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Combining genome-wide association study and transcriptome analysis to identify molecular markers and genetic basis of population-asynchronous ovarian development in Coilia nasus

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Zoological Research 2024年第3期45卷 491-505页

作者： Yue Yu Shi-Ming Wan Cheng-You Huang Shuang-Meng Zhang Ai-Li Sun Jun-Qi Liu Shun-Yao Li Yong-Fu Zhu Shu-Xin Gu ze-xia gao College of Fisheries Hubei Hongshan Laboratory/Key Lab of Freshwater Animal BreedingMinistry of Agriculture and Rural Affairs/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationHuazhong Agricultural UniversityWuhanHubei 430070China Laboratory for Marine Biology and Biotechnology Qingdao Marine Science and Technology CenterQingdaoShandong 266237China Wuhan Hengyuxin Technology Breeding Professional Cooperative WuhanHubei 430117China Hubei Provincial Aquatic Science Research Institute WuhanHubei 430208China Zhenjiang Jiangzhiyuan Fishery Technology Co. Ltd.ZhenjiangJiangsu 212213China

Coilia nasus,a migratory fish species found in the middle and lower reaches of the Yangtze River and along offshore areas of China,possesses considerable aquacultural and economic ***,the species faces challenges due to significant variation in the gonadal development rate among females,resulting in inconsistent ovarian maturation times at the population level,an extended reproductive period,and limitations on fish growth rate due to ovarian *** the present study,we combined genome-wide association study(GWAS)and comparative transcriptome analysis to investigate the potential single nucleotide polymorphisms(SNPs)and candidate genes associated with population-asynchronous ovarian development in *** of the female population based on whole-genome resequencing yielded 2120695 high-quality SNPs,39 of which were suggestively associated with ovarian *** note,a significant SNP peak on LG21 containing 30 suggestively associated SNPs was identified,with cpne5a determined as the causal gene of the ***,single-marker and haplotype association analyses were performed on cpne5a,revealing four genetic markers(P0.9)significantly associated with the *** transcriptome analysis of precociously and normally maturing individuals screened out 29 and 426 overlapping differentially expressed genes in the brain and ovary,respectively,between individuals of different body *** the GWAS and transcriptome analysis results,this study identified genes and pathways related to hypothalamic-pituitary-gonadal axis hormone secretion,extracellular matrix,angiogenesis,and gap junctions involved in population-asynchronous ovarian *** insights gained from this study provide a basis for a deeper understanding of the molecular mechanisms underlying ovarian development in fish and may facilitate the genetic breeding of *** strains exhibiting population-synchronous ovarian

关键词： Coilia nasus GWAS Transcriptome Ovarian development SNP

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Loss of scleraxis leads to distinct reduction of mineralized intermuscular bone in zebrafish

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Aquaculture and Fisheries 2021年第2期6卷 169-177页

作者： Chunhong Nie Shiming Wan Yulong Chen Dejie Zhu Xudong Wang xiaoru Dong ze-xia gao College of Fisheries Key Laboratory of Freshwater Animal BreedingMinistry of Agriculture and Rural Affair/Key Laboratory of Agricultural Animal GeneticsBreeding and ReproductionMinistry of EducationHuazhong Agricultural UniversityWuhanHubei430070China Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt Ministry of EducationWuhan430070China Hubei Engineering Technology Research Center for Fish Breeding and Healthy Aquaculture Wuhan430070China

Intermuscular bones(IBs)are ossified from tendons and only occur in lower *** association between the regulation of scleraxis gene(scx)and tendon development gave us reasons to speculate that the scx gene may play a potential role in regulating the development of IBs.A phylogenetic analysis conducted for this study revealed potential functional differentiation between two scx orthologues,scxa and *** scxa^(-/-) and scxb^(-/-) zebrafish were generated through CRISPR-Cas9 technology to study the role of scx in the IB and rib *** results showed a significant reduction of the number of IBs in adult scxa-1^(-/-) zebrafish,with almost 70%reduction(15-25 IBs)compared to the wild type scxa-1^(+/+)zebrafish(76-80 IBs).In the scxa-1^(+/+)adults,IBs were observed in both dorsal and tail segments;however,in scxa-1^(-/-)fish IBs were observed only in the tail segment(none in the dorsal segment).Although scxa-1^(-/-) zebrafish had rib defects,the mutants were viable and fertile as adult *** scxb^(-/-) zebrafish had the same number of IBs and same skeletal phenotype as the wild-type *** suggests that only scxa has a crucial role in the IB development,and confirms functional differentiation of scx *** further clarify the molecular mechanism by which scxa affects the IB development,we conducted comparative transcriptome analysis of dorsal tissue samples of scxa-1^(+/+)(with IBs)and scxa-1^(-/-) (without IBs),and further verified the expression of key genes via *** is the first study to identify a gene that controls the amount of IBs in fish,and it provides a new sight into the effects of scxa on the molecular mechanism of IB development in fish.

