuate foreign body reactions induced by exogenous biomaterials to treat chronic refractory wounds.

Context Acute pancreatitis (AP) is an acute abdominal inflammatory disease with episodes ranging from mild to fulminant symptoms which could include necrosis, systemic inflammation and multiple organ dysfunction. Increasing experimental evidence demonstrates that specific bioactive ingredients from natural plants have a favourable therapeutic effect on AP. Objective The objective of this review is to summarize the protective effects and potential mechanisms of action of phytochemicals on the attenuation of AP. Methods Experimental studies in vivo or in vitro between January 2016 and June 2021 were sought in PubMed and Web of Science using the following search terms: (‘phytochemicals’ OR ‘medicinal plant’ OR ‘traditional medicine’) AND (‘pancreatitis’ OR ‘pancreatic damage’ OR ‘pancreatic injury’). Data concerning the basic characteristics of phytochemicals, therapeutic dose and potential molecular mechanisms related to AP were extracted in this study. Results A total of 30 phytochemicals with potential therapeutic effects were reviewed and summarized systematically. According to their molecular pathways in AP, the underlying mechanisms of the phytochemicals were illustrated in detail. Discussion and conclusions The phytochemicals with anti-inflammatory and antioxidant abilities may be efficient candidate drugs for AP treatment. Importantly, more preclinical investigations are needed to illustrate the efficacy of future phytochemicals.

Abstract Background Peanut is the most essential oil and food crop globally due to its high oil and protein content. Root-knot nematode infects peanut roots, causing poor development and severely limiting peanut yields worldwide. The discovery of peanut genome identified a considerable number of genetic loci controlling the peanut root-knot nematode; however, the molecular mechanism of root-knot nematode remains unknown. Results The heterogeneous response to root-knot nematode stress in peanut roots was identified using whole-transcriptome RNA-seq. A total of 430 mRNAs, 111 miRNAs, 4453 lncRNAs, and 123 circRNAs were found to have differential expression between infected and non-infected peanuts. The expression profiles of the lncRNA/circRNA-miRNA-mRNA network were developed to understand the potential pathways that lead to root-knot nematodes in peanut roots. During root-knot nematodes stress, a total of 10 lncRNAs, 4 circRNAs, 5 miRNAs, and 13 mRNAs can create competing endogenous RNA and participate in the oxidation–reduction process as well as other biological metabolism processes in peanuts. The findings will highlight the role of peanut ceRNAs in response to root-knot nematodes. Conclusion The GO classification and KEGG pathway enrichment study of core regulatory networks revealed that ceRNAs are involved in oxidation–reduction, peroxidase activity, lignin synthesis in the xylem, and flavonoid synthesis. Overall, these findings may help researchers better understand the role of non-coding RNAs in response to root-knot nematodes.

Two-component system (TCS), which comprises histidine kinases (HKs), histidine phosphotransfer proteins (HPs), and response regulators (RRs), plays essential roles in regulating plant growth, development, and response to various environmental stimuli. TCS genes have been comprehensively identified in various plants, while studies on the genome-wide identification and analysis of TCS in sweet potato were still not reported. Therefore, in this study, a total of 90 TCS members consisting of 20 HK(L)s, 11 HPs, and 59 RRs were identified in the genome of Ipomoea batatas. Furthermore, their gene structures, conserved domains, and phylogenetic relationships were analyzed in detail. Additionally, the gene expression profiles in various organs were analyzed, and response patterns to adverse environmental stresses were investigated. The results showed that these 90 TCS genes were mapped on 15 chromosomes with a notably uneven distribution, and the expansion of TCS genes in sweet potato was attributed to both segmental and tandem duplications. The majority of the TCS genes showed distinct organ-specific expression profiles, especially in three types of roots (stem roots, fibrous roots, tuberous roots). Moreover, most of the TCS genes were either induced or suppressed upon treatment with abiotic stresses (drought, salinity, cold, heat) and exogenous phytohormone abscisic acid (ABA). In addition, the yeast-two hybrid system was used to reveal the HK-HP-RR protein-protein interactions. IbHP1, IbHP2, IbHP4, and IbHP5 could interact with three HKs (IbHK1a, IbHK1b, and IbHK5), and also interact with majority of the type-B RRs (IbRR20–IbRR28), while no interaction affinity was detected for IbHP3. Our systematic analyses could provide insights into the characterization of the TCS genes, and further the development of functional studies in sweet potato.

