Approximately 20%of colorectal cancer(CRC)patients present with metastasis at diagnosis.Among Stage I-III CRC patients who undergo surgical resection,18%typically suffer from distal metastasis within the first three y...Approximately 20%of colorectal cancer(CRC)patients present with metastasis at diagnosis.Among Stage I-III CRC patients who undergo surgical resection,18%typically suffer from distal metastasis within the first three years following initial treatment.The median survival duration after the diagnosis of metastatic CRC(mCRC)is only 9 mo.mCRC is traditionally considered to be an advanced stage malignancy or is thought to be caused by incomplete resection of tumor tissue,allowing cancer cells to spread from primary to distant organs;however,increa-sing evidence suggests that the mCRC process can begin early in tumor development.CRC patients present with high heterogeneity and diverse cancer phenotypes that are classified on the basis of molecular and morphological alterations.Different genomic and nongenomic events can induce subclone diversity,which leads to cancer and metastasis.Throughout the course of mCRC,metastatic cascades are associated with invasive cancer cell migration through the circulatory system,extravasation,distal seeding,dormancy,and reactivation,with each step requiring specific molecular functions.However,cancer cells presenting neoantigens can be recognized and eliminated by the immune system.In this review,we explain the biological factors that drive CRC metastasis,namely,genomic instability,epigenetic instability,the metastatic cascade,the cancer-immunity cycle,and external lifestyle factors.Despite remarkable progress in CRC research,the role of molecular classification in therapeutic intervention remains unclear.This review shows the driving factors of mCRC which may help in identifying potential candidate biomarkers that can improve the diagnosis and early detection of mCRC cases.展开更多
Assessment of past-climate simulations of regional climate models(RCMs)is important for understanding the reliability of RCMs when used to project future regional climate.Here,we assess the performance and discuss pos...Assessment of past-climate simulations of regional climate models(RCMs)is important for understanding the reliability of RCMs when used to project future regional climate.Here,we assess the performance and discuss possible causes of biases in a WRF-based RCM with a grid spacing of 50 km,named WRFG,from the North American Regional Climate Change Assessment Program(NARCCAP)in simulating wet season precipitation over the Central United States for a period when observational data are available.The RCM reproduces key features of the precipitation distribution characteristics during late spring to early summer,although it tends to underestimate the magnitude of precipitation.This dry bias is partially due to the model’s lack of skill in simulating nocturnal precipitation related to the lack of eastward propagating convective systems in the simulation.Inaccuracy in reproducing large-scale circulation and environmental conditions is another contributing factor.The too weak simulated pressure gradient between the Rocky Mountains and the Gulf of Mexico results in weaker southerly winds in between,leading to a reduction of warm moist air transport from the Gulf to the Central Great Plains.The simulated low-level horizontal convergence fields are less favorable for upward motion than in the NARR and hence,for the development of moist convection as well.Therefore,a careful examination of an RCM’s deficiencies and the identification of the source of errors are important when using the RCM to project precipitation changes in future climate scenarios.展开更多
Understanding the spatial variation,temporal changes,and their underlying driving forces of carbon sequestration in various forests is of great importance for understanding the carbon cycle and carbon management optio...Understanding the spatial variation,temporal changes,and their underlying driving forces of carbon sequestration in various forests is of great importance for understanding the carbon cycle and carbon management options.How carbon density and sequestration in various Cunninghamia lanceolata forests,extensively cultivated for timber production in subtropical China,vary with biodiversity,forest structure,environment,and cultural factors remain poorly explored,presenting a critical knowledge gap for realizing carbon sequestration supply potential through management.Based on a large-scale database of 449 permanent forest inventory plots,we quantified the spatial-temporal heterogeneity of aboveground carbon densities and carbon accumulation rates in Cunninghamia lanceolate forests in Hunan Province,China,and attributed the contributions of stand structure,environmental,and management factors to the heterogeneity using quantile age-sequence analysis,partial least squares path modeling(PLS-PM),and hot-spot analysis.The results showed lower values of carbon density and sequestration on average,in comparison with other forests in the same climate zone(i.e.,subtropics),with pronounced spatial and temporal variability.Specifically,quantile regression analysis using carbon accumulation rates along an age sequence showed large differences in carbon sequestration rates among underperformed and outperformed forests(0.50 and 1.80 Mg·ha^(-1)·yr^(-1)).PLS-PM demonstrated that maximum DBH and stand density were the main crucial drivers of aboveground carbon density from young to mature forests.Furthermore,species diversity and geotopographic factors were the significant factors causing the large discrepancy in aboveground carbon density change between low-and high-carbon-bearing forests.Hotspot analysis revealed the importance of culture attributes in shaping the geospatial patterns of carbon sequestration.Our work highlighted that retaining largesized DBH trees and increasing shade-tolerant tree species were important to enhance carbon sequestration in C.lanceolate forests.展开更多
The frequency and duration of observed concurrent hot and dry events(HDEs) over China during the growing season(April–September) exhibit significant decadal changes across the mid-1990s. These changes are characteriz...The frequency and duration of observed concurrent hot and dry events(HDEs) over China during the growing season(April–September) exhibit significant decadal changes across the mid-1990s. These changes are characterized by increases in HDE frequency and duration over most of China, with relatively large increases over southeastern China(SEC), northern China(NC), and northeastern China(NEC). The frequency of HDEs averaged over China in the present day(PD,1994–2011) is double that in the early period(EP, 1964–81);the duration of HDEs increases by 60%. Climate experiments with the Met Office Unified Model(MetUM-GOML2) are used to estimate the contributions of anthropogenic forcing to HDE decadal changes over China. Anthropogenic forcing changes can explain 60%–70% of the observed decadal changes,suggesting an important anthropogenic influence on HDE changes over China across the mid-1990s. Single-forcing experiments indicate that the increase in greenhouse gas(GHG) concentrations dominates the simulated decadal changes,increasing the frequency and duration of HDEs throughout China. The change in anthropogenic aerosol(AA) emissions significantly decreases the frequency and duration of HDEs over SEC and NC, but the magnitude of the decrease is much smaller than the increase induced by GHGs. The changes in HDEs in response to anthropogenic forcing are mainly due to the response of climatological mean surface air temperatures. The contributions from changes in variability and changes in climatological mean soil moisture and evapotranspiration are relatively small. The physical processes associated with the response of HDEs to GHG and AA changes are also revealed.展开更多
As a calculation method based on the Galerkin variation,the numerical manifold method(NMM)adopts a double covering system,which can easily deal with discontinuous deformation problems and has a high calculation accura...As a calculation method based on the Galerkin variation,the numerical manifold method(NMM)adopts a double covering system,which can easily deal with discontinuous deformation problems and has a high calculation accuracy.Aiming at the thermo-mechanical(TM)coupling problem of fractured rock masses,this study uses the NMM to simulate the processes of crack initiation and propagation in a rock mass under the influence of temperature field,deduces related system equations,and proposes a penalty function method to deal with boundary conditions.Numerical examples are employed to confirm the effectiveness and high accuracy of this method.By the thermal stress analysis of a thick-walled cylinder(TWC),the simulation of cracking in the TWC under heating and cooling conditions,and the simulation of thermal cracking of the SwedishÄspöPillar Stability Experiment(APSE)rock column,the thermal stress,and TM coupling are obtained.The numerical simulation results are in good agreement with the test data and other numerical results,thus verifying the effectiveness of the NMM in dealing with thermal stress and crack propagation problems of fractured rock masses.展开更多