关键词： Intermuscular bone Scleraxis CRISPR-Cas9 Phenotype Gene expression Gene function

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Single-cell transcriptomes and runx2b-/- mutants reveal the genetic signatures of intermuscular bone formation in zebrafish

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National Science Review 2022年第11期9卷 97-107页

作者： Chun-Hong Nie Shi-Ming Wan Yu-Long Chen Ann Huysseune Ya-Ming Wu Jia-Jia Zhou Alexandre Wagner Silva Hilsdorf Wei-Min Wang Paul Eckhard Witten Qiang Lin ze-xia gao College of Fisheries Key Lab of Freshwater Animal BreedingMinistry of Agriculture and Rural AffairsKey Lab of Agricultural Animal GeneticsBreeding and Reproduction of Ministry of EducationEngineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt Ministry of Education Huazhong Agricultural University Hubei Hongshan Laboratory CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology South China Sea Institute of Oceanology Innovation Academy of South China Sea Ecology and Environmental Engineering Chinese Academy of Sciences Department of Biology Ghent University Unit of Biotechnology University of Mogi das Cruzes Guangdong Laboratory for Lingnan Modern Agriculture

Intermuscular bones(IBs) are mineralized spicules, present in the myosepta of many, but not all, teleost species. IBs are often small and sharp, and they consequently limit how the fish can be processed; the IBs may cause injury or trauma if lodged in consumers’ throats or mouths, and therefore affect the appeal of the fish to many consumers. The development of IBs in teleosts is still not fully understood and the molecular basis of IB development remains to be established. Here, the characteristics of IB tissue are evaluated based on single-cell transcriptomics in wild-type zebrafish. The analysis defined 18 distinct cell *** trajectories showed that IBs are derived from tendons and that a core tendon-osteoblast cell lineage is related to IB formation. In particular, the functions of 10 candidate genes were evaluated via CRISPR-Cas9 mutants. Among those, runx2b-/-mutants completely lost IBs, while swimming performance, growth and bone mineral density were not significantly different from runx2b+/+*** single-cell RNA sequencing(sc RNA-seq) analysis in runx2b-/-and runx2b+/+zebrafish revealed the role of osteoblasts in IB formation. In addition, differentially expressed genes were enriched in the transforming growth factor β/bone morphogenetic protein(TGF-β/BMP) pathway after runx2b deletion. This study provides evidence for the crucial role of runx2b regulation in IB formation. Genetic breeding can target runx2b regulation and generate strains of commercial fish species without IBs, which can improve the safe consumption and economic value of many farmed fish species.

关键词： teleosts zebrafish intermuscular bones scRNA-seq tendon-osteoblast cell lineage runx2b genetic breeding

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Effect of FeSi additive in dual-chamber sample cup on thermal analysis characteristic values and vermiculating rate of compacted graphite iron

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China Foundry 2024年第1期21卷 91-100页

作者： De-quan Shi ze-yu Liu Gui-li gao Yi-cheng Feng School of Materials and Chemistry University of Shanghai for Science and TechnologyShanghai 200093China School of Materials Science and Chemical Engineering Harbin University of Science&TechnologyHarbin 150040China School of Mechanical and Energy Engineering Shanghai Technical Institute of Electronics and InformationShanghai 201411China

Thermal analysis plays a key role in the online inspection of molten iron *** solidification process of molten iron can be reflected by thermal analysis curves,and silicon is one of important elements affecting the solidification of molten *** this study,FeSi75 was added in one chamber of the dual-chamber sample cup,and the influences of FeSi75 additive on the characteristic values of thermal analysis curves and vermiculating rate were *** results show that with the increase of FeSi75,the start temperature of austenite formation TALfirstly decreases and then increases,but the start temperature of eutectic growth TSEF,the lowest eutectic temperature TEU,temperature at maximum eutectic reaction rate TEM,and highest eutectic temperature TERkeep always an *** temperature at final solidification point TEShas little *** FeSi75 additive has different influences on the vermiculating rate of molten iron with different vermiculation,and the vermiculating rate increases for lower vermiculation molten iron while decreases for higher *** to the thermal analysis curves obtained by a dual-chamber sample cup with 0.30wt.%FeSi75 additive in one chamber,the vermiculating rate of molten iron can be evaluated by comparing the characteristic values of these *** time differenceΔtERcorresponding to the highest eutectic temperature TERhas a closer relationship with the vermiculating rate,and a parabolic regression curve between the time differenceΔtERand vermiculating rateηhas been obtained within the range of 65%to 95%,which is suitable for the qualified melt.

