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Macroalgal deep genomics illuminate multiple paths to aquatic,photosynthetic multicellularity

Molecular Plant 2024年第5期17卷 747-771页

作者： David R.Nelson Alexandra Mystikou Ashish Jaiswal Cecilia Rad-Menendez Michael J.Preston Frederik De Boever Diana C.El Assal Sarah Daakour Michael W.Lomas Jean-Claude Twizere David H.Green William C.Ratcliff Kourosh Salehi-Ashtiani Division of Science and Math New York University Abu DhabiAbu DhabiUAE center for Genomics and Systems Biology(CGSB) New York University Abu DhabiAbu DhabiUAE Biotechnology Research center Technology Innovation InstitutePO Box 9639Masdar CityAbu DhabiUAE Culture Collection of algae and Protozoa Scottish Association for Marine ScienceObanScotlandUK national center for marine algae and microbiota Bigelow Laboratory for Ocean SciencesEast BoothbayMEUSA Laboratory of Viral Interactomes GIGA InstituteUniversity of LiegeLiegeBelgium School of Biological Sciences Georgia Institute of TechnologyAtlantaGAUSA

Macroalgae are multicellular,aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering,which are directly linked to their multicellularity ***,their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain *** this study,we sequenced 110 macroalgal genomes from diverse climates and phyla,and identified key genomic features that distinguish them from their microalgal *** for cell adhesion,extracellular matrix formation,cell polarity,transport,and cell differentiation distinguish macroalgae from microalgae across all three major phyla,constituting conserved and unique gene sets supporting multicellular *** genes show phylum-and climate-specific expansions that may facilitate niche ***,our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.

关键词： macroalgae multicellularity comparative genomics evolution adhesome endogenous viral elements

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Proteomic response of Phaeocystis globosa to nitrogen limitation

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Journal of Oceanology and Limnology 2024年第1期42卷 141-149页

作者： Haisu LIU Ruiwang WEI Qiangyong LEI Lei CUI Songhui LÜ Key Laboratory of Eutrophication and Red Tide Prevention Research Center for Harmful Algae and Marine BiologyJinan UniversityGuangzhou 510632China Southern marine Science and Engineering Guangdong Laboratory Zhuhai 519082China national Engineering Laboratory of Electronic and Information Standardization Shenzhen 518057China

Phaeocystis globosa is an important unicellular eukaryotic alga that can also form *** can cause massive harmful algal blooms and plays an important role in the global carbon or sulfur *** far,the ecophysiology of *** has been investigated by numerous ***,the proteomic response of *** to nitrogen depletion remains largely *** compared four protein preparation methods of *** for two-dimensional electrophoresis(2-DE)(Urea/Triton X-100 with trichloroacetic acid(TCA)/acetone precipitation;TCA/acetone precipitation;Radio Immuno Precipitation Assay(RIPA)with TCA/acetone precipitation;and Tris buffer).Results show that the combination of RIPA with TCA/acetone precipitation had a clear gel background and showed the best protein spot separation effect,based on which the proteomic response to nitrogen depletion was studied using *** addition,we identified six differentially expressed proteins whose relative abundance increased or decreased more than 1.5-fold(Pmarine microalgae.

关键词： Phaeocystis globosa nitrogen limitation proteomic response two-dimensional electrophoresis

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Characteristics Variation of Atmospheric CO_(2)and CH_(4)in Yongxing Island,South China Sea

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Journal of Ocean University of China 2024年第2期23卷 438-446页

作者： LV Honggang JIANG Yifei WANG Haiyan Key Laboratory of marine Hazards Forecasting National Marine Environmental Forecasting CenterMinistry of Natural Resources(MNR)Beijing 100081China national marine Environmental Forecasting center Beijing 100081China

Using the observation data in Yongxing Island,South China Sea(SCS)from December 2013 to November 2018,the multiple time scales variation of atmospheric CO_(2)and CH_(4)were analyzed to understand their temporal variation characteristics and controlling *** regional-averaged background mole fractions of CO_(2)and CH_(4)both show a single-period sinusoidal variation with a lower value at noon and a higher value in the wee *** the seasonal scale,they exhibited a significant seasonal difference with higher values in winter and lower values in *** the annual scale,CO_(2)and CH_(4)both show an increasing trend,with an annual growth rate of approximately 3.2 ppm and 12 ppb,*** annual growth rate at this site was higher than the global *** change in atmospheric CO_(2)and CH_(4)in Yongxing Island was probably caused by the higher emission of the surrounding areas and the airflows driven by ***,the long-term and high-resolution greenhouse gases(GHGs)dataset will aid relevent researchers and decision-makers in performing more in-depth studies for GHG sources in order to derive effective strategies.