As a stem variety of lettuce, the fleshy stem is the main product organ of stem lettuce. The molecular mechanism of fleshy stem expansion in stem lettuce is a complex biological process. In the study, the material accumulation, gene expression, and morphogenesis during fleshy stem expansion process were analyzed by the comparative analysis of metabolome, transcriptome and the anatomical studies. The anatomical studies showed that the occurrence and activity of vascular cambium mainly led to the development of fleshy stems; and the volume of pith cells gradually increased and arranged tightly during the expansion process. A total of 822 differential metabolites and 9,383 differentially expressed genes (DEGs) were identified by the metabolomics and transcriptomics analyses, respectively. These changes significantly enriched in sugar synthesis, glycolysis, and plant hormone anabolism. The expression profiles of genes in the sugar metabolic pathway gradually increased in fleshy stem expansion process. But the sucrose content was the highest in the early stage of fleshy stem expansion, other sugars such as fructose and glucose content increased during fleshy stem expansion process. Plant hormones, including IAA, GA, CTK, and JA, depicted important roles at different stem expansion stages. A total of 1,805 DEGs were identified as transcription factors, such as MYB, bHLH, and bZIP, indicating that these transcription factor families might regulate the fleshy stems expansion in lettuce. In addition, the expression patterns identified by qRT-PCR were consistent with the expression abundance identified by the transcriptome data. The important genes and metabolites identified in the lettuce fleshy stem expansion process will provide important information for the further molecular mechanism study of lettuce fleshy stem growth and development.

Abstract Background 3-Phenylpropanol with a pleasant odor is widely used in foods, beverages and cosmetics as a fragrance ingredient. It also acts as the precursor and reactant in pharmaceutical and chemical industries. Currently, petroleum-based manufacturing processes of 3-phenypropanol is environmentally unfriendly and unsustainable. In this study, we aim to engineer Escherichia coli as microbial cell factory for de novo production of 3-phenypropanol via retrobiosynthesis approach. Results Aided by in silico retrobiosynthesis analysis, we designed a novel 3-phenylpropanol biosynthetic pathway extending from l-phenylalanine and comprising the phenylalanine ammonia lyase (PAL), enoate reductase (ER), aryl carboxylic acid reductase (CAR) and phosphopantetheinyl transferase (PPTase). We screened the enzymes from plants and microorganisms and reconstructed the artificial pathway for conversion of 3-phenylpropanol from l-phenylalanine. Then we conducted chromosome engineering to increase the supply of precursor l-phenylalanine and combined the upstream l-phenylalanine pathway and downstream 3-phenylpropanol pathway. Finally, we regulated the metabolic pathway strength and optimized fermentation conditions. As a consequence, metabolically engineered E. coli strain produced 847.97 mg/L of 3-phenypropanol at 24 h using glucose-glycerol mixture as co-carbon source. Conclusions We successfully developed an artificial 3-phenylpropanol pathway based on retrobiosynthesis approach, and highest titer of 3-phenylpropanol was achieved in E. coli via systems metabolic engineering strategies including enzyme sources variety, chromosome engineering, metabolic strength balancing and fermentation optimization. This work provides an engineered strain with industrial potential for production of 3-phenylpropanol, and the strategies applied here could be practical for bioengineers to design and reconstruct the microbial cell factory for high valuable chemicals.

Due to frequent water level fluctuations and complex hydrochemical environments, rock slopes in reservoir areas progressively deteriorate and become unstable. This study investigated the coupling effect of drying−wetting cycles and acidic solutions on the physical and mechanical properties, strain field evolution, failure mode, and micro-mechanism of red sandstone using a series of laboratory experiments (wave velocity tests, uniaxial compression tests, the digital image correlation method, scanning electron microscopy, and X-ray diffraction). The results showed that with increasing drying−wetting cycles, the mass, P-wave velocity, elastic modulus, and uniaxial compressive strength decreased monotonically, while the water absorption and apparent strain in the strain localization band increased. Moreover, the failure mode transitioned gradually from tensile failure to shear failure or tensile-shear composite failure. The decrease in the solution pH values aggravated the changes in the physical and mechanical parameters and contributed to an increase in the secondary cracks and the occurrence of shear behavior. In addition, the coupling effect of drying−wetting cycles and acidic solutions accelerated the worsening of the microstructure and the dissolution of minerals, resulting in a loose structure with well-developed pores and fissures. These changes provide a favorable explanation for the mechanical property deterioration of red sandstone subjected to acidic drying−wetting cycles.