关键词： FeSi75 additive characteristic value vermiculating rate thermal analysis compacted graphite iron

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A NEW GLOBAL OPTIMIZATION ALGORITHM FOR MIXED-INTEGER QUADRATICALLY CONSTRAINED QUADRATIC FRACTIONAL PROGRAMMING PROBLEM

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Journal of Computational Mathematics 2024年第3期42卷 784-813页

作者： Bo Zhang Yuelin gao xia Liu xiaoli Huang School of Civil and Hydraulic Engineering School of Mathematics and StatisticsNingxia UniversityYinchuan 750021China School of Mathematics and Information Science North Minzu UniversityYinchuan 750021China Ningxia Province Key Laboratory of Intelligent Information and Data Processing Yinchuan 750021China School of Mathematics and Statistics Ningxia UniversityYinchuan 750021China

The mixed-integer quadratically constrained quadratic fractional programming(MIQCQFP)problem often appears in various fields such as engineering practice,management science and network ***,most of the solutions to such problems are often designed for their unique *** paper puts forward a new global optimization algorithm for solving the problem *** first convert the MIQCQFP into an equivalent generalized bilinear fractional programming(EIGBFP)problem with integer ***,we linearly underestimate and linearly overestimate the quadratic functions in the numerator and the denominator respectively,and then give a linear fractional relaxation technique for EIGBFP on the basis of non-negative *** that,combining rectangular adjustment-segmentation technique and midpointsampling strategy with the branch-and-bound procedure,an efficient algorithm for solving MIQCQFP globally is ***,a series of test problems are given to illustrate the effectiveness,feasibility and other performance of this algorithm.

关键词： Global optimization Branch and bound Quadratic fractional programming Mixed integer programming

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Acid-rock reaction kinetics in a two-scale model based on reaction order correction

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Petroleum Science 2024年第3期21卷 2089-2101页

作者： Xue-Song Li Ning Qi ze-Hui Zhang Lian Liu xia-Qing Li Xu-Hang Su School of Petroleum Engineering China University of Petroleum(East China)Qingdao266580ShandongChina Key Lab of Unconventional Oil&Gas Development Ministry of EducationChina University of Petroleum(East China)Qingdao26650ShandongChina SINOPEC Northwest Oilfield Branch Company Urumqi830011XinjiangChina Petroleum Engineering Technology Research Institute SINOPEC Shengli Oilfield CompanyDongying257000ShandongChina

The reaction order plays a crucial role in evaluating the response rate of ***,the conventional two-scale model typically assumes that the reaction order is constant as one,which can lead to significant deviations from *** address this issue,this study proposes a novel multi-order dynamic model for acid-rock reaction by combining rotating disk experimental data with theoretical *** numerical simulations,this model allows for the investigation of the impact of acidification conditions on different orders of reaction,thereby providing valuable insights for on-site *** analysis reveals that higher response orders require higher optimal acid liquid flow rates,and lower optimal H+diffusion coefficients,and demonstrate no significant correlation with acid ***,it is recommended to increase the displacement and use high-viscosity acid for reservoirs with high calcite content,while reducing the displacement and using low-viscosity acid for reservoirs with high dolomite content.

关键词： Reaction order Two-scale model Wormhole propagation Carbonate rocks Numerical simulation

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Effect of multiple coulomb scattering on the beam tests of silicon pixel detectors

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Nuclear Science and Techniques 2024年第4期35卷 200-207页

作者： Lan-Kun Li Ming-Yi Dong ze gao Liang-Cheng-Long Jin Shu-Jun Zhao School of Physics and Microelectronics Zhengzhou UniversityZhengzhou 450001China State Key Laboratory of Particle Detection and Electronics(Institute of High Energy Physics CAS)Beijing 100049China University of Chinese Academy of Science Beijing 100049China University of South China Hengyang 421001China

In the research and development of new silicon pixel detectors,a collimated monoenergetic charged-particle test beam equipped with a high-resolution pixel-beam telescope is crucial for prototype verification and performance *** the beam energy is low,the effect of multiple Coulomb scattering on the measured resolution of the Device Under Test(DUT)must be considered to accurately evaluate the performance of the pixel chips and *** study aimed to investigate the effect of multiple Coulomb scattering on the measured resolution,particularly at low beam *** were conducted using Allpix^(2) to study the effects of multiple Coulomb scattering under different beam energies,material budgets,and telescope *** simulations also provided the minimum energy at which the effect of multiple Coulomb scattering could be *** with the results of a five-layer detector system tested with an electron beam at DESY,the simulation results were consistent with the beam test results,confirming the reliability of the simulations.

