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Impacts of Aggregation Methods and Trophospecies Number on the Structure and Function of marine Food Webs

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Journal of Ocean University of China 2024年第1期23卷 190-198页

作者： LI Pengcheng ZHANG Chongliang XU Binduo JI Yupeng LI Fan REN Yiping XUE Ying Laboratory of fisheries Ecosystem Monitoring and Assessment College of FisheriesOcean University of ChinaQingdao 266003China Field Observation and research Station of Haizhou Bay Fishery Ecosystem Ministry of EducationQingdao 266003China shandong {1. Resources and Environment research institute Shandong Provincial Key Laboratory of Restoration for Marine EcologyYantai 264006China Laboratory for marine {1. Science and Food Production Processes Laoshan LaboratoryQingdao 266237China

Aggregation of species with similar ecological properties is one of the effective methods to simplify food web ***,species aggregation will affect not only the complexity of modeling process but also the accuracy of models’*** of aggregation methods and the number of trophospecies are the keys to study the simplification of food *** this study,three aggregation methods,including taxonomic aggregation(TA),structural equivalence aggregation(SEA),and self-organizing maps(SOM),were analyzed and compared with the linear inverse model–Markov Chain Monte Carlo(LIM-MCMC)*** of aggregation methods and trophospecies number on food webs were evaluated based on the robustness and unitless of ecological net-work *** showed that aggregation method of SEA performed better than the other two methods in estimating food web structure and function *** effects of aggregation methods were driven by the differences in species aggregation principles,which will alter food web structure and function through the redistribution of energy *** to the results of mean absolute percentage error(MAPE)which can be applied to evaluate the accuracy of the model,we found that MAPE in food web indices will increase with the reducing trophospecies number,and MAPE in food web function indices were smaller and more stable than those in food web structure ***,trade-off between simplifying food webs and reflecting the status of ecosystem should be con-sidered in food web *** findings highlight the importance of aggregation methods and trophospecies number in the analy-sis of food web *** study provided a framework to explore the extent to which food web models are affected by dif-ferent species aggregation,and will provide scientific basis for the construction of food webs.

关键词： LIM-MCMC model species aggregation trophospecies number aggregation methods food web indices

The environmental analysis and site selection of mussel and large yellow croaker aquaculture areas based on high resolution remote sensing

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Acta Oceanologica Sinica 2024年第3期43卷 66-86页

作者： Lina Cai Jie Yin Xiaojun Yan Yongdong Zhou Rong Tang Menghan Yu marine Science and Technology College Zhejiang Ocean UniversityZhoushan 316022China Zhejiang marine {1. research institute Zhejiang Ocean UniversityZhoushan 316004China

Mussel aquaculture and large yellow croaker aquaculture areas and their environmental characteristics in Zhoushan were analyzed using satellite data and in-situ surveys.A new two-step remote sensing method was proposed and applied to determine the basic environmental characteristics of the best mussel and large yellow croaker aquaculture *** methodology includes the first step of extraction of the location distribution and the second step of the extraction of internal environmental *** fishery ranching index(FRI1.FRI2)was established to extract the mussel and the large yellow croaker aquaculture area in Zhoushan,using Gaofen-1.GF-1.and Gaofen-6(GF-6)satellite data with a special resolution of 2 *** the second step,the environmental factors such as sea surface temperature(SST),chlorophyll a(Chl-a)concentration,current and tide,suspended sediment concentration(SSC)in mussel aquaculture area and large yellow croaker aquaculture area were extracted and analyzed in *** results show the following three points.(1.For the extraction of the mussel aquaculture area,FRI1.and FRI2 are complementary,and the combination of FRI1.and FRI2 is suitable to extract the mussel aquaculture *** for the large yellow croaker aquaculture area extraction,FRI2 is suitable.(2)Mussel aquaculture and the large yellow croaker aquaculture area in Zhoushan are mainly located on the side near the islands that are away from the eastern open *** water environment factor template suitable for mussel and large yellow croaker aquaculture was determined.(3)This two-step remote sensing method can be used for the preliminary screening of potential site selection for the mussels and large yellow croaker aquaculture area in the *** fishery ranching index(FRI1.FRI2)in this paper can be applied to extract the mussel and large yellow croaker aquaculture areas in coastal waters around the world.

