Structural basis for flagellin-induced NAIP5 activation.

The NAIP (NLR family apoptosis inhibitory protein)/NLRC4 (NLR family CARD containing protein 4) inflammasome senses Gram-negative bacterial ligand. In the ligand-bound state, the winged helix domain of NAIP forms a steric clash with NLRC4 to open it up. However, how ligand binding activates NAIP is less clear. Here, we investigated the dynamics of the ligand-binding region of inactive NAIP5 and solved the cryo-EM structure of NAIP5 in complex with its specific ligand, FliC from flagellin, at 2.9-Å resolution. The structure revealed a "trap and lock" mechanism in FliC recognition, whereby FliC-D0C is first trapped by the hydrophobic pocket of NAIP5, then locked in the binding site by ID (insertion domain) and C-terminal tail of NAIP5. The FliC-D0N domain further inserts into ID to stabilize the complex. According to this mechanism, FliC triggers the conformational change of NAIP5 by bringing multiple flexible domains together.

An Interpretable High-Accuracy Method for Rice Disease Detection Based on Multisource Data and Transfer Learning.

With the evolution of modern agriculture and precision farming, the efficient and accurate detection of crop diseases has emerged as a pivotal research focus. In this study, an interpretative high-precision rice disease detection method, integrating multisource data and transfer learning, is introduced. This approach harnesses diverse data types, including imagery, climatic conditions, and soil attributes, facilitating enriched information extraction and enhanced detection accuracy. The incorporation of transfer learning bestows the model with robust generalization capabilities, enabling rapid adaptation to varying agricultural environments. Moreover, the interpretability of the model ensures transparency in its decision-making processes, garnering trust for real-world applications. Experimental outcomes demonstrate superior performance of the proposed method on multiple datasets when juxtaposed against advanced deep learning models and traditional machine learning techniques. Collectively, this research offers a novel perspective and toolkit for agricultural disease detection, laying a solid foundation for the future advancement of agriculture.

Structural basis for flagellin induced NAIP5 activation.

The NAIP/NLRC4 inflammasome is activated when NAIP binds to a gram-negative bacterial ligand. Initially, NAIP exists in an inactive state with a wide-open conformation. Upon ligand binding, the winged helix domain (WHD) of NAIP is activated and forms steric clash with NLRC4 to open it up. However, how ligand binding induces the conformational change of NAIP is less clear. To understand this process, we investigated the dynamics of the ligand binding region of inactive NAIP5 and solved the cryo-EM structure of NAIP5 in complex with its specific ligand, FliC from flagellin, at 2.93 Å resolution. The structure revealed a "trap and lock" mechanism in FliC recognition, whereby FliC-D0C is first trapped by the hydrophobic pocket of NAIP5, then locked in the binding site by the insertion domain (ID) and C-terminal tail (CTT) of NAIP5. The FliC-D0N domain further inserts into the loop of ID to stabilize the complex. According to this mechanism, FliC activates NAIP5 by bringing multiple flexible domains together, particularly the ID, HD2, and LRR domains, to form the active conformation and support the WHD loop in triggering NLRC4 activation.

Mechanism of NAIP-NLRC4 inflammasome activation revealed by cryo-EM structure of unliganded NAIP5.

The nucleotide-binding domain (NBD), leucine rich repeat (LRR) domain containing protein family (NLR family) apoptosis inhibitory proteins (NAIPs) are cytosolic receptors that play critical roles in the host defense against bacterial infection. NAIPs interact with conserved bacterial ligands and activate the NLR family caspase recruitment domain containing protein 4 (NLRC4) to initiate the NAIP-NLRC4 inflammasome pathway. Here we found the process of NAIP activation is completely different from NLRC4. Our cryo-EM structure of unliganded mouse NAIP5 adopts an unprecedented wide-open conformation, with the nucleating surface fully exposed and accessible to recruit inactive NLRC4. Upon ligand binding, the winged helix domain (WHD) of NAIP5 undergoes roughly 20° rotation to form a steric clash with the inactive NLRC4, which triggers the conformational change of NLRC4 from inactive to active state. We also show the rotation of WHD places the 17-18 loop at a position that directly bind the active NLRC4 and stabilize the NAIP5-NLRC4 complex. Overall, these data provide structural mechanisms of inactive NAIP5, the process of NAIP5 activation and NAIP-dependent NLRC4 activation.

