ABSTRACT
Transition metal-nitrogen-carbon (M-N-C) catalysts have emerged as promising candidates for electrocatalytic CO2 reduction reaction (CO2RR) due to their uniform active sites and high atomic utilization rate. However, poor efficiency at low overpotentials and unclear reaction mechanisms limit the application of M-N-C catalysts. In this study, Fe-N-C catalysts are developed by incorporating S atoms onto ordered hierarchical porous carbon substrates with a molecular iron thiophenoporphyrin. The well-prepared FeSNC catalyst exhibits superior CO2RR activity and stability, attributes to an optimized electronic environment, and enhances the adsorption of reaction intermediates. It displays the highest CO selectivity of 94.0% at -0.58 V (versus the reversible hydrogen electrode (RHE)) and achieves the highest partial current density of 13.64 mA cm-2 at -0.88 V. Furthermore, when employed as the cathode in a Zn-CO2 battery, FeSNC achieves a high-power density of 1.19 mW cm-2 and stable charge-discharge cycles. Density functional theory calculations demonstrate that the incorporation of S atoms into the hierarchical porous carbon substrate led to the iron center becoming more electron-rich, consequently improving the adsorption of the crucial reaction intermediate *COOH. This study underscores the significance of hierarchical porous structures and heteroatom doping for advancing electrocatalytic CO2RR and energy storage technologies.
ABSTRACT
BACKGROUND: Metabolic score for insulin resistance (METS-IR) is a surrogate index to estimate insulin sensitivity. The aim of this study was to examine the association between METS-IR and regression to normoglycemia in Chinese adults with prediabetes. METHODS: A total of 15,415 Chinese adults with prediabetes defined by their fasting blood glucose were included in this retrospective study. The association between METS-IR and regression to normoglycemia from prediabetes was evaluated using the Cox proportional hazards regression model. A Cox proportional hazards regression with cubic spline function was performed to explore the nonlinear association between METS-IR and regression to normoglycemia. Kaplan-Meier curves was used to describe the probability of regression to normoglycemia from prediabetes. RESULTS: In multivariate Cox proportional hazards regression analyses, the increase in METS-IR was independently associated with a reduced probability of regression to normoglycemia from prediabetes (all p < 0.01 in models 1-3). A nonlinear association between METS-IR and the probability of regression to normoglycemia was observed, with an inflection point of 49.3. The hazard ratio on the left side of the inflection point was 0.965 (95% CI 0.953-0.976). Subgroup analyses demonstrated the robustness of our findings. CONCLUSION: This study demonstrated a negative and nonlinear association between METS-IR and regression to normoglycemia in Chinese adults with prediabetes. When METS-IR is below 49.3, reducing METS-IR could significantly increase the probability of regression to normoglycemia from prediabetes.
Subject(s)
Blood Glucose , Insulin Resistance , Prediabetic State , Humans , Prediabetic State/epidemiology , Prediabetic State/metabolism , Male , Female , Retrospective Studies , Middle Aged , Adult , Blood Glucose/metabolism , Blood Glucose/analysis , China/epidemiology , Proportional Hazards Models , Aged , Asian People , East Asian PeopleABSTRACT
Chromium-plated diamond/copper composite materials, with Cr layer thicknesses of 150 nm and 200 nm, were synthesized using a vacuum hot-press sintering process. Comparative analysis revealed that the thermal conductivity of the composite material with a Cr layer thickness of 150 nm increased by 266%, while that with a Cr layer thickness of 200 nm increased by 242%, relative to the diamond/copper composite materials without Cr plating. This indicates that the introduction of the Cr layer significantly enhanced the thermal conductivity of the composite material. The thermal properties of the composite material initially increased and subsequently decreased with rising sintering temperature. At a sintering temperature of 1050 °C and a diamond particle size of 210 µm, the thermal conductivity of the chromium-plated diamond/copper composite material reached a maximum value of 593.67 Wâm-1âK-1. This high thermal conductivity is attributed to the formation of chromium carbide at the interface. Additionally, the surface of the diamond particles in contact with the carbide layer exhibited a continuous serrated morphology due to the interface reaction. This "pinning effect" at the interface strengthened the bonding between the diamond particles and the copper matrix, thereby enhancing the overall thermal conductivity of the composite material.