关键词： carbon dioxide methane observation backward trajectory atmospheric transport

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Eutrophication of Jiangsu Coastal Water and Its Role in the Formation of Green Tide

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Journal of Ocean University of China 2024年第1期23卷 109-118页

作者： XIAO Mingyan SONG Weina ZHANG Haibo SHI Xiaoyong SU Rongguo Key Laboratory of marine Chemistry Theory and Technology Ministry of EducationOcean University of ChinaQingdao 266100China national marine Environmental Monitoring center Dalian 116000China national marine Hazard Mitigation Service Beijing 100194China

Since 2007,the large-scale green tide caused by Ulva prolifera(***)have occurred as a recurrent phenomenon in the southern Yellow Sea of *** surveys and satellite remote sensing showed that the small scattered patches of green tide algae were first observed along the Porphyra agriculture area of the Subei Shoal in late *** this study,we attempted to identify the role of eutrophication in the origin of the green tide in the Subei Shoal and its adjacent *** Shoal and its adjacent area are characterized by rich nutrients,especially NO_(3)^(-)-N,NH_(4)^(+)-N,PO_(4)^(3-)-P,and other bioavailable components(such as urea-N and amino acids).In the spring of 2017,the average concentrations of NO_(3)^(-)-N were 19.01±11.01μmolL^(-1),accounting for 86.68%of the dis-solved inorganic nitrogen(DIN).In addition,the average concentration of NH4^(+)-N was 2.51±1.60μmolL^(-1).PO_(4)^(3-)-P had an average concentration of 0.14±0.13μ*** average concentrations of urea-N and total hydrolyzed amino acids(THAA)were 1.73±1.36μmolL^(-1)and 1.33±0.80μmolL^(-1),*** nutritive substances play a key role in the rapid production of *** and make the Jiangsu coastal water an incubator for green tide.

关键词： green tide nutrients algae Ulva prolifera eutrophication Subei Shoal

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A typhoon-induced storm surge numerical model with GPU acceleration based on an unstructured spherical centroidal Voronoi tessellation grid

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Acta Oceanologica Sinica 2024年第3期43卷 40-47页

作者： Yuanyong Gao Fujiang Yu Cifu Fu Jianxi Dong Qiuxing Liu national marine Environmental Forecasting center Beijing 100081China Key Laboratory of marine Hazards Forecasting Ministry of Natural ResourcesBeijing 100081China

Storm surge is often the marine disaster that poses the greatest threat to life and property in coastal *** and timely issuance of storm surge warnings to take appropriate countermeasures is an important means to reduce storm surge-related *** surge numerical models are important for storm surge *** further improve the performance of the storm surge forecast models,we developed a numerical storm surge forecast model based on an unstructured spherical centroidal Voronoi tessellation(SCVT)*** model is based on shallow water equations in vector-invariant form,and is discretized by Arakawa C *** SCVT grid can not only better describe the coastline information but also avoid rigid transitions,and it has a better global consistency by generating high-resolution grids in the key areas through transition *** addition,the simulation speed of the model is accelerated by using the openACC-based GPU acceleration technology to meet the timeliness requirements of operational ensemble *** only takes 37 s to simulate a day in the coastal waters of *** newly developed storm surge model was applied to simulate typhoon-induced storm surges in the coastal waters of *** hindcast experiments on the selected representative typhoon-induced storm surge processes indicate that the model can reasonably simulate the distribution characteristics of storm *** simulated maximum storm surges and their occurrence times are consistent with the observed data at the representative tide gauge stations,and the mean absolute errors are 3.5 cm and 0.6 h respectively,showing high accuracy and application prospects.

关键词： typhoon-induced storm surge numerical model GPU acceleration unstructured grid spherical centroidal Voronoi tessellation(SCVT)

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New perspectives on the genetic structure of dotted gizzard shad(Konosirus punctatus)based on RAD-seq

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marine Life Science & Technology 2024年第1期6卷 50-67页

作者： Ying Peng Yifan Liu Jiasheng Li Kun Zhang Xun Jin Sixu Zheng Yunpeng Wang Zhenming Lu Liqin Liu Li Gong Bingjian Liu national Engineering Laboratory of marine Germplasm Resources Exploration and Utilization Zhejiang Ocean UniversityZhoushan 316022China national Engineering Research center for Facilitated marine Aquaculture Marine Science and Technology CollegeZhejiang Ocean UniversityZhoushan 316022China