The roles and therapeutic approaches of MSC-derived exosomes in colorectal cancer

Colorectal cancer (CRC) is the third most common cancer in both men and women, accounting for 8% of all new cancer cases in both. CRC is typically diagnosed at advanced stages, which leads to a higher mortality rate. The 5-year survival rate for CRC is 64% in all cases and just 12% in metastatic cases. Mesenchymal stem cells (MSCs) are one of the most recent approaches for therapeutic interventions in cancer. MSCs have multiple properties, including paracrine signaling, immunologic functions, and the ability to migrate to the targeted tissue. MSCs can produce and secrete exosomes in tumor microenvironments. These exosomes can transfer compounds across tumor cells, stromal cells, fibroblasts, endothelial cells, and immune cells. Studies showed that modified MCS-derived exosomes have enhanced specificity, reduced immunogenicity, and better targeting capabilities in comparison to other frequently used delivery systems such as liposomes. Therefore, this study aimed to provide a comprehensive view of the role of natural MSC-derived exosomes in CRC, as well as the most current and prospective advancements in MSC-derived exosome therapeutic modifications.

Structural mechanisms of inflammasome regulation revealed by cryo-EM studies.

Inflammasomes are cytosolic protein complexes that form in response to pathogen or damage signals and initiate inflammation. Signal transduction in the inflammasome pathway occurs via protein-protein interaction, protein conformational change, and oligomerization. Recent advances in structural biology have provided multiple insights in inflammasome regulation that are both biologically intriguing and therapeutically valuable. In this review, we summarize the current understanding of three most studied inflammasome complexes: the NAIP/NLRC4, NLRP1, and NLRP3 inflammasomes. We discuss the general mechanisms and unique features of their regulation and how investigating these systems may contribute to therapeutic applications.

Structural aspects of the MHC expression control system.

The major histocompatibility complex (MHC) spans innate and adaptive immunity by presenting antigenic peptides to CD4+ and CD8+ T cells. Multiple transcription factors form an enhanceosome complex on the MHC promoter and recruit transcriptional machinery to activate gene transcription. Immune signals such as interferon-γ (IFN-γ) control MHC level by up-regulating components of the enhanceosome complex. As MHC plays crucial roles in immune regulation, alterations in the MHC enhanceosome structure will alter the pace of rapid immune responses at the transcription level and lead to various diseases related to the immune system. In this review, we discuss the current understanding of the MHC enhanceosome, with a focus on the structures of MHC enhanceosome components and the molecular basis of MHC enhanceosome assembly.

Codon usage patterns across seven Rosales species.

BACKGROUND: Codon usage bias (CUB) analysis is an effective method for studying specificity, evolutionary relationships, and mRNA translation and discovering new genes among various species. In general, CUB analysis is mainly performed within one species or between closely related species and no such study has been applied among species with distant genetic relationships. Here, seven Rosales species with high economic value were selected to conduct CUB analysis. RESULTS: The results showed that the average GC1, GC2 and GC3 contents were 51.08, 40.52 and 43.12%, respectively, indicating that the A/T content is more abundant and the Rosales species prefer A/T as the last codon. Neutrality plot and ENc plot analysis revealed that natural selection was the main factor leading to CUB during the evolution of Rosales species. All 7 Rosales species contained three high-frequency codons, AGA, GTT and TTG, encoding Arg, Val and Leu, respectively. The 7 Rosales species differed in high-frequency codon pairs and the distribution of GC3, though the usage patterns of closely related species were more consistent. The results of the biclustering heat map among 7 Rosales species and 20 other species were basically consistent with the results of genome data, suggesting that CUB analysis is an effective method for revealing evolutionary relationships among species at the family or order level. In addition, chlorophytes prefer using G/C as ending codon, while monocotyledonous and dicotyledonous plants prefer using A/T as ending codon. CONCLUSIONS: The CUB pattern among Rosales species was mainly affected by natural selection. This work is the first to highlight the CUB patterns and characteristics of Rosales species and provides a new perspective for studying genetic relationships across a wide range of species.

The roles and therapeutic approaches of MSC-derived exosomes in colorectal cancer.

