Case histories have shown that the liquefaction-induced soil lateral spreading is one of the main causes of damage to pile foundations subjected to seismic loading. Post-liquefaction soil behaves similarly to a viscou...Case histories have shown that the liquefaction-induced soil lateral spreading is one of the main causes of damage to pile foundations subjected to seismic loading. Post-liquefaction soil behaves similarly to a viscous fluid. This study investigated the effect of soil lateral spreading on a single pile based on fluid mechanics in which the liquefied soils were treated as Newtonian fluids. A numerical simulation on a single pile embedded in a fully saturated sandy foundation was conducted and compared with shake table tests. The lateral flow effect and the effect of shear strain rate were discussed. After liquefaction, the acceleration of the foundation shows that there are no obvious spikes and finally reaches a stable state. The presented method can predict the pile response better than p-y curve method. A parametric study was performed to explore the effect of several influence factors on pile behaviors. The results show that the pile head displacement decreases and the maximum bending moment at pile bottom increases with the increase of bending stiffness. With the same pile bending stiffness, the displacement and bending moment of pile increase with the increase of soil viscosity and acceleration amplitude.展开更多
Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single n...Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms(SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here,we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs(FROH), homozygosity(FHOM), genomic relationship matrix(FGRM)and pedigree(FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.Results: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes(SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_totaland FHOM, while the lowest was-0.083 between FGRMand FPED. The correlations between FPEDand FROHusing four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes(SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4.Conclusion: FROHcan be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROHcan provide an alternative to inbreeding estimates.Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.展开更多
Background: RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has...Background: RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has enabled the identification of RNA edits at unprecedented throughput and resolution. However, our knowledge of RNA editing in swine is still limited.Results: Here, we utilized RES-Scanner to identify RNA editing sites in the brain, subcutaneous fat, heart, liver,muscle, lung and ovary in three 180-day-old Large White gilts based on matched strand-specific RNA sequencing and whole-genome resequencing datasets. In total, we identified 74863 editing sites, and 92.1% of these sites caused adenosine-to-guanosine(A-to-G) conversion. Most A-to-G sites were located in noncoding regions and generally had low editing levels. In total, 151 A-to-G sites were detected in coding regions(CDS), including 94 sites that could lead to nonsynonymous amino acid changes. We provide further evidence supporting a previous observation that pig transcriptomes are highly editable at PRE-1 elements. The number of A-to-G editing sites ranged from 4155(muscle) to 25001(brain) across the seven tissues. The expression levels of the ADAR enzymes could explain some but not all of this variation across tissues. The functional analysis of the genes with tissuespecific editing sites in each tissue revealed that RNA editing might play important roles in tissue function.Specifically, more pathways showed significant enrichment in the fat and liver than in other tissues, while no pathway was enriched in the muscle.Conclusions: This study identified a total of 74863 nonredundant RNA editing sites in seven tissues and revealed the potential importance of RNA editing in tissue function. Our findings largely extend the porcine editome and enhance our understanding of RNA editing in swine.展开更多
Background:The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms,which depend on chromatin accessibility.However,how chromatin accessibility plays a...Background:The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms,which depend on chromatin accessibility.However,how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported.To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development,we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45,70 and 100 days post coitus(dpc).Results:In total,21,638,35,447 and 60,181 unique regions(or peaks)were found across the embryos at 45 dpc(LW45),70 dpc(LW70)and 100 dpc(LW100),respectively.More than 91%of the peaks were annotated within−1 kb to 100 bp of transcription start sites(TSSs).First,widespread increases in specific accessible chromatin regions(ACRs)from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development.Second,the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes.Moreover,the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle developmentrelated genes,such as MyoG,Mef2c,and Mef2d.Several potential transcriptional repressors,including E2F6,OTX2 and CTCF,were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data.Conclusions:This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors.Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.展开更多
The Early Cretaceous deposits are composed of important source rocks in Boli Basin. The types of the source rocks include black mudstones and coal (with carbonaceous mudstone). By the organic geochemical analysis meth...The Early Cretaceous deposits are composed of important source rocks in Boli Basin. The types of the source rocks include black mudstones and coal (with carbonaceous mudstone). By the organic geochemical analysis methods, the authors discussed the organic petrological characters, abundance of organic matter, degree of maturity and the type of source rocks. The main micro-component of black mudstone is exinite or vitrinite, and the content of vitrinite is high in coal. The weathering of the outcrop is very serious. The abundance of organic matter in source rock reaches the poor to better rank. The major kerogens in mudstone are type-Ⅲ, type-Ⅱ 2 and some type-Ⅱ 1; the organic type of coal is type-Ⅲ. The thermal evolution of the source rocks in every structural unit is very different, from low-maturity to over-maturity. The depositional environment is reductive, which is good for the preservation of organic matter. The organic matter in source rocks is mainly from aquatic organisms and terrigenous input.展开更多
