Pathogen-secreted proteases activate a novel plant immune pathway.

Mitogen-activated protein kinase (MAPK) cascades play central roles in innate immune signalling networks in plants and animals. In plants, however, the molecular mechanisms of how signal perception is transduced to MAPK activation remain elusive. Here we report that pathogen-secreted proteases activate a previously unknown signalling pathway in Arabidopsis thaliana involving the Gα, Gß, and Gγ subunits of heterotrimeric G-protein complexes, which function upstream of an MAPK cascade. In this pathway, receptor for activated C kinase 1 (RACK1) functions as a novel scaffold that binds to the Gß subunit as well as to all three tiers of the MAPK cascade, thereby linking upstream G-protein signalling to downstream activation of an MAPK cascade. The protease-G-protein-RACK1-MAPK cascade modules identified in these studies are distinct from previously described plant immune signalling pathways such as that elicited by bacterial flagellin, in which G proteins function downstream of or in parallel to an MAPK cascade without the involvement of the RACK1 scaffolding protein. The discovery of the new protease-mediated immune signalling pathway described here was facilitated by the use of the broad host range, opportunistic bacterial pathogen Pseudomonas aeruginosa. The ability of P. aeruginosa to infect both plants and animals makes it an excellent model to identify novel immunoregulatory strategies that account for its niche adaptation to diverse host tissues and immune systems.

Genome sequence of the palaeopolyploid soybean.

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

LYK4, a lysin motif receptor-like kinase, is important for chitin signaling and plant innate immunity in Arabidopsis.

Chitin is commonly found in fungal cell walls and is one of the well-studied microbe/pathogen-associated molecular patterns. Previous studies showed that lysin motif (LysM)-containing proteins are essential for plant recognition of chitin, leading to the activation of plant innate immunity. In Arabidopsis (Arabidopsis thaliana), the LYK1/CERK1 (for LysM-containing receptor-like kinase1/chitin elicitor receptor kinase1) was shown to be essential for chitin recognition, whereas in rice (Oryza sativa), the LysM-containing protein, CEBiP (for chitin elicitor-binding protein), was shown to be involved in chitin recognition. Unlike LYK1/CERK1, CEBiP lacks an intracellular kinase domain. Arabidopsis possesses three CEBiP-like genes. Our data show that mutations in these genes, either singly or in combination, did not compromise the response to chitin treatment. Arabidopsis also contains five LYK genes. Analysis of mutations in LYK2, -3, -4, or -5 showed that LYK4 is also involved in chitin signaling. The lyk4 mutants showed reduced induction of chitin-responsive genes and diminished chitin-induced cytosolic calcium elevation as well as enhanced susceptibility to both the bacterial pathogen Pseudomonas syringae pv tomato DC3000 and the fungal pathogen Alternaria brassicicola, although these phenotypes were not as dramatic as that seen in the lyk1/cerk1 mutants. Similar to LYK1/CERK1, the LYK4 protein was also localized to the plasma membrane. Therefore, LYK4 may play a role in the chitin recognition receptor complex to assist chitin signal transduction and plant innate immunity.

[Overview and reflection on the development of the first batch of the inheritance studios of acupuncture and moxibustion academic schools].

The development status of the first 11 inheritance studios of acupuncture and moxibustion academic schools is summarized. Aiming at the current problems, it is suggested to establish qualitative and quantitative evaluation standards and establish a fair and reasonable evaluation system, build a systematic scientific theory and excavate the inherent laws of the schools, implement standardized management of the schools and protect the personalized characteristics of the schools, open outpatient clinic of acupuncture and moxibustion schools and promote the characteristic diagnosis and treatment technology, to promote the inheritance and development of acupuncture and moxibustion academic schools.

[Brief introduction of Qilu modern acupuncture methods].

Qilu acupuncture and moxibustion has promoted the formation and development of traditional Chinese medicine, which has a special historical position. By systematically collecting, sorting out and summarizing the characteristic acupuncture methods and academic ideas of several Qilu acupuncturists since the founding of the People's Republic of China, the understanding of the advantages and characteristics of Qilu modern acupuncture methods is deepened, aiming to exploring the inheritance and development pattern of Qilu acupuncture methods in the new era.

[Analysis of acupoints selection rules and efficacy evaluation of acupuncture and moxibustion for allergic rhinitis].

