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Abstract Elucidating cellular architecture and cell-type evolution across species is central to understanding immune system function and susceptibility to disease. Adaptive immunity is a shared trait of the common ancestor of cartilaginous and bony fishes. However, evolutionary features of lymphocytes in these two jawed vertebrates remain unclear. Here, we present a single-cell RNA sequencing atlas of immune cells from cartilaginous (white-spotted bamboo shark) and bony (zebrafish and Chinese tongue sole) fishes. Cross-species comparisons show that the same cell types across different species exhibit similar transcriptional profiles. In the bamboo shark, we identify a phagocytic B cell population expressing several pattern recognition receptors, as well as a T cell sub-cluster co-expressing both T and B cell markers. In contrast to a division by function in the bony fishes, we show close linkage and poor functional specialization among lymphocytes in the cartilaginous fish. Our cross-species single-cell comparison presents a resource for uncovering the origin and evolution of the gnathostome immune system.

A six-color fluorescent multiplex amplification system for 31 Y-chromosomal short tandem repeats (Y-STRs) (DYS19, DYS390, DYS391, DYF399S1, DYF404S1, DYS439, DYS444, DYS449, DYS452, DYS456, DYS458, DYS460, DYS481, DYS508, DYS513, DYS516, DYS518, DYS543, DYS547, DYS549, DYS552, DYS557, DYS570, DYS576, DYS612, DYS622, DYS626, DYS627, DYS630, DYS635, and Y-GATA-A10) was developed for investigating the mutation rates of 31 highly mutated Y-STR genes in the Han population of northern China. The mutation rates of the 31 highly mutated Y-STRs were calculated using the father–son pair study method after typing 526 Northern Han father–son pairs with this system. Statistically, 148 Y-STR mutations were found, with mutation rates ranging from 0 (95% confidence interval [CI] 0 to 9.0 × 10−3, DYS622) to 7.0 × 10−2 (95% CI 5.1 × 10−2 to 9.7 × 10−2, DYF399S1). Out of these, 126 father–son pairs were successfully identified, with a distinction rate of 24.0% (95% CI 20.4%–27.9%). The ability of the 31 highly mutated Y-STRs to distinguish closely related males from the same paternal lineage in the Northern Han population is extremely valuable for criminal investigations and other purposes.

Abstract The abundant genetic variation harbored by wild rice (Oryza rufipogon) has provided a reservoir of useful genes for rice breeding. However, the genome of wild rice has not yet been comprehensively assessed. Here, we report the haplotype-resolved gapless genome assembly and annotation of wild rice Y476. In addition, we develop two sets of chromosome segment substitution lines (CSSLs) using Y476 as the donor parent and cultivated rice as the recurrent parents. By analyzing the gapless reference genome and CSSL population, we identify 254 QTLs associated with agronomic traits, biotic and abiotic stresses. We clone a receptor-like kinase gene associated with rice blast resistance and confirm its wild rice allele improves rice blast resistance. Collectively, our study provides a haplotype-resolved gapless reference genome and demonstrates a highly efficient platform for gene identification from wild rice.

Abstract Chili pepper (Capsicum) is known for its unique fruit pungency due to the presence of capsaicinoids. The evolutionary history of capsaicinoid biosynthesis and the mechanism of their tissue specificity remain obscure due to the lack of high-quality Capsicum genomes. Here, we report two telomere-to-telomere (T2T) gap-free genomes of C. annuum and its wild nonpungent relative C. rhomboideum to investigate the evolution of fruit pungency in chili peppers. We precisely delineate Capsicum centromeres, which lack high-copy tandem repeats but are extensively invaded by CRM retrotransposons. Through phylogenomic analyses, we estimate the evolutionary timing of capsaicinoid biosynthesis. We reveal disrupted coding and regulatory regions of key biosynthesis genes in nonpungent species. We also find conserved placenta-specific accessible chromatin regions, which likely allow for tissue-specific biosynthetic gene coregulation and capsaicinoid accumulation. These T2T genomic resources will accelerate chili pepper genetic improvement and help to understand Capsicum genome evolution.

Abstract Pancreatic cancer is a malignant tumor of the digestive system. It is highly aggressive, easily metastasizes, and extremely difficult to treat. This study aimed to analyze the genes that might regulate pancreatic cancer migration to provide an essential basis for the prognostic assessment of pancreatic cancer and individualized treatment. A CRISPR knockout library directed against 915 murine genes was transfected into TB 32047 cell line to screen which gene loss promoted cell migration. Next-generation sequencing and PinAPL.py- analysis was performed to identify candidate genes. We then assessed the effect of serine/threonine kinase 11 (STK11) knockout on pancreatic cancer by wound-healing assay, chick agnosia (CAM) assay, and orthotopic mouse pancreatic cancer model. We performed RNA sequence and Western blotting for mechanistic studies to identify and verify the pathways. After accelerated Transwell migration screening, STK11 was identified as one of the top candidate genes. Further experiments showed that targeted knockout of STK11 promoted the cell migration and increased liver metastasis in mice. Mechanistic analyses revealed that STK11 knockout influences blood vessel morphogenesis and is closely associated with the enhanced expression of phosphodiesterases (PDEs), especially PDE4D, PDE4B, and PDE10A. PDE4 inhibitor Roflumilast inhibited STK11-KO cell migration and tumor size, further demonstrating that PDEs are essential for STK11-deficient cell migration. Our findings support the adoption of therapeutic strategies, including Roflumilast, for patients with STK11-mutated pancreatic cancer in order to improve treatment efficacy and ultimately prolong survival.

Abstract Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.

