It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms.De novo genes frequently emerge in proximity to existing genes,forming gene overlaps.Here,we p...It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms.De novo genes frequently emerge in proximity to existing genes,forming gene overlaps.Here,we present an analysis of the evolutionary history of a putative de novo gene,lawc,which overlaps with the conserved Trf2 gene,which encodes a general transcription factor in Drosophila melanogaster.We demonstrate that lawc emerged approximately 68 million years ago in the 5'-untranslated region(UTR)of Trf2 and displays an extensive spatiotemporal expression pattern.One of the most remarkable features of the lawc evolutionary history is that its emergence was facilitated by the engagement of Drosophilidae-specific short,highly conserved regions located in Trf2 introns.This represents a unique example of putative de novo gene birth involving conserved DNA regions localized in introns of conserved genes.The observed lawc expression pattern may be due to the overlap of lawc with the 5'-UTR of Trf2.This study not only enriches our understanding of gene evolution but also highlights the complex interplay between genetic conservation and innovation.展开更多
The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into...The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ruminant multi-chambered stomach innovation.We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific genes via batteries of active-RSCNEs during development.Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules.Notably,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the esophagus.Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.展开更多
Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms.Many conserved non-coding sequences(CNSs)function as cis-regulatory elements.They control the ...Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms.Many conserved non-coding sequences(CNSs)function as cis-regulatory elements.They control the development of various lineages.How-ever,predicting clade-wide cis-regulatory elements across several closely related species remains challenging.Based on the relationship between CNSs and cis-regulatory elements,we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes.Using 12-way whole-genome alignment,we first obtained 632112 CNSs in Cucurbitaceae.Next,we identified 16552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants.Furthermore,we predicted 3271 potential regulatory pairs in the cucumber genome,of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages.The CNSs,Cucurbitaceae-wide cis-regulatory elements,and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/.These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.展开更多
Element Transfer Reaction(ETR)theory is a new fundamental theory guiding the design of synthetic routes.It analyses problems from a brand-new perspective of element circulation,decomposing the factors affecting synthe...Element Transfer Reaction(ETR)theory is a new fundamental theory guiding the design of synthetic routes.It analyses problems from a brand-new perspective of element circulation,decomposing the factors affecting synthetic efficiency into three elements:element sources,driving force,and output.Different from the retrosynthetic analysis method and the atom economy theory,the ETR theory places more emphasis on examining the problem as a whole and comprehensively considering various factors involved in industrial applications.This perspective intends to elaborate on the scientific connotation of the ETR theory and explore its characteristics by discussing the practical application cases.展开更多
In this paper,a composite numerical scheme is proposed to solve the threedimensional Darcy-Forchheimer miscible displacement problem with positive semi-definite assumptions.A mixed finite element is used for the fow e...In this paper,a composite numerical scheme is proposed to solve the threedimensional Darcy-Forchheimer miscible displacement problem with positive semi-definite assumptions.A mixed finite element is used for the fow equation.The velocity and pressure are computed simultaneously.The accuracy of velocity is improved one order.The concentration equation is solved by using mixed finite element,multi-step difference and upwind approximation.A multi-step method is used to approximate time derivative for improving the accuracy.The upwind approximation and an expanded mixed finite element are adopted to solve the convection and diffusion,respectively.The composite method could compute the diffusion flux and its gradient.It possibly becomes an eficient tool for solving convection-dominated diffusion problems.Firstly,the conservation of mass holds.Secondly,the multi-step method has high accuracy.Thirdly,the upwind approximation could avoid numerical dispersion.Using numerical analysis of a priori estimates and special techniques of differential equations,we give an error estimates for a positive definite problem.Numerical experiments illustrate its computational efficiency and feasibility of application.展开更多
The development of a general discrete element method for irregularly shaped particles is the core issue of the simulation of the dynamic behavior of granular materials.The general energy-conserving contact theory is u...The development of a general discrete element method for irregularly shaped particles is the core issue of the simulation of the dynamic behavior of granular materials.The general energy-conserving contact theory is used to establish a universal discrete element method suitable for particle contact of arbitrary shape.In this study,three dimentional(3D)modeling and scanning techniques are used to obtain a triangular mesh representation of the true particles containing typical concave particles.The contact volumebased energy-conserving model is used to realize the contact detection between irregularly shaped particles,and the contact force model is refined and modified to describe the contact under real conditions.The inelastic collision processes between the particles and boundaries are simulated to verify the robustness of the modified contact force model and its applicability to the multi-point contact mode.In addition,the packing process and the flow process of a large number of irregular particles are simulated with the modified discrete element method(DEM)to illustrate the applicability of the method of complex problems.展开更多
Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. Howeve...Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.展开更多