Leakages from subsea oil and gas equipment cause substantial economic losses and damage to marine ecosystem,so it is essential to locate the source of the leak.However,due to the complexity and variability of the mari...Leakages from subsea oil and gas equipment cause substantial economic losses and damage to marine ecosystem,so it is essential to locate the source of the leak.However,due to the complexity and variability of the marine environment,the signals collected by hydrophone contain a variety of noises,which makes it challenging to extract useful signals for localization.To solve this problem,a hydrophone denoising algorithm is proposed based on variational modal decomposition(VMD)with grey wolf optimization.First,the average envelope entropy is used as the fitness function of the grey wolf optimizer to find the optimal solution for the parameters K andα.Afterward,the VMD algorithm decomposes the original signal parameters to obtain the intrinsic mode functions(IMFs).Subsequently,the number of interrelationships between each IMF and the original signal was calculated,the threshold value was set,and the noise signal was removed to calculate the time difference using the valid signal obtained by reconstruction.Finally,the arrival time difference is used to locate the origin of the leak.The localization accuracy of the method in finding leaks is investigated experimentally by constructing a simulated leak test rig,and the effectiveness and feasibility of the method are verified.展开更多
Seed germination with selenium(Se)is promising for producing Se-biofortified foods.Mungbean(Vigna radiata(L.)Wilczek)sprout is freshly eaten as a salad dressed with sauce,making it superior for Se biofortification.Since...Seed germination with selenium(Se)is promising for producing Se-biofortified foods.Mungbean(Vigna radiata(L.)Wilczek)sprout is freshly eaten as a salad dressed with sauce,making it superior for Se biofortification.Since the Se safety range for the human body is extremely narrow,it is imperative to evaluate the genotypic responses of mungbean sprouts to Se.This study evaluated the Se enrichment capacity and interaction withflavonoids and antioxidant systems in sprouts of 20 mungbean germplasms.Selenium treatment was done by immersing mung-bean seeds in 20μM sodium selenite solution for 8 h.Afterward,the biomass,Se amounts,flavonoid(particularly vitexin and isovitexin)contents,antioxidant capacity,and key biosynthetic gene expressions were measured.Sprout Se content was 2.0-7.0μg g^(-1) DW among the 20 mungbean germplasms.Selenium treatment differentially affected the biomass,totalflavonoid,vitexin,isovitexin,antioxidant enzyme activities,and antioxidant capacities of the mungbean germplasms.Eight germplasms showed increased biomass(p<0.05),the highest increasing by 127%,but 13 did not phenotypically respond to Se treatment.Seven and six germplasms showed varied levels of vitexin and isovitexin increment after Se treatment,the highest measuring 2.67-and 2.87-folds for vitexin and isovitexin,respectively.Two mungbeanflavonoid biosynthesis genes,chalcone synthase(VrCHS)and chalcone isomerase(VrCHI)were significantly up-regulated in the germplasms with increased vitexin and isovitexin levels(p<0.05).Moreover,Se enrichment capacity was significantly correlated with the vitexin,isovitexin,and antiox-idant capacities.In conclusion,mungbean sprouts could be a useful Se-biofortified food,but the Se enrichment capacity and nutritional response must be determined for each germplasm before commercialization.展开更多
Natural slopes usually display complicated exposed rock surfaces that are characterized by complex and substantial terrain undulation and ubiquitous undesirable phenomena such as vegetation cover and rockfalls.This st...Natural slopes usually display complicated exposed rock surfaces that are characterized by complex and substantial terrain undulation and ubiquitous undesirable phenomena such as vegetation cover and rockfalls.This study presents a systematic outcrop research of fracture pattern variations in a complicated rock slope,and the qualitative and quantitative study of the complex phenomena impact on threedimensional(3D)discrete fracture network(DFN)modeling.As the studies of the outcrop fracture pattern have been so far focused on local variations,thus,we put forward a statistical analysis of global variations.The entire outcrop is partitioned into several subzones,and the subzone-scale variability of fracture geometric properties is analyzed(including the orientation,the density,and the trace length).The results reveal significant variations in fracture characteristics(such as the concentrative degree,the average orientation,the density,and the trace length)among different subzones.Moreover,the density of fracture sets,which is approximately parallel to the slope surface,exhibits a notably higher value compared to other fracture sets across all subzones.To improve the accuracy of the DFN modeling,the effects of three common phenomena resulting from vegetation and rockfalls are qualitatively analyzed and the corresponding quantitative data processing solutions are proposed.Subsequently,the 3D fracture geometric parameters are determined for different areas of the high-steep rock slope in terms of the subzone dimensions.The results show significant variations in the same set of 3D fracture parameters across different regions with density differing by up to tenfold and mean trace length exhibiting differences of 3e4 times.The study results present precise geological structural information,improve modeling accuracy,and provide practical solutions for addressing complex outcrop issues.展开更多
Background The gut microbiota influences chicken health,welfare,and productivity.A diverse and balanced microbiota has been associated with improved growth,efficient feed utilisation,a well-developed immune system,dis...Background The gut microbiota influences chicken health,welfare,and productivity.A diverse and balanced microbiota has been associated with improved growth,efficient feed utilisation,a well-developed immune system,disease resistance,and stress tolerance in chickens.Previous studies on chicken gut microbiota have predominantly focused on broiler chickens and have usually been limited to one or two sections of the digestive system,under con-trolled research environments,and often sampled at a single time point.To extend these studies,this investigation examined the microbiota of commercially raised layer chickens across all major gut sections of the digestive system and with regular sampling from rearing to the end of production at 80 weeks.The aim was to build a detailed picture of microbiota development across the entire digestive system of layer chickens and study spatial and temporal dynamics.Results The taxonomic composition of gut microbiota differed significantly between birds in the rearing and pro-duction stages,indicating a shift after laying onset.Similar microbiota compositions were observed between proven-triculus and gizzard,as well as between jejunum and ileum,likely due to their anatomical proximity.Lactobacil-lus dominated the upper gut in pullets and the lower gut in older birds.The oesophagus had a high proportion of Proteobacteria,including opportunistic pathogens such as Gallibacterium.Relative abundance of Gallibacterium increased after peak production in multiple gut sections.Aeriscardovia was enriched in the late-lay phase compared to younger birds in multiple gut sections.Age influenced microbial richness and diversity in different organs.The upper gut showed decreased diversity over time,possibly influenced by dietary changes,while the lower gut,specifi-cally cecum and colon,displayed increased richness as birds matured.However,age-related changes were inconsist-ent across all organs,suggesting the influence of organ-specific factors in microbiota maturation.Conclusion Addressing a gap in previous research,this study explored the microbiota across all major gut sections and tracked their dynamics from rearing to the end of the production cycle in commercially raised layer chickens.This study provides a comprehensive understanding of microbiota structure and development which help to develop targeted strategies to optimise gut health and overall productivity in poultry production.展开更多