The pearlite phase transition behavior of the high-carbon steel (0.82% C) under different holding temperatures (1050 °C and 1450 °C) and cooling rates (60, 300 and 600 °C/min）were investigated using a confocal laser scanning microscope (CLSM). The phase diagram of the researched steel in an equilibrium state was calculated by JMatPro software, and the identifications of the pearlite lamellar spacing and dislocation density were conducted by SEM and TEM analysis, respectively. The in situ observation showed that the pearlite formed at the grain boundary and grew into austenite grains. As the cooling rate increased, the beginning and finishing temperature of pearlite transition moved in a lower direction as a whole. Compared with the normal heat treatment of 1050 °C, the pearlite formation temperature increased by 30 °C with a holding temperature of 1450 °C at the same cooling rate of 60 °C/min, which was contributed to the enhancement of dislocation density along the grain boundary. In addition, the liner relationship between average phase transition temperature and reciprocal of pearlite lamellar spacing was obtained.

Triticeae, the wheatgrass tribe, includes several major cereal crops and their wild relatives. Major crops within the Triticeae are wheat, barley and rye which are important for human consumption, animal feed, and rangeland protection. Species within this tribe are known for their large genomes and complex genetic histories. Powered by recent advances in sequencing technology, researchers worldwide have made progress in elucidating the genomes of Triticeae crops. In addition to assemblies of high-quality reference genomes, pan-genome studies have just started to capture the genomic diversities of these species, shedding light on our understanding of the genetic basis of domestication and environmental adaptation of Triticeae crops. In this review, we focus on recent signs of progress in genome sequencing, pan-genome analyses, and resequencing analysis of Triticeae crops. We also propose future research avenues in Triticeae crop genomes, including identifying genome structure variations, the association of genomic regions with desired traits, mining functions of the non-coding area, introgression of high-quality genes from wild Triticeae resources, genome editing, and integration of genomic resources.

With the emergence of various new power systems, accurate wind power prediction plays a critical role in their safety and stability. However, due to the historical wind power data with few samples, it is difficult to ensure the accuracy of power system prediction for new wind farms. At the same time, wind power data show significant uncertainty and fluctuation. To address this issue, it is proposed in this research to build a novel few-sample wind power prediction model based on the least-square generative adversarial network (LSGAN) and quadratic mode decomposition (QMD). Firstly, a small amount of original wind power data are generated to improve the data by least-square generative adversarial network, which solves the error in prediction with limited sample data. Secondly, a quadratic mode decomposition method based on ensemble empirical mode decomposition (EEMD) and variational mode decomposition (VMD) is developed to address the instability of wind power data and extract hidden temporal characteristics. Specifically, ensemble empirical mode decomposition decomposes the data once to obtain a set of intrinsic mode functions (IMFs), and then variational mode decomposition is used to decompose the fuzzy irregular IMF1 function twice. Finally, a bidirectional long short-term memory network (BiLSTM) based on particle swarm optimization (PSO) is applied to predict wind power data. The LSGAN-QMD-PSO-BiLSTM model proposed in this research is verified on a wind farm located in Spain, which indicates that the proposed model achieves the lowest root mean square error (RMSE) and mean absolute error (MAE) errors of 100.6577 and 66.5175 kW, along with the highest R2 of 0.9639.

High-speed elevator systems comprise numerous components, and vibration issues are prevalent. The evident non-linear behavior resulting from changes in the wire rope length adds complexity to the investigation of elevator dynamics issues. This paper investigates dynamics modeling and numerical solution methods for longitudinal vibrations in a typical high-speed elevator system. The primary contributions of this paper include constructing a dynamics model for high-speed elevators using a substructure dynamics modeling approach. This model incorporates Newton’s law and the Lagrange equation to comprehensively represent the dynamics of the elevator car, car frame, traction system, and tension system. Additionally, a non-linear dynamics model of the steel wire rope is developed using the centralized mass method. This paper also presents an algorithm to solve the time-domain dynamics based on the variable-step-length Runge–Kutta method. Furthermore, it investigates the non-linear dynamics of elevators considering variations in the elevator’s intrinsic frequency and different elevator control strategies, focusing on the response characteristics of high-speed elevator dynamics. The findings of this thesis hold significant importance in the field of high-speed elevator dynamics. They aid in the design and debugging of high-speed elevator systems and serve as a foundation for future research into the non-linear aspects of elevators.

MicroRNAs (miRNAs) are trans-acting small regulatory RNAs that work coordinately with transcription factors (TFs) to shape the repertoire of cellular mRNAs available for translation. Despite our growing knowledge of individual plant miRNAs, their global roles in gene regulatory networks remain mostly unassessed. Based on interactions obtained from public databases and curated from the literature, we reconstructed an integrated miRNA network in Arabidopsis that includes 66 core TFs, 318 miRNAs, and 1712 downstream genes. We found that miRNAs occupy distinct niches and enrich miRNA-containing feed-forward loops (FFLs), particularly those with miRNAs as intermediate nodes. Further analyses revealed that miRNA-containing FFLs coordinate TFs located in different hierarchical layers and that intertwined miRNA-containing FFLs are associated with party and date miRNA hubs. Using the date hub MIR858A as an example, we performed detailed molecular and genetic analyses of three interconnected miRNA-containing FFLs. These analyses revealed individual functions of the selected miRNA-containing FFLs and elucidated how the date hub miRNA fulfills multiple regulatory roles. Collectively, our findings highlight the prevalence and importance of miRNA-containing FFLs, and provide new insights into the design principles and control logics of miRNA regulatory networks governing gene expression programs in plants.

Key points 1. t-SNE instructed transcriptomic stratification discriminates FAB subgroups of AML. 2. Potential association of the prioritized genes with Venetoclax resistance at single-cell resolution.