Mitogen-activated protein kinases (MAPKs) play essential roles in the process of stress response and plant growth and development. MAPK family genes have been identified in many plant species. In this study, 18 LsMAPK genes were identified in lettuce (Lactuca sativa). The LsMAPK members were divided into Group A, B, C, and D by phylogenetic tree analysis among Arabidopsis, rice, and lettuce. Cis-elements, which relate to abiotic stress, phytohormone response, and transcription factor binding site, were identified to exist in the promoter region of LsMAPK genes. Chromosomal location analysis showed the LsMAPK genes were distributed on eight chromosomes except chromosome 6. Interaction network analysis showed that LsMAPKs could interact with MAPK kinase (MAPKK), protein-tyrosine-phosphatase (PTP), and transcription factors (WRKY, bZIP). Quantitative reverse transcription PCR (qRT-PCR) showed that LsMAPK genes were induced by different abiotic stresses, hormone response, and stem enlargement. The comprehensive identification and characterization of LsMAPK genes in stem lettuce will lay a theoretical foundation for the functional analysis of LsMAPK genes and advance our knowledge of the regulatory mechanism of MAPK genes in plants.

A proof of quantumness is a type of challenge-response protocol in which a classical verifier can efficiently certify the $\textit{quantum advantage}$ of an untrusted prover. That is, a quantum prover can correctly answer the verifier's challenges and be accepted, while any polynomial-time classical prover will be rejected with high probability, based on plausible computational assumptions. To answer the verifier's challenges, existing proofs of quantumness typically require the quantum prover to perform a combination of polynomial-size quantum circuits and measurements. In this paper, we give two proof of quantumness constructions in which the prover need only perform $\textit{constant-depth quantum circuits}$ (and measurements) together with log-depth classical computation. Our first construction is a generic compiler that allows us to translate all existing proofs of quantumness into constant quantum depth versions. Our second construction is based around the $\textit{learning with rounding}$ problem, and yields circuits with shorter depth and requiring fewer qubits than the generic construction. In addition, the second construction also has some robustness against noise.

Paraquat (PQ) can cause multiorgan failure including acute kidney injury (AKI). Our prior study showed that Toll-interacting protein (TOLLIP) protected against PQ-induced acute lung injury. However, the role of TOLLIP in PQ-induced AKI remains undefined. This study was aimed at understanding the role and mechanism of TOLLIP in AKI. Six-eight-week-old male Wistar rats were intraperitoneally injected with 25 mg/kg PQ to induce AKI for 24 h in vivo. HK-2 cells were treated with 300 μM PQ for 24 h to induce cellular injury in vitro or 300 μM PQ and 5 μM nuclear factor-κB (NF-κB) inhibitor BAY11-7082 for 24 h. Rats were infected with adenovirus carrying TOLLIP shRNA via tail vein injection and HK-2 cells with adenovirus carrying TOLLIP shRNA or TOLLIP 48 h before PQ exposure. Results showed that TOLLIP and Toll-like receptor 2/4 (TLR2/4) expressions were boosted in the kidney after PQ intoxication. The toxic effect of PQ on the kidney and HK-2 cells was exacerbated by TOLLIP knockdown, as evidenced by aggravated glomerulus and tubule injury, inflammatory infiltration, and cell apoptosis in the kidney and increased loss of cell viability and apoptotic cells in HK-2 cells. TOLLIP knockdown also enhanced PQ-induced NLR family pyrin domain-containing 3 (NLRP3) inflammasome activation in vivo and in vitro and TLR2/4-NF-κB signaling in vitro, reflected by increased contents of proinflammatory cytokines and expressions of NLRP3 inflammasome-related proteins in the kidney and HK-2 cells and expressions of TLR2, TLR4, and nuclear NF-κB p65 in HK-2 cells. However, TOLLIP overexpression inhibited PQ-induced loss of cell viability, cell apoptosis, NLRP3 inflammasome activation, and TLR2/4-NF-κB signaling in vitro. Additionally, BAY11-7082 abolished TOLLIP knockdown-induced NLRP3 inflammasome activation in vitro, indicating that TOLLIP protected against NLRP3 inflammasome activation in PQ-induced AKI through inhibiting TLR2/4-NF-κB signaling. This study highlights the importance of TOLLIP in AKI after PQ intoxication.