This study compared the differences in the wave climate in the South China Sea and North Indian Ocean under these two datasets:ERA-40 wave reanalysis and Mei’s hindcast wave data.In the numerical calculation of regio...This study compared the differences in the wave climate in the South China Sea and North Indian Ocean under these two datasets:ERA-40 wave reanalysis and Mei’s hindcast wave data.In the numerical calculation of regional ocean waves,the wave climate characteristics exhibited significant bias if the influence of external swells(swells from afar)was not fully considered,which may provide an incorrect basis for global climate change analysis.1)The trends of the significant wave height(SWH)obtained from the two datasets showed significant differences,such as those of the Bay of Bengal and the Java Sea in June-July-August.For the past 45 years,SWH from ERA-40(SWH-ERA)exhibited a significant annual increase in low-latitude waters of the North Indian Ocean(0.2-0.6 cm yr^(-1))and South China Sea(0.2-0.8 cm yr^(-1)).2)In the Bay of Bengal,the SWH-ERA in each month was generally 0.5 m higher than the SWH from Mei’s hindcast wave data(SWH-Mei)and can reach 1.0 m higher in some months.3)In the Bay of Bengal,SWH-ERA and SWH-Mei increased significantly at annual rates of 0.13 and 0.27 cm yr^(-1),respectively.This increasing trend was mainly reflected after 1978.SWH-ERA showed a trough in 1975(1.33 m)and a crest in 1992(1.83 m),which were not reflected in SWH-Mei.展开更多
Multiplicative noise removal problems have attracted much attention in recent years.Unlike additive noise,multiplicative noise destroys almost all information of the original image,especially for texture images.Motiva...Multiplicative noise removal problems have attracted much attention in recent years.Unlike additive noise,multiplicative noise destroys almost all information of the original image,especially for texture images.Motivated by the TV-Stokes model,we propose a new two-step variational model to denoise the texture images corrupted by multiplicative noise with a good geometry explanation in this paper.In the first step,we convert the multiplicative denoising problem into an additive one by the logarithm transform and propagate the isophote directions in the tangential field smoothing.Once the isophote directions are constructed,an image is restored to fit the constructed directions in the second step.The existence and uniqueness of the solution to the variational problems are proved.In these two steps,we use the gradient descent method and construct finite difference schemes to solve the problems.Especially,the augmented Lagrangian method and the fast Fourier transform are adopted to accelerate the calculation.Experimental results show that the proposed model can remove the multiplicative noise efficiently and protect the texture well.展开更多
Variations of picoplankton groups were investigated over a one-month period in Daya Bay and Sanya Bay,in the northern South China Sea.The two coastal regions exhibited different variation patterns in physicochemical p...Variations of picoplankton groups were investigated over a one-month period in Daya Bay and Sanya Bay,in the northern South China Sea.The two coastal regions exhibited different variation patterns in physicochemical parameters.Moreover,the diel variations of picoplankton groups were different between the two bays.The abundance of the picoplankton in Sanya Bay displayed a pronounced diel variation,while it was not significant in Daya Bay.In addition,some similar patterns of picoplankton abundance were discovered.In the two bays,virioplankton exhibited the smallest fluctuation range,whereas picocyanobacteria fluctuated most markedly.The fluctuation range of picoplankton groups was larger in spring tide than in neap tide,especially in Sanya Bay.Random forest model analysis demonstrated that the variation of picoplankton groups was attributed to physical and chemical factors in Sanya Bay and Daya Bay,respectively.Therefore,our findings suggest that virioplankton abundance can persist more stably in response to changing environmental conditions compared to bacterioplankton and picophytoplankton.展开更多
Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability ...Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.展开更多
Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and ...Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and other phenotypic traits.Constructing a pan-genome facilitates a thorough identification of genetic variations,thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.Results To comprehensively facilitate population genomic and pan-genomic analyses in geese,we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples.By constructing the pan-genome for geese,we generated non-reference contigs totaling 612 Mb,unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes,1,324 softcore genes,2,734 shell genes,and 878 cloud genes in goose genomes.Furthermore,we detected an 81.97 Mb genomic region showing signs of genome selection,encompassing the TGFBR2 gene correlated with variations in body weight among geese.Genome-wide association studies utilizing single nucleotide polymorphisms(SNPs)and presence-absence variation revealed significant genomic associations with various goose meat quality,reproductive,and body composition traits.For instance,a gene encoding the SVEP1 protein was linked to carcass oblique length,and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length.Notably,the pan-genome analysis revealed enrichment of variable genes in the“hair follicle maturation”Gene Ontology term,potentially linked to the selection of feather-related traits in geese.A gene presence-absence variation analysis suggested a reduced frequency of genes associated with“regulation of heart contraction”in domesticated geese compared to their wild counterparts.Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation.Conclusion This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits,thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese.Moreover,assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome,establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.展开更多
Plankton are an important component of marine protected areas(MPAs),and its communities would require much smaller interpatch distances to ensure connection among MPAs.According to the survey from MPAs dominated by ar...Plankton are an important component of marine protected areas(MPAs),and its communities would require much smaller interpatch distances to ensure connection among MPAs.According to the survey from MPAs dominated by artificial reefs and adjacent waters(estuary area(EA),aquaculture area(AA),artificial reef area(ARA),natural area(NA)and comprehensive effect area(CEA))in Haizhou Bay in spring and autumn,we analyzed phyto-zooplankton composition,abundance and biomass,and correlation with hydrologic variables to gain information about the forces that structure the plankton.The results showed that the dominant zooplankton were copepods(spring,98.9%;autumn,94.2%),while the phytoplankton were mainly composed of Bacillariophyta(spring,61.8%;autumn,95.6%).The RDA results showed that temperature,salinity and depth highly associated with the distribution and composition of plankton species among the habitats than other factors in spring;temperature,Chla and DO had the strongest influence in autumn.The zooplankton in the ARA and AA ecosystems basically contained the same species as those in other habitats,and each habitat also exhibited a relatively unique combination of plankton species.The structures of the EA zooplankton in spring and the EA phytoplankton in both seasons were much different than other habitats,which may have been caused by factors such as currents and tides.We concluded that there exists similarity of the plankton community between artificial reef area and adjacent waters,whereas the EAs may be relatively independent systems.Therefore,these interaction between plankton community should be considered when designing MPA networks,and ocean circulations should be considered more than the environmental factors.展开更多