To maintain,develop and rationally utilize marine organisms,understanding their genetic structure and habitat adaptation pattern is *** punctatus,which is a commercial fish species inhabiting the Indo-west Pacific Ocean,has shown an obvious annual global capture and aquaculture production decline due to climate changes and human *** the present study,restriction-site associated DNA sequencing(RAD-seq)was used to describe its genome-wide single nucleotide polymorphisms panel(SNPs).Among 146 individuals collected at nine locations scattered in China,Korea and Japan,a set of 632,090 SNPs were *** genetic analysis showed that *** individuals were divided into two significant genetic ***,potential genetic differentiation between northern and southern population of *** was *** results indicated that gene flow existed among sampling locations of ***,especially from southern Japan to ***,candidate genes associated with habitat adaptations of *** were identified,which are involved in diverse physiological processes of *** including growth and development(e.g.,KIDINS220,PAN3),substance metabolism(e.g.,PGM5)and immune response(e.g.,VAV3,CCT7,HSPA12B).Our findings may aid in understanding the possible mechanisms for the population genetic structure and local adaptation of ***,which is beneficial to establish the management and conservation units of ***,guiding the rational use of resources,with reference significance for a profound understanding of the adaptative mechanisms of other marine organisms to the environment.

关键词： Population structure Konosirus punctatus SNP RAD-seq Local adaptation

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Identification and Expression Profile of a Neuropeptide LFRFamide-Like Gene During Different Stages of Gonadal Development in the Cephalopod Sepia pharaonis

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Journal of Ocean University of China 2024年第2期23卷 499-508页

作者： QIU Jiayin SUN Lianlian LI Shuang ZHOU Xu CHI Changfeng ZHENG Libing national and Provincial Joint Engineering Research center for marine Germplasm Resources Exploration and Utilization School of Marine Science and TechnologyZhejiang Ocean UniversityZhoushan 316022China

Neuropeptides are widely distributed in vertebrates and invertebrates,regulating a variety of physiological activities in the organisms,such as metabolism,feeding and *** this study,to explore the function of neuropeptide LFRFamide in Sepia pharaonis,the full-length cDNA of LFRFamide-like gene(named SpLFRFL,MG869822.1)was identified with rapid amplification of cDNA ends(RACE)*** sequence of SpLFRFL was 860 bp in length and encoded 188 amino acids containing 4 different mature peptides:1 copy of PHTPFRFamide,NSLFRFamide,TIFRFamide,and 3 copies of *** alignment and phylogenetic analysis results showed that SpLFRFL shared high identity with LFRFamides of Sepia officinalis and Sepiella japonica and had the closest relationship with *** quantitative Real-time PCR(qRT-PCR),it was found that the SpLFRFL gene was highly expressed in the optic lobe and brain at three different stages during gonad development in both ***,the four mature peptides at a concentration of 0.01μmol L^(−1) could inhibit the protein synthesis in the Chinese hamster ovary cell strain-K1(CHOK1)induced by *** data suggest that SpLFRFL might be involved in the development and reproduction of *** results can contribute to future studies on neuropeptide evolution and function and benefit the cuttlefish farming.

关键词： neuropeptide LFRFamide-like cephalopod cuttlefish Sepia pharaonis development reproduction

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Numerical Simulation on Production Trials by Using Depressurization for Typical marine Hydrate Reservoirs:Well Type and Formation Dip

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Journal of Ocean University of China 2024年第3期23卷 661-675页

作者： QIN Fanfan SUN Jiaxin GU Yuhang CAO Xinxin MAO Peixiao NING Fulong JIANG Guosheng national center for International Research on Deep Earth Drilling and Resource Development Faculty of EngineeringChina University of GeosciencesWuhan 430074China Laboratory for marine Mineral Resources Qingdao National Laboratory for Marine Science and TechnologyQingdao 266237China

Natural gas hydrate has huge reserves and is widely distributed in marine *** commercial development is of great significance for alleviating the contradiction between energy supply and *** an efficient research method,numerical simulation can provide valuable insights for the design and optimization of hydrate ***,most of the current production models simplify the reservoir as a two-dimensional(2D)horizontal layered model,often ignoring the impact of formation dip *** improve the accuracy of production prediction and provide theoretical support for the optimization of production well design,two three-dimensional(3D)geological models with different dip angles based on the geological data from two typical sites are *** vertical well,horizontal well and multilateral wells are deployed in these reservoirs with different permeabilities to perform production trial,and the sensitivity analysis of dip angles is also carried *** short-term production behaviors in high and low permeability reservoirs with different dip angles are *** simulation results show that 1)the gas and water production behaviors for different well types in the two typical reservoirs show obviously different variation laws when the short-term depressurization is conducted in the inclined formation;2)the inclined formation will reduce the gas production and increase the water extraction,and the phenomena becomes pronounced as the dip angle increases,particularly in the low-permeability reservoirs;3)and the impact of formation dip on hydrate recovery does not change significantly with the variation of well type.