ABSTRACT
BACKGROUND: There are limited data on the effect of different sutures and surgical approaches on the quality of pancreaticojejunostomy in minimally invasive pancreaticoduodenectomy (MIPD). This study compares the incidence of clinically relevant postoperative pancreatic fistula (CR-POPF) between the use of barbed sutures (BSs) and conventional sutures (CSs). METHODS: A retrospective cohort study was conducted on 253 consecutive patients who had undergone MIPD from July 2016 to April 2023. Patients were excluded if conversion to open surgery or open anastomosis was necessary. 220 patients were enrolled and divided into BS (n = 148) and CS (n = 72) groups. After 1:1 propensity score matching (PSM), 67 cases remained in each group. Univariate and multivariate analyses identified factors associated with CR-POPF. Comparisons were also made between laparoscopic (LPD) and robotic (RPD) pancreaticoduodenectomy. RESULTS: After PSM, BSs were associated with significantly lower rates of CR-POPF (7.5 vs. 22.4%, P = 0.015) and severe complications (Clavien-Dindo ≥ III) (7.5vs. 19.4%, P = 0.043). No significant differences were found in operative time, length of postoperative hospital stay, or other major morbidities. Multivariate analyses revealed BMI ≥ 22 kg/m2 (OR = 5.048, 95% CI: 1.256-20.287, P = 0.023) and the use of BSs (OR = 0.196, 95% CI: 0.059-0.653, P = 0.008) as the independent predictors of CR-POPF. There were no significant differences in postoperative outcomes between the LPD and RPD groups, but RPD was associated with significantly shorter operative time (402.8 min vs. 429.4 min, P = 0.015). CONCLUSIONS: In conclusion, using BSs for PJ during MIPD is feasible and has the potential to reduce CR-POPF and severe complications.
ABSTRACT
Carotenoid biosynthesis is closely associated with abscisic acid (ABA) during the ripening process of non-climacteric fruits, but the regulatory mechanism between ABA signaling and carotenoid metabolism remains largely unclear. Here, we identified two master regulators of ABA-mediated citrus fruit coloration, CsERF110 and CsERF53, which activated the expression of carotenoid metabolism genes (CsGGPPS, CsPSY, CsPDS, CsCRTISO, CsLCYB2, CsLCYE, CsHYD, CsZEP, and CsNCED2) to facilitate carotenoid accumulation. Further investigations showed that CsERF110 not only activated the expression of CsERF53 by binding to its promoter, but also interacted with CsERF53 to form a transcriptional regulatory module CsERF110-CsERF53. Furthermore, we discovered a positive feedback regulation loop between the ABA signal and carotenoid metabolism regulated by the transcriptional regulatory module CsERF110-CsERF53. Our results reveal that the transcriptional regulatory module CsERF110-CsERF53 responded to ABA signaling, thereby orchestrating citrus fruit coloration. Considering the importance of carotenoid content for citrus and many other carotenoid-rich crops, the revelation of molecular mechanisms underlying ABA-mediated carotenoid biosynthesis in plants will facilitate transgenic/gene editing approach development, further contributing to improving the quality of citrus and other carotenoid-rich crops.
ABSTRACT
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants raises concerns regarding the effectiveness of immunity acquired from previous Omicron subvariants breakthrough infections (BTIs) or reinfections (RIs) against the current circulating Omicron subvariants. In this study, we prospectively investigate the dynamic changes of virus-specific antibody and T cell responses among 77 adolescents following Omicron BA.2.3 BTI with or without subsequent Omicron BA.5 RI. Notably, the neutralizing antibodies (NAbs) titers against various detected SARS-CoV-2 variants, especially the emerging Omicron CH.1.1, XBB.1.5, XBB.1.16, EG.5.1, and JN.1 subvariants, exhibited a significant decrease along the time. A lower level of IgG and NAbs titers post-BTI was found to be closely associated with subsequent RI. Elevated NAbs levels and shortened antigenic distances were observed following Omicron BA.5 RI. Robust T cell responses against both Omicron BA.2- and CH.1.1-spike peptides were observed at each point visited. The exposure to Omicron BA.5 promoted phenotypic differentiation of virus-specific memory T cells, even among the non-seroconversion adolescents. Therefore, updated vaccines are needed to provide effective protection against newly emerging SARS-CoV-2 variants among adolescents.