关键词： mussel aquaculture area large yellow croaker aquaculture area high resolution satellite site selection environmental analysis

Full-length transcriptome sequencing analysis reveals differential skin color regulation in snakeheads fish Channa argus

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Aquaculture and fisheries 2024年第4期9卷 590-596页

作者： Leigang Mao Yongan Zhu Jiaren Yan Longgang Zhang Shuren Zhu Li An Qinglei Meng Zhishan Zhang Xirong Wang College of fisheries and Life Science Shanghai Ocean UniversityShanghai201306China shandong Freshwater {1. research institute Jinan250017China

Albinism is a genetic disorder caused by a series of genetic abnormalities that result in a decrease in *** yellow snakehead fish(GCAS)has been discovered while the Channa argus(CAS)breeding,but the genetic mechanism that causes its albinism is not *** sequencing and comparison of CAS and GCAS skin using Oxford Nanopore Technologies(ONT)technology to elucidate the molecular mechanisms of snakehead albinism.27.1.G clean reads and 26,1.8 full-length non-redundant sequences were generated via ONT ***,8079 new transcripts and 7231.genes were identified by comparing and analyzing redundant removed transcripts and known reference genome *** results of DEGs analysis showed that a total of 59 transcripts were differentially expressed in the two groups,including 22 up-regulated transcripts and 37 down-regulated *** causative genes associated with albinism have been identified,including TYR(Tyrosinase)and SOX1.(SRY-box transcription factor 1.)(tyrosinase synthesis and metabolism),S-1.0(S1.0 calcium binding protein A1.(melanin production),NLRC3(NLR family CARD domain containing 3)(disease immunity)are significantly down-regulated in GCAS,while RhoGEFs expression(melanin synthesis)is *** interaction analysis revealed that GAPDH(Glyceraldehyde-3-phosphate dehydrogenase)is the top hub gene in the regulation of skin color in *** addition,the skin of snakehead fish is regulated by metabolic(GAPDH),immune[Tumor protein p53(TP53),C-X-C motif chemokine ligand 8(CXCL8),SRC proto-oncogene,non-receptor tyrosine kinase(SRC),CD274]and neural[Notch receptor 1.NOTCH1.,C-X-C motif chemokine ligand 1.(CXCL1.)]related genes to achieve differences in skin *** findings in understanding the process by which albinism in fish develops.

关键词： Albinism Channa argus Nanopore-based RNA sequencing Melanin

First record of abnormal body coloration in a rockfish Sebastes koreanus(Scorpaenoidei:Sebastidae)from coastal water of China based on morphological characteristics and DNA barcoding

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Journal of Oceanology and Limnology 2024年第2期42卷 640-646页

作者： Ang LI Huan WANG Changting AN Shufang LIU Yellow Sea fisheries {1. institute Chinese Academy of Fishery SciencesQingdao 266071China Laboratory for marine {1. Science and Food Production Processes Laoshan LaboratoryQingdao 266071China

The first record of abnormal body coloration in Sebastes koreanus Kim and Lee,1.94,from the Yellow Sea of China,was documented based on morphological characteristics and DNA *** two rockfish specimens were collected from the coastal waters of Qingdao,China,and the whole body and all fins of them were *** the two red-colored rockfish,there were tiny deep red spots on each fin,2 red radial stripes behind and below the eyes and 1.large deep red blotch on the opercula,while the similar stripe and spot patterns are also present in the *** specimens with normal body *** countable characteristics of the two specimens are in the range of the morphometry of *** further clarify the species identity and taxonomic status of the two specimens,DNA barcode analysis was carried *** genetic distance between the red-colored rockfish and *** was 0,and the minimum net genetic distances between the red-colored rockfish and other Sebastes species except for *** were 3.0%,which exceeds the threshold of species *** phylogenetic analysis showed that the DNA barcoding sequences of the two red-colored rockfish clustered with the *** *** above results of DNA barcode analysis also support that the two red-colored rockfish could be identified as the species of *** mechanism of color variation in *** is desirable for further research and the species could be an ideal model to study the color-driven speciation of the rockfishes.

