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Incorporating adaptive genomic variation into predictive models for invasion risk assessment

Environmental Science and Ecotechnology 2024年第2期18卷 83-90页

作者： Yiyong Chen Yangchun Gao Xuena Huang Shiguo Li Zhixin Zhang Aibin Zhan research Center for Eco-Environmental Sciences Chinese Academy of SciencesBeijing100085China Guangdong Key Laboratory of Animal Conservation and Resource Utilization Guangdong Public Laboratory of Wild Animal Conservation and UtilizationInstitute of ZoologyGuangdong Academy of ScienceGuangzhou510260China University of Chinese Academy of Sciences Chinese Academy of SciencesBeijing100049China CAS Key Laboratory of Tropical Marine Bio-resources and Ecology South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou510275China Global Ocean and Climate research Center South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhou510275China

Global climate change is expected to accelerate biological invasions,necessitating accurate risk forecasting and management ***,current invasion risk assessments often overlook adaptive genomic variation,which plays a significant role in the persistence and expansion of invasive *** we used Molgula manhattensis,a highly invasive ascidian,as a model to assess its invasion risks along Chinese coasts under climate *** population genomics analyses,we identified two genetic clusters,the north and south clusters,based on geographic *** predict invasion risks,we employed the gradient forest and species distribution models to calculate genomic offset and species habitat suitability,*** approaches yielded distinct predictions:the gradient forest model suggested a greater genomic offset to future climatic conditions for the north cluster(i.e.,lower invasion risks),while the species distribution model indicated higher future habitat suitability for the same cluster(i.e,higher invasion risks).By integrating these models,we found that the south cluster exhibited minor genome-niche disruptions in the future,indicating higher invasion *** study highlights the complementary roles of genomic offset and habitat suitability in assessing invasion risks under climate ***,incorporating adaptive genomic variation into predictive models can significantly enhance future invasion risk predictions and enable effective management strategies for biological invasions in the future.

关键词： Invasion risk Climate change Adaptive genomic variation Genomic offset Habitat suitability

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Imaging the western boundary of the Sichuan Craton from multiple geophysical observations

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Journal of Earth Science 2024年

作者： Qihang Yin Xi Xu Xiaodong Yang Xuhua Shi Lei Wu Andrew V.Zuza Liu Yang Hefeng Tian Yuanhai Shu Shufeng Yang Nevada Bureau of Mines and Geology， University of Nevada China Aero Geophysical Survey and Remote Sensing Center for Natural Resources，China Geological Survey School of Earth Sciences， Zhejiang University research Center for Structures in Oil and Gas Bearing Basins， Ministry of Education Key Laboratory of Ocean and Marginal sea Geology， South China sea Institute of Oceanology， Innovation Academy of South China sea Ecology and Environmental Engineering， Chinese Academy of Sciences School of Mechanical and Electrical Engineering， Hubei Open University

The boundary between the cratonic and orogenic lithospheres is one of the most significant seismogenic zones characterized by strong lithospheric deformation. As the essential tectonic block bounding the eastern Tibetan Plateau， the Sichuan Craton (SCC) resists the eastward escape of Plateau’s crustal materials， resulting in the uplift of the Songpan-Ganzi Block (SGB) and the crustal deformation of the Longmenshan tectonic belt (LMTB). To uncover the compressional structures and deformational mode of the LMTB and SCC， it is crucial to determine the precise location and geometry of the western boundary of the SCC. To address this issue， the lithospheric properties of the obduction SGB， the underthrusting SCC， and the LMTB were analyzed using a series of geophysical data， including seismic reflection profiles， magnetotellurics， aeromagnetics， gravity， and seismic tomography. The crust of the SGB is characterized by low magnetism， low seismic velocity， low resistivity and low Bouguer gravity， while that of the SCC features non-uniform high magnetism， high seismic velocity， high resistivity and high Bouguer gravity. The LMTB， as the boundary between the SGB and SCC， shows the geophysical characteristics similar to the SCC along the southern and central segments. The integration of all these geophysical observations suggests that the SCC’s western boundary follows the Yingxiu-Beichuan fault along the northern segment， without obvious underthrust. However， this boundary is located west of the Wenchuan-Maoxian fault zone along the southern and central segments， with distinct westward wedging/underthrusting. The irregular geometry of the SCC’s western boundary can further explain the variation in structural deformation along the LMTB. By comparing the differences in crustal thickness and lithospheric strength between the SGB and SCC， this study suggests that the varying crustal strength between tectonic blocks may be the controlling factor for the irregular geometry of the

