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Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane's tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia , which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia , Pseudomonas , Paraburkholderia , and Chryseobacterium . This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields., Importance: This work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.

Three-dimensional (3D) reduced graphene oxide (rGO)/Ti2CTx MXene hybrid aerogels were effectively prepared by a two-step method involving hydrothermal reaction and freeze-drying. The intimately coupled rGO/Ti2CTx hybrid aerogel combined high electrical conductivity, large interlayer spacing, and excellent mechanical stability of Ti2CTx, which not only effectively prevents the self-restacking of Ti2CTx nanosheets, exposes more active sites exposed, and improves the volume change during the charge/discharge process but also increases the accessibility of ions and promotes the rapid transfer of ions/electrons. As a result, rGO/Ti2CTx 17.5-2.5 as the working electrode of electric double layer capacitors delivers a large specific capacity (107.05 F g-1 at 0.5 A g-1 in a 1M Na2SO4 electrolyte), a high rate capability (maintains 30% of its initial capacitance at 10 A g-1, which is much better than rGO and Ti2CTx), and excellent long-term large-current cycle stability (the initial capacitance remains above 71.1% after 10 000 cycles at 1 A g-1). In addition to providing a high-performance electrode for supercapacitors, this study proposes an efficient and time-saving strategy for constructing 3D structures from 2D materials., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The basic tribological experiments have reported that nano-graphene lubricating oil has excellent anti-friction and anti-wear properties, which has been widely concerned. However, the real anti-friction effect of nano-graphene lubricating oil and its impact on engine power performance, economic performance and emission performance remain to be proved. This has seriously hindered the popularization and application of nano-graphene lubricating oil in the engine field. In this paper, nano-graphene powder was chemically grafted to prepare nano-graphene lubricating oil with high dispersion stability. The influence of nano-graphene on physicochemical properties of lubricating oil was studied, and the influence of nano-graphene on engine power performance, economic performance and emission performance was explored. The results show that after modification, the dispersion of nano-graphene in lubricating oil is improved. Compared with pure lubricating oil, the addition of nano-graphene makes the kinematic viscosity of lubricating oil slightly lower, and has little effect on the density, flash point, pour point and total acid value of lubricating oil. The reversed towing torque of nano-graphene lubricating oil is reduced by 1.82-5.53%, indicating that the friction loss decreases. The specific fuel consumption of the engine is reduced, which indicates that the fuel economic performance is improved. Engine HC+NOX, CH4, CO2 emissions do not change much, but particulate matter (PM) emissions increase by 8.85%. The quantity concentration of nuclear particles, accumulated particles and total particles of nano-graphene lubricating oil are significantly higher than that of pure lubricating oil. And the increase of the quantity concentration of accumulated particles is more obvious than that of nuclear particles, and the larger the load, the more obvious this phenomenon. In order to apply nano-graphene lubricating oil to the engine, it is also necessary to further study its impact on the post-processing system, adjust the control strategy of the post-processing system and then test and calibrate., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Kuang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Saccharum complex includes genera Saccharum , Miscanthus , Erianthus , Narenga , and Tripidium . Since the Saccharum complex/Saccharinae constitutes the gene pool used by sugarcane breeders to introduce useful traits into sugarcane, studying the genomic characterization of the Saccharum complex has become particularly important. Here, we assembled graph-based mitochondrial genomes (mitogenomes) of four Saccharinae species ( T. arundinaceum , E. rockii, M. sinensis , and N. porphyrocoma ) using Illumina and PacBio sequencing data. The total lengths of the mitogenomes of T. arundinaceum , M. sinensis , E. rockii and N. porphyrocoma were 549,593 bp, 514,248 bp, 481,576 bp and 513,095 bp, respectively. Then, we performed a comparative mitogenomes analysis of Saccharinae species, including characterization, organelles transfer sequence, collinear sequence, phylogenetics analysis, and gene duplicated/loss. Our results provided the mitogenomes of four species closely related to sugarcane breeding, enriching the mitochondrial genomic resources of the Saccharinae. Additionally, our study offered new insights into the evolution of mitogenomes at the family and genus levels and enhanced our understanding of organelle evolution in the highly polyploid Saccharum genus., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Li, Yang, Wang, Xu, Zhang, Huang, Zhang, Zhou, Gao, Zong, Duan and Yang.)

Key Message: We reported the graph-based mitochondrial genomes of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) for the first time. The results revealed pan-structural variation and evolutionary processes in the mitochondrial genomes within Saccharum. Saccharum belongs to the Andropogoneae, and cultivars species in Saccharum contribute nearly 80% of sugar production in the world. To explore the genomic studies in Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) using Illumina and Oxford Nanopore Technologies sequencing data. The mitogenomes of the three species were divided into a total of eight types based on contig numbers and linkages. All mitogenomes in the three species encoded 51 unique genes, including 32 protein-coding, 3 ribosomal RNA (rRNA) and 16 transfer RNA (tRNA) genes. The existence of long and short-repeat-mediated recombinations in the mitogenome of S. officinarum and S. robustum was revealed and confirmed through PCR validation. Furthermore, employing comparative genomics and phylogenetic analyses of the organelle genomes, we unveiled the evolutionary relationships and history of the major interspecific lineages in Saccharum genus. Phylogenetic analyses of homologous fragments between S. officinarum and S. robustum showed that S. officinarum and S. robustum are phylogenetically distinct and that they were likely parallel rather than domesticated. The variations between ancient (S. sinense and S. barberi) and modern cultivated species (S. hybrid) possibly resulted from hybridization involving different S. officinarum accessions. Lastly, this project reported the first graph-based mitogenomes of three Saccharum species, and a systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitogenomes revealed the differential features of the Saccharum mitogenomes., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks., (© 2024 Institute of Botany, Chinese Academy of Sciences.)

Stem color is an important agronomic trait of wax gourds. However, its regulatory genes have not been identified. In this study, 105 inbred lines constructed from two parents (GX-71 and MY-1) were sequenced and quantitative trait loci sequencing was used to mine the genes that regulate stem color in wax gourds. The results identified two quantitative trait loci related to stem color, qSC5 and qSC12 , located on Chr05 (11,134,567-16,459,268) and Chr12 (74,618,168-75,712,335), respectively. The qSC5 had a phenotypic variation rate of 36.9% and a maximum limit of detection of 16.9. And the qSC12 had a phenotypic variation rate of 20.9%, and a maximum limit of detection of 11.2. Bch05G003950 (named BchAPRR2 ) and Bch12G020400 were identified as candidate genes involved in stem color regulation in wax gourds. The chlorophyll content and expression of BchAPRR2 and Bch12G020400 were significantly higher in green-stemmed wax gourds than in white-stemmed ones. Therefore, BchAPRR2 and Bch12G020400 were considered the main and secondary regulatory genes for wax gourd stem color, respectively. Finally, InDel markers closely linked to BchAPRR2 were developed to validate the prediction of wax gourd stem color traits in 55 germplasm lines, with an accuracy of 81.8%. These findings lay the foundation for exploring the genetic regulation of wax gourd stem color and future research on wax gourd breeding.