This paper discusses the k-degree averaging discontinuous finite element solution for the initial value problem of ordinary differential equations. When k is even, the averaging numerical flux （the average of left an...This paper discusses the k-degree averaging discontinuous finite element solution for the initial value problem of ordinary differential equations. When k is even, the averaging numerical flux （the average of left and right limits for the discontinuous finite element at nodes） has the optimal-order ultraconvergence 2k ＋ 2. For nanlinear Hamiltonian systems （e.g., SchrSdinger equation and Kepler system） with momentum conservation, the discontinuous finite element methods preserve momentum at nodes. These properties are confirmed by numerical experiments.展开更多
Energy conservation of nonlinear Schrodinger ordinary differential equation was proved through using continuous finite element methods of ordinary differential equation; Energy integration conservation was proved thro...Energy conservation of nonlinear Schrodinger ordinary differential equation was proved through using continuous finite element methods of ordinary differential equation; Energy integration conservation was proved through using space-time continuous fully discrete finite element methods and the electron nearly conservation with higher order error was obtained through using time discontinuous only space continuous finite element methods of nonlinear Schrodinger partial equation. The numerical results are in accordance with the theory.展开更多
The hierarchical reconstruction （HR） [Liu, Shu, Tadmor and Zhang, SINUM ＇07] has been successfully applied to prevent oscillations in solutions computed by finite volume, Runge-Kutta discontinuous Galerkin, spectra...The hierarchical reconstruction （HR） [Liu, Shu, Tadmor and Zhang, SINUM ＇07] has been successfully applied to prevent oscillations in solutions computed by finite volume, Runge-Kutta discontinuous Galerkin, spectral volume schemes for solving hyperbolic conservation laws. In this paper, we demonstrate that HR can also be combined with spectral/hp element method for solving hyperbolic conservation laws. An orthogonal spectral basis written in terms of Jacobi polynomials is applied. High computational efficiency is obtained due to such matrix-free algorithm. The formulation is conservative, and essential nomoscillation is enforced by the HR limiter. We show that HR preserves the order of accuracy of the spectral/hp element method for smooth solution problems and generate essentially non-oscillatory solutions profiles for capturing discontinuous solutions without local characteristic decomposition. In addition, we introduce a postprocessing technique to improve HR for limiting high degree numerical solutions.展开更多
In this paper we propose a spectral element: vanishing viscosity (SEW) method for the conservation laws on the semi-infinite interval. By using a suitable mapping, the problem is first transformed into a modified cons...In this paper we propose a spectral element: vanishing viscosity (SEW) method for the conservation laws on the semi-infinite interval. By using a suitable mapping, the problem is first transformed into a modified conservation law in a bounded interval, then the well-known spectral vanishing viscosity technique is generalized to the multi-domain case in order to approximate this trarsformed equation more efficiently. The construction details and convergence analysis are presented. Under a usual assumption of boundedness of the approximation solutions, it is proven that the solution of the SEW approximation converges to the uniciue entropy solution of the conservation laws. A number of numerical tests is carried out to confirm the theoretical results.展开更多
The scientific community faces the challenge of measuring progress toward biodiversity targets and indices have been traditionally used.However,recent inventories in secondary tropical mountain forests using tradition...The scientific community faces the challenge of measuring progress toward biodiversity targets and indices have been traditionally used.However,recent inventories in secondary tropical mountain forests using traditional biodiversity indices have yielded results that are indistinct with primary ones.This shows the need to develop complementary indices that goes beyond species count but integrates the distribution and conservation status of the species.This study developed endemicity and conservation importance index for tropical forest that incorporated the distribution and conservation status of the species.These indices were applied to Mt.Natoo,a remnant primary mossy forest in Buguias,Benguet,Philippines,that resulted to endemicity index of 81.07 and conservation importance index of 42.90.Comparing these with secondary forest sites with comparable Shannon-Wiener,Simpson,Evenness and Margalef’s indices,our endemicity and conservation indices clearly differentiates primary forest(our study site)with higher values from secondary forests with much lower values.Thus,we are proposing these indices for a direct but scientifically-informed identification of specific sites for conservation and protection in tropical forests.Additionally,our study documented a total of 168 vascular plant species(79 endemic and 12 locally threatened species)in Mt.Nato-o.Majority are of tropical elements for both generic and species levels with some temperate elements that could be attributed to the site's high elevation and semi-temperate climate.These are important baseline information for conservation plans and monitoring of tropical mossy forests.展开更多
基金funded by a grant from the Russian Science Foundation № 24-24-00354
文摘It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms.De novo genes frequently emerge in proximity to existing genes,forming gene overlaps.Here,we present an analysis of the evolutionary history of a putative de novo gene,lawc,which overlaps with the conserved Trf2 gene,which encodes a general transcription factor in Drosophila melanogaster.We demonstrate that lawc emerged approximately 68 million years ago in the 5'-untranslated region(UTR)of Trf2 and displays an extensive spatiotemporal expression pattern.One of the most remarkable features of the lawc evolutionary history is that its emergence was facilitated by the engagement of Drosophilidae-specific short,highly conserved regions located in Trf2 introns.This represents a unique example of putative de novo gene birth involving conserved DNA regions localized in introns of conserved genes.The observed lawc expression pattern may be due to the overlap of lawc with the 5'-UTR of Trf2.This study not only enriches our understanding of gene evolution but also highlights the complex interplay between genetic conservation and innovation.