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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&Marine Biodiversity Ocean University of ChinaQingdao 266003China Yellow sea Fisheries research 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 ***,21conserved miRNAs in ***(mja-miRNAs),belonging to 19 miRNA families,were identified and *** the 21 mja-miRNAs,15 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,120 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

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Geometry and 3D seismic characterisation of post-rift normal faults in the Pearl River Mouth Basin,northern South China sea

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Acta Oceanologica Sinica 2024年第4期43卷 25-39页

作者： Yuanhang Liu Jinwei Gao Wanli Chen Jiliang Wang Umair Khan Laboratory of Marine Geophysics and Georesources Institute of Deep-sea Science and EngineeringChinese Academy of SciencesSanya 572000China University of Chinese Academy of Sciences Beijing 100049China

Based on high-resolution 3D seismic data acquired in the Pearl(Zhujiang)River Mouth Basin of the northern South China sea,this study investigated the geometry,spatial extension,and throw distribution of the post-rift normal fault through detailed seismic interpretation and fault modeling.A total of 289 post-rift normal faults were identified in the study area and can be classified into four types:(1)isolated normal faults above the carbonate platform;(2)isolated normal faults cutting through the carbonate platform;(3)conjugate normal faults,and(4)connecting normal *** distribution analysis on the fault planes show that the vertical throw profiles of most normal fault exhibit flat-topped *** normal faults above the carbonate platform exhibit roughly concentric ellipses with maximum throw zones in the central section whereas the normal faults cutting through the carbonate platform miss the lowermost section due to the chaotic seismic reflections in the interior of the carbonate *** vertical throws of conjugate normal faults anomalously decrease toward their intersection region on the fault plane whereas the connecting normal faults present two maximum throw zones in the central section of the fault *** to the symmetric elliptical distribution model of fault throw,an estimation was made indicating that normal faults cutting through the carbonate platform extended downward between-1308 s and-1780 s(two-way travel time)in depth and may not penetrate the entire Liuhua carbonate ***,it is observed that the distribution of karst caves on the top of the carbonate platform disaccord with those of hydrocarbon reservoirs and the post-rift normal faults cutting through the carbonate platform in the study *** propose that these karst caves formed most probably by corrosive fluids derived from magmatic activities during the Dongsha event,rather than pore waters or hydrocarbons.

关键词： Post-rift normal faults fault throw Karst caves Corrosive fluids Pearl River Mouth Basin South China sea

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An ensemble learning method to retrieve sea ice roughness from Sentinel-1 SAR images

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Acta Oceanologica Sinica 2024年第5期43卷 78-90页

作者： Pengyi Chen Zhongbiao Chen Runxia Sun Yijun He School of Marine Sciences Nanjing University of Information Science&TechnologyNanjing 210044China East sea Information Center of State Oceanic Administration Shanghai 200136China

sea ice surface roughness(SIR)affects the energy transfer between the atmosphere and the ocean,and it is also an important indicator for sea ice *** obtain a small-scale SIR with high spatial resolution,a novel method is proposed to retrieve SIR from Sentinel-1 synthetic aperture radar(SAR)images,utilizing an ensemble learning ***,the two-dimensional continuous wavelet transform is applied to obtain the spatial information of sea ice,including the scale and direction of ice ***,a model is developed using the Adaboost Regression model to establish a relationship among SIR,radar backscatter and the spatial information of sea *** proposed method is validated by using the SIR retrieved from SAR images and comparing it to the measurements obtained by the Airborne Topographic Mapper(ATM)in the summer Beaufort *** determination of coefficient,mean absolute error,root-mean-square error and mean absolute percentage error of the testing data are 0.91,1.71 cm,2.82 cm,and 36.37%,respectively,which are ***,K-fold cross-validation and learning curves are analyzed,which also demonstrate the method’s applicability in retrieving SIR from SAR images.

关键词： 2-D Cauchy continuous wavelet transform(CWT) Adaboost Regression sea ice sea ice surface roughness

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Isotope constraints on seasonal dynamics of nitrogen in Zhanjiang Bay, a typical mariculture bay in South China

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Acta Oceanologica Sinica 2024年第6期43卷 60-70页

作者： Chunqing Chen Qibin Lao Fajin Chen Guangzhe Jin Jiacheng Li Qingmei Zhu College of Ocean and Meteorology Guangdong Ocean UniversityZhanjiang 524088China School of Chemistry and Environment Guangdong Ocean UniversityZhanjiang 524088China Key Laboratory for Coastal Ocean Variation and Disaster Prediction Guangdong Ocean UniversityZhanjiang 524088China Key Laboratory of Climate Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong ProvinceGuangdong Ocean UniversityZhanjiang 524088China