关键词： natural gas hydrate inclined formation depressurization production well type

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Application of the finite analytic numerical method to a flowdependent variational data assimilation

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Acta Oceanologica Sinica 2024年第3期43卷 30-39页

作者： Yan Hu Wei Li Xuefeng Zhang Guimei Liu Liang Zhang Tianjin Key Laboratory for marine Environmental Research and Service School of Marine Science and TechnologyTianjin UniversityTianjin 300072China School of marine Science and Technology Tianjin UniversityTianjin 300072China national marine Environmental Forecasting center Ministry of Natural ResourcesBeijing 100081China

An anisotropic diffusion filter can be used to model a flow-dependent background error covariance matrix,which can be achieved by solving the advection-diffusion *** of the directionality of the advection term,the discrete method needs to be chosen very *** finite analytic method is an alternative scheme to solve the advection-diffusion *** a combination of analytical and numerical methods,it not only has high calculation accuracy but also holds the characteristic of the auto *** demonstrate its ability,the one-dimensional steady and unsteady advection-diffusion equation numerical examples are respectively solved by the finite analytic *** more widely used upwind difference method is used as a control *** result indicates that the finite analytic method has higher accuracy than the upwind difference *** the two-dimensional case,the finite analytic method still has a better *** the three-dimensional variational assimilation experiment,the finite analytic method can effectively improve analysis field accuracy,and its effect is significantly better than the upwind difference and the central difference ***,it is still a more effective solution method in the strong flow region where the advective-diffusion filter performs most prominently.

关键词： finite analytic method advection-diffusion equation data assimilation flow-dependent

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Evaluation of a hepatic biomarker of nutritional imbalance in juvenile red drum(Sciaenops ocellatus) fed 60% soybean meal-based diets using NMR-based metabolomics

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Animal Nutrition 2024年第1期16卷 45-61页

作者： Fabio Casu Aaron M.Watson Justin Yost T.Gibson Gaylord Daniel W.Bearden Michael R.Denson marine Resources Research Institute South Carolina Department of Natural Resources Bozeman Fish Technology center United States Fish and Wildlife Service marine Biochemical Sciences Group Chemical Sciences Division National Institute of Standards and Technology Hollings Marine Laboratory

A 12-week feeding trial with juvenile red drum(Sciaenops ocellatus) fed high-soybean meal(SBM) diets was conducted to investigate a putative biomarker of nutritional imbalance, N-formimino-L-glutamate(FIGLU). Three fishmeal-free, 60% SBM pelleted diets(named B12, Fol, and Met, respectively) were tested to evaluate the effects on growth performance and tissue metabolite profiles of supplementation of vitamin B12(0.012 mg/kg), folate(10 mg/kg), methionine(1 g/kg) respectively, above basal supplementation levels. A fourth SBM-based diet(named B12/Fol/Met) was formulated with a combination of B12, folate, and methionine to attain the above-mentioned target concentrations. A fifth 60% SBM diet(named FWS) with methionine supplementation(1 g/kg above basal supplementation levels), enriched with taurine, lysine and threonine as well as minerals, was also tested. This diet contained formulation targets and additives which have allowed for replacing fishmeal with plant proteins in rainbow trout feeds. Control diets included a fishmeal-based diet(named FM), an unsupplemented basal 60% SBM diet(named SBM60), and a “natural” diet(named N) made up of equal parts of fish(cigar minnows), squid and shrimp as a positive reference for growth performance. Formulated feeds contained approximately 37% total crude protein, approximately 14% total crude lipid and were energetically balanced. Standard growth performance metrics were measured, and tissues(liver, muscle) were collected at week 12 to evaluate diet-induced metabolic changes using nuclear magnetic resonance(NMR)-based *** results show that the FWS diet outperformed all other SBM diets and the FM diet under all performance metrics(P<0.05). FIGLU was not detected in fish fed the N diet but was detected in those fed the SBM diets and the FM diet. Fish fed the FWS diet and the Met diet showed lower hepatic levels of FIGLU compared with the other SBM-based diets(P<0.05), suggesting that among the different supplementatio

关键词： Aquaculture Metabolomics Nuclear magnetic resonance Red drum Soybean meal N-Formimino-L-glutamate

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