基金supported by the National Key R&D Program of China(Grant No.2020YFA0712402)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDPB17)+3 种基金the CAS Project for Young Scientists in Basic Research(Grant No.YSBR-077)the National Natural Science Foundation of China(Grant Nos.12025107,11871463,11688101,and 61621003)the National Thousand Youth Talents Plan,and the CAS“Light of West China”Program(Grant No.xbzg-zdsys-201913)China.We thank High Performance Computing(HPC)of Northwest A&F University(NWAFU)for providing computing resources。
文摘The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ruminant multi-chambered stomach innovation.We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific genes via batteries of active-RSCNEs during development.Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules.Notably,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the esophagus.Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data.
基金supported by the National Natural Science Foundation of China(grant number:31571361).
文摘Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms.Many conserved non-coding sequences(CNSs)function as cis-regulatory elements.They control the development of various lineages.How-ever,predicting clade-wide cis-regulatory elements across several closely related species remains challenging.Based on the relationship between CNSs and cis-regulatory elements,we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes.Using 12-way whole-genome alignment,we first obtained 632112 CNSs in Cucurbitaceae.Next,we identified 16552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants.Furthermore,we predicted 3271 potential regulatory pairs in the cucumber genome,of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages.The CNSs,Cucurbitaceae-wide cis-regulatory elements,and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/.These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.
基金Industry Foresight and Key Core Technology(No.YZ2023019)Cooperation Project of Yangzhou City with Yangzhou University(No.YZ2023209)+3 种基金Sichuan Tianfu Talent Programme(No.A.2200732)Chengdu Rongpiao Talent Programme(No.1043)SeleValley Scholars Basic Research Project(No.2301)Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)for financial support。
文摘Element Transfer Reaction(ETR)theory is a new fundamental theory guiding the design of synthetic routes.It analyses problems from a brand-new perspective of element circulation,decomposing the factors affecting synthetic efficiency into three elements:element sources,driving force,and output.Different from the retrosynthetic analysis method and the atom economy theory,the ETR theory places more emphasis on examining the problem as a whole and comprehensively considering various factors involved in industrial applications.This perspective intends to elaborate on the scientific connotation of the ETR theory and explore its characteristics by discussing the practical application cases.
基金supported by the Natural Science Foundation of Shandong Province(ZR2021MA019)the National Natural Science Foundation of China(11871312)。
文摘In this paper,a composite numerical scheme is proposed to solve the threedimensional Darcy-Forchheimer miscible displacement problem with positive semi-definite assumptions.A mixed finite element is used for the fow equation.The velocity and pressure are computed simultaneously.The accuracy of velocity is improved one order.The concentration equation is solved by using mixed finite element,multi-step difference and upwind approximation.A multi-step method is used to approximate time derivative for improving the accuracy.The upwind approximation and an expanded mixed finite element are adopted to solve the convection and diffusion,respectively.The composite method could compute the diffusion flux and its gradient.It possibly becomes an eficient tool for solving convection-dominated diffusion problems.Firstly,the conservation of mass holds.Secondly,the multi-step method has high accuracy.Thirdly,the upwind approximation could avoid numerical dispersion.Using numerical analysis of a priori estimates and special techniques of differential equations,we give an error estimates for a positive definite problem.Numerical experiments illustrate its computational efficiency and feasibility of application.
基金supported by the National Key Research and Development Program of China(2018YFA0605902)the National Natural Science Foundation of China(42176241 and 11872136).