Eutrophication in coastal waters has been increasing remarkably,severely impacting the water quality in mariculture *** this study,we conducted multiple isotopic measurements on suspended particulate nitrogen(δ^(15)N-PN) and dissolved nitrate(δ^(15)N-NO_(3)^(-)and δ^(18)O-NO_(3)^(-)) in Zhanjiang Bay,a typical mariculture bay with a high level of eutrophication in South China,to investigate the changes in nitrogen sources and their cycling between the rainy and dry *** the rainy season,the study found no significant relation between δ^(15)NPN and δ^(15)N-NO_(3)^(-)due to the impact of heavy rainfall and terrestrial *** the upper bay,a slight nitrate loss and slightly higher δ_(15)N-NO_(3)^(-)and δ^(18)O-NO_(3)^(-)values were observed,attributed to intense physical sedimentwater *** some fluctuations,nitrate concentrations in the lower bay mainly aligned with the theoretical mixing line during the rainy season,suggesting that nitrate was primarily influenced by terrestrial erosion and that nitrate isotopes resembled the ***,the isotopic values of nitrate can be used for source apportionment in the rainy *** results indicated that soil nitrogen(36%) and manure and sewage(33%) were the predominant nitrogen sources contributing to nitrogen loads during this *** contrast,the dry season saw a deficient ammonium concentration(red tide ***,the significant loss of nitrate and simultaneous increase in the stable isotopes of dissolved and particulate nitrogen suggest a strong coupling of assimilation and mineralization during the dry *** active biogeochemical processes during the dry season may be related to decreased runoff and increased water retention ***,our study illustrated the major seasonal nitrogen sources and their dynamics in Zhanjiang B ay,providing valuable insights for formulati

关键词： nitrogen stable nitrogen isotopes biogeochemical processes eutrophication Zhanjiang Bay

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Photobiomodulation:a novel approach to promote trans-differentiation of adipose-derived stem cells into neuronal-like cells

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Neural Regeneration research 2025年第2期20卷 598-608页

作者： Daniella Da Silva Madeleen Jansen van Rensburg Anine Crous Heidi Abrahamse Laser research centre Faculty of Health SciencesUniversity of JohannesburgDoornfonteinJohannesburgSouth Africa

Photobiomodulation,originally used red and near-infrared lasers,can alter cellular *** has been demonstrated that the visible spectrum at 451-540 nm does not necessarily increase cell proliferation,near-infrared light promotes adipose stem cell proliferation and affects adipose stem cell migration,which is necessary for the cells homing to the site of *** this in vitro study,we explored the potential of adipose-derived stem cells to differentiate into neurons for future translational regenerative treatments in neurodegenerative disorders and brain *** investigated the effects of various biological and chemical inducers on trans-differentiation and evaluated the impact of photobiomodulation using 825 nm near-infrared and 525 nm green laser light at 5 J/*** adipose-derived stem cells can be used in autologous grafting and photobiomodulation has been shown to have biostimulatory *** findings reveal that adipose-derived stem cells can indeed trans-differentiate into neuronal cells when exposed to inducers,with pre-induced cells exhibiting higher rates of proliferation and trans-differentiation compared with the control ***,green laser light stimulation led to notable morphological changes indicative of enhanced trans-differentiation,while near-infrared photobiomodulation notably increased the expression of neuronal *** biochemical analysis and enzyme-linked immunosorbent assays,we observed marked improvements in viability,proliferation,membrane permeability,and mitochondrial membrane potential,as well as increased protein levels of neuron-specific enolase and ciliary neurotrophic ***,our results demonstrate the efficacy of photobiomodulation in enhancing the trans-differentiation ability of adipose-derived stem cells,offering promising prospects for their use in regenerative medicine for neurodegenerative disorders and brain injuries.

关键词： differentiation inducers green photobiomodulation immortalized adipose-derived stem cell near-infrared photobiomodulation neurodegenerative disease neurogenesis photobiomodulation trans-differentiation

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Lignocellulosic fraction-induced niche differentiation within dissimilatory iron reducing bacterial groups in a paddy soil

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Soil Ecology Letters 2024年第1期6卷 77-88页

作者： Yunbin Jiang Wenting Hu Kailou Liu Shangshu Huang Fengwu Zhou Cheng Han Huan Deng Wenhui Zhong Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control School of GeographyNanjing Normal UniversityNanjing 210023China Jiangsu Centerfor Collaborative Innovation in Geographical Information Resource Development and Application Nanjing 210023China National Engineering and Technology research Center for red Soil Improvement Jiangxi Institute of Red Soil and Germplasm ResourcesNanchang 331717China Schoolof Environment Nanjing Normal UniversityNanjing 210023China