Subject(s)
Antibodies, Neutralizing , Antibodies, Viral , COVID-19 , Memory T Cells , Reinfection , SARS-CoV-2 , Humans , Adolescent , COVID-19/immunology , COVID-19/virology , SARS-CoV-2/immunology , Antibodies, Viral/blood , Antibodies, Viral/immunology , Antibodies, Neutralizing/immunology , Antibodies, Neutralizing/blood , Male , Reinfection/immunology , Reinfection/virology , Female , Memory T Cells/immunology , Prospective Studies , Immunoglobulin G/blood , Immunoglobulin G/immunology , Antibody Formation , Spike Glycoprotein, Coronavirus/immunology , Immunologic Memory , Child , T-Lymphocytes/immunologyABSTRACT
Self-reaction of propargyl (C3H3) radical is the main pathway to benzene, the formation of which is the rate-controlling step toward the formation of polycyclic aromatic hydrocarbons (PAHs) and soot. Oxidation of C3H3 is a promising strategy to inhibit the formation of hazardous PAHs and soot. In the present study, we studied the C3H3 + O2 reaction from 650 to 1100 K in a laminar flow reactor and identified the intermediates and products by synchrotron VUV photoionization mass spectrometry. 2-Propynal, ethenone, formaldehyde, CO, CO2, C2H2, C2H4, and C3O2 were identified. Among them, 2-propynal, ethenone, and formaldehyde provided direct evidence for the branching reaction of C3H3 + O2 â HCCCHO + OH, C3H3 + O2 â H2CCO + CHO, and C3H3 + O2 â H2CO + CHCO, respectively. Potential energy surface calculation and mechanistic analysis of the C3O2 formations implied that C3H3 + O2 â CCCHO + H2O and C3H3 + O2 â HCCCO + H2O could occur, despite lacking direct observations of CCCHO and HCCCO radicals. The formation of ethenone and CO suggested the occurrence of the two CO elimination channels. We incorporated these validated reactions and the corresponding rate coefficients in the kinetic model of NUIGMech1.3, and the simulation showed obvious improvements toward the measured mole fractions of C3H3 and H2CCO, suggesting that the new C3H3 + O2 reaction channels were crucial in the overall combustion modeling of the important intermediate propyne (C3H4).
ABSTRACT
OBJECTIVE: Previous studies have reported that the inappropriate use of allopurinol may increase the risk of cerebrovascular accidents, but some studies have also confirmed that allopurinol is a protective factor against stroke. To clarify whether there is a relevant causal relationship between allopurinol and cerebral infarction, we conducted a two-sample Mendelian randomization (MR) study. METHODS: Data on single nucleotide polymorphisms (SNPs) associated with allopurinol and genome-wide association studies of cerebral infarction were obtained from the genome-wide association study (GWAS) web site. Five basic MR analyses were performed using MR-Egger regression, weighted median (WM1), inverse variance weighting (IVW), weighted mode (WM2), and simple mode. Sensitivity analysis was subsequently performed to detect horizontal pleiotropy, heterogeneity, and potential outliers. The final analysis results were mainly based on the IVW estimates. RESULTS: A total of 10 SNPs were used as instrumental variables (IVs). MR analysis [(IVW: odds ratio (OR) = 1.053, 95% confidence interval (CI): 1.019-1.088, P = 0.002), (WM1: OR = 1.053, 95% CI: 1.009-1.098, P = 0.017), (WM2: OR = 1.050, 95% CI: 1.008-1.095, P = 0.044), (MR Egger: Q = 4.285, P = 0.830)] showed a positive causal association between allopurinol and the risk of cerebral infarction. Sensitivity analysis such as horizontal pleiotropy and heterogeneity increased the reliability of this result. CONCLUSION: The results of this study provide direct evidence that there is a causal relationship between allopurinol and cerebral infarction and that allopurinol may increase the risk of cerebral infarction.