Combining biodegradable materials with bioactive factors for skin wound healing has been receiving significant attention. This study was inspired by the adhesion mechanism of a marine organism, the mussel. 3,4-Dihydroxyphenylalanine (DOPA) was introduced to basic fibroblast growth factor (bFGF) and ponericin G1 (PonG1) using tyrosine hydroxylation, which are expected to have strong binding affinities to the surfaces of materials. DOPA-bFGF and DOPA-PonG1 were applied for the surface modification of patterned poly(lactic-co-glycolic acid) (PLGA) electrospun nanofibrous films for skin wound healing. The DOPA-bFGF- and DOPA-PonG1-modified patterned PLGA nanofibrous films were analysed using scanning electron microscopy (SEM), contact angle, and materials testing machine. Then, the immobilization efficiencies and antibacterial abilities of the different films were examined. The results show that the DOPA-bFGF- and DOPA-PonG1-modified PLGA nanofibrous films exhibited bionic performance, improved tensile strength, and hydrophilicity. DOPA-bFGF and DOPA-PonG1 exhibited stronger binding abilities to films compared with bFGF and PonG1. DOPA-bFGF and DOPA-PonG1 films can significantly promote BALB/c 3T3 cell attachment, proliferation and tissue repair-related gene expression. In vivo experiments indicated that DOPA-PonG1/DOPA-bFGF@PLGA nanofibrous films shortened the wound healing time, accelerated epithelialization and promoted skin remodelling. Keywords: DOPA-bFGF, DOPA-PonG1, PLGA, Patterned, Nanofibrous films, Skin tissue engineering

Oxygen reduction reaction (ORR) electrocatalysts derived from biomass have become one of the research focuses in hetero-catalysis due to their low cost, high performance, and reproducibility properties. Related researches are of great significance for the development of next-generation fuel cells and metal-air batteries. Herein, the preparation methods of various biomass-derived catalysts and their performance in alkaline, neutral, and acidic media are summarized. This review clarifies the research progress of biomass carbon-based electrocatalysts for ORR in acidic, alkaline and neutral media, and discusses the future development trends. This minireview can give us an important enlightenment to practical application in the future.

Abstract Background Cytokinin is a classical phytohormone that plays important roles in numerous plant growth and development processes. In plants, cytokinin signals are transduced by a two-component system, which involves many genes, including cytokinin response factors (CRFs). Although CRFs take vital part in the growth of Arabidopsis thaliana and Solanum lycopersicum, little information of the CRFs in the Brassica U-triangle species has been known yet. Results We identified and compared 141 CRFs in the diploids and amphidiploids of Brassica species, including B. rapa, B. oleracea, B. nigra, B. napus, and B. juncea. For all the 141 CRFs, the sequence and structure analysis, physiological and biochemical characteristics analysis were performed. Meanwhile, the Ka/Ks ratios of orthologous and paralogous gene pairs were calculated, which indicated the natural selective pressure upon the overall length or a certain part of the CRFs. The expression profiles of CRFs in different tissues and under various stresses were analyzed in B. oleracea, B. nigra, and B. napus. The similarities and differences in gene sequences and expression profiles among the homologous genes of these species were discussed. In addition, AtCRF11 and its ortholog BrCRF11a were identified to be related to primary root growth in Arabidopsis. Conclusion This study performed a genome-wide comparative analysis of the CRFs in the diploids and amphidiploids of the Brassica U-triangle species. Many similarities and differences in gene sequences and expression profiles existed among the CRF homologous genes of these species. In the bioinformatics analysis, we found the close relativity of the CRF homologous genes in the Brassica A and C genomes and the distinctiveness of those in the B genome, and the CRF homologous genes in B subgenome were considerably influenced by the A subgenome of B. juncea. In addition, we identified a new function of the Clade V CRFs related to root growth, which also clarified the functional conservation between Arabidopsis and B. rapa. These results not only offer useful information on the functional analysis of CRFs but also provide new insights into the evolution of Brassica species.

The AP2/ERF transcription factor family is one of the largest families involved in growth and development, hormone responses, and biotic or abiotic stress responses in plants. In this study, 281 AP2/ERF transcription factor unigenes were identified in Chinese cabbage. These superfamily members were classified into three families (AP2, ERF, and RAV). The ERF family was subdivided into the DREB subfamily and the ERF subfamily with 13 groups (I- XI) based on sequence similarity. Duplication, evolution and divergence of the AP2/ERF genes in B. rapa and Arabidopsis thaliana were investigated and estimated. Cytokinin response factors (CRFs), as a subclade of the AP2/ERF family, are important transcription factors that define a branch point in the cytokinin two-component signal (TCS) transduction pathway. Up to 21 CRFs with a conserved CRF domain were retrieved and designated as BrCRFs. The amino acid sequences, conserved regions and motifs, phylogenetic relationships, and promoter regions of the 21 BrCRFs were analyzed in detail. The BrCRFs broadly expressed in various tissues and organs. The transcripts of BrCRFs were regulated by factors such as drought, high salinity, and exogenous 6-BA, NAA, and ABA, suggesting their involvement in abiotic stress conditions and regulatory mechanisms of plant hormone homeostasis. These results provide new insight into the divergence, variation, and evolution of AP2/ERF genes at the genome-level in Chinese cabbage.