OBJECTIVE: To explore the rules of acupoints selection of acupuncture and moxibustion in the treatment of allergic rhinitis (AR) by using data mining technology, as well as to compare the efficacy of different acupoints selection methods. METHODS: Papers about acupuncture and moxibustion for treating AR published from January 2002 to August 2022 was retrieved from Chinese and English databases including CNKI, Wanfang, VIP, SinoMed and PubMed by using keywords of "acupuncture", "moxibustion" and "allergic rhinitis". According to the inclusion and exclusion criteria, the collected literature was screened to establish the AR database. Frequency statistic analysis was conducted for detecting high-frequency acupoints and specific acupoints frequency, and the curative effects of different acupoints selection methods were compared. SPSS26.0 software was used for factor analysis, cluster analysis and QUEST decision tree model identification. RESULTS: A total of 289 papers were included, with 384 acupuncture prescriptions extracted. A total of 99 acupoints were involved with the application frequency of 2 430 times. Among them, the application frequency of Yingxiang (LI20) is the highest (296 times, 12.18%), followed by Yintang (GV24+) and Hegu (LI4), etc. The main invloved meridians are the Bladder Meridian of Foot-Taiyang, the Large Intestine Meridian of Hand-Yangming and the Governor Vessel. The involved specific acupoints with the highest frequency of application is the crossing acupoints. Nine common factors of acupoints combinations units were extracted by factor analysis, and two cluster prescriptions of acupoints combinations correlation were obtained by cluster analysis. Three decision paths of simplified acupoints selection were simulated by the decision tree, with LI20 as the dependent variable. CONCLUSION: In the treatment of AR with acupuncture and moxibustion, the regularities and characteristics of acupoints selection are as follows: 1) often selecting local acupoints and acupoint combinations along meridians, 2) focusing on combination of dispelling pathogenic factors with strengthening vital energy, 3) advocating diversification of acupoint matching methods. The combination of factor analysis, cluster analysis and QUEST decision tree application provides three directions for clinical acupoints selection of AR.

PSKR1 balances the plant growth-defence trade-off in the rhizosphere microbiome.

Microbiota benefit their hosts by improving nutrient uptake and pathogen protection. How host immunity restricts microbiota while avoiding autoimmunity is poorly understood. Here we show that the Arabidopsis phytosulfokine receptor 1 (pskr1) mutant displays autoimmunity (plant stunting, defence-gene expression and reduced rhizosphere bacterial growth) in response to growth-promoting Pseudomonas fluorescens. Microbiome profiling and microbiota colonization showed that PSKR1-mediated reduction in bacterial growth and stunting is largely specific to Pseudomonas. Transcriptional profiling demonstrated that PSKR1 regulates the growth-defence trade-off during Pseudomonas colonization: PSKR1 upregulates plant photosynthesis and root growth but suppresses salicylic-acid-mediated defences. Genetic epistasis experiments showed that pskr1 stunting and restriction of bacterial growth are salicylic acid dependent. Finally, we showed that Pseudomonas, but not other bacteria, induces PSKR1 expression in roots, suggesting that Pseudomonas might manipulate plant signalling to promote its colonization. Our data demonstrate a genetic mechanism to coordinate beneficial functions of the microbiome while preventing autoimmunity.

Clinical evidence of three traditional Chinese medicine drugs and three herbal formulas for COVID-19: A systematic review and meta-analysis of the Chinese population.