ABSTRACT
Obesity is a significant risk factor for various cancers, including pancreatic cancer (PC), but the underlying mechanisms are still unclear. In our study, pancreatic ductal epithelial cells were cultured using serum from human subjects with diverse metabolic statuses, revealing that serum from patients with obesity alters inflammatory cytokine signaling and ferroptosis, where a mutual enhancement between interleukin 34 (IL-34) expression and ferroptosis defense was observed in these cells. Notably, oncogenic KRASG12D amplified their interaction and this leads to the initiation of pancreatic ductal adenocarcinoma (PDAC) in diet-induced obese mice via macrophage-mediated immunosuppression. Single-cell RNA sequencing (scRNA-seq) of human samples showed that cytokine signaling, ferroptosis defense, and immunosuppression are correlated with the patients' body mass index (BMI) during PDAC progression. Our findings provide a mechanistic link between obesity, inflammation, ferroptosis defense, and pancreatic cancer, suggesting novel therapeutic targets for the prevention and treatment of obesity-associated PDAC.
ABSTRACT
Neurological disorders such as Parkinson's disease, stroke, and spinal cord injury can result in impairments of motor function, consciousness, cognition, and sensory processing. Brain-Computer Interface (BCI) technology, which facilitates direct communication between the brain and external devices, emerges as an innovative key to unlocking neurological conditions, demonstrating significant promise in this context. This comprehensive review uniquely synthesizes the latest advancements in BCI research across multiple neurological disorders, offering an interdisciplinary perspective on both clinical applications and emerging technologies. We explore the progress in BCI research and its applications in addressing various neurological conditions, with a particular focus on recent clinical studies and prospective developments. Initially, the review provides an up-to-date overview of BCI technology, encompassing its classification, operational principles, and prevalent paradigms. It then critically examines specific BCI applications in movement disorders, disorders of consciousness, cognitive and mental disorders, as well as sensory disorders, highlighting novel approaches and their potential impact on patient care. This review reveals emerging trends in BCI applications, such as the integration of artificial intelligence and the development of closed-loop systems, which represent significant advancements over previous technologies. The review concludes by discussing the prospects and directions of BCI technology, underscoring the need for interdisciplinary collaboration and ethical considerations. It emphasizes the importance of prioritizing bidirectional and high-performance BCIs, areas that have been underexplored in previous reviews. Additionally, we identify crucial gaps in current research, particularly in long-term clinical efficacy and the need for standardized protocols. The role of neurosurgery in spearheading the clinical translation of BCI research is highlighted. Our comprehensive analysis presents BCI technology as an innovative key to unlocking neurological disorders, offering a transformative approach to diagnosing, treating, and rehabilitating neurological conditions, with substantial potential to enhance patients' quality of life and advance the field of neurotechnology.
ABSTRACT
Chloroplasts are key players in photosynthesis and immunity against microbial pathogens. However, the precise and timely regulatory mechanisms governing the control of photosynthesis-associated nuclear genes (PhANGs) expression in plant immunity remain largely unknown. Here we report that TaPIR1, a Pst-induced RING-finger E3 ubiquitin ligase, negatively regulates Pst resistance by specifically interacting with TaHRP1, an atypical transcription factor histidine-rich protein. TaPIR1 ubiquitinates the lysine residues K131 and K136 in TaHRP1 to regulate its stability. TaHRP1 directly binds to the TaHRP1-binding site elements within the PhANGs promoter to activate their transcription via the histidine-rich domain of TaHRP1. PhANGs expression induces the production of chloroplast-derived ROS. Although knocking out TaHRP1 reduces Pst resistance, TaHRP1 overexpression contributes to photosynthesis, and chloroplast-derived ROS production, and improves disease resistance. TaPIR1 expression inhibits the downstream activation of TaHRP1 and TaHRP1-induced ROS accumulation in chloroplasts. Overall, we show that the TaPIR1-mediated ubiquitination and degradation of TaHRP1 alters PhANGs expression to disrupt chloroplast function, thereby increasing plant susceptibility to Pst.