Abstract Background Heterosis is a phenomenon that hybrids show superior performance over their parents. The successful utilization of heterosis has greatly improved rice productivity, but the molecular basis of heterosis remains largely unclear. Results Here, the transcriptomes of young panicles and leaves of the two widely grown two-line super hybrid rice varieties (Jing-Liang-You-Hua-Zhan (JLYHZ) and Long-Liang-You-Hua-Zhan (LLYHZ)) and their parents were analyzed by RNA-seq. Transcriptome profiling of the hybrids revealed 1,778 ~ 9,404 differentially expressed genes (DEGs) in two tissues, which were identified by comparing with their parents. GO, and KEGG enrichment analysis showed that the pathways significantly enriched in both tissues of two hybrids were all related to yield and resistance, like circadian rhythm (GO:0,007,623), response to water deprivation (GO:0,009,414), and photosynthetic genes (osa00196). Allele-specific expression genes (ASEGs) were also identified in hybrids. The ASEGs were most significantly enriched in ionotropic glutamate receptor signaling pathway, which was hypothesized to be potential amino acid sensors in plants. Moreover, the ASEGs were also differentially expressed between parents. The number of variations in ASEGs is higher than expected, especially for large effect variations. The DEGs and ASEGs are the potential reasons for the formation of heterosis in the two elite super hybrid rice. Conclusions Our results provide a comprehensive understanding of the heterosis of two-line super hybrid rice and facilitate the exploitation of heterosis in hybrid rice breeding with high yield heterosis.

Seeds are an indispensable part of the flowering plant life cycle and a critical determinant of agricultural production. Distinct differences in the anatomy and morphology of seeds separate monocots and dicots. Although some progress has been made with respect to understanding seed development in Arabidopsis, the transcriptomic features of monocotyledon seeds at the cellular level are much less understood. Since most important cereal crops, such as rice, maize, and wheat, are monocots, it is essential to study transcriptional differentiation and heterogeneity during seed development at a finer scale. Here, we present single-nucleus RNA sequencing (snRNA-seq) results of over three thousand nuclei from caryopses of the rice cultivars Nipponbare and 9311 and their intersubspecies F1 hybrid. A transcriptomics atlas that covers most of the cell types present during the early developmental stage of rice caryopses was successfully constructed. Additionally, novel specific marker genes were identified for each nuclear cluster in the rice caryopsis. Moreover, with a focus on rice endosperm, the differentiation trajectory of endosperm subclusters was reconstructed to reveal the developmental process. Allele-specific expression (ASE) profiling in endosperm revealed 345 genes with ASE (ASEGs). Further pairwise comparisons of the differentially expressed genes (DEGs) in each endosperm cluster among the three rice samples demonstrated transcriptional divergence. Our research reveals differentiation in rice caryopsis from the single-nucleus perspective and provides valuable resources to facilitate clarification of the molecular mechanism underlying caryopsis development in rice and other monocots.

PurposeAdjacent segment degeneration (ASD) following lumbar fusion is technically challenging for spine surgeons. Posterolateral open fusion surgery with pedicle screw fixation is an effective way to treat symptomatic ASD with favorable clinical outcomes; however, it is associated with an increased morbidity rate. Therefore, minimally invasive spine surgery is advocated. This study was designed to compare clinical outcomes among patients with symptomatic ASD who underwent percutaneous transforaminal endoscopic discectomy (PTED) with the transforaminal approach, posterior lumbar interbody fusion (PLIF) with cortical bone trajectory screw fixation (CBT-PLIF), and PLIF with traditional trajectory screw fixation (TT-PLIF).MethodsA retrospective study was conductedon 46 patients (26 men and 20 women; average age 60.8 ± 6.78 years) with symptomatic ASD. The patients were treated with three approaches. The operation time, incision length, time to return to work, complications, and the like were compared among three groups. Intervertebral disc (IVD) space height, angular motion, and vertebral slippage were obtained to assess spine biomechanical stability following surgery. The visual analog scale (VAS) score and Oswestry disability index were evaluated at preoperation and 1-week, 3-month, and the latest follow-ups. Clinical global outcomes were also estimated using modified MacNab criteria.ResultsThe operation time, incision length, intraoperative blood loss, and time to return to work for the PTED group were significantly decreased compared with those for the other two groups (P

The hot deformation behavior and flow stress characteristics of experimental 26CrMo7S steel were analyzed using a thermal simulator under a range of conditions, including a strain rate range of 0.01~10 s−1, a temperature range of 850~1250 °C, and a maximum deformation amount of 70%. The Arrhenius constitutive model was built for the corresponding conditions, and the model’s accuracy was verified through error analysis. Additionally, hot processing maps were constructed to analyze the processing zone of the steel under different hot deformation conditions. Finally, the microstructure of the processing zones was observed and verified using the electron backscattered diffraction (EBSD). The results indicate that the interaction of work hardening and dynamic softening influences the hot deformation behavior of 26CrMo7S steel. The Arrhenius constitutive equation with a value of the correlation coefficient (r = 0.99523) accurately predicts the flow behavior of 26CrMo7S steel under different strains. The optimal processing zone obtained with the hot processing maps is within a deformation range of 1010~1190 °C and a strain rate range of 0.01~10−1.5 s−1, and the obtained microstructure is in good agreement with the analysis results.

Exosomes are small vesicles that contain diverse miRNA, mRNA, and proteins that are secreted by multiple cells, and play a vital function in cell–cell communication. Numerous exosomes produced by cells have been demonstrated to be protective against spinal cord injury (SCI). This study aims to investigate the neuroprotective effect of Schwann cells-derived exosomes (SCs-Exos) on spinal cord injury. We found that SCs-Exos can be taken directly by brain-derived endothelial cells.3 (bEnd.3 cells) and promoted to proliferate, migrate, and form bEnd.3 tube. Additionally, our results showed that the pro-angiogenesis molecules, Integrin-β1, were highly expressed in SCs-Exos. Moreover, we used special shRNA technology to investigate the role of Integrin-β1 in mediating the effect of SCs-Exos-induced angiogenesis on bEnd.3 cells. We observed that the pro-angiogenic effect of SCs-Exos on bEnd.3 cells was suppressed by inhibiting the expression of integrin-β1 in SCs-Exos. In the SCI model, we found that SCs-Exos attenuated tissue damage and improved functional recovery after SCI. Using immunofluorescence staining, we observed that SCs-Exos treatment promoted angiogenesis in SCI, and integrin-β1 was required to promote angiogenesis. In conclusion, our results indicate that SCs-Exos promote angiogenesis by delivering integrin-β1 and may serve as a promising novel therapeutic agent for enhancing neurological functional recovery after SCI.