1.Introduction Hydrogen is an ideal energy carrier to tackle the energy crisis and greenhouse effect,because of its high energy density and low emission.The production,storage and transportation of hydrogen are key fa...1.Introduction Hydrogen is an ideal energy carrier to tackle the energy crisis and greenhouse effect,because of its high energy density and low emission.The production,storage and transportation of hydrogen are key factors to the practical application of hydrogen energy.As the scientific and technological understanding of the electrochemical devices was advancing in the past few decades,water electrolyzers based on the proton exchange membrane (PEM) have attracted much focus for its huge potential on the production of hydrogen via water splitting.PEM electrolyzers use perfluorinated sulfonic acid (PFSA) based membranes as the electrolyte.展开更多
Ex situ conservation is the main method for the protection of endangered wildlife.To explore the effect of ex situ conservation on the gut microbiota of the kiang(Equus kiang),metagenomic sequencing combined with bioi...Ex situ conservation is the main method for the protection of endangered wildlife.To explore the effect of ex situ conservation on the gut microbiota of the kiang(Equus kiang),metagenomic sequencing combined with bioinformatics analysis was used to investigate the composition and function of the gut microbiota of the kiang.The results showed that ex situ conservation not only protected wildlife,but also affected the composition and function of gut microbiota,as well as the health of animals.In the zoo,the ratio of the relative abundance of Firmicutes to that of Bacteroidetes(F/B)is higher,clusters of potentially pathogenic bacteria(such as Catonella,Catonella,and Mycoplasma)are more numerous,the abundance of resistance genes is higher,and the abundance of metabolic functions is increased.The dynamic changes of the gut microbiota also played an important role in the nutritional absorption,energy metabolism,and environmental adaptation of the kiang.Improving the rearing environment and increasing food diversity play important roles for increasing the diversity of gut microbiota,reducing the spread of potentially pathogenic bacteria,and reducing diseases.In the wild,especially in winter and in food-deficient areas,food supplementation can enhance the gut microbial homeostasis of wild animals and reduce the impact of crises.In depth studies of the gut microbial function of wildlife have important implications for improving ex situ conservation.展开更多
文摘Case histories have shown that the liquefaction-induced soil lateral spreading is one of the main causes of damage to pile foundations subjected to seismic loading. Post-liquefaction soil behaves similarly to a viscous fluid. This study investigated the effect of soil lateral spreading on a single pile based on fluid mechanics in which the liquefied soils were treated as Newtonian fluids. A numerical simulation on a single pile embedded in a fully saturated sandy foundation was conducted and compared with shake table tests. The lateral flow effect and the effect of shear strain rate were discussed. After liquefaction, the acceleration of the foundation shows that there are no obvious spikes and finally reaches a stable state. The presented method can predict the pile response better than p-y curve method. A parametric study was performed to explore the effect of several influence factors on pile behaviors. The results show that the pile head displacement decreases and the maximum bending moment at pile bottom increases with the increase of bending stiffness. With the same pile bending stiffness, the displacement and bending moment of pile increase with the increase of soil viscosity and acceleration amplitude.
基金supported by the Natural Science Foundation of China (No.31572357) to FPZthe National Swine Industry Technology System(CARS-35) to LXW。
文摘Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms(SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here,we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs(FROH), homozygosity(FHOM), genomic relationship matrix(FGRM)and pedigree(FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.Results: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes(SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_totaland FHOM, while the lowest was-0.083 between FGRMand FPED. The correlations between FPEDand FROHusing four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes(SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4.Conclusion: FROHcan be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROHcan provide an alternative to inbreeding estimates.Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.
基金supported by the National Key Technology R&D Program of China(2015BAD03B02–2)Beijing Natural Science Foundation(6174047)+1 种基金earmarked fund for Modern Agro-industry Technology Research System(CARS-35)Agricultural Science and Technology Innovation Program(ASTIP-IAS02)
文摘Background: RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has enabled the identification of RNA edits at unprecedented throughput and resolution. However, our knowledge of RNA editing in swine is still limited.Results: Here, we utilized RES-Scanner to identify RNA editing sites in the brain, subcutaneous fat, heart, liver,muscle, lung and ovary in three 180-day-old Large White gilts based on matched strand-specific RNA sequencing and whole-genome resequencing datasets. In total, we identified 74863 editing sites, and 92.1% of these sites caused adenosine-to-guanosine(A-to-G) conversion. Most A-to-G sites were located in noncoding regions and generally had low editing levels. In total, 151 A-to-G sites were detected in coding regions(CDS), including 94 sites that could lead to nonsynonymous amino acid changes. We provide further evidence supporting a previous observation that pig transcriptomes are highly editable at PRE-1 elements. The number of A-to-G editing sites ranged from 4155(muscle) to 25001(brain) across the seven tissues. The expression levels of the ADAR enzymes could explain some but not all of this variation across tissues. The functional analysis of the genes with tissuespecific editing sites in each tissue revealed that RNA editing might play important roles in tissue function.Specifically, more pathways showed significant enrichment in the fat and liver than in other tissues, while no pathway was enriched in the muscle.Conclusions: This study identified a total of 74863 nonredundant RNA editing sites in seven tissues and revealed the potential importance of RNA editing in tissue function. Our findings largely extend the porcine editome and enhance our understanding of RNA editing in swine.