Macrophyte habitats exhibit remarkable heterogeneity,encompassing the spatial variation of abiotic and biotic components such as changes in water conditions and weather as well as anthropogenic stressors.Environmental...Macrophyte habitats exhibit remarkable heterogeneity,encompassing the spatial variation of abiotic and biotic components such as changes in water conditions and weather as well as anthropogenic stressors.Environmental factors are thought to be important drivers shaping the genetic and epigenetic variation of aquatic plants.However,the links among genetic diversity,epigenetic variation,and environmental variables remain largely unclear,especially for clonal aquatic plants.Here,we performed population genetic and epigenetic analyses in conjunction with habitat discrimination to elucidate the environmental factors driving intraspecies genetic and epigenetic variation in hornwort(Ceratophyllum demersum)in a subtropical lake.Environmental factors were highly correlated with the genetic and epigenetic variation of C.demersum,with temperature being a key driver of the genetic variation.Lower temperature was detected to be correlated with greater genetic and epigenetic variation.Genetic and epigenetic variation were positively driven by water temperature,but were negatively affected by ambient air temperature.These findings indicate that the genetic and epigenetic variation of this clonal aquatic herb is not related to the geographic feature but is instead driven by environmental conditions,and demonstrate the effects of temperature on local genetic and epigenetic variation in aquatic systems.展开更多
Spatiotemporal variation of seed rain reflects the response of plants in terms of their reproductive strategy to environmental gradients.In this study,we collected seeds from four sites in the Dalaoling Nature Reserve...Spatiotemporal variation of seed rain reflects the response of plants in terms of their reproductive strategy to environmental gradients.In this study,we collected seeds from four sites in the Dalaoling Nature Reserve,Hubei Province,China,between 2011 and 2014,measured seed output and seed mass as seed rain traits,and compared their interannual and elevational variation.Then,we ran phylogenetic generalized mixed linear models(PGLMMs) to explore the effects of temperature and precipitation as well as interspecific differences on seed rain,and fitted the best regression models for seed rain vs.weather of canopy and understory species.The results showed no correlation between values of seed output and seed mass.However,the variation of the two traits showed significantly positive correlation.Seed output of canopy species generally decreased with increasing elevation,and showed significant interannual difference;however,seed output of understory species and seed mass for both canopy and understory species did not show consistency tends along elevational or in interannual variation.Seed output was significantly affected by temperature and precipitation,while seed mass mainly varied due to interspecific differences.Weather explained more the variation of the seed output of canopy species than that of understory species,with R^(2) values of 43.0%and 29.9%,respectively.These results suggested that canopy plants contributed more to the reproductive dynamics of the whole communities,and the canopy's buffer effect on the underground weakened the response of understory plants to weather variation in terms of their reproductive strategy.展开更多
Seed size is an important agronomic trait in melons that directly affects seed germination and subsequent seedling growth.However,the genetic mechanism underlying seed size in melon remains unclear.In the present stud...Seed size is an important agronomic trait in melons that directly affects seed germination and subsequent seedling growth.However,the genetic mechanism underlying seed size in melon remains unclear.In the present study,we employed Bulked-Segregant Analysis sequencing(BSA-seq)to identify a candidate region(~1.35 Mb)on chromosome 6 that corresponds to seed size.This interval was confirmed by QTL mapping of three seed size-related traits from an F2 population across three environments.This mapping region represented nine QTLs that shared an overlapping region on chromosome 6,collectively referred to as qSS6.1.New InDel markers were developed in the qSS6.1 region,narrowing it down to a 68.35 kb interval that contains eight annotated genes.Sequence variation analysis of the eight genes identified a SNP with a C to T transition mutation in the promoter region of MELO3C014002,a leucine-rich repeat receptor-like kinase(LRR-RLK)gene.This mutation affected the promoter activity of the MELO3C014002 gene and was successfully used to differentiate the large-seeded accessions(C-allele)from the small-seeded accessions(T-allele).qRT-PCR revealed differential expression of MELO3C014002 between the two parental lines.Its predicted protein has typical LRR-RLK family domains,and phylogenetic analyses reveled its similarity with the homologs in several plant species.Altogether,these findings suggest MELO3C014002 as the most likely candidate gene involved in melon seed size regulation.Our results will be helpful for better understanding the genetic mechanism regulating seed size in melons and for genetically improving this important trait through molecular breeding pathways.展开更多
The heterogeneous variational nodal method(HVNM)has emerged as a potential approach for solving high-fidelity neutron transport problems.However,achieving accurate results with HVNM in large-scale problems using high-...The heterogeneous variational nodal method(HVNM)has emerged as a potential approach for solving high-fidelity neutron transport problems.However,achieving accurate results with HVNM in large-scale problems using high-fidelity models has been challenging due to the prohibitive computational costs.This paper presents an efficient parallel algorithm tailored for HVNM based on the Message Passing Interface standard.The algorithm evenly distributes the response matrix sets among processors during the matrix formation process,thus enabling independent construction without communication.Once the formation tasks are completed,a collective operation merges and shares the matrix sets among the processors.For the solution process,the problem domain is decomposed into subdomains assigned to specific processors,and the red-black Gauss-Seidel iteration is employed within each subdomain to solve the response matrix equation.Point-to-point communication is conducted between adjacent subdomains to exchange data along the boundaries.The accuracy and efficiency of the parallel algorithm are verified using the KAIST and JRR-3 test cases.Numerical results obtained with multiple processors agree well with those obtained from Monte Carlo calculations.The parallelization of HVNM results in eigenvalue errors of 31 pcm/-90 pcm and fission rate RMS errors of 1.22%/0.66%,respectively,for the 3D KAIST problem and the 3D JRR-3 problem.In addition,the parallel algorithm significantly reduces computation time,with an efficiency of 68.51% using 36 processors in the KAIST problem and 77.14% using 144 processors in the JRR-3 problem.展开更多
文摘Approximately 20%of colorectal cancer(CRC)patients present with metastasis at diagnosis.Among Stage I-III CRC patients who undergo surgical resection,18%typically suffer from distal metastasis within the first three years following initial treatment.The median survival duration after the diagnosis of metastatic CRC(mCRC)is only 9 mo.mCRC is traditionally considered to be an advanced stage malignancy or is thought to be caused by incomplete resection of tumor tissue,allowing cancer cells to spread from primary to distant organs;however,increa-sing evidence suggests that the mCRC process can begin early in tumor development.CRC patients present with high heterogeneity and diverse cancer phenotypes that are classified on the basis of molecular and morphological alterations.Different genomic and nongenomic events can induce subclone diversity,which leads to cancer and metastasis.Throughout the course of mCRC,metastatic cascades are associated with invasive cancer cell migration through the circulatory system,extravasation,distal seeding,dormancy,and reactivation,with each step requiring specific molecular functions.However,cancer cells presenting neoantigens can be recognized and eliminated by the immune system.In this review,we explain the biological factors that drive CRC metastasis,namely,genomic instability,epigenetic instability,the metastatic cascade,the cancer-immunity cycle,and external lifestyle factors.Despite remarkable progress in CRC research,the role of molecular classification in therapeutic intervention remains unclear.This review shows the driving factors of mCRC which may help in identifying potential candidate biomarkers that can improve the diagnosis and early detection of mCRC cases.