TaMs1 encodes a non-specific lipid transfer protein (nsLTP) and is required for pollen development in wheat. Although MS1 is a Poaceae-specific gene, the roles of MS1 genes in other Poaceae plants are unknown, especially in rice and maize. Here, we identified one ortholog in rice (OsLTPg29) and two orthologs in maize (ZmLTPg11 and ZmLTPx2). Similar to TaMs1, both OsLTPg29 and ZmLTPg11 genes are specifically expressed in the microsporocytes, and both OsLTPg29 and ZmLTPg11 proteins showed lipid-binding ability to phosphatidic acid and several phosphoinositides. To determine their roles in pollen development, we created osltpg29 mutants and zmltpg11zmltpx2 double mutants by CRISPR/Cas9. osltpg29, not zmltpg11zmltpx2, is defective in pollen development, and only OsLTPg29, not ZmLTPg11, can rescue the male sterility of tams1 mutant. Our results demonstrate that the biological function of MS1 in pollen development differs in the evolution of Poaceae plants.

Bioactive organic compounds (BOCs) contained in bio-stabilized products of waste activated sludge (WAS) have attracted considerable attention, as they can enhance the fertilizing effect of WAS in land applications. This study investigated the molecular composition and plant-growth-promoting mechanisms of various BOCs in the bio-stabilized products of WAS. After stepwise fractionation, aerobic composting sludge (ACS) and anaerobic digestion sludge (ADS) were chemically fractioned into five subcomponents, namely dissolved organic matter (DOM) (C1), weakly interacted organic matter (OM) (C2), metal-bonded OM (C3), NaOH-extracted OM (C4), and strongly interacted OM (C5), in sequence. The results showed that fatty acids and carboxylic acid (CAs) present in ACS C2 promoted plant growth and enhanced the ability of plants against stresses by upregulating pathways related to “carbohydrate metabolism,” “lipid metabolism,” “amino acid metabolism,” and “phenylpropanoid biosynthesis.” However, in ACS C4, plenty of amino acids could promote plant growth via upregulating “carbohydrate metabolism” and “amino acid metabolism” pathways. As an important precursor, aromatic amino acids inside ACS C4 also stimulated the production of indoleacetic acids. In ADS C1, amino sugar and phytohormone were the major BOCs causing the up-regulation of “carbohydrate metabolism” and AAA catabolism in “amino acid metabolism” pathways. CAs enriched in ADS C2 stimulated plant growth through “amino acid metabolism” pathway. In summary, alkali extraction can recycle a large proportion of BOCs with low environmental risk from the bio-stabilization products of WAS. The results from this study provide scientific guidance for safe and value-added resource utilization of bio-stabilization products of WAS in land applications.

Abstract Members of the Enterobacter genus are gram-negative bacteria, which are used as plant growth-promoting bacteria, and increasingly recovered from economic plants as emerging pathogens. A new Enterobacter mori strain, designated CX01, was isolated as an emerging bacterial pathogen of a recent outbreak of kiwifruit canker-like disease in China. The main symptoms associated with this syndrome are bleeding cankers on the trunk and branch, and brown leaf spots. The genome sequence of E. mori CX01 was determined as a single chromosome of 4,966,908 bp with 4640 predicted open reading frames (ORFs). To better understand the features of the genus and its potential pathogenic mechanisms, five available Enterobacter genomes were compared and a pan-genome of 4870 COGs with 3158 core COGs were revealed. An important feature of the E. mori CX01 genome is that it lacks a type III secretion system often found in pathogenic bacteria, instead it is equipped with type I, II, and VI secretory systems. Besides, the genes encoding putative virulence effectors, two-component systems, nutrient acquisition systems, proteins involved in phytohormone synthesis, which may contribute to the virulence and adaption to the host plant niches are included. The genome sequence of E. mori CX01 has high similarity with that of E. mori LMG 25,706, though the rearrangements occur throughout two genomes. Further pathogenicity assay showed that both strains can either invade kiwifruit or mulberry, indicating they may have similar host range. Comparison with a closely related isolate enabled us to understand its pathogenesis and ecology.

Chlorination disinfection has been widely used to kill the pathogenic microorganisms in wastewater sludge during the special Covid-19 period, but sludge chlorination might cause the generation of harmful disinfection byproducts (DBPs). In this work, the transformation of extracellular polymeric substance (EPS) and mechanisms of Cl-DBPs generation during sludge disinfection by sodium hypochlorite (NaClO) were investigated using multispectral analysis in combination with Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). The microorganism Escherichia coli (E. coli) was effectively inactivated by active chlorine generated from NaClO. However, a high diversity of Cl-DBPs were produced with the addition of NaClO into sludge, causing the increase of acute toxicity on Q67 luminous bacteria of chlorinated EPS. A variety of N-containing molecular formulas were produced after chlorination, but N-containing DBPs were not detected, which might be the indicative of the dissociation of –NH2 groups after Cl-DBPs generated. Additionally, the release of N-containing compounds was increased in alkaline environment caused by NaClO addition, resulted in more Cl-DBPs generation via nucleophilic substitutions. Whereas, less N-compounds and Cl-DBPs were detected after EPS chlorination under acidic environment, leading to lower cell cytotoxicity. Therefore, N-containing compounds of lignin derivatives in sludge were the major Cl-DBPs precursors, and acidic environment could control the release of N-compounds by eliminating the dissociation of functional groups in lignin derivatives, consequently reducing the generation and cytotoxicity of Cl-DBPs. This study highlights the importance to control the alkalinity of sludge to reduce Cl-DBPs generation prior to chlorination disinfection process, and ensure the safety of subsequential disposal for wastewater sludge.

Gravitropism is the process by which plants perceive and respond to gravity. Here the authors identify a minus-end-directed kinesin required for gravity-triggered actin filament rearrangement and negative gravitropic response in the moss Physcomitrella patens, thus linking a microtubule-based cellular motor to gravitropism via actin.