Lithium-sulfur (Li-S) batteries with high specific energy density, low cost, and environmental friendliness of sulfur have been regarded as a competitive alternative to replace lithium-ion batteries. However, the shuttle effect and the sluggish conversion rate of lithium polysulfides (LiPSs) have seriously limited the practical application of Li-S batteries. Herein, high-entropy oxides grown on the carbon cloth (CC/HEO) are synthesized by a simple and ultrafast solution combustion method for the sulfur cathode. The as-prepared composites possess abundant HEO active sites for strong interaction with LiPSs, which can significantly promote redox kinetics. Besides, the carbon fiber substrate not only ensures high electrical conductivity but also accommodates large volume change, leading to a stable sulfur electrochemistry. Benefiting from the rational design, the Li-S batteries with CC/HEO as cathode skeleton exhibits good cyclability with a capacity decay rate of 0.057% per cycle after 1000 cycles at 2 C. More importantly, the Li-S batteries with 4.3 mg cm -2 high sulfur loading can still retain a high capacity retention of 78.2% after 100 cycles.

Microbes living inside or around sugarcane (Saccharum spp.) are crucial for their resistance to abiotic and biotic stress, growth, and development. Sequences of microbial genomes and genes are helpful to understand the function of these microbes. However, there is currently a lack of such knowledge in sugarcane. Here, we combined Nanopore and Illumina sequencing technologies to successfully construct the first high-quality metagenome-assembled genomes (MAGs) and gene catalogues of sugarcane culturable microbes (GCSCMs), which contained 175 species-level genome bins (SGBs), and 7,771,501 non-redundant genes. The SGBs included 79 novel culturable bacteria genomes, and 3 bacterial genomes with nitrogen-fixing gene clusters. Four single scaffold near-complete circular MAGs (cMAGs) with 0% contamination were obtained from Nanopore sequencing data. In conclusion, we have filled a research gap in the genomes and gene catalogues of culturable microbes of sugarcane, providing a vital data resource for further understanding the genetic basis and functions of these microbes. In addition, our methodology and results can provide guidance and reference for other plant microbial genome and gene catalogue studies., (© 2024. The Author(s).)

Objective: Sphingosine-1-phosphate receptor (S1PR) modulators have recently attracted increasing attention for the treatment of multiple sclerosis (MS). Despite their preference in the clinic, multiple adverse events (AEs) continue to be reported every year. This study aimed to investigate the potential AEs as well as related important medical events (IMEs) signal associated with S1PR modulators, including fingolimod, siponimod and ozanimod in a real-world study using the FDA Adverse Event Reporting System (FAERS) database., Methods: All data were collected from the FAERS database, spanning from the fourth quarter of 2010(2010Q4) to the second quarter of 2023 (2023Q2). Potential AE and IME signals of S1PR modulators were identified based on a disproportionality analysis using the reporting odds ratio (ROR), proportional reporting ratio (PRR), and the bayesian confidence propagation neural network of information components (IC)., Results: Overall, 276,436 reports of fingolimod, 20,972 reports of siponimod and 10,742 reports of ozanimod were analyzed from the FAERS database. Among reports, females were more prone to develop AEs (73.71% for females vs. 23.21% for males), and more than 50% of patients suffered from AEs were between 18 and 64 years. Subsequently, we investigated the top 20 AEs associated with the signal strength of S1PR modulators at the preferred term (PT) level, and identified 31 (8 vs. 11 vs. 12, respectively) unlabeled risk signals such as thrombosis, uterine disorder and reproductive system and breast disorders. Furthermore, we discovered that the S1PR modulator reported variations in the possible IMEs, and that the IMEs associated with ocular events were reported frequently. It's interesting to note that infection and malignancy are prominent signals with both fingolimod and siponimod in the top 20 PTs related to mortality reports., Conclusion: The present investigation highlights the possible safety risks associated with S1PR modulators. The majority of AEs are generally consistent with previous studies and are mentioned in the prescribing instructions, however, several unexpected AE signals have also been observed. Ozanimod showed the lowest signal intensity and a better safety profile than the other S1PR modulators. Due to the short marketing time of drugs and the limitations of spontaneous reporting database, further research is required to identify potential AEs related to S1PR modulators., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Yang, Yan, Liu, Wang and Feng.)

Nano-graphene lubricating oil with appropriate concentration shows excellent performance in reducing friction and wear under different working conditions of diesel engines, and has been widely concerned. Lubricating oil has a significant impact on particulate matter (PM) emissions. At present, there are few studies on the impact of nano-graphene lubricating oil on the physicochemical properties of PM. In order to comprehensively evaluate the impact of nano-graphene lubricating oil on diesel engines, this paper mainly focused on the effects of lubricating oil nano-graphene additives on the particle size distribution and physicochemical properties of PM. The results show that, compared with pure lubricating oil, the total number of nuclear PM and accumulated PM of nano-graphene lubricating oil is significantly increased. The fractal dimension of PM of nano-graphene lubricating oil increases and its structure becomes more compact. The average fringe separation distance of basic carbon particles decreases, the average fringe length increases. The degree of ordering and graphitization of basic carbon particles are higher. The fringe tortuosity of basic carbon particles decreases, and the fluctuation of carbon layer structure of basic carbon particles decreases. Aliphatic substances in PM are basically unchanged, aromatic components and oxygen functional groups increase. The initial PM oxidation temperature and burnout temperature increase, the maximum oxidation rate temperature and combustion characteristic index decrease, and the activation energy increases, making it more difficult to oxidize. This was mainly caused by the higher graphitization degree of PM of nano-graphene lubricating oil and the increased content of aromatic substances., (© 2024. The Author(s).)

Objective: Identifying the gut microbiota associated with host immunity in the AIDS stage., Design: We performed a cross-sectional study., Methods: We recruited people with HIV (PWH) in the AIDS or non-AIDS stage and evaluated their gut microbiota and metabolites by using 16S ribosomal RNA (rRNA) sequencing and liquid chromatography-mass spectrometry (LC-MS). Machine learning models were used to analyze the correlations between key bacteria and CD4 + T cell count, CD4 + T cell activation, bacterial translocation, gut metabolites, and KEGG functional pathways., Results: We recruited 114 PWH in the AIDS stage and 203 PWH in the non-AIDS stage. The α-diversity of gut microbiota was downregulated in the AIDS stage ( P  < 0.05). Several machine learning models could be used to identify key gut microbiota associated with AIDS, including the logistic regression model with area under the curve (AUC), sensitivity, specificity, and Brier scores of 0.854, 0.813, 0.813, and 0.160, respectively. The decreased key bacteria ASV1 ( Bacteroides sp.), ASV8 ( Fusobacterium sp.), ASV30 ( Roseburia sp.), ASV37 ( Bacteroides sp.), and ASV41 ( Lactobacillus sp.) in the AIDS stage were positively correlated with the CD4 + T cell count, the EndoCAb IgM level, 4-hydroxyphenylpyruvic acid abundance, and the predicted cell growth pathway, and negatively correlated with the CD3 + CD4 + CD38 + HLA-DR + T cell count and the sCD14 level., Conclusion: Machine learning has the potential to recognize key gut microbiota related to AIDS. The key five bacteria in the AIDS stage and their metabolites might be related to CD4 + T cell reduction and immune activation., (Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc.)