文摘Assessment of past-climate simulations of regional climate models(RCMs)is important for understanding the reliability of RCMs when used to project future regional climate.Here,we assess the performance and discuss possible causes of biases in a WRF-based RCM with a grid spacing of 50 km,named WRFG,from the North American Regional Climate Change Assessment Program(NARCCAP)in simulating wet season precipitation over the Central United States for a period when observational data are available.The RCM reproduces key features of the precipitation distribution characteristics during late spring to early summer,although it tends to underestimate the magnitude of precipitation.This dry bias is partially due to the model’s lack of skill in simulating nocturnal precipitation related to the lack of eastward propagating convective systems in the simulation.Inaccuracy in reproducing large-scale circulation and environmental conditions is another contributing factor.The too weak simulated pressure gradient between the Rocky Mountains and the Gulf of Mexico results in weaker southerly winds in between,leading to a reduction of warm moist air transport from the Gulf to the Central Great Plains.The simulated low-level horizontal convergence fields are less favorable for upward motion than in the NARR and hence,for the development of moist convection as well.Therefore,a careful examination of an RCM’s deficiencies and the identification of the source of errors are important when using the RCM to project precipitation changes in future climate scenarios.
基金the National Natural Science Foundation of China(Nos.U20A2089 and 41971152)the Research Foundation of the Department of Natural Resources of Hunan Province(No.20230138ST)to SLthe open research fund of Technology Innovation Center for Ecological Conservation and Restoration in Dongting Lake Basin,Ministry of Natural Resources(No.2023005)to YZ。
文摘Understanding the spatial variation,temporal changes,and their underlying driving forces of carbon sequestration in various forests is of great importance for understanding the carbon cycle and carbon management options.How carbon density and sequestration in various Cunninghamia lanceolata forests,extensively cultivated for timber production in subtropical China,vary with biodiversity,forest structure,environment,and cultural factors remain poorly explored,presenting a critical knowledge gap for realizing carbon sequestration supply potential through management.Based on a large-scale database of 449 permanent forest inventory plots,we quantified the spatial-temporal heterogeneity of aboveground carbon densities and carbon accumulation rates in Cunninghamia lanceolate forests in Hunan Province,China,and attributed the contributions of stand structure,environmental,and management factors to the heterogeneity using quantile age-sequence analysis,partial least squares path modeling(PLS-PM),and hot-spot analysis.The results showed lower values of carbon density and sequestration on average,in comparison with other forests in the same climate zone(i.e.,subtropics),with pronounced spatial and temporal variability.Specifically,quantile regression analysis using carbon accumulation rates along an age sequence showed large differences in carbon sequestration rates among underperformed and outperformed forests(0.50 and 1.80 Mg·ha^(-1)·yr^(-1)).PLS-PM demonstrated that maximum DBH and stand density were the main crucial drivers of aboveground carbon density from young to mature forests.Furthermore,species diversity and geotopographic factors were the significant factors causing the large discrepancy in aboveground carbon density change between low-and high-carbon-bearing forests.Hotspot analysis revealed the importance of culture attributes in shaping the geospatial patterns of carbon sequestration.Our work highlighted that retaining largesized DBH trees and increasing shade-tolerant tree species were important to enhance carbon sequestration in C.lanceolate forests.
基金the University of Reading, funded by the UK–China Research and Innovation Partnership Fund through the Met Office Climate Science for Service Partnership (CSSP) China as part of the Newton Fundsupported by the National Natural Science Foundation of China (Grant Nos. 42030603 and 42175044)+1 种基金supported by CSSP-China. NPK was supported by an Independent Research Fellowship from the Natural Environment Research Council (Grant No. NE/L010976/1)supported by the National Centre for Atmospheric Science via the NERC/GCRF programme “Atmospheric hazards in developing countries: risk assessment and early warnings ” (ACREW)。
文摘The frequency and duration of observed concurrent hot and dry events(HDEs) over China during the growing season(April–September) exhibit significant decadal changes across the mid-1990s. These changes are characterized by increases in HDE frequency and duration over most of China, with relatively large increases over southeastern China(SEC), northern China(NC), and northeastern China(NEC). The frequency of HDEs averaged over China in the present day(PD,1994–2011) is double that in the early period(EP, 1964–81);the duration of HDEs increases by 60%. Climate experiments with the Met Office Unified Model(MetUM-GOML2) are used to estimate the contributions of anthropogenic forcing to HDE decadal changes over China. Anthropogenic forcing changes can explain 60%–70% of the observed decadal changes,suggesting an important anthropogenic influence on HDE changes over China across the mid-1990s. Single-forcing experiments indicate that the increase in greenhouse gas(GHG) concentrations dominates the simulated decadal changes,increasing the frequency and duration of HDEs throughout China. The change in anthropogenic aerosol(AA) emissions significantly decreases the frequency and duration of HDEs over SEC and NC, but the magnitude of the decrease is much smaller than the increase induced by GHGs. The changes in HDEs in response to anthropogenic forcing are mainly due to the response of climatological mean surface air temperatures. The contributions from changes in variability and changes in climatological mean soil moisture and evapotranspiration are relatively small. The physical processes associated with the response of HDEs to GHG and AA changes are also revealed.
基金supported by the National Natural Science Foundation of China(Grant No.42277165)the Fundamental Research Funds for the Central Universities,China University of Geosciences(Wuhan)(Grant No.CUGCJ1821)the National Overseas Study Fund(Grant No.202106410040).
文摘As a calculation method based on the Galerkin variation,the numerical manifold method(NMM)adopts a double covering system,which can easily deal with discontinuous deformation problems and has a high calculation accuracy.Aiming at the thermo-mechanical(TM)coupling problem of fractured rock masses,this study uses the NMM to simulate the processes of crack initiation and propagation in a rock mass under the influence of temperature field,deduces related system equations,and proposes a penalty function method to deal with boundary conditions.Numerical examples are employed to confirm the effectiveness and high accuracy of this method.By the thermal stress analysis of a thick-walled cylinder(TWC),the simulation of cracking in the TWC under heating and cooling conditions,and the simulation of thermal cracking of the SwedishÄspöPillar Stability Experiment(APSE)rock column,the thermal stress,and TM coupling are obtained.The numerical simulation results are in good agreement with the test data and other numerical results,thus verifying the effectiveness of the NMM in dealing with thermal stress and crack propagation problems of fractured rock masses.