Abstract Background Effective tiller number (ETN) has a pivotal role in determination of rice (Oryza sativa L.) grain yield. ETN is a complex quantitative trait regulated by both genetic and environmental factors. Despite multiple tillering-related genes have been cloned previously, few of them have been utilized in practical breeding programs. Results In this study, we conducted a genome-wide association study (GWAS) for ETN using a panel of 490 rice accessions derived from the 3 K rice genomes project. Thirty eight ETN-associated QTLs were identified, interestingly, four of which colocalized with the OsAAP1, DWL2, NAL1, and OsWRKY74 gene previously reported to be involved in rice tillering regulation. Haplotype (Hap) analysis revealed that Hap5 of OsAAP1, Hap3 and 6 of DWL2, Hap2 of NAL1, and Hap3 and 4 of OsWRKY74 are favorable alleles for ETN. Pyramiding favorable alleles of all these four genes had more enhancement in ETN than accessions harboring the favorable allele of only one gene. Moreover, we identified 25 novel candidate genes which might also affect ETN, and the positive association between expression levels of the OsPILS6b gene and ETN was validated by RT-qPCR. Furthermore, transcriptome analysis on data released on public database revealed that most ETN-associated genes showed a relatively high expression from 21 days after transplanting (DAT) to 49 DAT and decreased since then. This unique expression pattern of ETN-associated genes may contribute to the transition from vegetative to reproductive growth of tillers. Conclusions Our results revealed that GWAS is a feasible way to mine ETN-associated genes. The candidate genes and favorable alleles identified in this study have the potential application value in rice molecular breeding for high ETN and grain yield.

In situ conserved wild rice (Oryza rufipogon Griff.) is a promising source of alleles for improving rice production worldwide. In this study, we conducted a genomic analysis of an in situ conserved wild rice population (Guiping wild rice) growing at the center of wild rice genetic diversity in South China. Differences in the plant architecture in this population were investigated. An analysis using molecular markers revealed the substantial genetic diversity in this population, which was divided into subgroups according to the plant architecture. After resequencing representative individuals, the Guiping wild rice population was compared with other O. rufipogon and Oryza sativa populations. The results indicated that this in situ conserved wild rice population has a unique genetic structure, with genes that were introgressed from aromatic and O. sativa ssp. indica and japonica populations. The QTLs associated with plant architecture in this population were detected via a pair-wise comparison analysis of the sequencing data for multiple DNA pools. The results suggested that a heading date-related gene (DHD1) might be associated with variations in plant architecture and may have originated in cultivated rice. Our findings provide researchers with useful insights for future genomic analyses of in situ conserved wild rice populations.

Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.

Fusarium ear rot (FER) caused by Fusarium verticillioides is one of the most common diseases affecting maize production worldwide. FER results in severe yield losses and grain contamination with health-threatening mycotoxins. Although most studies to date have focused on comprehensive analysis of gene regulation in maize during defense responses against F. verticillioides infection, less is known about the role of microRNAs (miRNAs) in this process. We used deep sequencing to compare small RNA libraries from the maize kernels of susceptible (N6) or resistant (BT-1) inbred lines from uninfected plants and upon F. verticillioides infection. We found that pathogen exposure was accompanied by dynamic alterations in expression levels of multiple miRNAs, including new members of previously annotated miRNA families. A combination of transcriptomic, degradomic, and bioinformatics analyses revealed that F. verticillioides-responsive miRNAs and their potential target genes displayed opposite expression patterns in the susceptible and resistant genotypes. Functional category analysis uncovered preferential enrichment of the pathogen-responsive miRNAs and their targets in the phenylpropanoid metabolic processes, plant–pathogen interactions, and plant phytohormone signal transduction pathways. Furthermore, transgenic maize plants overexpressing miR408b exhibited reduced resistance to F. verticillioides infection in a susceptible maize line. These findings provide new insights into the regulatory roles of miRNAs in maize immunity against FER and new resources for breeding disease resistance into maize.

Heat stress can activate heterochromatin-associated transposon elements (TEs). Here, the authors show that heat stress leads to global rearrangement of 3D genome and TEs activation closely correlates with 3D chromatin organization rearrangement in Arabidopsis.

This paper proposes an improved internal-model-control (IMC)-based proportional-integral (PI) current controller for a permanent magnet synchronous motor (PMSM) drive system to solve the parameter dependence problem. The parameter sensitivity of the conventional IMC-based PI controller is analyzed, which indicates that the parameters mismatch would cause oscillation or overshoot. Therefore, this paper utilizes an uncertainty and disturbance estimator to eliminate the impact of the parameters mismatch disturbance caused by the parameters variation. The proposed controller includes an IMC-based PI controller, which is responsible for tracking, and a disturbance estimator, which deals with other control difficulties. The performance and robustness are easily achieved by separately tuning the only two parameters (the desired closed-loop bandwidth and the estimator bandwidth). The frequency-domain characteristic of the proposed current controller indicates that it can effectively suppress the parameters mismatch disturbance. Simulations and experiments have verified the effectiveness of the proposed method.

Exosomes are nano-sized vesicles that contain a variety of mRNAs, miRNAs, and proteins. They are capable of being released by a variety of cells and are essential for cell–cell communication. The exosomes produced by cells have shown protective benefits against spinal cord damage (SCI). Recently, it was discovered that M2 macrophages aid in the angiogenesis of numerous illnesses. However, the functional role of M2 macrophage-derived exosomes on SCI is unclear. Here, we investigate the pro-angiogenesis of M2 macrophage-derived exosomes on SCI. We founded that M2 macrophage exosomes alleviated tissue damage and enhanced functional recovery post-SCI. We discovered that M2 macrophage exosome administration increased angiogenesis after SCI in vivo using immunohistochemistry, immunofluorescence labeling, and Western blot analysis. Additionally, the expression of the pro-angiogenesis factors, HIF-1α and VEGF, were enhanced with the treatment of the M2 macrophage exosomes. Furthermore, we found that M2 macrophage exosomes enhanced neurogenesis after SCI in vivo. In vitro, we found that M2 macrophage exosomes can be taken up by the brain endothelial cell line (bEnd.3) and that they enhanced the tube formation, migration, and proliferation of bEnd.3 cells. Furthermore, by using special siRNA to inhibit HIF-1α expression, we observed that the expression of VEGF decreased, and the tube formation, migration, and proliferation of bEnd.3 cells were attenuated with the treatment of HIF-1α-siRNA. In conclusion, our findings reveal that M2 macrophage exosomes improve neurological functional recovery and angiogenesis post-SCI, and this process is partially associated with the activation of the HIF-1/VEGF signaling pathway.