Driven by the strong adsorptive and catalytic ability of metal sulfides for soluble polysulfides, it is considered as a potential mediator to resolve the problems of shuttle effect and slow reaction kinetics of polysulfides in lithium-sulfur (Li-S) batteries. However, their further development is limited by poor electrical conductivity and bad long-term durability. Herein, one type of new catalyst composed of SnS/SnS 2 heterostructures on hierarchical porous carbon (denoted as SnS/SnS 2 -HPC) by a simple hydrothermal method is reported and used as an interlayer coating on the conventional separator for blocking polysulfides. The SnS/SnS 2 -HPC integrates the advantages of a porous conductive network for promoting the transport of electrons and an enhanced electrocatalyst for accelerating polysulfides conversion. As a result, such a cell coupled with a SnS/SnS 2 -HPC interlayer exhibits a long-term lifespan of 1200 cycles. This work provides a new cell configuration by using heterostructures with a built-in electric field formed from a p-n heterojunction to improve the performance of Li-S batteries.

Purinergic signaling plays a causal role in the pathogenesis of inflammatory bowel disease. Among purinoceptors, only P2Y 14 R is positively correlated with inflammatory score in mucosal biopsies of ulcerative colitis patients, nevertheless, the role of P2Y 14 R in ulcerative colitis remains unclear. Here, based on the over-expressions of P2Y 14 R in the intestinal epithelium of mice with experimental colitis, we find that male mice lacking P2Y 14 R in intestinal epithelial cells exhibit less intestinal injury induced by dextran sulfate sodium. Mechanistically, P2Y 14 R deletion limits the transcriptional activity of cAMP-response element binding protein through cAMP/PKA axis, which binds to the promoter of Ripk1, inhibiting necroptosis of intestinal epithelial cells. Furthermore, we design a hierarchical strategy combining virtual screening and chemical optimization to develop a P2Y 14 R antagonist HDL-16, which exhibits remarkable anti-colitis effects. Summarily, our study elucidates a previously unknown mechanism whereby P2Y 14 R participates in ulcerative colitis, providing a promising therapeutic target for inflammatory bowel disease., (© 2024. The Author(s).)

Background: Bladder cancer (BLCA) is a prevalent malignancy worldwide. Anoikis remains a new form of cell death. It is necessary to explore Anoikis-related genes in the prognosis of BLCA., Methods: We obtained RNA expression profiles from the The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases for dimensionality reduction analysis and isolated epithelial cells, T cells and fibroblasts for copy number variation analysis, pseudotime analysis and transcription factor analysis based on R package. We integrated machine-learning algorithms to develop the artificial intelligence-derived prognostic signature (AIDPS)., Results: The performance of AIDPS with clinical indicators was stable and robust in predicting BLCA and showed better performance in every validation dataset compared to other models. Mendelian randomization analysis was conducted. Single nucleotide polymorphism (SNP) sites of rs3100578 (HK2) and rs66467677 (HSP90B1) exhibited significant correlation of bladder problem (not cancer) and bladder cancer, whereasSNP sites of rs3100578 (HK2) and rs947939 (BAD) had correlation between bladder stone and bladder cancer. The immune infiltration analysis of the TCGA-BLCA cohort was calculated via the ESTIMATE (i.e. Estimation of STromal and Immune cells in MAlignantTumours using Expression data) algorithm which contains stromal, immune and estimate scores. We also found significant differences in the IC 50 values of Bortezomib&#95;1191, Docetaxel&#95;1007, Staurosporine&#95;1034 and Rapamycin&#95;1084 among the high- and low-risk groups., Conclusions: In conclusion, these findings indicated Anoikis-related prognostic genes in BLCA and constructed an innovative machine-learning model of AIDPS with high prognostic value for BLCA., (© 2024 John Wiley & Sons Ltd.)

Introduction: Modern sugarcane cultivars (Saccharum spp. hybrids) derived from crosses between S. officinarum and S. spontaneum, with high-sugar traits and excellent stress tolerance inherited respectively. However, the contribution of the S. spontaneum subgenome to sucrose accumulation is still unclear., Objective: To compensate for the absence of a high-quality reference genome, a transcriptome analysis method is needed to analyze the molecular basis of differential sucrose accumulation in sugarcane hybrids and to find clues to the contribution of the S. spontaneum subgenome to sucrose accumulation., Methods: PacBio full-length sequencing was used to complement genome annotation, followed by the identification of differential genes between the high and low sugar groups using differential alternative splicing analysis and differential expression analysis. At the subgenomic level, the factors responsible for differential sucrose accumulation were investigated from the perspective of transcriptional and post-transcriptional regulation., Results: A full-length transcriptome annotated at the subgenomic level was provided, complemented by 263,378 allele-defined transcript isoforms and 139,405 alternative splicing (AS) events. Differential alternative splicing (DA) analysis and differential expression (DE) analysis identified differential genes between high and low sugar groups and explained differential sucrose accumulation factors by the KEGG pathways. In some gene models, different or even opposite expression patterns of alleles from the same gene were observed, reflecting the potential evolution of these alleles toward novel functions in polyploid sugarcane. Among DA and DE genes in the sucrose source-sink complex pathway, we found some alleles encoding sucrose accumulation-related enzymes derived from the S. spontaneum subgenome were differentially expressed or had DA events between the two contrasting sugarcane hybrids., Conclusion: Full-length transcriptomes annotated at the subgenomic level could better characterize sugarcane hybrids, and the S. spontaneum subgenome was found to contribute to sucrose accumulation., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Production and hosting by Elsevier B.V.)

Background: The studies on SARS-CoV-2 and human microbiota have yielded inconsistent results regarding microbiota α-diversity and key microbiota. To address these issues and explore the predictive ability of human microbiota for the prognosis of SARS-CoV-2 infection, we conducted a reanalysis of existing studies., Methods: We reviewed the existing studies on SARS-CoV-2 and human microbiota in the Pubmed and Bioproject databases (from inception through October 29, 2021) and extracted the available raw 16S rRNA sequencing data of human microbiota. Firstly, we used meta-analysis and bioinformatics methods to reanalyze the raw data and evaluate the impact of SARS-CoV-2 on human microbial α-diversity. Secondly, machine learning (ML) was employed to assess the ability of microbiota to predict the prognosis of SARS-CoV-2 infection. Finally, we aimed to identify the key microbiota associated with SARS-CoV-2 infection., Results: A total of 20 studies related to SARS-CoV-2 and human microbiota were included, involving gut (n = 9), respiratory (n = 11), oral (n = 3), and skin (n = 1) microbiota. Meta-analysis showed that in gut studies, when limiting factors were studies ruled out the effect of antibiotics, cross-sectional and case-control studies, Chinese studies, American studies, and Illumina MiSeq sequencing studies, SARS-CoV-2 infection was associated with down-regulation of microbiota α-diversity (P < 0.05). In respiratory studies, SARS-CoV-2 infection was associated with down-regulation of α-diversity when the limiting factor was V4 sequencing region (P < 0.05). Additionally, the α-diversity of skin microbiota was down-regulated at multiple time points following SARS-CoV-2 infection (P < 0.05). However, no significant difference in oral microbiota α-diversity was observed after SARS-CoV-2 infection. ML models based on baseline respiratory (oropharynx) microbiota profiles exhibited the ability to predict outcomes (survival and death, Random Forest, AUC = 0.847, Sensitivity = 0.833, Specificity = 0.750) after SARS-CoV-2 infection. The shared differential Prevotella and Streptococcus in the gut, respiratory tract, and oral cavity was associated with the severity and recovery of SARS-CoV-2 infection., Conclusions: SARS-CoV-2 infection was related to the down-regulation of α-diversity in the human gut and respiratory microbiota. The respiratory microbiota had the potential to predict the prognosis of individuals infected with SARS-CoV-2. Prevotella and Streptococcus might be key microbiota in SARS-CoV-2 infection., (© 2023. The Author(s).)