关键词： Silicon Pixel Detectors Beam Telescope Multiple Coulomb Scattering Spatial Resolution

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ControlService: a containerized solution for control-algorithm-as-a-service in cloud control systems

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Science China(Information Sciences) 2024年第8期67卷 172-189页

作者： Chenggang SHAN Runze gao Zhen YANG Wei ZHANG Yuanqing xia School of Artificial Intelligence Zaozhuang University School of Automation Beijing Institute of Technology

As an extension of networked control systems, cloud control systems(CCSs) have emerged as a new control paradigm to improve the service quality of emerging control missions, such as data-driven modeling and automated vehicles. Existing studies have used the workflow-based restructured method to optimize the computation-intensive algorithms in the CCSs. However, the challenges here are how to define and submit these algorithms' workflows as cloud services and execute these algorithms' workflows in a containerized manner. Based on these challenges, we propose a containerized solution for the control-algorithm-as-a-service(C3aS) in the CCSs, namely Control Service. It offers the control algorithm as a cloud workflow service and uses a customized workflow engine to realize the containerized execution. First, we employ a cloud workflow representation method to define a control algorithm into an abstract cloud workflow form. Afterward, we provide a cloud service representation of the abstract cloud workflow. Next, we design a workflow engine and submit the cloud service to this workflow engine to implement containerized execution of this cloud service in the CCSs. In the experiment, we discuss the cloud service form and containerized implementation of the subspace identification method. Experimental results show that the proposed Control Service has significant performance advantages in computational time, reduction percentage, and speedup ratio compared with the baseline method.

关键词： cloud control systems control-algorithm-as-a-service containerization workflow engine cloud workflow service subspace identification

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Preface to the special topic on metals and their compounds for lithium ion/metal batteries

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Tungsten 2024年第1期6卷 162-163页

作者： Ying-ze Song Wen-Long Cai gao-Ran Li State Key Laboratory of Environment-Friendly Energy Materials Southwest University of Science and TechnologyMianyang 621010China College of Materials Science and Engineering Sichuan UniversityChengdu 610064China School of Materials Science and Engineering Nanjing University of Science and TechnologyNanjing 210094China

The fast development of electronics and electric devices has inspired the practical application of lithium ion/metal *** this line,the metals and their compounds as electrode materials as well as the corresponding mechanism for energy storage have gained extensive international *** as-organized special topic focuses on W,Mo,Co,Zr,Hf,Re,Ta,Nb,V-based metals and their compounds for lithium ion/metal *** special topic involves four reviews and four research papers totally,providing the latest advances of transition metals and their related compounds for rechargeable lithium ion/metal batteries.

关键词： lithium metals gained

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Three dimensional discrete element modelling of the conventional compression behavior of gas hydrate bearing coal

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International Journal of Coal Science & Technology 2024年第1期11卷 61-77页

作者： xia gao Nannan Wang Baoyong Zhang Qiqi Lin Qiang Wu Wei Meng xia Liu Department of Architecture and Civil Engineering Heilongjiang University of Science and TechnologyHarbin150022China School of Qilu Transportation Shandong UniversityJinan250061China Department of Safety Engineering Heilongjiang University of Science and TechnologyHarbin150022China Jining Hongxiang Highway Survey Design and Research Institute Co.Ltd Jining272000China

To analyze the relationship between macro and meso parameters of the gas hydrate bearing coal(GHBC)and to calibrate the meso-parameters,the numerical tests were conducted to simulate the laboratory triaxial compression tests by PFC3D,with the parallel bond model employed as the particle contact constitutive ***,twenty simulation tests were conducted to quantify the relationship between the macro–meso ***,nine orthogonal simulation tests were performed using four meso-mechanical parameters in a three-level to evaluate the sensitivity of the meso-mechanical ***,the calibration method of the meso-parameters were then ***,the contact force chain,the contact force and the contact number were examined to investigate the saturation effect on the meso-mechanical behavior of *** results show that:(1)The elastic modulus linearly increases with the bonding stiffness ratio and the friction coefficient while exponentially increasing with the normal bonding strength and the bonding radius *** failure strength increases exponentially with the increase of the friction coefficient,the normal bonding strength and the bonding radius coefficient,and remains constant with the increase of bond stiffness ratio;(2)The friction coefficient and the bond radius coefficient are most sensitive to the elastic modulus and the failure strength;(3)The number of the force chains,the contact force,and the bond strength between particles will increase with the increase of the hydrate saturation,which leads to the larger failure strength.

关键词： Gas hydrate bearing coal Discrete element method Triaxial compression test Macro-meso mechanical propertie

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