Subject(s)
Chloroplasts , Gene Expression Regulation, Plant , Triticum , Ubiquitin-Protein Ligases , Arabidopsis/metabolism , Arabidopsis/genetics , Arabidopsis/immunology , Chloroplasts/metabolism , Disease Resistance/genetics , Nicotiana/metabolism , Nicotiana/genetics , Photosynthesis , Plant Diseases/microbiology , Plant Diseases/immunology , Plant Diseases/genetics , Plant Immunity , Plants, Genetically Modified , Promoter Regions, Genetic , Proteolysis , Reactive Oxygen Species/metabolism , Transcription Factors/metabolism , Transcription Factors/genetics , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitination , Triticum/cytology , Triticum/metabolismABSTRACT
Systemic lupus erythematosus (SLE) affects many populations. This study aims to develop a predictive model and create a nomogram for assessing the risk of end-stage renal disease (ESRD) in patients diagnosed with SLE. Data from electronic health records of SLE patients treated at the Affiliated Hospital of North Sichuan Medical College between 2013 and 2023 were collected. The dataset underwent thorough cleaning and variable assignment procedures. Subsequently, variables were selected using one-way logistic regression and lasso logistic regression methods, followed by multifactorial logistic regression to construct nomograms. The model's performance was assessed using calibration, receiver operating characteristic (ROC), and decision curve analysis (DCA) curves. Statistical significance was set at P < 0.05. The predictive variables for ESRD development in SLE patients included anti-GP210 antibody presence, urinary occult blood, proteinuria, white blood cell count, complement 4 levels, uric acid, creatinine, total protein, globulin, glomerular filtration rate, pH, specific gravity, very low-density lipoprotein, homocysteine, apolipoprotein B, and absolute counts of cytotoxic T cells. The nomogram exhibited a broad predictive range. The ROC area under the curve (AUC) was 0.886 (0.858-0.913) for the training set and 0.840 (0.783-0.897) for the testing set, indicating good model performance. The model demonstrated both applicability and significant clinical benefits. The developed model presents strong predictive capabilities and considerable clinical utility in estimating the risk of ESRD in patients with SLE.
ABSTRACT
OBJECTIVE: To examine the application of a novel pedagogical approach multidimensional supportive psychological intervention (MSPI) in the clinical practice teaching of andrological nursing care. METHODS: Using the Hamilton Depression Scale (HAMD), we assessed the psychology of 100 nursing interns about to enter clinical practice in the Department of Andrology from December 2021 to December 2022. We equally randomized the subjects into an experimental and a control group, the former receiving MSPI and the latter trained on the conventional teaching model without any psychological support intervention. RESULTS: Compared with the baseline, the HAMD scores were significantly decreased in the experimental group after intervention (12.4±2.1 vs 8.9±2.4, P<0.01), but increased in the controls (13.1±1.8 vs 14.7±1.9, P<0.01); the skill scores dramatically increased in the experimental group (82.6±4.7 vs 91.2±2.4, P<0.01), but decreased in the control group after intervention (81.0±3.5 vs 80.4±2.7, P = 0.28). CONCLUSION: MSPI can significantly enhance the learning enthusiasm of nursing students in a short period, reduce their psychological stress and improve teaching outcomes. This approach, combining psychology with teaching, can also strengthen the mental resilience of nursing students and better confront them with future professional challenges.