Sugarcane, a major sugar and energy crop worldwide faces an increasing demand for higher yields. Identifying yield-related markers and candidate genes is valuable for breeding high-yield varieties using molecular techniques. In this work, seven yield-related traits were evaluated in a diversity panel of 159 genotypes, derived from Tripidium arundinaceum , Saccharum spontaneum , and modern sugarcane genotypes. All traits exhibited significant genetic variance with high heritability and high correlations. Genetic diversity analysis reveals a genomic decay of 23 kb and an average single nucleotide polymorphism (SNP) number of 25,429 per genotype. These 159 genotypes were divided into 4 subgroups. Genome-wide association analysis identified 47 SNPs associated with brix, spanning 36 quantitative trait loci (QTLs), and 138 SNPs for other traits across 104 QTLs, covering all 32 chromosomes. Interestingly, 12 stable QTLs associated with yield-related traits were identified, which contained 35 candidate genes. This work provides markers and candidate genes for marker-assisted breeding to improve sugarcane yields.

Background: Gut microbiota is the largest population of microorganisms and is closely related to health. Many studies have explored changes in gut microbiota in viral hepatitis. However, the correlation between gut microbiota and the occurrence and progression of viral hepatitis has not been fully clarified., Methods: PubMed and BioProject databases were searched for studies about viral hepatitis disease and 16S rRNA gene sequencing of gut microbiota up to January 2023. With bioinformatics analyses, we explored changes in microbial diversity of viral hepatitis, screened out crucial bacteria and microbial functions related to viral hepatitis, and identified the potential microbial markers for predicting risks for the occurrence and progression of viral hepatitis based on ROC analysis., Results: Of the 1389 records identified, 13 studies met the inclusion criteria, with 950 individuals including 656 patient samples (HBV, n = 546; HCV, n = 86; HEV, n = 24) and 294 healthy controls. Gut microbial diversity is significantly decreased as the infection and progression of viral hepatitis. Alpha diversity and microbiota including Butyricimonas , Escherichia-Shigella , Lactobacillus , and Veillonella were identified as the potential microbial markers for predicting the risk of development of viral hepatitis (AUC>0.7). Microbial functions including tryptophan metabolism, fatty acid biosynthesis, lipopolysaccharide biosynthesis, and lipid metabolism related to the microbial community increased significantly as the development of viral hepatitis., Conclusions: This study demonstrated comprehensively the gut microbiota characteristics in viral hepatitis, screened out crucial microbial functions related to viral hepatitis, and identified the potential microbial markers for predicting the risk of viral hepatitis., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Yang, Mai, Zhou, Li, Wang, Lan, Lu, Yang, Guo, Ye, Cui, Liang and Huang.)

Introduction: During plant evolution, nucleotide-binding sites (NBS) and leucine-rich repeat (LRR) genes have made significant contributions to plant disease resistance. With many high-quality plant genomes sequenced, identification and comprehensive analyses of NBS-LRR genes at whole genome level are of great importance to understand and utilize them., Methods: In this study, we identified the NBS-LRR genes of 23 representative species at whole genome level, and researches on NBS-LRR genes of four monocotyledonous grass species, Saccharum spontaneum, Saccharum officinarum, Sorghum bicolor and Miscanthus sinensis, were focused., Results and Discussion: We found that whole genome duplication, gene expansion, and allele loss could be factors affecting the number of NBS-LRR genes in the species, and whole genome duplication is likely to be the main cause of the number of NBS-LRR genes in sugarcane. Meanwhile, we also found a progressive trend of positive selection on NBS-LRR genes. These studies further elucidated the evolutionary pattern of NBS-LRR genes in plants. Transcriptome data from multiple sugarcane diseases revealed that more differentially expressed NBS-LRR genes were derived from S. spontaneum than from S. officinarum in modern sugarcane cultivars, and the proportion was significantly higher than the expected. This finding reveals that S. spontaneum has a greater contribution to disease resistance for modern sugarcane cultivars. In addition, we observed allelespecific expression of seven NBS-LRR genes under leaf scald, and 125 NBS-LRR genes responding to multiple diseases were identified. Finally, we built a plant NBS-LRR gene database to facilitate subsequent analysis and use of NBSLRR genes obtained here. In conclusion, this study complemented and completed the research of plant NBS-LRR genes, and discussed how NBS-LRR genes responding to sugarcane diseases, which provided a guide and genetic resources for further research and utilization of NBS-LRR genes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Jiang, Zhao, Qin, Li and Yang.)

Nitrogen (N) is a vital mineral component that can restrict the growth and development of plants if supplied inappropriately. In order to benefit their growth and development, plants have complex physiological and structural responses to changes in their nitrogen supply. As higher plants have multiple organs with varying functions and nutritional requirements, they coordinate their responses at the whole-plant level based on local and long-distance signaling pathways. It has been suggested that phytohormones are signaling substances in such pathways. The nitrogen signaling pathway is closely associated with phytohormones such as auxin (AUX), abscisic acid (ABA), cytokinins (CKs), ethylene (ETH), brassinosteroid (BR), strigolactones (SLs), jasmonic acid (JA), and salicylic acid (SA). Recent research has shed light on how nitrogen and phytohormones interact to modulate physiology and morphology. This review provides a summary of the research on how phytohormone signaling affects root system architecture (RSA) in response to nitrogen availability. Overall, this review contributes to identifying recent developments in the interaction between phytohormones and N, as well as serving as a foundation for further study.

Predicting urban crowd flow spatial distributions plays a critical role in optimizing urban public safety and traffic congestion management. The spatial dependency between regions and the temporal dynamics of the local crowd flow are two important features in urban crowd flow prediction. However, few studies considered geographic characteristic in terms of spatial features. To fill this gap, we propose an urban crowd flow prediction model integrating geographic characteristics (FPM-geo). First, three geographic characteristics, proximity, functional similarity, and road network connectivity, are fused by a residual multigraph convolution network to model the spatial dependency relationship. Then, a long short-term memory network is applied as a framework to integrate both the temporal dynamic patterns of local crowd flow and the spatial dependency between regions. A 4-day mobile phone dataset validates the effectiveness of the proposed method by comparing it with several widely used approaches. The result shows that the root mean square error decreases by 15.37% compared with those of the typical models with the prediction interval at the 15-min level. The prediction error increases with the crowd flow size in a local area. Moreover, the error reaches the top of the morning peak and the evening peak and slopes down to the bottom at night., (© 2023. The Author(s).)

Introduction: Traditional chemical control methods pose a damaging effect on farmland ecology, and their long-term use has led to the development of pest resistance., Methods: Here, we analyzed the correlations and differences in the microbiome present in the plant and soil of sugarcane cultivars exhibiting different insect resistance to investigate the role played by microbiome in crop insect resistance. We evaluated the microbiome of stems, topsoil, rhizosphere soil, and striped borers obtained from infested stems, as well as soil chemical parameters., Results and Discussion: Results showed that microbiome diversity was higher in stems of insect-resistant plants, and contrast, lower in the soil of resistant plants, with fungi being more pronounced than bacteria. The microbiome in plant stems was almost entirely derived from the soil. The microbiome of insect-susceptible plants and surrounding soil tended to change towards that of insect-resistant plants after insect damage. Insects' microbiome was mainly derived from plant stems and partly from the soil. Available potassium showed an extremely significant correlation with soil microbiome. This study validated the role played by the microbiome ecology of plant-soil-insect system in insect resistance and provided a pre-theoretical basis for crop resistance control., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Li, Liu, Zhao, Su, Zhao, Jiang, Zhao and Yang.)