BACKGROUND: The coronavirus disease 2019 (COVID-19) continues to spread worldwide. Integrated Chinese and Western medicine have had some successes in treating COVID-19. OBJECTIVE: This study aims to evaluate the efficacy and safety of three traditional Chinese medicine drugs and three herbal formulas (3-drugs-3-formulas) in patients with COVID-19. SEARCH STRATEGY: Relevant studies were identified from 12 electronic databases searched from their establishment to April 7, 2022. INCLUSION CRITERIA: Randomized controlled trials (RCTs), non-RCTs and cohort studies that evaluated the effects of 3-drugs-3-formulas for COVID-19. The treatment group was treated with one of the 3-drugs-3-formulas plus conventional treatment. The control group was treated with conventional treatment. DATA EXTRACTION AND ANALYSIS: Two evaluators screened and selected literature independently, then extracted basic information and assessed risk of bias. The treatment outcome measures were duration of main symptoms, hospitalization time, aggravation rate and mortality. RevMan 5.4 was used to analyze the pooled results reported as mean difference (MD) with 95% confidence interval (CI) for continuous data and risk ratio (RR) with 95% CI for dichotomous data. RESULTS: Forty-one studies with a total of 13,260 participants were identified. Our analysis suggests that compared with conventional treatment, the combination of 3-drugs-3-formulas might shorten duration of fever (MD = -1.39; 95% CI: -2.19 to -0.59; P < 0.05), cough (MD = -1.57; 95% CI: -2.16 to -0.98; P < 0.05) and fatigue (MD = -1.36; 95% CI: -2.21 to -0.51; P < 0.05), decrease length of hospital stay (MD = -2.62; 95% CI -3.52 to -1.72; P < 0.05), the time for nucleic acid conversion (MD = -2.92; 95% CI: -4.26 to -1.59; P < 0.05), aggravation rate (RR = 0.49; 95% CI: 0.38 to 0.64; P < 0.05) and mortality (RR = 0.34; 95% CI: 0.19 to 0.62; P < 0.05), and increase the recovery rate of chest computerized tomography manifestations (RR = 1.22; 95% CI: 1.14 to 1.3; P < 0.05) and total effectiveness (RR = 1.24; 95% CI: 1.09 to 1.42; P < 0.05). CONCLUSION: The 3-drugs-3-formulas can play an active role in treating all stages of COVID-19. No severe adverse events related to 3-drugs-3-formulas were observed. Hence, 3-drugs-3-formulas combined with conventional therapies have effective therapeutic value for COVID-19 patients. Further long-term high-quality studies are essential to demonstrate the clinical benefits of each formula. Please cite this article as: You LZ, Dai QQ, Zhong XY, Yu DD, Cui HR, Kong YF, Zhao MZ, Zhang XY, Xu QQ, Guan ZY, Wei XX, Zhang XC, Han SJ, Liu WJ, Chen Z, Zhang XY, Zhao C, Jin YH, Shang HC. Clinical evidence of three traditional Chinese medicine drugs and three herbal formulas for COVID-19: A systematic review and meta-analysis of the Chinese population. J Integr Med. 2023; 21(5): 441-454.

Evolutionary dynamics of protein domain architecture in plants.

BACKGROUND: Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s) in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. RESULTS: Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. CONCLUSIONS: Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing the notion that plant genomes have undergone dynamic evolution.

Calcium regulates caveolin-1 expression at the transcriptional level.

Caveolin-1, an indispensable component of caveolae serving as a transformation suppressor protein, is highly expressed in poorly metastatic mouse osteosarcoma FBJ-S1 cells while highly metastatic FBJ-LL cells express low levels of caveolin-1. Calcium concentration is higher in FBJ-S1 cells than in FBJ-LL cells; therefore, we investigated the possibility that calcium signaling positively regulates caveolin-1 in mouse FBJ-S1 cells. When cells were treated with the calcium channel blocker nifedipine, cyclosporin A (a calcineurin inhibitor), or INCA-6 (a nuclear factor of activated T-cells [NFAT] inhibitor), caveolin-1 expression at the mRNA and protein levels decreased. RNA silencing of voltage-dependent L-type calcium channel subunit alpha-1C resulted in suppression of caveolin-1 expression. This novel caveolin-1 regulation pathway was also identified in mouse NIH 3T3 cells and Lewis lung carcinoma cells. These results indicate that caveolin-1 is positively regulated at the transcriptional level through a novel calcium signaling pathway mediated by L-type calcium channel/Ca(2+)/calcineurin/NFAT.

[Analysis on combination regularities of Houxi (SI3) in ancient times of China based on latent structure model].

OBJECTIVE: To explore the feasibility and application value of combination regularities of acupoint Houxi (SI3) in Chinese ancient times based on latent structure model. METHODS: Relevant articles about SI3 for treating various diseases with acupuncture, moxibustion, acupoint application, etc. were mainly searched from book Chinese Medical Classics (5th edition), followed by establishment of a Database of Houxi Acupoint Recipes. The Lantern 5.0 software was used to construct and analyze the latent structure model of high-frequently-used acupoints. RESULTS: A total of 46 high frequently-used acupoints contained in 240 articles of 26 medical books were collected. The top 7 acupoints are Shenmai (BL62), Hegu (LI4), Qiangu (SI2), Fengchi (GB20), Jianshi (PC5), Wangu (SI4) and Quchi (LI11) in sequence. After modeling the 46 high-frequently used adjunct acupoints, 12 latent variables (Y0-Y11) and 24 latent classes were obtained by setting the cumulative coverage threshold ratio to be 95%. According to the Bayesian information criterion (BIC) measure, the model score was -2 170.68 points. Seven comprehensive clustering models were summarized up according to the latent structure. Compared with the yin meridians, the yang meridians played a more significant role. The multiple combinations of SI3 with specific acupoints provided a reference for clinical practice. The supplementary acupoints mainly distribute in the upper and lower limbs, head, face, neck, etc. and the SI3 acupoint recipes function mainly in dredging and activating meridians and collaterals, clearing away pathologic heat and wind, improving eyesight, and relieving swelling and pain. CONCLUSION: The latent structure model is applicable in analysis of the regularities of SI3 acupoint combination for treating some diseases. Comprehensive clustering is employed to determine the primary acupoint SI3 and adjunct acupoint matching, revealing the common regularity and logical progressive relationship between the primary and secondary points, which may be helpful for teaching, clinical and scientific research.