Subject(s)
Students, Nursing , Humans , Students, Nursing/psychology , Teaching , Psychosocial Intervention/methodsABSTRACT
Genetic generalized epilepsies (GGE) exhibit widespread morphometric alterations in the subcortical structures. Subcortical structures are essential for understanding GGE pathophysiology, but their fine-grained morphological diversity has yet to be comprehensively investigated. Furthermore, the relationships between macroscale morphological disturbances and microscale molecular chemoarchitectures are unclear. High-resolution structural images were acquired from patients with GGE (n = 97) and sex- and age-matched healthy controls (HCs, n = 184). Individual measurements of surface shape features (thickness and surface area) of seven bilateral subcortical structures were quantified. The patients and HCs were then compared vertex-wise, and shape anomalies were co-located with brain neurotransmitter profiles. We found widespread morphological alterations in GGE and prominent disruptions in the thalamus, putamen, and hippocampus. Shape area dilations were observed in the bilateral ventral, medial, and right dorsal thalamus, as well as the bilateral lateral putamen. We found that the shape area deviation pattern was spatially correlated with the norepinephrine transporter and nicotinic acetylcholine (Ach) receptor (α4ß2) profiles, but a distinct association was seen in the muscarinic Ach receptor (M1). The findings provided a comprehensive picture of subcortical morphological disruptions in GGE, and further characterized the associated molecular mechanisms. This information may increase our understanding of the pathophysiology of GGE.
Subject(s)
Epilepsy, Generalized , Humans , Female , Male , Epilepsy, Generalized/pathology , Epilepsy, Generalized/physiopathology , Adult , Young Adult , Magnetic Resonance Imaging , Thalamus/pathology , Thalamus/diagnostic imaging , Thalamus/metabolism , Brain/pathology , Brain/diagnostic imaging , Adolescent , Putamen/pathology , Putamen/diagnostic imaging , Putamen/metabolism , Case-Control Studies , Hippocampus/pathologyABSTRACT
Robotic surgery has been increasingly adopted in various surgical fields, but the cost-effectiveness of this technology remains controversial due to its high cost and limited improvements in clinical outcomes. This study aims to explore the health economic implications of robotic pancreatic surgery, to investigate its impact on hospitalization costs and consumption of various medical resources. Data of patients who underwent pancreatic surgery at our institution were collected and divided into robotic and traditional groups. Statistical analyses of hospitalization costs, length of stay, costs across different service categories, and subgroup cost analyses based on age, BMI class, and procedure received were performed using t tests and linear regression. Although the total hospitalization cost for the robotic group was significantly higher than that for the traditional group, there was a notable reduction in the cost of medical consumables. The reduction was more prominent among elderly patients, obese patients, and those undergoing pancreaticoduodenectomy, which could be attributed to the technological advantages of the robotic surgery platform that largely facilitate blood control, tissue protection, and suturing. The study concluded that despite higher overall costs, robotic pancreatic surgery offers significant savings in medical consumables, particularly benefiting certain patient subgroups. The findings provide valuable insights into the economic viability of robotic surgery, supporting its adoption from a health economics perspective.
Subject(s)
Pancreatectomy , Robotic Surgical Procedures , Tertiary Care Centers , Robotic Surgical Procedures/economics , Robotic Surgical Procedures/statistics & numerical data , Robotic Surgical Procedures/methods , Humans , China , Tertiary Care Centers/economics , Middle Aged , Female , Male , Aged , Pancreatectomy/economics , Pancreatectomy/methods , Pancreaticoduodenectomy/economics , Pancreaticoduodenectomy/methods , Pancreaticoduodenectomy/statistics & numerical data , Length of Stay/economics , Length of Stay/statistics & numerical data , Cost-Benefit Analysis , Adult , Costs and Cost Analysis , Pancreas/surgery , Hospitalization/economics , Hospitalization/statistics & numerical data , Hospital Costs/statistics & numerical dataABSTRACT
Quantum entanglement serves as an essential resource across various fields, including quantum communication, quantum computing, and quantum precision measurement. Quantum microscope, as one of the significant applications in quantum precision measurement, could bring revolutionary advancements in both signal-to-noise ratio (SNR) and spatial resolution of imaging. Here, we present a quantum microscopy system that relies on a fully fiber-integrated high-performance energy-time entangled light source operating within the near-infrared II (NIR-II) window. Complemented by tailored real-time data acquisition and processing software, we successfully demonstrate the quantum imaging of a standard target, achieving a SNR of 131.51 ± 6.74 and a spatial resolution of 4.75 ± 0.27 µm. Furthermore, we showcase quantum imaging of cancer cells, unveiling the potential of quantum entanglement in biomedical applications. Our fiber-integrated quantum microscope, characterized by high imaging SNR, instantaneous image capture, and analysis capabilities, marks an important step toward the practical application in life sciences.
