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A catalog of genetic variation in a crop species facilitates marker-assisted breeding, gene mapping and analysis of elite traits. Xu et al . resequenced 40 cultivated and 10 wild rice accessions to >15 × coverage, yielding 6.5 million single-nucleotide polymorphisms and 808,000 small insertions and deletions. Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors ( Oryza rufipogon and Oryza nivara ) to >15 × raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.

KIF22, also known as kinesin-like DNA-binding protein (Kid), is a member of the Kinesin superfamily proteins (KIFs). Available evidence indicated that KIF22 was associated with cancer occurrence and development. However, the functions and underlying mechanisms of KIF22 in carcinogenesis and cancer progression remain largely unknown. In this study, we examined the expression profile and methylation status of KIF22 in different cancers, as well as its associations with prognosis, tumor stemness, genomic heterogeneity, immune evasion, immune infiltration, and therapeutic response in various tumor types. The results demonstrated that the expression level of KIF22 was higher in tumors than nontumor tissues and had strong relationships with prognosis, genomic heterogeneity, tumor stemness, neoantigen, ESTIMATE, and immune infiltration. KIF22 methylation status showed strong relationships with immunomodulators and chemokines. KIF22 had a significant relevance with drug susceptibility and could be a useful biomarker for forecasting survival probability and therapeutic reaction. Furthermore, KIF22 interaction and coexpression networks were mainly involved in cell division, cell cycle, DNA repair, and antigen processing and presentation. KIF22 could be used as a pan-cancer biomarker for clinical diagnosis, therapeutic schedule, prognosis, and cancer monitoring.

Introduction/background The specific role of efferocytosis-related long noncoding RNAs (ERLncRNAs) in Clear Cell Renal Cell Carcinoma (ccRCC) has not been thoroughly examined. This study aims to identify and validate a signature of ERLncRNAs for prognostic prediction and characterization of the immune landscape in individuals with ccRCC. Materials and methods Analysis of ccRCC samples was conducted by utilizing clinical and RNA sequencing information obtained from The Cancer Genome Atlas (TCGA). Pearson correlation analysis was utilized to identify lncRNAs associated with efferocytosis, which was then used to create a new prognostic model through univariate Cox regression, Least Absolute Shrinkage and Selection Operator (LASSO) regression, and stepwise multivariate Cox analysis. In order to investigate the biological significance, we performed a functional enrichment analysis to assess how well the model predicts outcomes. Differences in the immune landscape were observed through a comparison of immune cell infiltration, tumor mutational burden (TMB), and tumor microenvironment (TME) characteristics. Following this, drug sensitivity analysis was conducted. Results This led to the identification of a unique signature consisting of seven ERLncRNAs (LINC01615, RUNX3-AS1, FOXD2-AS1, AC002070.1, LINC02747, LINC00944, and AC092296.1). Model performance was measured by Kaplan–Meier curves and receiver operating characteristic (ROC) curves. The nomogram and C-index provided additional validation of the strong correlation between the risk signature and clinical decision-making . Conclusion On the whole, our innovative signature exhibits potential for prognostic prediction and assessment of immunotherapeutic response in patients with ccRCC.

The underwater curing agents have demonstrated promising potential in various applications, especially in underwater repair engineering, yet have proven considerable challenging. Here, we report a cardanol-based curing agent for epoxy resin that achieves robust adhesion to steel and concrete substrates both in air and underwater. Cardanol, paraformaldehyde, and -phenyldimethylamine are selected as the polymeric monomers to synthesize curing agent by Mannich reaction in the absence of chemical cross-linker agents. The coating is completely cured within 46 ± 1 min in air and 54 ± 2 min under water with an adhesion of 0 or 1 and a hardness of 5H. The impact strength, shear strength, and tensile strength of coating on underwater concrete were 9.58 ± 0.41 kJ·m , 13.1 ± 0.3, and 10.5 ± 0.2 MPa, respectively, demonstrating exceptional flexibility and mechanical strength as well as favorable hydrophobicity. This work paves the way for the rehabilitation of underwater drainage network for urban infrastructure and water conservancy projects.

Lubrication and friction conditions vary with deformation during metal forming processes. Significant macro-variations can be observed when a threshold of deformation is reached. This study shows that during the cold compression processing of #45 (AISI 1045) steel rings, the magnitude of friction and surface roughness ( R a ) changes significantly upon reaching a 45% reduction in ring height. For example, the R a of compressed ring specimens increased by approximately 55% immediately before and after reaching this threshold, compared to an 18% or 25%variation over a 35%-45% or a 45%-55% reduction in height, respectively. The ring compression test conducted by this study indicates that the Coulomb friction coefficient μ and Tresca friction factor m are 0.105 and 0.22, respectively, when the reduction in height is less than 45%; and 0.11 and 0.24, respectively, when the reduction in height is greater than 45%.