Colorectal cancer (CRC) is the third most common cancer in both men and women, accounting for 8% of all new cancer cases in both. CRC is typically diagnosed at advanced stages, which leads to a higher mortality rate. The 5-year survival rate for CRC is 64% in all cases and just 12% in metastatic cases. Mesenchymal stem cells (MSCs) are one of the most recent approaches for therapeutic interventions in cancer. MSCs have multiple properties, including paracrine signaling, immunologic functions, and the ability to migrate to the targeted tissue. MSCs can produce and secrete exosomes in tumor microenvironments. These exosomes can transfer compounds across tumor cells, stromal cells, fibroblasts, endothelial cells, and immune cells. Studies showed that modified MCS-derived exosomes have enhanced specificity, reduced immunogenicity, and better targeting capabilities in comparison to other frequently used delivery systems such as liposomes. Therefore, this study aimed to provide a comprehensive view of the role of natural MSC-derived exosomes in CRC, as well as the most current and prospective advancements in MSC-derived exosome therapeutic modifications.

ZjSEP3 modulates flowering time by regulating the LHY promoter.

BACKGROUND: SEPALLATA3 (SEP3), which is conserved across various plant species, plays essential and various roles in flower and fruit development. However, the regulatory network of the role of SEP3 in flowering time at the molecular level remained unclear. RESULTS: Here, we investigated that SEP3 in Ziziphus jujuba Mill. (ZjSEP3) was expressed in four floral organs and exhibited strong transcriptional activation activity. ZjSEP3 transgenic Arabidopsis showed an early-flowering phenotype and altered the expression of some genes related to flowering. Among them, the expression of LATE ELONGATED HYPOCOTYL (AtLHY), the key gene of circadian rhythms, was significantly suppressed. Yeast one-hybrid (Y1H) and electrophoretic mobility shift assays (EMSAs) further verified that ZjSEP3 inhibited the transcription of AtLHY by binding to the CArG-boxes in its promoter. Moreover, ZjSEP3 also could bind to the ZjLHY promoter and the conserved binding regions of ZjSEP3 were found in the LHY promoter of various plant species. The ectopic regulatory pathway of ZjSEP3-AtLHY was further supported by the ability of 35S::AtLHY to rescue the early-flowering phenotype in ZjSEP3 transgenic plants. In ZjSEP3 transgenic plants, total chlorophyll content and the expression of genes involved in chlorophyll synthesis increased during vegetative stages, which should contribute to its early flowering and relate to the regulatory of AtLHY. CONCLUSION: Overall, ZjSEP3-AtLHY pathway represents a novel regulatory mechanism that is involved in the regulation of flowering time.

Process optimization and mechanism study of acid red G degradation by electro-Fenton-Feox process as an in situ generation of H2O2.

Dye-contaminated wastewaters are industrial wastewaters that are difficult to treat using traditional biochemical and physicochemical methods. In the present work, the acid red G was removed as a model pollutant by the electro-Fenton process for the first time. The anode and cathode used by the electro-Fenton process were iron plate and graphite felt, respectively. It was concluded that under the optimal conditions of current density = 20 mA cm-2, pH = 3 and initial Na2SO4 concentration = 0.2 M, the removal rate of acid red G (ARG) with an initial concentration of 300 mg L-1 could reach 94.05% after 80 min of electrolysis. This reveals that the electro-Fenton-Feox process used in this work has an excellent removal efficiency on acid red G. The required reagents (Fe2+ and H2O2) were generated by the electrode reaction, while the optimal generation conditions and mechanism of •OH, H2O2, and Fe2+ were investigated. By testing •OH, H2O2, and Fe2+ agents at different pH and current densities, it was revealed that the electro-Fenton reaction was most efficient when the current density was 20 mA cm-2, and the pH was 3. Moreover, the removal rate of ARG is consistent with first-order reaction kinetics.

Functional regions in the 5' external transcribed spacer of yeast pre-rRNA.

Ribosomal subunits are assembled on a precursor rRNA that includes four spacers in addition to mature rRNA sequences. The 5' external transcribed spacer (5' ETS) is the most prominent one that recruits U3 snoRNA and a plethora of proteins during the early assembly of 90S small subunit preribosomes. Here, we have conducted a comprehensive mutational analysis of 5' ETS by monitoring the processing and assembly of a plasmid-expressed pre-18S RNA. Remarkably, nearly half of the 5' ETS sequences, when depleted individually, are dispensable for 18S rRNA processing. The dispensable elements largely bind at the surface of the 90S structure. Defective assembly of 5' ETS completely blocks the last stage of 90S formation yet has little effect on the early assembly of 5' and central domains of 18S rRNA. Our study reveals the functional regions of 5' ETS and provides new insight into the assembly hierarchy of 90S preribosomes.