Background: Sucrose phosphate synthase B (SPSB) gene encoding an important rate-limiting enzyme for sucrose synthesis in sugarcane is mainly expressed on leaves, where its alleles control sucrose synthesis. In this study, genetic variation of SPSB gene represented by different haplotypes in sugarcane was investigated in hybrid clones with high and low sugar content and various accessory species., Results: A total of 39 haplotypes of SPSB gene with 2, 824 bp in size were identified from 18 sugarcane accessions. These haplotypes mainly distributed on Chr3B, Chr3C, and Chr3D according to the AP85-441 reference genome. Single nucleotide polymorphisms (SNPs) and insertion/deletion (InDels) were very dense (42 bp/sequence variation) including 44 transitional and 23 transversional SNPs among the 39 haplotypes. The sequence diversity related Hd, Eta, and Pi values were all lower in clones of high sucrose content (HS) than those in clones of low sucrose content (LS). The evolutionary network analysis showed that about half SPSB haplotypes (19 out of 39) were clustered into one group, including 6 (HAP4, HAP6, HAP7, HAP9, HAP17 and HAP20) haplotypes under positive selection in comparison to HAP26 identified in Badila (S. officinarum), an ancestry noble cane species and under purification selection (except HAP19 under neutral selection) in comparison to HAP18 identified from India1 (S. spontaneum), an ancestry species with low sugar content but high stress tolerance. The average number of haplotypes under positive selection in HS clones was twice as that in LS. Most of the SNPs and InDels sequence variation sites were positively correlated with sucrose and fiber content and negatively correlated with reducing sugar., Conclusions: A total of 39 haplotypes of SPSB gene were identified in this study. Haplotypes potentially associated with high sucrose synthesis efficiency were identified. The mutations of SPSB haplotypes in HS were favorable and tended to be selected and fixed. The results of this study are informative and beneficial to the molecular assisted breeding of sucrose synthesis in sugarcane in the future., (© 2023. The Author(s).)

High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the ' Saccharum Complex', and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of Saccharum (among them, S. robustum , S. sinense , and S. barberi firstly reported in this study) and 2 sugarcane relative species, Tripidium arundinaceum and Narenga porphyrocoma . The plastid phylogenetic signal demonstrated that S. officinarum and S. robustum shared a common ancestor, and that the cytoplasmic origins of S. sinense and S. barberi were much more ancient than the S. offcinarum / S. robustum linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing Saccharum from its relative species, 4 dCAPS markers for distinguishing S. officinarum from S. robustum, and 1 dCAPS marker for distinguishing S. sinense and S. barberi from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in Saccharum and relative species.

Background: Sugarcane (Saccharum) is the most critical sugar crop worldwide. As one of the most enriched transcription factor families in plants, MYB genes display a great potential to contribute to sugarcane improvement by trait modification. We have identified the sugarcane MYB gene family at a whole-genome level through systematic evolution analyses and expression profiling. R2R3-MYB is a large subfamily involved in many plant-specific processes., Results: A total of 202 R2R3-MYB genes (356 alleles) were identified in the polyploid Saccharum spontaneum genomic sequence and classified into 15 subgroups by phylogenetic analysis. The sugarcane MYB family had more members by a comparative analysis in sorghum and significant advantages among most plants, especially grasses. Collinearity analysis revealed that 70% of the SsR2R3-MYB genes had experienced duplication events, logically suggesting the contributors to the MYB gene family expansion. Functional characterization was performed to identify 56 SsR2R3-MYB genes involved in various plant bioprocesses with expression profiling analysis on 60 RNA-seq databases. We identified 22 MYB genes specifically expressed in the stem, of which RT-qPCR validated MYB43, MYB53, MYB65, MYB78, and MYB99. Allelic expression dominance analysis implied the differential expression of alleles might be responsible for the high expression of MYB in the stem. MYB169, MYB181, MYB192 were identified as candidate C 4 photosynthetic regulators by C 4 expression pattern and robust circadian oscillations. Furthermore, stress expression analysis showed that MYB36, MYB48, MYB54, MYB61 actively responded to drought treatment; 19 and 10 MYB genes were involved in response to the sugarcane pokkah boeng and mosaic disease, respectively., Conclusions: This is the first report on genome-wide analysis of the MYB gene family in sugarcane. SsMYBs probably played an essential role in stem development and the adaptation of various stress conditions. The results will provide detailed insights and rich resources to understand the functional diversity of MYB transcription factors and facilitate the breeding of essential traits in sugarcane., (© 2021. The Author(s).)

Sugarcane is of important economic value for producing sugar and bioethanol. Tripidium &nbsp; arundinaceum (old name: Erianthus &nbsp; arundinaceum ) is an intergeneric wild species of sugarcane that has desirable resistance traits for improving sugarcane varieties. However, the scarcity of chromosome markers has hindered the cytogenetic study of T. arundinaceum . Here we applied maize chromosome painting probes (MCPs) to identify chromosomes in sorghum and T. arundinaceum using a repeated fluorescence in situ hybridization (FISH) system. Sequential FISH revealed that these MCPs can be used as reliable chromosome markers for T. arundinaceum , even though T. arundinaceum has diverged from maize over 18 MYs (million years). Using these MCPs, we identified T. arundinaceum chromosomes based on their sequence similarity compared to sorghum and labeled them 1 through 10. Then, the karyotype of T. arundinaceum was established by multiple oligo-FISH. Furthermore, FISH results revealed that 5S rDNA and 35S rDNA are localized on chromosomes 5 and 6, respectively, in T. arundinaceum . Altogether, these results represent an essential step for further cytogenetic research of T. arundinaceum in sugarcane breeding.

Apoptosis signal-regulating kinase 1 (ASK1, MAP3K5), a member of the mitogen-activated protein kinase (MAPK) signaling pathway, is involved in cell survival, differentiation, stress response, and apoptosis. ASK1 kinase inhibition has emerged as a promising therapeutic strategy for inflammatory disease. A series of novel ASK1 inhibitors with 1H-indazole scaffold were designed, synthesized and evaluated for their ASK1 kinase activity and AP1-HEK293 cell inhibitory effect. Systematic structure-activity relationship (SAR) efforts led to the discovery of promising compound 15, which showed excellent in vitro ASK1 kinase activity and potent inhibitory effects on ASK1 in AP1-HEK293 cells. In a tumor necrosis factor-α (TNF-α)-induced HT-29 intestinal epithelial cell model, compound 15 exhibited a significantly protective effect on cell viability comparable to that of GS-4997; moreover, compound 15 exhibited no obvious cytotoxicity against HT-29 cells at concentrations up to 25 μM. Mechanistic research demonstrated that compound 15 suppresses phosphorylation in the ASK1-p38/JNK signaling pathway in HT-29 cells, and regulates the expression levels of apoptosis-related proteins. Altogether, these results show that compound 15 may serve as a potential candidate compound for the treatment of inflammatory bowel disease (IBD)., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Masson SAS. All rights reserved.)