Aquatic macrophytes are a vital component of lake ecosystems, profoundly influencing ecosystem structure and function. Under future scenarios of more frequent extreme floods and intensified lake eutrophication, aquatic macrophytes will face increasing challenges. Therefore, understanding aquatic macrophyte responses to flood disturbances and nutrient enrichment is crucial for predicting future vegetation dynamics in lake ecosystems. This study focuses on Huangmaotan Lake, a Yangtze River floodplain lake, where we reconstructed 200-year successional trajectories of macrophyte communities and their driving mechanisms. With a multiproxy approach we analyzed a well-dated sediment core incorporating plant macrofossils, grain size, nutrient elements, heavy metals, and historical flood records from the watershed. The results demonstrate a significant shift in the macrophyte community, from species that existed before 1914 to species that existed by 2020. Unlike the widespread macrophyte degradation seen in most regional lakes, this lake has maintained clear-water plant dominance and experienced continuous vegetation expansion over the past 50 years. We attribute this to the interrelated effects of floods and the enrichment of ecosystems with nutrients. Specifically, our findings suggest that nutrient enrichment can mitigate the stress effects of floods on aquatic macrophytes, while flood disturbances help reduce excess nutrient concentrations in the water column. These findings offer applicable insights for aquatic vegetation restoration in the Yangtze River floodplain and other comparable lake systems worldwide.

Autophagy acts as a pivotal innate immune response against infection. Some virulence effectors subvert the host autophagic machinery to escape the surveillance of autophagy. The mechanism by which pathogens interact with host autophagy remains mostly unclear. However, traditional strategies often have difficulty identifying host proteins that interact with effectors due to the weak, dynamic, and transient nature of these interactions. Here, we found that Enteropathogenic Escherichia coli (EPEC) regulates autophagosome formation in host cells dependent on effector NleE. The 26S Proteasome Regulatory Subunit 10 (PSMD10) was identified as a direct interaction partner of NleE in living cells by employing genetically incorporated crosslinkers. Pairwise chemical crosslinking revealed that NleE interacts with the N-terminus of PSMD10. We demonstrated that PSMD10 homodimerization is necessary for its interaction with ATG7 and promotion of autophagy, but not necessary for PSMD10 interaction with ATG12. Therefore, NleE-mediated PSMD10 in monomeric state attenuates host autophagosome formation. Our study reveals the mechanism through which EPEC attenuates host autophagy activity.

Identification of genomic structural variation from short-read sequencing data is typically accomplished by mapping reads to a reference genome. Li et al . show that de novo assembly of the reads followed by whole-genome alignment to the reference is a more comprehensive method that can also resolve complex rearrangements. Here we use whole-genome de novo assembly of second-generation sequencing reads to map structural variation (SV) in an Asian genome and an African genome. Our approach identifies small- and intermediate-size homozygous variants (1–50 kb) including insertions, deletions, inversions and their precise breakpoints, and in contrast to other methods, can resolve complex rearrangements. In total, we identified 277,243 SVs ranging in length from 1–23 kb. Validation using computational and experimental methods suggests that we achieve overall <6% false-positive rate and <10% false-negative rate in genomic regions that can be assembled, which outperforms other methods. Analysis of the SVs in the genomes of 106 individuals sequenced as part of the 1000 Genomes Project suggests that SVs account for a greater fraction of the diversity between individuals than do single-nucleotide polymorphisms (SNPs). These findings demonstrate that whole-genome de novo assembly is a feasible approach to deriving more comprehensive maps of genetic variation.

The high frequency double-servo direct drive rotary valve (DDRV) stated in this paper put forward a new kind of drive method and novel structure satisfied highly adjusting reversal frequency and adequate flow as well. The basic structure and working principle of the new type valve were explained at first. Theoretical analysis and calculation of the DDRV were conduct to study the mathematical model on fluid force and torque. A high linear correlation of flow rate and opening of valve port was achieved, and the hydraulic simulation based on AMESim is carried out as evaluation and validation for the theoretical calculation. In addition, the preliminary experiment laid emphasis on the reversing function of DDRV at different working frequency like 80 Hz and 200 Hz and both the simulated and experimental results show a relatively satisfying performance.

In this study, the gap viscous loss of a self-designed automotive electronic water pump is analyzed and discussed through CFD simulation (two models) and theoretical methods. The multi-objective optimization design incorporating the gap viscous loss factor into the electronic water pump motor is realized. Each method indicates that the gap viscous loss value of the electronic water pump is negatively correlated with the gap diameter. However, the laminar flow equation is obviously not applicable to the electronic water pump in this study. The hydraulic performance of the pump is basically not affected by the internal flow channel. In addition, a set of motors with different air gap diameters matching the pump shaft power was simulated. A conclusion is drawn that the optimal gap length is shifted after considering the gap viscous loss factor, and the actual rated point efficiency after considering the gap viscous loss factor is higher than that of the prototype motor. The magnitude of the boosting efficiency is related to factors affecting the gap viscous loss value such as glycol concentration. A regression model with a 95% confidence level was developed by response surface methodology to predict motor performance. Compared with the prototype motor, the cogging torque of the motor after multi-objective optimization is reduced by more than 60%, and the rated point efficiency is increased by 0.72%. Sensitivity analysis was applied to demonstrate the stability of the results after weight changes. Finally, the simulation results of this work are verified by experiments.