文摘The development of a general discrete element method for irregularly shaped particles is the core issue of the simulation of the dynamic behavior of granular materials.The general energy-conserving contact theory is used to establish a universal discrete element method suitable for particle contact of arbitrary shape.In this study,three dimentional(3D)modeling and scanning techniques are used to obtain a triangular mesh representation of the true particles containing typical concave particles.The contact volumebased energy-conserving model is used to realize the contact detection between irregularly shaped particles,and the contact force model is refined and modified to describe the contact under real conditions.The inelastic collision processes between the particles and boundaries are simulated to verify the robustness of the modified contact force model and its applicability to the multi-point contact mode.In addition,the packing process and the flow process of a large number of irregular particles are simulated with the modified discrete element method(DEM)to illustrate the applicability of the method of complex problems.
文摘Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.
基金Project supported by the National Natural Science Foundation of China (No. 10771063)
文摘This paper discusses the k-degree averaging discontinuous finite element solution for the initial value problem of ordinary differential equations. When k is even, the averaging numerical flux （the average of left and right limits for the discontinuous finite element at nodes） has the optimal-order ultraconvergence 2k ＋ 2. For nanlinear Hamiltonian systems （e.g., SchrSdinger equation and Kepler system） with momentum conservation, the discontinuous finite element methods preserve momentum at nodes. These properties are confirmed by numerical experiments.
基金Project supported by the National Basic Research Program of China (973 program) (No.G1999032804)
文摘Energy conservation of nonlinear Schrodinger ordinary differential equation was proved through using continuous finite element methods of ordinary differential equation; Energy integration conservation was proved through using space-time continuous fully discrete finite element methods and the electron nearly conservation with higher order error was obtained through using time discontinuous only space continuous finite element methods of nonlinear Schrodinger partial equation. The numerical results are in accordance with the theory.
基金Research was supported in part by NSF grant DMS-0800612Research was supported by Applied Mathematics program of the US DOE Office of Advanced Scientific Computing ResearchThe Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830
文摘The hierarchical reconstruction （HR） [Liu, Shu, Tadmor and Zhang, SINUM ＇07] has been successfully applied to prevent oscillations in solutions computed by finite volume, Runge-Kutta discontinuous Galerkin, spectral volume schemes for solving hyperbolic conservation laws. In this paper, we demonstrate that HR can also be combined with spectral/hp element method for solving hyperbolic conservation laws. An orthogonal spectral basis written in terms of Jacobi polynomials is applied. High computational efficiency is obtained due to such matrix-free algorithm. The formulation is conservative, and essential nomoscillation is enforced by the HR limiter. We show that HR preserves the order of accuracy of the spectral/hp element method for smooth solution problems and generate essentially non-oscillatory solutions profiles for capturing discontinuous solutions without local characteristic decomposition. In addition, we introduce a postprocessing technique to improve HR for limiting high degree numerical solutions.
文摘In this paper we propose a spectral element: vanishing viscosity (SEW) method for the conservation laws on the semi-infinite interval. By using a suitable mapping, the problem is first transformed into a modified conservation law in a bounded interval, then the well-known spectral vanishing viscosity technique is generalized to the multi-domain case in order to approximate this trarsformed equation more efficiently. The construction details and convergence analysis are presented. Under a usual assumption of boundedness of the approximation solutions, it is proven that the solution of the SEW approximation converges to the uniciue entropy solution of the conservation laws. A number of numerical tests is carried out to confirm the theoretical results.
文摘The scientific community faces the challenge of measuring progress toward biodiversity targets and indices have been traditionally used.However,recent inventories in secondary tropical mountain forests using traditional biodiversity indices have yielded results that are indistinct with primary ones.This shows the need to develop complementary indices that goes beyond species count but integrates the distribution and conservation status of the species.This study developed endemicity and conservation importance index for tropical forest that incorporated the distribution and conservation status of the species.These indices were applied to Mt.Natoo,a remnant primary mossy forest in Buguias,Benguet,Philippines,that resulted to endemicity index of 81.07 and conservation importance index of 42.90.Comparing these with secondary forest sites with comparable Shannon-Wiener,Simpson,Evenness and Margalef’s indices,our endemicity and conservation indices clearly differentiates primary forest(our study site)with higher values from secondary forests with much lower values.Thus,we are proposing these indices for a direct but scientifically-informed identification of specific sites for conservation and protection in tropical forests.Additionally,our study documented a total of 168 vascular plant species(79 endemic and 12 locally threatened species)in Mt.Nato-o.Majority are of tropical elements for both generic and species levels with some temperate elements that could be attributed to the site's high elevation and semi-temperate climate.These are important baseline information for conservation plans and monitoring of tropical mossy forests.