Crop domestication occurred ~10,000-12,000 years ago when humans shifted from a hunter-gatherer to an agrarian society. Crops were domesticated by selecting the traits in wild plant species that were suitable for human use. Research is crucial to elucidate the mechanisms and processes involved in modern crop improvement and breeding. Recent advances in genomics have revolutionized our understanding of crop domestication. In this review, we summarized cutting-edge crop domestication research by presenting its (1) methodologies, (2) current status, (3) applications, and (4) perspectives. Advanced genomics approaches have clarified crop domestication processes and mechanisms, and supported crop improvement.

Background: Piperine is a great lead compound, as a phytopharmaceutical with reported neuroprotective effects in neurodegenerative diseases. HJ105, a piperine derivative with high affinity to Keap1 receptor, attracts increasing attention in Alzheimer's disease (AD) treatment., Purpose: This work mainly aimed to study HJ105's therapeutic effects on Aβ 1-42 -associated AD and the underpinning mechanisms., Methods: In the in vivo part, a rat model of AD was established by bilateral intra-hippocampal administration of aggregated Aβ 1-42 , followed by a month of intragastric HJ105 or donepezil administration. Spatial and learning memories were detected by the Morris water maze assay, passive avoidance learning as well as Y-maze test. The morphology of hippocampal neurons was assessed by hematoxylin-eosin (H&E) staining. In addition, the amounts of the IL-1β and TNF-α were obtained with specific ELISA kits. More importantly, apoptosis-related proteins and factors involved in Nrf2/TXNIP/NLPR3 pathways were detected by Western blot, while the interaction between Keap1 and Nrf2 was assessed by co-immunoprecipitation. In the in vitro part, human neuroblastoma (SH-SY5Y) cells were applied to evaluate the role of HJ105 on Aβ 1-42 -induced neuronal damage., Results: Treatment of HJ105 not only reversed memory impairment, but also protected neurons in the hippocampus by inhibiting Bax/Bcl2 ratio increase. HJ105 decreased TXNIP expression, suppressing NLRP3 inflammasome activation in the hippocampus, which in turn counteracted the upregulation of IL-1β and TNF-α. Notably, HJ105 exerted an inhibitory effect on Keap1-Nrf2 interaction and upregulated nuclear Nrf2, which conversely increased the expression levels of superoxide dismutase, catalase and glutathione peroxidase and downregulated malondialdehyde. Additionally, neurotoxicity induced by Aβ 1-42 in SH-SY5Y cells was alleviated by HJ105., Conclusion: Overall, HJ105 exerts neuroprotective effects in SH-SY5Y cells induced by Aβ 1-42 as well as in experimental rats with AD by decreasing apoptosis, oxidative stress and neuroinflammation, partly via suppression of Keap1-Nrf2 complex generation. HJ105 might represent a promising compound for AD treatment., (Copyright © 2021. Published by Elsevier GmbH.)

Apoptosis signal-regulating kinase 1 (ASK1), a member of the mitogen-activated protein kinase (MAPK) family, is implicated in many human diseases. Here, we describe the structural optimization of hit compound 7 and conduct further structure-activity relationship (SAR) studies that result in the development of compound 19 with a novel indole-2-carboxamide hinge scaffold. Compound 19 displays potent anti-ASK1 kinase activity and stronger inhibitory effect on ASK1 in AP1-HEK293 cells than previously described ASK1 inhibitor GS-4997. Besides improved in vitro activity, compound 19 also exhibits an appropriate in vivo PK profile. In a dextran sulfate sodium (DSS)-induced mouse model of ulcerative colitis (UC), compound 19 shows significant anti-UC efficacy and markedly attenuates DSS-induced body weight loss, colonic shortening, elevation in disease activity index (DAI) and inflammatory cell infiltration in colon tissues. Mechanistically, compound 19 represses the phosphorylation of ASK1-p38/JNK signaling pathways and suppresses the overexpression of inflammatory cytokines. Together, these findings suggest that ASK1 inhibitors can potentially be used as a therapeutic strategy for UC., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Masson SAS. All rights reserved.)

Brain death is the irreversible loss of all the functions of the brain and brainstem. Compared to traditional diagnostic methods of brain death, near-infrared spectroscopy (NIRS) is a noninvasive, objective, cost-effective, and safe way of assessment of brain death. Eighteen brain dead patients and 20 healthy subjects were studied by NIRS, with a multiple-phase protocol at varied fractions of inspired O 2 (FIO 2 ). We found that the changes in the concentration ratios of oxyhemoglobin to deoxyhemoglobin (Δ[HbO 2 ]/Δ[Hb]) in the cerebral cortex of brain dead patients were significantly higher than those of healthy subjects, and its low-to-high FIO 2 phase was most sensitive, with a recommended threshold in the range 1.40-1.50. Our study indicated that NIRS is a promising technology for assessing brain death. The success of this application potentially offers a supplementary technique for the assessment of brain death in real time in order to be able to promptly offer quality-assured donor organs.

Sugarcane (Saccharum spp.) is an important economic crop, supplying up to 80% of the table sugar and ~60% of bio-ethanol worldwide. Due to population growth and dwindling fossil-fuel reserves, the demand for sugar and bio-ethanol requires significant improvement in sugarcane production. Breeding sugarcane cultivars with high-performance agronomic traits is undoubtedly the most efficient way to achieve this goal. Therefore, evaluating agronomic traits and dissecting underlying loci are critically important for this aim steps in providing genetic resources and molecular markers for selection. In this study, we assembled a diversity panel of 236 elite sugarcane germplasms originally collected from 12 countries. We evaluated 28 agronomic traits in the diversity panel with three replicates. The diversity panel was genotyped using amplified fragment length polymorphism markers, and a total of 1,359 markers were generated. Through the genome-wide association study, we identified three markers significantly associated with three traits evaluated at a stringent threshold (P < 0.05 after Bonferroni correction). The genotypes of the three associated markers grouped respective trait values into two distinct groups, supporting the reliability of these markers for breeding selection. Our study provides putative molecular markers linked to agronomic traits for breeding robust sugarcane cultivars. Additionally, this study emphasized the importance of sugarcane germplasm introduced from other countries and suggested that the use of these germplasms in breeding programs depends on local industrial needs., Competing Interests: The authors have declared that no competing interests exist.

It was previously confirmed that the apoptotic and necrotic neurons are found during the acute post-traumatic period, suggesting the induction of apoptosis after traumatic brain injury (TBI). To further explore the involvement of apoptotic factors in TBI, an apoptosis antibody array was conducted to measure the alterations of apoptotic factors in rat brain cortex after TBI. As a result, the Neurological Severity Scale (NSS) scores after TBI were increased, and the cell morphology of the brain cortex was destructed with increased neuronal apoptosis. Furthermore, the caspase-3 activity was increased, and the apoptotic-related factors TNF-α and p53 were up-regulated in the brain cortex. More importantly, in vitro experiments demonstrated that down-regulation of TNF-α in oxygen-glucose deprivation/reoxygenation (OGD/R) cells increased cell viability and decreased apoptosis and the p53 expression. These results suggested the involvement of TNF-α-induced apoptotic signalling pathway by activating p53 in the molecular mechanism of neurological injury., (© 2020 The Authors. Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.)