关键词： abnormal body coloration Sebastes koreanus coastal water of China Yellow Sea morphological characteristics DNA barcoding

Decoding the fish genome opens a new era in important trait research and molecular breeding in China

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Science China(Life Sciences) 2024年第10期67卷 2064-2083页

作者： Qian Zhou Jialin Wang Jiongtang Li Zhangfan Chen Na Wang Ming Li Lei Wang Yufeng Si Sheng Lu Zhongkai Cui Xuhui Liu Songlin Chen State Key Laboratory of Mariculture Biobreeding and Sustainable Goods Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoShandong 266071China Laboratory for marine {1. Science and Food Production Processes Qingdao Marine Science and Technology CenterQingdaoShandong 266237China Key Laboratory of Aquatic Genomics Ministry of Agriculture and Rural AffairsBeijing Key Laboratory of Fishery BiotechnologyChinese Academy of Fishery SciencesBeijing 100041China

Aquaculture represents the fastest-growing global food production sector,as it has become an essential component of the global food *** has the world's largest aquaculture industry in terms of production ***,the sustainable development of fish culture is hindered by several concerns,including germplasm degradation and disease *** practice of genomic breeding,which relies heavily on genome information and genotypephenotype relationships,has significant potential for increasing the efficiency of aquaculture *** 201.,the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in *** then,domestic researchers have made dramatic progress in functional genomic *** date,the genomes of more than 60 species of fish in China have been assembled and *** on these reference genomes,evolutionary,comparative,and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes,including growth and development,sex determination,disease resistance,metamorphosis,and ***,genomic tools and breeding techniques such as SNP arrays,genomic selection,and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding *** review aims to summarize the current status,advances,and perspectives of the genome resources,genomic study of important traits,and genomic breeding techniques of fish in *** review will provide aquaculture researchers,fish breeders,and farmers with updated information concerning fish genomic research and breeding *** summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.

关键词： fish genomics economic traits genomic selection genome editing genomic breeding

Combined ATAC-seq,RNA-seq,and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster(Crassostrea ariakensis)

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Zoological research 2024年第1期45卷 201-214页

作者： Biao Wu Xi Chen Jie Hu Zhen-Yuan Wang Yan Wang Da-You Xu Hao-Bing Guo Chang-Wei Shao Li-Qing Zhou Xiu-Jun Sun Tao Yu Xiao-Mei Wang Yan-Xin Zheng Guang-Yi Fan Zhi-Hong Liu State Key Laboratory of Mariculture Biobreeding and Sustainable Goods Yellow Sea Fisheries Research InstituteChinese Academy of Fishery SciencesQingdaoShandong 266071China Laboratory for marine {1. Science and Food Production Processes Laoshan LaboratoryQingdaoShandong 266071China BGI-Qingdao BGI-ShenzhenQingdaoShandong 266426China National Demonstration Center for Experimental fisheries Science Education Shanghai Ocean UniversityShanghai 201306China Changdao Enhancement and Experiment Station Chinese Academy of Fishery SciencesYantaiShandong 265800China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhenGuangdong 518083China

Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of *** Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in *** the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen *** identified 9483 differentially expressed genes(DEGs)and 721. genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between ***,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen *** loci corresponded to 241.genes,63 of which were categorized as both DEGs and *** study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in ***.

关键词： Crassostrea ariakensis Glycogen Transcriptome ATAC GWAS

Integrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of Marsupenaeus japonicas

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Journal of Oceanology and Limnology 2024年第1期42卷 201-215页

作者： Jing WANG Longjun PU Xiaojuan ZHANG Cuicui LIANG Dandan DONG Jiantao GUAN Huarong GUO Ministry of Education Key Laboratory of marine Genetics and Breeding College of Marine Life SciencesOcean University of ChinaQingdao 266003China institute of Evolution&{1. Biodiversity Ocean University of ChinaQingdao 266003China Yellow Sea fisheries {1. institute Chinese Academy of Fishery SciencesQingdao 266071China

Regulation of microRNAs(miRNAs)on various biological processes has been a surprising and exciting *** of miRNAs is the first step to comprehensively understand their ***,attempts on global identification and functional verification of miRNAs are very limited in penaeid shrimp Marsupenaeus japonicus,an economically important aquatic *** performing an integrated analysis of transcriptomic profile from gastrula embryos of ***,21.onserved miRNAs in ***(mja-miRNAs),belonging to 1. miRNA families,were identified and *** the 21.mja-miRNAs,1. miRNAs were successfully verified to be predominantly expressed in gastrula stage,where they displayed dynamic expression patterns compared with those in naupliuin *** on perfect or near-perfect match to target region,1.0 target genes were predicted at transcriptome-wide ***,gene ontology(GO)classification and metabolic pathway annotation revealed eight targets that were actively involved in developmental *** the predicted miRNA-mRNA pairs,six targets were then randomly selected and experimentally validated by dual luciferase reporter assay,where three pairs were proved with potential targeting ***,to search for conserved miRNAs potentially involved in early development of ***,we combined in silico and experimental methods,which can be applied in other organisms as *** data implied important roles of miRNAs in the early embryonic development and also suggested the presence of complex miRNA-mRNA functional networks in ***.