A member of the highly conserved FWL (tomato FW2.2-like) gene family is essential for soybean nodule organogenesis.

A soybean homolog of the tomato FW2.2 gene, here named GmFWL1 (Glycine max FW2.2-like 1), was found to respond strongly to inoculation with the nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum. In tomato, the FW2.2 gene is hypothesized to control 30% of the variance in fruit weight by negatively regulating cell division. In the present study, the induction of GmFWL1 expression in root hair cells and nodules in response to B. japonicum inoculation was documented using quantitative RT-PCR and transcriptional fusions to both beta-glucuronidase (GUS) and green fluorescent protein (GFP). RNAi-mediated silencing of GmFWL1 expression resulted in a significant reduction in nodule number, with a concomitant reduction in nuclear size and changes in chromatin structure. The reduction in nuclear size is probably due to a change in DNA heterochromatinization, as the ploidy level of wild-type and RNAi-silenced nodule cells was similar. GmFWL1 was localized to the plasma membrane. The data suggest that GmFWL1 probably acts indirectly, perhaps through a cellular cascade, to affect chromatin structure/nuclei architecture. As previously proposed in tomato, this function may be a result of effects on plant cell division.

Activity-based metagenomic screening and biochemical characterization of bovine ruminal protozoan glycoside hydrolases.

The rumen, the foregut of herbivorous ruminant animals such as cattle, functions as a bioreactor to process complex plant material. Among the numerous and diverse microbes involved in ruminal digestion are the ruminal protozoans, which are single-celled, ciliated eukaryotic organisms. An activity-based screen was executed to identify genes encoding fibrolytic enzymes present in the metatranscriptome of a bovine ruminal protozoan-enriched cDNA expression library. Of the four novel genes identified, two were characterized in biochemical assays. Our results provide evidence for the effective use of functional metagenomics to retrieve novel enzymes from microbial populations that cannot be maintained in axenic cultures.

Preparation and Properties of Thrombus-Targeted Urokinase/Multi-Walled Carbon Nanotubes (MWCNTs)-Chitosan (CS)-RGD Drug Delivery System.

In order to improve the therapeutic effect, prolong the action time and reduce the side effects of the first generation thrombolytic drug urokinase (UK), a novel UK/multi-walled carbon nanotubes (MWCNTs)-chitosan (CS)-arginine-glycine-aspartic acid (Arg-Gly-Asp) (RGD) drug delivery system was synthesized by chemical bonding/non covalent bond modification/ultrasonic dispersion. The results showed that the diameter of the UK/MWCNTs-CS-RGD drug delivery system was about 30-40 nm, there was a layer of UK was attached to the surface of the tube wall, and the distribution was relatively uniform. The average encapsulation efficiency was 83.10%, and the average drug loading was 12.81%. Interestingly, it also had a certain sustained-release effect, and its release law was best fitted by first-order kinetic equation. Moreover, the accelerated and long-term stability test results show that it had good stability. Compared with free UK, UK/MWCNTs-CS-RGD had thrombolytic effect in vitro. In addition, MTT experiment showed that the prepared MWCNTs-CS-RGD nanomaterials had good biocompatibility. A rabbit model of carotid artery thrombosis was used to conduct targeted thrombolysis experiments in vivo. Compared with free UK, UK/MWCNTs-CS-RGD could be enriched in the thrombosis site to achieve thrombus targeting. UK/MWCNTs-CS-RGD drug delivery system was expected to become an effective thrombolytic drug for targeted therapy of thrombosis.

[Discussion on the theory of he-sea point in Neijing (Inner Canon of Yellow Emperor) and Nanjing (Yellow Emperor's Classic of Eighty-one Difficult Issues )].

By collecting and analyzing the explanation/conception, acupoint name, acupoint location, indications, acupuncture and moxibustion techniques and contraindications of he-sea point recorded in Neijing (Inner Canon of Yellow Emperor) and Nanjing (Yellow Emperor 's Classic of Eighty-one Difficult Issues), it is found that conception of he-sea point of five-shu points has been specifically formed, the names of he-sea points of eleven meridians, the locations and the ways to locate them were recorded. But, the summaries relevant to the indications of the many he-sea points have not been included in teaching materials, thus, it needs to be further analyzed. The acupuncture-moxibustion techniques at he-sea point are flexible and the attention should be paid to distinguish "needling he-sea point in autumn" from "needling he-sea point in winter". Besides, the consideration should be given on coma/fainting induced by arterial bleeding when needling he-sea point, as well as the joint motor impairment caused by over deep insertion in acupuncture.