Kelch-like ECH-associated protein (Keap1)-nuclear factor erythroid-2-related factor 2 (Nrf2) protein-protein interaction has become an important drug target for the treatment of Alzheimer's disease. In this study, we found a novel piperine derivative (HJ22) synthesized by our group with great ability to bind to Keap-1 and activate Keap1-Nrf2-ARE signaling pathway in vitro, driving us to investigate the beneficial effects of HJ22 on ibotenic acid (IBO)-induced neurological disorders in rats and underlying mechanisms. Interestingly, HJ22 significantly ameliorated IBO-induced cognitive impairment in Morris water maze, Y-maze and passive avoidance tests. Moreover, HJ22 significantly attenuated cholinergic dysfunction and neuronal morphological changes via inhibiting apoptotic cell death induced by IBO. Notably, HJ22 inhibited the interaction between Keap1 and Nrf2, and subsequently up-regulated nuclear Nrf2 expression, thereby inhibiting oxidative stress and Thioredoxin-interacting protein (TXNIP)-mediated Nod-like receptor protein 3 (NLRP3) inflammasome activation. These findings demonstrated that HJ22 exhibited potent therapeutic effects against IBO-induced cognitive impairment by alleviating cholinergic damage, oxidative stress, apoptosis and neuroinflammation, which might be partly attributed to its inhibitory activity on Keap1-Nrf2 protein-protein interaction., Competing Interests: Declaration of Competing Interest The authors declare that they have no conflict of interest., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Nod-like receptor protein 3 (NLRP3)-mediated pyroptosis has a causal role in the pathogenesis of gout. P2Y 14 receptor (P2Y 14 R) distributed in immune cells including macrophages is a Gi-coupled receptor that inhibits the synthesis of cAMP, which has been regarded as a potential regulator of inflammatory response. Nevertheless, the role of P2Y 14 R in MSU-induced pyroptosis of macrophages involved in acute gouty arthritis is still unclear. In our present study, P2Y 14 R knockout (P2Y 14 R-KO) disrupted MSU-induced histopathologic changes in rat synoviums, accompanied with a significant inhibition of pyroptotic cell death characterized by Caspase-1/PI double-positive and blockade of NLRP3 inflammasome activation in synovial tissues, which was consistent with that observed in in vitro studies. Owing to the interaction of NLRP3 inflammasome and cAMP, we then investigated the effect of adenylate cyclase activator (Forskolin) on macrophage pyroptosis and gout flare caused by MSU stimulation. The reversal effect of Forskolin verified the negative regulatory role of cAMP in MSU-induced pyroptosis. More importantly, adenylate cyclase inhibitor (SQ22536) intervention led to a reversal of protection attributed to P2Y 14 R deficiency. Findings in air pouch animal models also verified aforementioned experimental results. Our study first identified the role of P2Y 14 R/cAMP/NLRP3 signaling pathway in acute gouty arthritis, which provides a novel insight into the pathological mechanisms of pyroptosis-related diseases.

Key Message: A total of 33 additive stem rot QTLs were identified in peanut genome with nine of them consistently detected in multiple years or locations. And 12 pairs of epistatic QTLs were firstly reported for peanut stem rot disease. Stem rot in peanut (Arachis hypogaea) is caused by the Sclerotium rolfsii and can result in great economic loss during production. In this study, a recombinant inbred line population from the cross between NC 3033 (stem rot resistant) and Tifrunner (stem rot susceptible) that consists of 156 lines was genotyped by using 58 K peanut single nucleotide polymorphism (SNP) array and phenotyped for stem rot resistance at multiple locations and in multiple years. A linkage map consisting of 1451 SNPs and 73 simple sequence repeat (SSR) markers was constructed. A total of 33 additive quantitative trait loci (QTLs) for stem rot resistance were detected, and six of them with phenotypic variance explained of over 10% (qSR.A01-2, qSR.A01-5, qSR.A05/B05-1, qSR.A05/B05-2, qSR.A07/B07-1 and qSR.B05-1) can be consistently detected in multiple years or locations. Besides, 12 pairs of QTLs with epistatic (additive × additive) interaction were identified. An additive QTL qSR.A01-2 also with an epistatic effect interacted with a novel locus qSR.B07&#95;1-1 to affect the percentage of asymptomatic plants in a row. A total of 193 candidate genes within 38 stem rot QTLs intervals were annotated with functions of biotic stress resistance such as chitinase, ethylene-responsive transcription factors and pathogenesis-related proteins. The identified stem rot resistance QTLs, candidate genes, along with the associated SNP markers in this study, will benefit peanut molecular breeding programs for improving stem rot resistance.

Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of sugar and approximately 60% of biofuel globally. To meet the increased demand for sugar and biofuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield traits. Therefore, dissection of causal DNA sequence variants is of great importance, as it provides genetic resources and fundamental information for crop improvement. In this study, we analyzed nine yield traits in a sugarcane diversity panel consisting of 308 accessions primarily selected from the World Collection of Sugarcane and Related Grasses. By genotyping the diversity panel via target enrichment sequencing, we identified a large number of sequence variants. Genome-wide association studies between the markers and traits were conducted, taking dosages and gene actions into consideration. In total, 217 nonredundant markers and 225 candidate genes were identified to be significantly associated with the yield traits, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 ROHs and found that the occurrence of ROHs in the genome were nonrandom and probably under selection. The ROHs were associated with total weight and dry weight, and high ROHs resulted in a decrease in the two traits. This study suggests that genomic inbreeding has led to negative impacts on sugarcane yield., (© 2020 The Authors. The Plant Genome published by Wiley Periodicals, Inc. on behalf of Crop Science Society of America.)

The loss of urban vitality is an important problem in the development of urban central areas. Analyzing the correlation between urban built environment and urban vitality supports urban planning and design. However, current research excludes the study of how consistent built environment factors affect urban vitality of cities with different development situations. Therefore, using social media check-in data, this paper measures neighborhood vibrancy in urban central areas in Beijing and Chengdu, China. Four levels of spatial information were used to measure the built environment: regulatory planning management unit (RPMU), land use, road network, and building. Regression model is used to quantify the correlation between urban vitality and the built environment of these two cities. The study found a strong correlation between built environment factors and urban vitality. Among the built environment factors, points of interest (POI) diversity and public transport accessibility indicators were strongly positively correlated with neighborhood vibrancy. However, the density indicators had totally different effects on urban vitality of cities with different development situations, which is excluded in existing studies. This research strengthens the practical understanding of the compact city concept, and can support the design and planning of urban built environment.

Key Message: An Axiom Sugarcane100K SNP array has been designed and successfully utilized to construct the sugarcane genetic map and to identify the QTLs associated with SCYLV resistance. To accelerate genetic studies in sugarcane, an Axiom Sugarcane100K single-nucleotide polymorphism (SNP) array was designed and customized in this study. Target enrichment sequencing 300 sugarcane accessions selected from the world collection of sugarcane and related grass species yielded more than four million SNPs, from which a total of 31,449 single-dose (SD) SNPs and 68,648 low-dosage (33,277 SD and 35,371 double dose) SNPs from two datasets, respectively, were selected and tiled on Affymetrix Axiom SNP array. Most of selected SNPs (91.77%) were located within genic regions (12,935 genes), with an average of 7.1 SNPs/gene according to sorghum gene models. This array was used to genotype 469 sugarcane clones, including one F 1 population derived from the cross between Green German and IND81-146, one selfing population derived from CP80-1827, and 11 diverse sugarcane accessions as controls. Results of genotyping revealed a high polymorphic SNP rate (77.04%) among the 469 samples. Three linkage maps were constructed by using SD SNP markers, including a genetic map for Green German with 3482 SD SNP markers spanning 3336 cM, a map for IND81-146 with 1513 SD SNP markers spanning 2615 cM, and a map for CP80-1827 with 536 SD SNP markers spanning 3651 cM. Quantitative trait loci (QTL) analysis identified 18 QTLs controlling Sugarcane yellow leaf virus resistance segregating in the two mapping populations, harboring 27 disease-resistant genes. This study demonstrated the successful development and utilization of a SNP array as an efficient genetic tool for high-throughput genotyping in highly polyploid sugarcane.