Electrochemical oxidation treatment of coal tar wastewater with lead dioxide anodes.

In this study, coal tar wastewater was treated by electrochemical oxidation technology using lead dioxide anodes. The influence of operating parameters, including applied current density, electrode gap and initial pH value, on the removal ratio of chemical oxygen demand (COD) was investigated. The results demonstrated that the COD removal ratio reached 90.5% after 3.5 h electrolysis with the current density at 3 A dm-2 and electrode gap at 1.0 cm. Correspondingly, the COD decreased from 5,125 mg L-1 to 487 mg L-1, which fitted the wastewater discharge standards of China, and the specific energy consumption (SECCOD) was 35.3 kWh kgCOD -1. Not only was the COD removal ratio only 77.1% after 2 h electrolysis but the BOD5/COD ratio of the wastewater reached 0.44, which could be biochemically treated, and the SECCOD decreased by 34.3%. Moreover, the main composition of pristine wastewater before and after 2 h electrolysis was analyzed by GC-MS, and the disappearance of macromolecules (such as ethyl-2-pyrenemethanol) and the production of small molecules (such as propane-1,3-diol) could improve the biodegradability of the wastewater. Therefore, electrochemical oxidation for 2 h is a promising alternative for pretreatment of coal tar wastewater prior to biological treatment.

Electrocatalytic degradation of the herbicide metamitron using lead dioxide anode: influencing parameters, intermediates, and reaction pathways.

In the present study, the electrocatalytic degradation of triazine herbicide metamitron using Ti/PbO2-CeO2 composite anode was studied in detail. The effects of the current density, initial metamitron concentration, supporting electrolyte concentration, and initial pH value were investigated and optimized. The results revealed that an electrocatalytic approach possessed a high capability of metamitron removal in aqueous solution. After 120 min, the removal ratio of metamitron could reach 99.0% in 0.2 mol L-1 Na2SO4 solution containing 45 mg L-1 metamitron with the current density at 90 mA cm-2 and pH value at 5.0. The reaction followed the pseudo-first-order kinetics model. HPLC and HPLC-MS were employed to analyze the degradation by-products in the metamitron oxidization process, and the degradation pathway was also proposed, which was divided into two sub-routes according to the different initial attacking positions on metamitron by hydroxyl radicals. Therefore, the electrocatalytic approach was considered as a very promising technology in practical application for herbicide wastewater treatment.

Bad germs are trapped.

Activation of the NAIP/NLRC4 inflammasomes initiates inflammatory responses against bacterial invasion. Two recent reports described the cryo-EM structure of the flagellin/NAIP5 complex, providing important insights into the mechanism of bacterial sensing by innate immunity.

Structural basis for specific flagellin recognition by the NLR protein NAIP5.

The nucleotide-binding domain- and leucine-rich repeat (LRR)-containing proteins (NLRs) function as intracellular immune receptors to detect the presence of pathogen- or host-derived signals. The mechanisms of how NLRs sense their ligands remain elusive. Here we report the structure of a bacterial flagellin derivative in complex with the NLR proteins NAIP5 and NLRC4 determined by cryo-electron microscopy at 4.28 Å resolution. The structure revealed that the flagellin derivative forms two parallel helices interacting with multiple domains including BIR1 and LRR of NAIP5. Binding to NAIP5 results in a nearly complete burial of the flagellin derivative, thus stabilizing the active conformation of NAIP5. The extreme C-terminal side of the flagellin is anchored to a sterically constrained binding pocket of NAIP5, which likely acts as a structural determinant for discrimination of different bacterial flagellins by NAIP5, a notion further supported by biochemical data. Taken together, our results shed light on the molecular mechanisms underlying NLR ligand perception.

Genome-wide identification and analysis of MAPK and MAPKK gene family in Chinese jujube (Ziziphus jujuba Mill.).