FERONIA restricts Pseudomonas in the rhizosphere microbiome via regulation of reactive oxygen species.

Maintaining microbiome structure is critical for the health of both plants and animals. By re-screening a collection of Arabidopsis mutants affecting root immunity and hormone crosstalk, we identified a FERONIA (FER) receptor kinase mutant (fer-8) with a rhizosphere microbiome enriched in Pseudomonas fluorescens without phylum-level dysbiosis. Using microbiome transplant experiments, we found that the fer-8 microbiome was beneficial. The effect of FER on rhizosphere pseudomonads was largely independent of its immune scaffold function, role in development and jasmonic acid autoimmunity. We found that the fer-8 mutant has reduced basal levels of reactive oxygen species (ROS) in roots and that mutants deficient in NADPH oxidase showed elevated rhizosphere pseudomonads. The addition of RALF23 peptides, a FER ligand, was sufficient to enrich P. fluorescens. This work shows that FER-mediated ROS production regulates levels of beneficial pseudomonads in the rhizosphere microbiome.

Evolutionary genomics of LysM genes in land plants.

BACKGROUND: The ubiquitous LysM motif recognizes peptidoglycan, chitooligosaccharides (chitin) and, presumably, other structurally-related oligosaccharides. LysM-containing proteins were first shown to be involved in bacterial cell wall degradation and, more recently, were implicated in perceiving chitin (one of the established pathogen-associated molecular patterns) and lipo-chitin (nodulation factors) in flowering plants. However, the majority of LysM genes in plants remain functionally uncharacterized and the evolutionary history of complex LysM genes remains elusive. RESULTS: We show that LysM-containing proteins display a wide range of complex domain architectures. However, only a simple core architecture is conserved across kingdoms. Each individual kingdom appears to have evolved a distinct array of domain architectures. We show that early plant lineages acquired four characteristic architectures and progressively lost several primitive architectures. We report plant LysM phylogenies and associated gene, protein and genomic features, and infer the relative timing of duplications of LYK genes. CONCLUSION: We report a domain architecture catalogue of LysM proteins across all kingdoms. The unique pattern of LysM protein domain architectures indicates the presence of distinctive evolutionary paths in individual kingdoms. We describe a comparative and evolutionary genomics study of LysM genes in plant kingdom. One of the two groups of tandemly arrayed plant LYK genes likely resulted from an ancient genome duplication followed by local genomic rearrangement, while the origin of the other groups of tandemly arrayed LYK genes remains obscure. Given the fact that no animal LysM motif-containing genes have been functionally characterized, this study provides clues to functional characterization of plant LysM genes and is also informative with regard to evolutionary and functional studies of animal LysM genes.

Comparison of Prognostic Indices in NSCLC Patients with Brain Metastases after Radiosurgery.

Prognostic indices are commonly used in the context of brain metastases radiotherapy to guide patient decision-making and clinical trial stratification. This study is to choose an appropriate prognostic index (PI) for non-small cell lung cancer (NSCLC) patients with brain metastases (BM) who underwent radiosurgery. A total of 103 patients with BM from NSCLC receiving radiosurgery were analyzed retrospectively. There are six prognostic factors were analyzed, including age, primary tumor control, extracranial metastasis, KPS score, number of lesions, max lesion volume; and four prognostic indices were compared, include Recursive Partitioning Analysis (RPA),Graded Prognostic Assessment (GPA), Score Index for Radiosurgery (SIR), Basic Score for Brain Metastases (BSBM). Survival curves were estimated with the Kaplan-Meier method and compared with a log-rank test stratified according to the PIs. Univariate and multivariate analysis was performed using the Cox regression analysis. The PI's predictive capacity was compared in terms of Akaike information criterion (AIC), Log-rank × 2, Concordance index (C-index) and calibration curve. The median survival time was 8 months, and the 6-months and 12-months survival rate were 61% and 26% respectively. All four prognostic indices were correlated with prognosis (P<0.005).The AIC for BSBM (686.317) was the minimum in the four PIs(range,686.317-739.113).The Log-rank × 2 value for BSBM (77.62) was the maximum in the four PIs (range,23.32-77.62).The C-index for BSBM (0.758)was superior than the other PIs predictive capacity (range,0.611-0.758). The calibration curve showed that the BSBM was able to predict 6-months and 12-months overall survival accurately. In conclusion, the BSBM may be the most accurate prognostic index for patients with BM from NSCLC who underwent radiosurgery.