ABSTRACT
Tandem repeats (TRs) are genomic regions that tandemly change in repeat number, which are often multiallelic. Their characteristics and contributions to gene expression and quantitative traits in rice are largely unknown. Here, we survey rice TR variations based on 231 genome assemblies and the rice pan-genome graph. We identify 227,391 multiallelic TR loci, including 54,416 TR variations that are absent from the Nipponbare reference genome. Only 1/3 TR variations show strong linkage with nearby bi-allelic variants (SNPs, Indels and PAVs). Using 193 panicle and 202 leaf transcriptomic data, we reveal 485 and 511 TRs act as QTLs independently of other bi-allelic variations to nearby gene expression, respectively. Using plant height and grain width as examples, we identify and validate TRs contributions to rice agronomic trait variations. These findings would enhance our understanding of the functions of multiallelic variants and facilitate rice molecular breeding.
Subject(s)
Alleles , Gene Expression Regulation, Plant , Genome, Plant , Oryza , Quantitative Trait Loci , Tandem Repeat Sequences , Oryza/genetics , Oryza/growth & development , Oryza/metabolism , Tandem Repeat Sequences/genetics , Chromosome Mapping , Polymorphism, Single Nucleotide , Phenotype , Genetic VariationABSTRACT
Transposable elements (TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms (SNPs), such as OsRbohB, and validated OsRbohB's relative expression activity using a dual-Luciferase (LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.
ABSTRACT
BACKGROUND: Nipah virus is a zoonotic paramyxovirus responsible for disease outbreaks with high fatality rates in south and southeast Asia. However, knowledge of the potential geographical extent and risk patterns of the virus is poor. We aimed to establish an integrated spatiotemporal and phylogenetic database of Nipah virus infections in humans and animals across south and southeast Asia. METHODS: In this geospatial modelling analysis, we developed an integrated database containing information on the distribution of Nipah virus infections in humans and animals from 1998 to 2021. We conducted phylodynamic analysis to examine the evolution and migration pathways of the virus and meta-analyses to estimate the adjusted case-fatality rate. We used two boosted regression tree models to identify the potential ecological drivers of Nipah virus occurrences in spillover events and endemic areas, and mapped potential risk areas for Nipah virus endemicity. FINDINGS: 749 people and eight bat species across nine countries were documented as being infected with Nipah virus. On the basis of 66 complete genomes of the virus, we identified two clades-the Bangladesh clade and the Malaysia clade-with the time of the most recent common ancestor estimated to be 1863. Adjusted case-fatality rates varied widely between countries and were higher for the Bangladesh clade than for the Malaysia clade. Multivariable meta-regression analysis revealed significant relationships between case-fatality rate estimates and viral clade (p=0·0021), source country (p=0·016), proportion of male patients (p=0·036), and travel time to health-care facilities (p=0·036). Temperature-related bioclimate variables and the probability of occurrence of Pteropus medius were important contributors to both the spillover and the endemic infection models. INTERPRETATION: The suitable niches for Nipah virus are more extensive than previously reported. Future surveillance efforts should focus on high-risk areas informed by updated projections. Specifically, intensifying zoonotic surveillance efforts, enhancing laboratory testing capacity, and implementing public health education in projected high-risk areas where no human cases have been reported to date will be crucial. Additionally, strengthening wildlife surveillance and investigating potential modes of transmission in regions with documented human cases is needed. FUNDING: The Key Research and Development Program of China.