基金financially supported by the National Key Research and Development Program of China(Grant No.2022YFC2806102)the National Natural Science Foundation of China(Grant Nos.52171287,52325107)+2 种基金High Tech Ship Research Project of Ministry of Industry and Information Technology(Grant Nos.2023GXB01-05-004-03,GXBZH2022-293)the Science Foundation for Distinguished Young Scholars of Shandong Province(Grant No.ZR2022JQ25)the Taishan Scholars Project(Grant No.tsqn201909063)。
文摘Leakages from subsea oil and gas equipment cause substantial economic losses and damage to marine ecosystem,so it is essential to locate the source of the leak.However,due to the complexity and variability of the marine environment,the signals collected by hydrophone contain a variety of noises,which makes it challenging to extract useful signals for localization.To solve this problem,a hydrophone denoising algorithm is proposed based on variational modal decomposition(VMD)with grey wolf optimization.First,the average envelope entropy is used as the fitness function of the grey wolf optimizer to find the optimal solution for the parameters K andα.Afterward,the VMD algorithm decomposes the original signal parameters to obtain the intrinsic mode functions(IMFs).Subsequently,the number of interrelationships between each IMF and the original signal was calculated,the threshold value was set,and the noise signal was removed to calculate the time difference using the valid signal obtained by reconstruction.Finally,the arrival time difference is used to locate the origin of the leak.The localization accuracy of the method in finding leaks is investigated experimentally by constructing a simulated leak test rig,and the effectiveness and feasibility of the method are verified.
基金This study was supported by the Key Project of Natural Science Research for Colleges and Universities in Anhui Province(KJ2021A0533,2023AH050345)the Excellent Scientific Research and Innovation Team of Universities in Anhui Province(2022AH010029).
文摘Seed germination with selenium(Se)is promising for producing Se-biofortified foods.Mungbean(Vigna radiata(L.)Wilczek)sprout is freshly eaten as a salad dressed with sauce,making it superior for Se biofortification.Since the Se safety range for the human body is extremely narrow,it is imperative to evaluate the genotypic responses of mungbean sprouts to Se.This study evaluated the Se enrichment capacity and interaction withflavonoids and antioxidant systems in sprouts of 20 mungbean germplasms.Selenium treatment was done by immersing mung-bean seeds in 20μM sodium selenite solution for 8 h.Afterward,the biomass,Se amounts,flavonoid(particularly vitexin and isovitexin)contents,antioxidant capacity,and key biosynthetic gene expressions were measured.Sprout Se content was 2.0-7.0μg g^(-1) DW among the 20 mungbean germplasms.Selenium treatment differentially affected the biomass,totalflavonoid,vitexin,isovitexin,antioxidant enzyme activities,and antioxidant capacities of the mungbean germplasms.Eight germplasms showed increased biomass(p<0.05),the highest increasing by 127%,but 13 did not phenotypically respond to Se treatment.Seven and six germplasms showed varied levels of vitexin and isovitexin increment after Se treatment,the highest measuring 2.67-and 2.87-folds for vitexin and isovitexin,respectively.Two mungbeanflavonoid biosynthesis genes,chalcone synthase(VrCHS)and chalcone isomerase(VrCHI)were significantly up-regulated in the germplasms with increased vitexin and isovitexin levels(p<0.05).Moreover,Se enrichment capacity was significantly correlated with the vitexin,isovitexin,and antiox-idant capacities.In conclusion,mungbean sprouts could be a useful Se-biofortified food,but the Se enrichment capacity and nutritional response must be determined for each germplasm before commercialization.
基金supported by the National Key Research and Development Program of China(Grant No.2022YFC3080200)the National Natural Science Foundation of China(Grant No.42022053)the China Postdoctoral Science Foundation(Grant No.2023M731264).
文摘Natural slopes usually display complicated exposed rock surfaces that are characterized by complex and substantial terrain undulation and ubiquitous undesirable phenomena such as vegetation cover and rockfalls.This study presents a systematic outcrop research of fracture pattern variations in a complicated rock slope,and the qualitative and quantitative study of the complex phenomena impact on threedimensional(3D)discrete fracture network(DFN)modeling.As the studies of the outcrop fracture pattern have been so far focused on local variations,thus,we put forward a statistical analysis of global variations.The entire outcrop is partitioned into several subzones,and the subzone-scale variability of fracture geometric properties is analyzed(including the orientation,the density,and the trace length).The results reveal significant variations in fracture characteristics(such as the concentrative degree,the average orientation,the density,and the trace length)among different subzones.Moreover,the density of fracture sets,which is approximately parallel to the slope surface,exhibits a notably higher value compared to other fracture sets across all subzones.To improve the accuracy of the DFN modeling,the effects of three common phenomena resulting from vegetation and rockfalls are qualitatively analyzed and the corresponding quantitative data processing solutions are proposed.Subsequently,the 3D fracture geometric parameters are determined for different areas of the high-steep rock slope in terms of the subzone dimensions.The results show significant variations in the same set of 3D fracture parameters across different regions with density differing by up to tenfold and mean trace length exhibiting differences of 3e4 times.The study results present precise geological structural information,improve modeling accuracy,and provide practical solutions for addressing complex outcrop issues.
基金This study was conducted in compliance with the standards stated in the eighth edition(2013)of the Australian Code for the Care and Use of Animals for Scientific Purposes,and the study was approved by the institutional Animal Ethics Committee of The University of Adelaide under the approval No.S-2018-015.
文摘Background The gut microbiota influences chicken health,welfare,and productivity.A diverse and balanced microbiota has been associated with improved growth,efficient feed utilisation,a well-developed immune system,disease resistance,and stress tolerance in chickens.Previous studies on chicken gut microbiota have predominantly focused on broiler chickens and have usually been limited to one or two sections of the digestive system,under con-trolled research environments,and often sampled at a single time point.To extend these studies,this investigation examined the microbiota of commercially raised layer chickens across all major gut sections of the digestive system and with regular sampling from rearing to the end of production at 80 weeks.The aim was to build a detailed picture of microbiota development across the entire digestive system of layer chickens and study spatial and temporal dynamics.Results The taxonomic composition of gut microbiota differed significantly between birds in the rearing and pro-duction stages,indicating a shift after laying onset.Similar microbiota compositions were observed between proven-triculus and gizzard,as well as between jejunum and ileum,likely due to their anatomical proximity.Lactobacil-lus dominated the upper gut in pullets and the lower gut in older birds.The oesophagus had a high proportion of Proteobacteria,including opportunistic pathogens such as Gallibacterium.Relative abundance of Gallibacterium increased after peak production in multiple gut sections.Aeriscardovia was enriched in the late-lay phase compared to younger birds in multiple gut sections.Age influenced microbial richness and diversity in different organs.The upper gut showed decreased diversity over time,possibly influenced by dietary changes,while the lower gut,specifi-cally cecum and colon,displayed increased richness as birds matured.However,age-related changes were inconsist-ent across all organs,suggesting the influence of organ-specific factors in microbiota maturation.Conclusion Addressing a gap in previous research,this study explored the microbiota across all major gut sections and tracked their dynamics from rearing to the end of the production cycle in commercially raised layer chickens.This study provides a comprehensive understanding of microbiota structure and development which help to develop targeted strategies to optimise gut health and overall productivity in poultry production.