The present study was conducted to investigate the effects of dietary yeast culture (YC) supplementation on growth performance, nutrient digestibility, blood metabolites, and immune functions in geese. One-day-old Sichuan white geese (n = 300) were randomly divided into five groups containing 0 (control), 0.5%, 1.0%, 2.0%, and 4.0% of YC in the diet for 70 days. In general, the dietary supplementation of YC significantly increased the average daily gain and feed conversion ratio (p < 0.05) in which the 1.0% or 2.0% levels were better and significantly reduced the average daily feed intake at the 2.0% level (p < 0.05). YC supplementation increased digestibility of P (quadratic, p = 0.01) and gross energy (quadratic, p = 0.04) from days 23 to 27 and crude protein from days 23 to 27 and days 64 to 68 (quadratic, p ≤ 0.05), with the 2.0% level being the most effective. Serum metabolites were significantly affected by dietary YC (p < 0.05). Supplemental YC increased IL-2 on day 28 (linear, p = 0.01; quadratic, p = 0.04) and lysozyme on day 70 (quadratic, p = 0.04) and decreased complement C4 on day 70 (linear, p = 0.05). Interferon-γ, interleukin-2, and tumor necrosis factor-α genes were mostly up-regulated after YC supplementation, and interferon-γ and interleukin-2 gene expression levels were significantly increased at the 2.0% level (p < 0.05). Taken together, dietary YC supplementation improved growth performance and affected nutrient digestibility, serum metabolites, and immune function in geese, which was optimized at the 2% YC level in the present study.

Background: : Postoperative pancreatic fistula (POPF) is one of the most common complications and the leading cause of morbidity and mortality after pancreatic operation with pancreatojejunostomy (PJ). Many strategies have been used to prevent the incidence of POPF, among which drainage of pancreatic juice is effective. There are two types of drainage methods used in clinical practice; however, the method with a superior effect remains unknown. This study compared the effect of external and internal drainage without stent (in other words, no drainage, only PJ by duct-to-mucosa) on the incidence of clinically relevant POPF (CR-POPF) to provide evidence to select a better drainage scheme in clinical practice. Methods: Overall, 520 patients undergoing pancreatic operation, including PJ were included in this single-centre study and were divided into two groups according to drainage methods. We compared the incidence of CR-POPF between the two groups and performed stratified analysis according to the Fistula Risk Score (FRS) and pancreatic gland texture. Factors such as gender, age, Body Mass Index (BMI), operative procedure, and drainage methods were included in univariable and multivariable analyses. Results: The incidence rate of CR-POPF between two groups was significantly different (23.3% vs 13.6%, P

Summary: The asymmetric distribution of auxin leads to the bending growth of hypocotyls during gravitropic and phototropic responses, but the signaling events downstream of auxin remain unclear. Here, we identify many SAUR genes showing asymmetric expression in soybean hypocotyls during gravistimulation and then study their homologs in Arabidopsis. SAUR19 subfamily genes have asymmetric expression in Arabidopsis hypocotyls during gravitropic and phototropic responses, induced by the lateral redistribution of auxin. Both the mutation of SAUR19 subfamily genes and the ectopic expression of SAUR19 weaken these tropic responses, indicating the critical role of their asymmetric expression. The auxin-responsive transcription factor ARF7 may directly bind the SAUR19 promoter and activate SAUR19 expression asymmetrically in tropic responses. Taken together, our results reveal that a gravity- or light-triggered asymmetric auxin distribution induces the asymmetric expression of SAUR19 subfamily genes by ARF7 and ARF19 in the hypocotyls, which leads to bending growth during gravitropic and phototropic responses. : Gravitropism and phototropism are important for sessile plants to adapt to various environments. Wang et al. show that gravity- or light-triggered asymmetric distribution of auxin induces the asymmetric expression of SAUR19 subfamily genes by ARF7 and ARF19, which directs the bending growth of Arabidopsis hypocotyls. Keywords: gravitropism, phototropism, SAUR, ARF, auxin, asymmetric, SAUR19, ARF7, Arabidopsis, soybean

Concrete pipe may suffer joint failure under the coupling effect of internal fluid and overlying load, which may lead to pipe leakage. Based on Abaqus and Fluent finite element software, a three-dimensional refined model of drainage pipeline with gasketed bell-and-spigot joints and flow field model inside the pipeline was established. Fully considering the compression of the gasket during pipeline assembly and pipe-soil interaction, the fluid-structure coupling numerical simulation was carried out by using the MpCCI (Mesh-based parallel Code Coupling Interface) platform, and the mechanical response of the concrete pipe joint under the multifield loads coupling effects of burial condition, traffic load, and internal fluid was studied. The accuracy of the coupling model was verified through the full-scale tests that have been carried out. The influences of various factors on the circumferential stress and vertical deformation of the joint were mainly studied. The result reveals that the influence of different working conditions on the circumferential stress of the pipe joint is mainly concentrated on the crown and the invert of the joint, the areas vulnerable to tensile damage. The change of flow field leads to a slight difference in the vertical deformation of the joint, while variation in gasket hardness and cushion compactness has a certain influence on the vertical deformation of the joint. The change of buried depth has a negative correlation to the vertical deformation of the joint, and the change of load position has a significant nonlinear effect. The result provides a theoretical basis for further research on the mechanical mechanism of the pipeline joints during operation.