关键词： microRNAs(miRNAs) identification Marsupenaeus japonicus embryo transcriptome

Time-sensitive prediction of NO_(2) concentration in China using an ensemble machine learning model from multi-source data

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Journal of Environmental Sciences 2024年第3期137卷 30-40页

作者： Chenliang Tao Man Jia Guoqiang Wang Yuqiang Zhang Qingzhu Zhang Xianfeng Wang Qiao Wang Wenxing Wang Big Data research Center for Ecology and Environment Environment Research InstituteShandong UniversityQingdao 266237China shandong Provincial Eco-environment Monitoring Center Jinan 250101China

Nitrogen dioxide(NO_(2))poses a critical potential risk to environmental quality and public health.A reliable machine learning(ML)forecasting framework will be useful to provide valuable information to support government *** on the data from1.09 air quality monitors across China from 201.-2020,this study designed an ensemble ML model by integrating multiple types of spatial-temporal variables and three sub-models for time-sensitive prediction over a wide *** ensemble ML model incorporates a residual connection to the gated recurrent unit(GRU)network and adopts the advantage of Transformer,extreme gradient boosting(XGBoost)and GRU with residual connection network,resulting in a 4.1.±1.0%lower root mean square error over XGBoost for the test *** ensemble model shows great prediction performance,with coefficient of determination of 0.91.0.86,and 0.77 for 1.hr,3-hr,and 24-hr averages for the test results,*** particular,this model has achieved excellent performance with low spatial uncertainty in Central,East,and North China,the major site-dense *** the interpretability analysis based on the Shapley value for different temporal resolutions,we found that the contribution of atmospheric chemical processes is more important for hourly predictions compared with the daily scale predictions,while the impact of meteorological conditions would be ever-prominent for the *** with existing models for different spatiotemporal scales,the present model can be implemented at any air quality monitoring station across China to facilitate achieving rapid and dependable forecast of NO_(2),which will help developing effective control policies.

关键词： Air quality prediction Deep learning Ensemble method Nitrogen dioxide Spatiotemporal covariates

Application of Bionic Technology in marine Cruise Equipment:{1. Progress and Development Trends

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Journal of Bionic Engineering 2024年第3期21卷 1117-1155页

作者： Kunhui Luo Lan Yan Zhiyi Zhu Zhongqiu Wang Hongru Wang Feng Jiang School of Electromechanical and Automation Huaqiao UniversityXiamen36102China National Local Joint Engineering research Center for Intelligent Manufacturing Technology of Brittle Material Products Xiamen361021China institute of Oceanographic Instrumentation Shandong Academy of SciencesQilu University of Technology(Shandong Academy of Sciences)Qingdao266100China shandong Provincial Key Laboratory of {1. Monitoring Instrument Equipment Technology Qingdao266100China National Engineering and Technological research Center of {1. Monitoring Equipment Qingdao266100China institute of Manufacturing Engineering Huaqiao UniversityXiamen361021China

This article provides an overview of the application of bionic technology in marine cruising equipment,discussing its {1. progress and future development *** cruising is a crucial means of gaining insights into the marine environment and conducting scientific ***,conventional marine cruising equipment faces numerous challenges when dealing with complex and ever-changing marine *** technology,as a means of drawing inspiration from the structure and functions of living organisms,offers new approaches and methods to address the challenges faced by marine cruising equipment and has found widespread *** article primarily focuses on the applications and historical developments of bionic technology in propulsion methods,drag reduction,and surface *** summarizes the design principles,manufacturing techniques,and optimization methods for marine biomimetic cruising ***,this paper analyzes the achievements,challenges,and future directions of bionic technology in marine cruising *** application of bionic technology in marine cruising equipment holds vast potential for development,enabling us to better confront the challenges of marine exploration and {1. by drawing wisdom from nature and driving advancements in marine science.

关键词： marine cruising equipment Bionic technology Propulsion methods Drag reduction Surface antifouling