基金supported by the open fund project of Shandong Provincial Key Laboratory of Ocean Engineering,Ocean University of China(No.kloe201901)the State Key Laboratory of Estuarine and Coastal Research(No.SKLEC-KF201707).
文摘This study compared the differences in the wave climate in the South China Sea and North Indian Ocean under these two datasets:ERA-40 wave reanalysis and Mei’s hindcast wave data.In the numerical calculation of regional ocean waves,the wave climate characteristics exhibited significant bias if the influence of external swells(swells from afar)was not fully considered,which may provide an incorrect basis for global climate change analysis.1)The trends of the significant wave height(SWH)obtained from the two datasets showed significant differences,such as those of the Bay of Bengal and the Java Sea in June-July-August.For the past 45 years,SWH from ERA-40(SWH-ERA)exhibited a significant annual increase in low-latitude waters of the North Indian Ocean(0.2-0.6 cm yr^(-1))and South China Sea(0.2-0.8 cm yr^(-1)).2)In the Bay of Bengal,the SWH-ERA in each month was generally 0.5 m higher than the SWH from Mei’s hindcast wave data(SWH-Mei)and can reach 1.0 m higher in some months.3)In the Bay of Bengal,SWH-ERA and SWH-Mei increased significantly at annual rates of 0.13 and 0.27 cm yr^(-1),respectively.This increasing trend was mainly reflected after 1978.SWH-ERA showed a trough in 1975(1.33 m)and a crest in 1992(1.83 m),which were not reflected in SWH-Mei.
文摘Multiplicative noise removal problems have attracted much attention in recent years.Unlike additive noise,multiplicative noise destroys almost all information of the original image,especially for texture images.Motivated by the TV-Stokes model,we propose a new two-step variational model to denoise the texture images corrupted by multiplicative noise with a good geometry explanation in this paper.In the first step,we convert the multiplicative denoising problem into an additive one by the logarithm transform and propagate the isophote directions in the tangential field smoothing.Once the isophote directions are constructed,an image is restored to fit the constructed directions in the second step.The existence and uniqueness of the solution to the variational problems are proved.In these two steps,we use the gradient descent method and construct finite difference schemes to solve the problems.Especially,the augmented Lagrangian method and the fast Fourier transform are adopted to accelerate the calculation.Experimental results show that the proposed model can remove the multiplicative noise efficiently and protect the texture well.
基金Supported by the National Natural Science Foundation of China(Nos.42176116,41576126,41890851,U21A6001)the Natural Science Foundation of Guangdong Province(No.2017A030306020)+4 种基金the Guangdong Major Project of Basic and Applied Basic Research(No.2019B030302004)the Rising Star Foundation of the South China Sea Institute of Oceanology(No.NHXX2019ST0101)the Youth Innovation Promotion Association of the Chinese Academy of Sciences(No.2018377)the Science and Technology Planning Project of Guangdong Province of China(No.2021B1212050023)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA19060503)。
文摘Variations of picoplankton groups were investigated over a one-month period in Daya Bay and Sanya Bay,in the northern South China Sea.The two coastal regions exhibited different variation patterns in physicochemical parameters.Moreover,the diel variations of picoplankton groups were different between the two bays.The abundance of the picoplankton in Sanya Bay displayed a pronounced diel variation,while it was not significant in Daya Bay.In addition,some similar patterns of picoplankton abundance were discovered.In the two bays,virioplankton exhibited the smallest fluctuation range,whereas picocyanobacteria fluctuated most markedly.The fluctuation range of picoplankton groups was larger in spring tide than in neap tide,especially in Sanya Bay.Random forest model analysis demonstrated that the variation of picoplankton groups was attributed to physical and chemical factors in Sanya Bay and Daya Bay,respectively.Therefore,our findings suggest that virioplankton abundance can persist more stably in response to changing environmental conditions compared to bacterioplankton and picophytoplankton.
基金supported by the National Key R&D Program of China(2021YFD1301101)National Swine Industry Technology System(CARS-35)Agricultural Science and Technology Innovation Program(ASTIP-IAS02)。
文摘Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.
基金funding from several sources,including the Chongqing Scientific Research Institution Performance Incentive Project(grant number cstc2022jxjl80007)the Earmarked Fund for China Agriculture Research System(grant number CARS-42-51)+5 种基金the Chongqing Scientific Research Institution Performance Incentive Project(grant number 22527 J)the Key R&D Project in Agriculture and Animal Husbandry of Rongchang(grant number No.22534C-22)Natural Science Foundation of Chongqing Project,grant number CSTB2022NSCQ-MSX0434Natural Science Foundation of Sichuan Project,grant number 2022NSFSC0605Natural Science Foundation of Sichuan Project,grant number 2021YFS0379the Chongqing Technology Innovation and Application Development Project(grant number No.cstc2021ycjh-bgzxm0248)。
文摘Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and other phenotypic traits.Constructing a pan-genome facilitates a thorough identification of genetic variations,thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.Results To comprehensively facilitate population genomic and pan-genomic analyses in geese,we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples.By constructing the pan-genome for geese,we generated non-reference contigs totaling 612 Mb,unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes,1,324 softcore genes,2,734 shell genes,and 878 cloud genes in goose genomes.Furthermore,we detected an 81.97 Mb genomic region showing signs of genome selection,encompassing the TGFBR2 gene correlated with variations in body weight among geese.Genome-wide association studies utilizing single nucleotide polymorphisms(SNPs)and presence-absence variation revealed significant genomic associations with various goose meat quality,reproductive,and body composition traits.For instance,a gene encoding the SVEP1 protein was linked to carcass oblique length,and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length.Notably,the pan-genome analysis revealed enrichment of variable genes in the“hair follicle maturation”Gene Ontology term,potentially linked to the selection of feather-related traits in geese.A gene presence-absence variation analysis suggested a reduced frequency of genes associated with“regulation of heart contraction”in domesticated geese compared to their wild counterparts.Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation.Conclusion This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits,thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese.Moreover,assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome,establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.
基金financed by the Jiangsu Haizhou Bay National Sea Ranching Demonstration Project(No.D-8005-18-0188)the Shanghai Municipal Science and Technology Commission Local Capacity Construction Project(No.21010502200).