In order to explore the influence of the types of waste gypsum on the properties of alkali slag cement, fluorogypsum (FG) and flue-gas desulfurization (FGD) gypsum were comparatively investigated. Moreover, the action mechanisms of FG and FGD gypsum on the properties of alkali slag cement were analyzed. The results show that both the FG and FGD gypsum prolonged the setting time of the alkali slag cement paste. However, the prolongation effect of FG was more pronounced than the FGD gypsum. When the compressive strength was maximum, the contents of FG and FGD gypsum were 5 and 6 wt.%, respectively. At 3 and 28 days, compared to the control sample, the compressive strengths increased by 59.3% and 24.3%, and 66.9% and 33.9%, respectively. Furthermore, the XRD, TG-DTA and SEM-EDS results showed that, with the increase in the contents of FG and FGD gypsum, ettringite was more easily produced and the hydration products were more abundant in the system. The greater the gypsum content of the paste, the less accumulated was the heat of hydration. The change of micro-structure caused by the formation of ettringite was the main reason for the difference in the properties of cement.

Abstract Heterosis has been widely utilized in agriculture and is important for world food safety. Many genetic models have been proposed as mechanisms underlying heterosis during the past century, yet more evidence is needed to support such models. To investigate heterosis in two-line hybrid rice, we generated a partial diallel crossing scheme, which consisted of approximately 500 F1 hybrids derived from 14 male sterile lines and 39 restorer lines. In this population, increased panicle number played the most important role in yield heterosis of hybrid rice. Genome-wide association studies identified many QTLs related to the yield traits of F1 hybrids, better paternal heterosis and special combining ability. Relevant genes, including Hd3a, qGL3, OsmiR156h, and LAX2, were identified as candidates within these QTLs. Nearly forty percent of the QTLs had only two genotypes in the F1 hybrids, mainly because the maternal lines were under intense selective pressure. Further analysis found male sterile lines and restorer lines made different superior allele contributions to F1 hybrids, and their contributions varied among different traits. These results extend our understanding of the molecular basis of heterosis in two-line hybrid rice.

We study the doubly charmed baryon Ξcc+ structure and production in high energy nuclear collisions. By solving the three-quark Schrödinger equation including relativistic correction and calculating the yield via coalescence mechanism, we find that, the Ξcc+ created in nuclear collisions is in the quark–diquark state as a consequence of chiral symmetry restoration in hot medium, and the production is extremely enhanced due to the large number of charm quarks.

Current research was not dedicated to investigate the mechanical behavior of a concrete drainage pipe under multiphysical coupling conditions of overburden pressure, traffic loads, groundwater, and pipe fluids. This study proposes a new numerical solution method for coupled stress, seepage, and flow fields based on a validated finite element model. The model was developed by ABAQUS and FLUENT and then solved simultaneously using the MpCCI (mesh-based parallel-code coupling interface) platform. Results show that the tensile stress at the springline and the radial displacement at the crown (or invert) of the bell under the effect of groundwater alone were reduced by 50.5% and 38.1%, respectively, compared to the effect of traffic load alone. Parametric analyses show that vehicle speed and fluid height have a slight impact on the pipes. The soil cover depth, wheel pressure, and gasket strength are directly proportional to the pipe stress and vertical displacement. Within the scope of their respective changes, the pipe stresses were increased by 34.4%, 36.7%, and 28.5%, and the vertical displacements were increased by 124%, 95.85%, and 87.7%. The bedding and backfill strengths are proportional to the pipe stress and inversely proportional to the vertical displacement. Within the scope of their respective changes, the pipe stresses were increased by 18.2% and 20.0%, and the vertical displacements were decreased by 11.4% and 10.4%. Sensitivity analyses show that soil cover depth has a greatest impact on the pipe, followed by traffic load.

In order to improve the early age strength of ordinary Portland cement-based materials, many early strength agents were applied in different conditions. Different from previous research, the nano calcium silicate hydrate (C-S-H) particles used in this study were synthesized through the chemical reaction of CaO, SiO2, and H2O under 120 °C using the hydrothermal method, and the prepared nano C-S-H particles were highly crystalized. The influences of different amounts of nano C-S-H particles (0%, 0.5%, 1%, 2% and 3% by weight of cement) on the setting time, compressive strength, and hydration heat of cement paste were studied. The hydration products and microstructure of the cement paste with different additions of nano C-S-H particles were investigated through thermogravimetry-differential thermal analysis (TG-DTA), X-ray powder diffraction (XRD), and scanning electron microscope (SEM) tests. The results show that the nano C-S-H particles could be used as an early strength agent, and the early strength of cement paste can be increased by up to 43% through accelerating the hydration of tricalcium silicate (C3S). However, the addition of more than 2% nano C-S-H particles was unfavorable to the later strength development due to more space being left during the initial accelerated hydration process. It is suggested that the suitable content of the nano C-S-H particles is 0.5%−1% by weight of cement.

We investigate the production of Ωccc baryon in high energy nuclear collisions via quark coalescence mechanism. The wave function of Ωccc is solved from the Schrödinger equation for the bound state of three charm quarks by using the hyperspherical method. The production cross section of Ωccc per binary collision in a central Pb+Pb collision at sNN=2.76 TeV reaches 9 nb, which is at least two orders of magnitude larger than that in a p+p collision at the same energy. Therefore, it is most probable to discover Ωccc in heavy ion collisions at LHC, and the observation will be a clear signature of the quark–gluon plasma formation.

In the process of acid hydrolysis of cellulose, hydrolyzing the amorphous regions while retaining the crystalline regions is the key technology for obtaining microcrystalline cellulose products. This paper investigated the influence of FeCl3 on selective acid hydrolysis of crystalline regions and amorphous regions of cellulose. X-ray diffraction data indicated that FeCl3 can enhance the selectivity of acid hydrolysis for amorphous regions of cellulose, thus improving the crystallinity of hydrocellulose. Meanwhile, the crystalline structure did not change. Response surface methodology (RSM) was employed to optimize the crystallinity of hydrocellulose with respect to FeCl3 concentration, HCl concentration, reaction time, and temperature, and the relevant mathematical regression equation model was established. Under optimal conditions, the crystallinity of hydrocellulose was as high as 63.59% at 88.28 °C, 2.46 M HCl, 0.4 M FeCl3, and reaction duration of 64.02 min, which was in agreement with the predicted value.