基金supported by the Agricultural Science and Technology Innovation Program(ASTIP-IAS02).
文摘Background:The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms,which depend on chromatin accessibility.However,how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported.To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development,we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45,70 and 100 days post coitus(dpc).Results:In total,21,638,35,447 and 60,181 unique regions(or peaks)were found across the embryos at 45 dpc(LW45),70 dpc(LW70)and 100 dpc(LW100),respectively.More than 91%of the peaks were annotated within−1 kb to 100 bp of transcription start sites(TSSs).First,widespread increases in specific accessible chromatin regions(ACRs)from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development.Second,the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes.Moreover,the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle developmentrelated genes,such as MyoG,Mef2c,and Mef2d.Several potential transcriptional repressors,including E2F6,OTX2 and CTCF,were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data.Conclusions:This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors.Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.
文摘The Early Cretaceous deposits are composed of important source rocks in Boli Basin. The types of the source rocks include black mudstones and coal (with carbonaceous mudstone). By the organic geochemical analysis methods, the authors discussed the organic petrological characters, abundance of organic matter, degree of maturity and the type of source rocks. The main micro-component of black mudstone is exinite or vitrinite, and the content of vitrinite is high in coal. The weathering of the outcrop is very serious. The abundance of organic matter in source rock reaches the poor to better rank. The major kerogens in mudstone are type-Ⅲ, type-Ⅱ 2 and some type-Ⅱ 1; the organic type of coal is type-Ⅲ. The thermal evolution of the source rocks in every structural unit is very different, from low-maturity to over-maturity. The depositional environment is reductive, which is good for the preservation of organic matter. The organic matter in source rocks is mainly from aquatic organisms and terrigenous input.
基金supported by the National Key R&D Program of China(2021YFA1500900,2020YFA0710000)the National Natural Science Foundation of China(22172047,22002039,21825201 and U19A2017)+3 种基金the Provincial Natural Science Foundation of Hunan(2021JJ30089,2016TP1009 and 2020JJ5045)the China Postdoctoral Science Foundation(2019M662759,2020M682541 and 2020M682549)the Shenzhen Science and Technology Program(JCYJ20210324122209025)the Changsha Municipal Natural Science Foundation(kq2107008 and kq2007009)。
文摘1.Introduction Hydrogen is an ideal energy carrier to tackle the energy crisis and greenhouse effect,because of its high energy density and low emission.The production,storage and transportation of hydrogen are key factors to the practical application of hydrogen energy.As the scientific and technological understanding of the electrochemical devices was advancing in the past few decades,water electrolyzers based on the proton exchange membrane (PEM) have attracted much focus for its huge potential on the production of hydrogen via water splitting.PEM electrolyzers use perfluorinated sulfonic acid (PFSA) based membranes as the electrolyte.
基金We would like to express our heartfelt thanks to the keepers of the Qinghai-Tibet Plateau Wildlife Park for their help in collecting fecal samples from the Tibetan wild ass in zoo.This study was financially supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA23060602 and XDA2002030302)the Qinghai Province Science and Technology Plan(2021-ZJ-951Q)+3 种基金the Second Tibetan Plateau Scientific Expedition and Research Program(STEP)(2019QZKK0501)Qinghai Key R&D and Transformation Program(2019-SF-150)the Joint Grant from Chinese Academy of Sciences-People’s Government of Qinghai Province on Sanjiangyuan National Park(LHZX-2020-01)the Science and Technology Department of Qinghai Province Major Project“Sanjiangyaun National Park Animal Genome Program.”。
文摘Ex situ conservation is the main method for the protection of endangered wildlife.To explore the effect of ex situ conservation on the gut microbiota of the kiang(Equus kiang),metagenomic sequencing combined with bioinformatics analysis was used to investigate the composition and function of the gut microbiota of the kiang.The results showed that ex situ conservation not only protected wildlife,but also affected the composition and function of gut microbiota,as well as the health of animals.In the zoo,the ratio of the relative abundance of Firmicutes to that of Bacteroidetes(F/B)is higher,clusters of potentially pathogenic bacteria(such as Catonella,Catonella,and Mycoplasma)are more numerous,the abundance of resistance genes is higher,and the abundance of metabolic functions is increased.The dynamic changes of the gut microbiota also played an important role in the nutritional absorption,energy metabolism,and environmental adaptation of the kiang.Improving the rearing environment and increasing food diversity play important roles for increasing the diversity of gut microbiota,reducing the spread of potentially pathogenic bacteria,and reducing diseases.In the wild,especially in winter and in food-deficient areas,food supplementation can enhance the gut microbial homeostasis of wild animals and reduce the impact of crises.In depth studies of the gut microbial function of wildlife have important implications for improving ex situ conservation.