Automatic Identification System (AIS) data could support ship movement analysis, and maritime network construction and dynamic analysis. This study examines the global maritime network dynamics from multi-layers (bulk, container, and tanker) and multidimensional (e.g., point, link, and network) structure perspectives. A spatial-temporal framework is introduced to construct and analyze the global maritime transportation network dynamics by means of big trajectory data. Transport capacity and stability are exploited to infer spatial-temporal dynamics of system nodes and links. Maritime network structure changes and traffic flow dynamics grouping are then possible to extract. This enables the global maritime network between 2013 and 2016 to be investigated, and the differences between the countries along the 21st-century Maritime Silk Road and other countries, as well as the differences between before and after included by 21st-century Maritime Silk Road to be revealed. Study results indicate that certain countries, such as China, Singapore, Republic of Korea, Australia, and United Arab Emirates, build new corresponding shipping relationships with some ports of countries along the Silk Road and these new linkages carry significant traffic flow. The shipping dynamics exhibit interesting geographical and spatial variations. This study is meaningful to policy formulation, such as cooperation and reorientation among international ports, evaluating the adaptability of a changing traffic flow and navigation environment, and integration of the maritime economy and transportation systems.

Sugarcane (Saccharum spp.) supplies globally ∼80% of table sugar and 60% of bioethanol. Sugarcane orange rust and Sugarcane yellow leaf virus (SCYLV) are major sugarcane diseases, causing up to 50 and 40% yield losses, respectively. Sugarcane cultivars resistant to these diseases are needed to sustain sugarcane production in several regions. Dissecting DNA sequence variants controlling disease resistance provides a valuable tool for fulfilling a breeding strategy to develop resistant cultivars. In this study, we evaluated disease reactions to orange rust and SCYLV of a sugarcane diversity panel in repeated trials. We conducted a genome-wide association study between high-density markers and disease resistance reactions. We identified 91 putative DNA markers and 82 candidate genes significantly associated with resistance to one of the two diseases. These provide an important genetic resource for finding genes and molecular markers for disease resistance. Our results emphasized the importance of utilizing a wide germplasm collection for breeding resistant sugarcane cultivars.

Traumatic brain injury (TBI) is the most common cause of death and permanent disability in people aged <45, and is associated with secondary brain injury and bleed progression, resulting in increased morbidity and mortality. TBI may also induce innate host defense responses characterized by activation of resident microglia and astrocytes, brain microvascular endothelial cells and peripheral blood monocytes. In the present study, 34 patients with moderate‑to‑severe traumatic brain injury were randomly divided into two groups, including a 7.5% hypertonic saline (HS) treatment group (4 ml/kg) and 3% HS treatment group (4 ml/kg). The results demonstrated that treatment with 7.5% HS decreased the intracranial pressure and improved coagulofibrinolytic homeostasis. Analysis of the monocyte subsets revealed significant reduction in the proportion of cluster of differentiation (CD)14++CD16+ circulating inflammatory monocytes in the 7.5% HS group. In addition, 7.5% HS treatment downregulated the expression of long non‑coding (lnc) RNA2448‑11 and lncRNA1403 in the peripheral blood mononuclear cells of patients with TBI. Using reverse transcription‑quantitative polymerase chain reaction, it was determined that 7.5% HS regulated the expression of tumor necrosis factor‑α, interleukin‑1β, transforming growth factor‑β and thrombomodulin, which are the target genes of lncRNA2448‑11 and lncRNA1403. These results indicated that 7.5% HS improved the intracranial pressure and coagulofibrinolytic homeostasis by modulating the phenotype of monocytes through lncRNA2448‑11 and lncRNA1403. These findings provided evidence that initial resuscitation with HS imparts functional changes to inflammatory cells following TBI, thereby reducing potential neuroinflammatory events associated with secondary brain injury.

Sugarcane (Saccharum spp.) is a highly energy-efficient crop primarily for sugar and bio-ethanol production. Sugarcane genetics and cultivar improvement have been extremely challenging largely due to its complex genomes with high polyploidy levels. In this study, we deeply sequenced the coding regions of 307 sugarcane germplasm accessions. Nearly five million sequence variations were catalogued. The average of 98× sequence depth enabled different allele dosages of sequence variation to be differentiated in this polyploid collection. With selected high-quality genome-wide SNPs, we performed population genomic studies and environmental association analysis. Results illustrated that the ancient sugarcane hybrids, S. barberi and S. sinense, and modern sugarcane hybrids are significantly different in terms of genomic compositions, hybridization processes and their potential ancestry contributors. Linkage disequilibrium (LD) analysis showed a large extent of LD in sugarcane, with 962.4 Kbp, 2739.2 Kbp and 3573.6 Kbp for S. spontaneum, S. officinarum and modern S. hybrids respectively. Candidate selective sweep regions and genes were identified during domestication and historical selection processes of sugarcane in addition to genes associated with environmental variables at the original locations of the collection. This research provided an extensive amount of genomic resources for sugarcane community and the in-depth population genomic analyses shed light on the breeding and evolution history of sugarcane, a highly polyploid species., (© 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Aim: To evaluate the effect of umbilical cord derived mesenchymal stem cells (UC-MSCs) transplantation on traumatic brain injury (TBI)., Material and Methods: UC-MSCs were isolated from human umbilical cord and TBI rat model was constructed. 30 male SD rats were randomly divided into 3 groups: control group, TBI group and MSCs transplantation group. Rats in MSCs group received the injection of a total of 1.5 Ć- 106 MSCs (25 Ī¼l) via ventricle at operated ventricular coordinates (0 at bregma, 1.5 mm at lateral, 1.1 mm at behind, 4.5 mm in depth)., Results: 80% confluence of cells was formed from tissue at day 10 and the amount of CD90, CD73, CD105 positive cells increased correspondingly. In TBI model, clear hyperemia, edema and obvious infiltration of inflammatory cells in brain tissue were found. However, the manifestations were alleviated after the treatment of MSCs. In MSCs group, GFP in the brain tissue and the area around the vessels were found after the injection, while the expression levels of micro-vessel density (MVD), brain-derived neurotrophic factor (BDNF) and glial fibrillary acidic protein (GFAP) were elevated., Conclusion: UC-MSCs transplantation for treatment of acute TBI could effectively reduce the injury and improve the vascular reconstruction.

In the version of this article originally published, the accession codes listed in the data availability section were incorrect and the section was incomplete. The text for this section should have read "The genome assembly and gene annotation have been deposited in the NCBI database under accession number QVOL00000000, BioProject number PRJNA483885 and BioSample number SAMN09753102. The data can also be downloaded from the following link: http://www.life.illinois.edu/ming/downloads/Spontaneum&#95;genome/ ." The errors have been corrected in the HTML and PDF versions of the article.

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.