BACKGROUND: Chinese jujube (Ziziphus jujuba Mill.) is one of the most important members in the Rhamnaceae family. The whole genome sequence and more than 30,000 proteins of Chinese jujube have been obtained in 2014. Mitogen-activated protein kinase cascades are universal signal transduction modules in plants, which is rapidly activated under various biotic and abiotic stresses. To date, there has been no comprehensive analysis of the MAPK and MAPKK gene family in Chinese jujube at the whole genome level. RESULTS: By performing a series of bioinformatics analysis, ten MAPK and five MAPKK genes were identified from the genome database of Chinese jujube, and then compared with the homologous genes from Arabidopsis. Phylogenetic analysis showed that ZjMAPKs was classified into four known groups, including A, B, C and D. ZjMAPKs contains five members of the TEY phosphorylation site and five members with the TDY motif. The ZjMAPKK family was subsequently divided into three groups, A, B and D. The gene structure, conserved motifs, functional annotation and chromosome distribution of ZjMAPKs and ZjMAPKKs were also predicted. ZjMAPKs and ZjMAPKKs were distributed on nine pseudo-chromosomes of Chinese jujube. Subsequently, expression analysis of ZjMAPK and ZjMAPKK genes using reverse transcription PCR and quantitative real-time PCR was carried out. The majority of ZjMAPK and ZjMAPKK genes were expressed in all tested organs/tissues with considerable differences in transcript levels indicating that they might be constitutively expressed. Moreover, ZjMKK5 was specific expressed in early development stage of jujube flower bud, indicating it plays some roles in reproductive organs development. The transcript expression of most ZjMAPK and ZjMAPKK genes was down-regulated in response to plant growth regulators, darkness treatment and phytoplasma infection. CONCLUSIONS: We identified ten ZjMAPK and five ZjMAPKK genes from the genome database of Chinese jujube, the research results shown that ZjMPKs and ZjMKKs have the different expression patterns, indicating that they might play different roles in response to various treatments. The results provide valuable information for the further elucidation of physiological functions and biological roles of jujube MAPKs and MAPKKs.

Genome-wide identification, characterization of the MADS-box gene family in Chinese jujube and their involvement in flower development.

MADS-box genes encode transcription factors that are involved in plant development control (particularly in floral organogenesis) and signal transduction pathways, though a comprehensive analysis of MADS-box family proteins in Chinese jujube (Ziziphus jujuba Mill.) is still missing. Here, we report a genome-wide analysis of the MADS-box gene family in Chinese jujube. Based on phylogenetic analyses, 52 jujube MADS-box genes were classified into 25 MIKCC-type, 3 MIKC*-type, 16 Mα, 5 Mß and 3 Mγ genes. 37 genes were randomly distributed across all 12 putative chromosomes. We found that the type II genes are more complex than the type I genes and that tandem duplications have occurred in three groups of MADS-box genes. Meanwhile, some gene pairs in the same clade displayed similar or distinct expression profiles, suggesting possible functional redundancy or divergence. MIKCC-type genes exhibited typical temporal and spatial expression patterns in the four whorls of floral tissues. The expressions of B, C/D and E-type genes were significantly suppressed in phyllody as compared to flower, providing valuable evidence for their involvement in flower development. This study is the first comprehensive analysis of the MADS-box family in jujube, and provides valuable information for elucidating molecular regulation mechanism of jujube flower development.

Stepwise and dynamic assembly of the earliest precursors of small ribosomal subunits in yeast.

The eukaryotic ribosomal RNA (rRNA) is associated cotranscriptionally with numerous factors into an enormous 90S preribosomal particle that conducts early processing of small ribosomal subunits. The assembly pathway and structure of the 90S particle is poorly understood. Here, we affinity-purified and analyzed the constituents of yeast 90S particles that were assembled on a series of plasmid-encoded 3'-truncated pre-18S RNAs. We determined the assembly point of 65 proteins and the U3, U14, and snR30 small nucleolar RNAs (snoRNAs), revealing a stepwise and dynamic assembly map. The 5' external transcribed spacer (ETS) alone can nucleate a large complex. When the 18S rRNA is nearly complete, the 90S structure undergoes a dramatic reorganization, releasing U14, snR30, and 14 protein factors that bind earlier. We also identified a reference state of 90S that is fully assembled yet has not undergone 5'ETS processing. The assembly map present here provides a new framework to understand small subunit biogenesis.