With the depletion and increasing demand of river sand, machine-made sand could be used more and more in concrete. In order to improve the properties of machine-made sand concrete, the effects of the aggregate micro fines (AMF) content, aluminum sulfate, and polypropylene fibers (PPF) on the slump, compressive strength, water permeability, and the chloride permeability coefficients were investigated through a single factor test method, and related mechanisms were analyzed. The results show that the optimum contents of AMF, aluminum sulfate, and the polypropylene fiber are 10 wt%, 1 wt%, and 0.6 kg/m3, respectively. The optimum content of AMF improved the compactness of concrete. The addition of aluminum sulfate promoted the initial formation of ettringite, and thereby improved the compressive strength and the permeability resistance. The polypropylene fiber can modify the pore structure distribution of concrete and reduce the porosity, thereby improving the impermeability of the concrete. The compressive strength of the machine-made sand concrete could be increased by more than 20%, and the water/chloride permeability coefficients could be decreased by more than 45%.

The transcriptional coactivator Yes-associated protein (Yap) promotes proliferation and inhibits apoptosis, suggesting that Yap functions as an oncogene. Most oncogenes, however, require a combination of at least two signals to promote proliferation. In this study, we present evidence that Yap activation is insufficient to promote growth in the otherwise normal tissue. Using a mosaic mouse model, we demonstrate that Yap overexpression in a fraction of hepatocytes does not lead to their clonal expansion, as proliferation is counterbalanced by increased apoptosis. To shift the activity of Yap towards growth, a second signal provided by tissue damage or inflammation is required. In response to liver injury, Yap drives clonal expansion, suppresses hepatocyte differentiation, and promotes a progenitor phenotype. These results suggest that Yap activation is insufficient to promote growth in the absence of a second signal thus coordinating tissue homeostasis and repair.

The mitogen-activated protein kinase (MAPK) cascade is an evolutionarily conserved signal transduction pathway that is involved in plant development and stress responses. As the first component of this phosphorelay cascade, mitogen-activated protein kinase kinase kinases (MAPKKKs) act as adaptors linking upstream signaling steps to the core MAPK cascade to promote the appropriate cellular responses; however, the functions of MAPKKKs in maize are unclear. Here, we identified 71 MAPKKK genes, of which 14 were novel, based on a computational analysis of the maize (Zea mays L.) genome. Using an RNA-seq analysis in the leaf, stem and root of maize under well-watered and drought-stress conditions, we identified 5,866 differentially expressed genes (DEGs), including 8 MAPKKK genes responsive to drought stress. Many of the DEGs were enriched in processes such as drought stress, abiotic stimulus, oxidation-reduction, and metabolic processes. The other way round, DEGs involved in processes such as oxidation, photosynthesis, and starch, proline, ethylene, and salicylic acid metabolism were clearly co-expressed with the MAPKKK genes. Furthermore, a quantitative real-time PCR (qRT-PCR) analysis was performed to assess the relative expression levels of MAPKKKs. Correlation analysis revealed that there was a significant correlation between expression levels of two MAPKKKs and relative biomass responsive to drought in 8 inbred lines. Our results indicate that MAPKKKs may have important regulatory functions in drought tolerance in maize.

Pulmonary fibrosis is a progressive and fatal fibrotic disease of the lungs with unclear etiology. Recent insight has suggested that early injury/inflammation of alveolar epithelial cells could lead to dysregulation of tissue repair driven by multiple cytokines. Although dysregulation of interleukin- (IL-) 22 is involved in various pulmonary pathophysiological processes, the role of IL-22 in fibrotic lung diseases is still unclear and needs to be further addressed. Here we investigated the effect of IL-22 on alveolar epithelial cells in the bleomycin- (BLM-) induced pulmonary fibrosis. BLM-treated mice showed significantly decreased level of IL-22 in the lung. IL-22 produced γδT cells were also decreased significantly both in the tissues of lungs and spleens. Administration of recombinant human IL-22 to alveolar epithelial cell line A549 cells ameliorated epithelial to mesenchymal transition (EMT) and partially reversed the impaired cell viability induced by BLM. Furthermore, blockage of IL-22 deteriorated pulmonary fibrosis, with elevated EMT marker (α-smooth muscle actin (α-SMA)) and overactivated Smad2. Our results indicate that IL-22 may play a protective role in the development of BLM-induced pulmonary fibrosis and may suggest IL-22 as a novel immunotherapy tool in treating pulmonary fibrosis.

Genome tiling microarray studies have consistently documented rich transcriptional activity beyond the annotated genes. However, systematic characterization and transcriptional profiling of the putative novel transcripts on the genome scale are still lacking. We report here the identification of 25,352 and 27,744 transcriptionally active regions (TARs) not encoded by annotated exons in the rice (Oryza. sativa) subspecies japonica and indica, respectively. The non-exonic TARs account for approximately two thirds of the total TARs detected by tiling arrays and represent transcripts likely conserved between japonica and indica. Transcription of 21,018 (83%) japonica non-exonic TARs was verified through expression profiling in 10 tissue types using a re-array in which annotated genes and TARs were each represented by five independent probes. Subsequent analyses indicate that about 80% of the japonica TARs that were not assigned to annotated exons can be assigned to various putatively functional or structural elements of the rice genome, including splice variants, uncharacterized portions of incompletely annotated genes, antisense transcripts, duplicated gene fragments, and potential non-coding RNAs. These results provide a systematic characterization of non-exonic transcripts in rice and thus expand the current view of the complexity and dynamics of the rice transcriptome.