文摘Plankton are an important component of marine protected areas(MPAs),and its communities would require much smaller interpatch distances to ensure connection among MPAs.According to the survey from MPAs dominated by artificial reefs and adjacent waters(estuary area(EA),aquaculture area(AA),artificial reef area(ARA),natural area(NA)and comprehensive effect area(CEA))in Haizhou Bay in spring and autumn,we analyzed phyto-zooplankton composition,abundance and biomass,and correlation with hydrologic variables to gain information about the forces that structure the plankton.The results showed that the dominant zooplankton were copepods(spring,98.9%;autumn,94.2%),while the phytoplankton were mainly composed of Bacillariophyta(spring,61.8%;autumn,95.6%).The RDA results showed that temperature,salinity and depth highly associated with the distribution and composition of plankton species among the habitats than other factors in spring;temperature,Chla and DO had the strongest influence in autumn.The zooplankton in the ARA and AA ecosystems basically contained the same species as those in other habitats,and each habitat also exhibited a relatively unique combination of plankton species.The structures of the EA zooplankton in spring and the EA phytoplankton in both seasons were much different than other habitats,which may have been caused by factors such as currents and tides.We concluded that there exists similarity of the plankton community between artificial reef area and adjacent waters,whereas the EAs may be relatively independent systems.Therefore,these interaction between plankton community should be considered when designing MPA networks,and ocean circulations should be considered more than the environmental factors.
基金supported by Liangzi Lake reservesupported by the International Partnership Program of Chinese Academy of Sciences [Grant number, 152342KYSB20200021]+1 种基金the National Key R and D Program of China [Grant numbers, 2020YFD0900305, 2018YFD0900801]National Natural Science Foundation of China [Grant numbers, 32001107, 32201285, 32101254]
文摘Macrophyte habitats exhibit remarkable heterogeneity,encompassing the spatial variation of abiotic and biotic components such as changes in water conditions and weather as well as anthropogenic stressors.Environmental factors are thought to be important drivers shaping the genetic and epigenetic variation of aquatic plants.However,the links among genetic diversity,epigenetic variation,and environmental variables remain largely unclear,especially for clonal aquatic plants.Here,we performed population genetic and epigenetic analyses in conjunction with habitat discrimination to elucidate the environmental factors driving intraspecies genetic and epigenetic variation in hornwort(Ceratophyllum demersum)in a subtropical lake.Environmental factors were highly correlated with the genetic and epigenetic variation of C.demersum,with temperature being a key driver of the genetic variation.Lower temperature was detected to be correlated with greater genetic and epigenetic variation.Genetic and epigenetic variation were positively driven by water temperature,but were negatively affected by ambient air temperature.These findings indicate that the genetic and epigenetic variation of this clonal aquatic herb is not related to the geographic feature but is instead driven by environmental conditions,and demonstrate the effects of temperature on local genetic and epigenetic variation in aquatic systems.
基金the Second Tibetan Plateau Scientific Expedition and Research Program (STEP)(No.2019QZKK0402)。
文摘Spatiotemporal variation of seed rain reflects the response of plants in terms of their reproductive strategy to environmental gradients.In this study,we collected seeds from four sites in the Dalaoling Nature Reserve,Hubei Province,China,between 2011 and 2014,measured seed output and seed mass as seed rain traits,and compared their interannual and elevational variation.Then,we ran phylogenetic generalized mixed linear models(PGLMMs) to explore the effects of temperature and precipitation as well as interspecific differences on seed rain,and fitted the best regression models for seed rain vs.weather of canopy and understory species.The results showed no correlation between values of seed output and seed mass.However,the variation of the two traits showed significantly positive correlation.Seed output of canopy species generally decreased with increasing elevation,and showed significant interannual difference;however,seed output of understory species and seed mass for both canopy and understory species did not show consistency tends along elevational or in interannual variation.Seed output was significantly affected by temperature and precipitation,while seed mass mainly varied due to interspecific differences.Weather explained more the variation of the seed output of canopy species than that of understory species,with R^(2) values of 43.0%and 29.9%,respectively.These results suggested that canopy plants contributed more to the reproductive dynamics of the whole communities,and the canopy's buffer effect on the underground weakened the response of understory plants to weather variation in terms of their reproductive strategy.
基金the Henan Special Funds for Major Science and Technology,China(221100110400)the Henan Scienti?c and Technological Joint Project for Agricultural Improved Varieties,China(2022010503)the National Natural Science Foundation of China(31902038 and 32072564)。
文摘Seed size is an important agronomic trait in melons that directly affects seed germination and subsequent seedling growth.However,the genetic mechanism underlying seed size in melon remains unclear.In the present study,we employed Bulked-Segregant Analysis sequencing(BSA-seq)to identify a candidate region(~1.35 Mb)on chromosome 6 that corresponds to seed size.This interval was confirmed by QTL mapping of three seed size-related traits from an F2 population across three environments.This mapping region represented nine QTLs that shared an overlapping region on chromosome 6,collectively referred to as qSS6.1.New InDel markers were developed in the qSS6.1 region,narrowing it down to a 68.35 kb interval that contains eight annotated genes.Sequence variation analysis of the eight genes identified a SNP with a C to T transition mutation in the promoter region of MELO3C014002,a leucine-rich repeat receptor-like kinase(LRR-RLK)gene.This mutation affected the promoter activity of the MELO3C014002 gene and was successfully used to differentiate the large-seeded accessions(C-allele)from the small-seeded accessions(T-allele).qRT-PCR revealed differential expression of MELO3C014002 between the two parental lines.Its predicted protein has typical LRR-RLK family domains,and phylogenetic analyses reveled its similarity with the homologs in several plant species.Altogether,these findings suggest MELO3C014002 as the most likely candidate gene involved in melon seed size regulation.Our results will be helpful for better understanding the genetic mechanism regulating seed size in melons and for genetically improving this important trait through molecular breeding pathways.
基金supported by the National Key Research and Development Program of China(No.2020YFB1901900)the National Natural Science Foundation of China(Nos.U20B2011,12175138)the Shanghai Rising-Star Program。
文摘The heterogeneous variational nodal method(HVNM)has emerged as a potential approach for solving high-fidelity neutron transport problems.However,achieving accurate results with HVNM in large-scale problems using high-fidelity models has been challenging due to the prohibitive computational costs.This paper presents an efficient parallel algorithm tailored for HVNM based on the Message Passing Interface standard.The algorithm evenly distributes the response matrix sets among processors during the matrix formation process,thus enabling independent construction without communication.Once the formation tasks are completed,a collective operation merges and shares the matrix sets among the processors.For the solution process,the problem domain is decomposed into subdomains assigned to specific processors,and the red-black Gauss-Seidel iteration is employed within each subdomain to solve the response matrix equation.Point-to-point communication is conducted between adjacent subdomains to exchange data along the boundaries.The accuracy and efficiency of the parallel algorithm are verified using the KAIST and JRR-3 test cases.Numerical results obtained with multiple processors agree well with those obtained from Monte Carlo calculations.The parallelization of HVNM results in eigenvalue errors of 31 pcm/-90 pcm and fission rate RMS errors of 1.22%/0.66%,respectively,for the 3D KAIST problem and the 3D JRR-3 problem.In addition,the parallel algorithm significantly reduces computation time,with an efficiency of 68.51% using 36 processors in the KAIST problem and 77.14% using 144 processors in the JRR-3 problem.