Responses of soil DIRB to lignocellulosic fractions during a 6-week microcosm incubation were ***,Bacillus,and Clostridium maintained their domi-nance throughout the *** DIRB groups proliferated under specific lignocellulosic fraction *** of insufficient ferric iron on the proliferation varied by DIRB *** iron reducing bacteria(DIRB)are phylogenetically and physi-ologically diverse in paddy soils,where iron reduction closely couples with the oxidation of rice straw-derived carbon in the straw returning ***,few studies have addressed the niche differentiation within DIRB groups during the degradation of lignocellulosic fractions of rice *** study conducted a 6-week microcosm incubation experiment to reveal the distinct responses of DIRB groups under specific lignocellulosic fraction amendments with and without ferrihydrite(Fh)addition in a flooded paddy *** showed that the total absolute abundance of the 19 detected DIRB groups did not vary significantly during the ***,Bacillus,and Clostridium were the dominant DIRB groups for all lignocellulosic treatments whereas Thermincola was dominant but only under xylan amendment with Fh ***-nodes in the co-occurrence networks of bacterial community mainly belonged to Anaeromyxobacter and *** and Thermincola,Alkaliphilus and Anaeromyxobacter,and Alicyclobacillus,Desulfobulbus,and Desulfosporosinus were specifically proliferated under xylan,cellulose,and lignin amendments,*** the proliferation was limited by insufficient ferric iron varied by bacterial *** findings suggested the lignocellulosic fraction-induced niche differentiation within DIRB groups,which advanced our understanding of the ecology of DIRB in paddy soils under straw returning.

关键词： cellulose hemicellulose lignin bacterial community diversity co-occurrence networks

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Validating the use of ROS-scavenging bacteria as probiotics to increase coral resilience to thermal stress

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Journal of Oceanology and Limnology 2024年第4期42卷 1242-1260页

作者： Xiaoyu TANG Qingsong YANG Ying ZHANG Hanzhang WANG Juan LING Haiyan SUN Junde DONG Yanying ZHANG CAS Key Laboratory of Tropical Marine Bio-resources and Ecology South China Sea Institute of Oceanology(SCSIO)Guangzhou 510301China Ocean School Yantai UniversityYantai 264005China Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou) Guangzhou 511458China Sanya National Marine Ecosystem research Station and Key Laboratory of Tropical Marine Biotechnology of Hainan Province Sanya Institute of OceanologySCSIOSanya 572000China Institute of Deep-sea Science and Engineering Chinese Academy of SciencesSanya 572000China University of Chinese Academy of Sciences Beijing 100049China

Thermal stress causes the overproduction and toxic accumulation of reactive oxygen species(ROS),which seems to be correlated with coral bleaching and,ultimately,*** reduction of ROS concentration within the coral holobiont could minimize the effects of thermal stress and support efforts to reduce coral decline *** the current study,we explored the physiological responses of Pocillopora damicornis to ROS-scavenging bacteria inoculation as well as the microbiome restructuring that correlates with ***’s resilience to thermal stress after probiotic *** of corals with ROS-scavenging bacteria enhanced coral health and reduced ROS ***,the enhanced coral thermal resistance promoted by ROS-scavenging bacteria was also correlated with an overall coral microbiome *** addition,the complex network relationships between bacteria and Symbiodiniaceae in corals after ROS-scavenging bacteria inoculation contributed to corals’resilience to high ***,coral heat tolerance bacterial biomarkers,such as Myxococcota,were enriched in corals with added ROS-scavenging ***,our findings validate the selected ROS-scavenging bacteria as coral probiotics that could help corals resist thermal stress on a short ***,our data contribute to our understanding of the potential interactions between different members of the coral holobiont and the use of probiotics as tools to aid coral restoration efforts.

关键词： coral beneficial microorganisms for corals(BMCs) Symbiodiniaceae thermal stress coral bleaching

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Development of SNP parentage assignment techniques in the yellowfin seabream Acanthopagrus latus

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Acta Oceanologica Sinica 2024年第2期43卷 151-155页

作者： Hongbo Zhao Liangmin Huang Jing Zhang Songyuan You Qingmin Zeng Xiande Liu Fisheries College of Jimei University Xiamen 361021China Key Laboratory of Healthy Mariculture for the East China sea Ministry of Agriculture and Rural AffairsXiamen 361021China Bureau of Agriculture and Rural Affairs of Wudang District Guiyang CityGuizhou ProvinceGuiyang 550018China Fisheries research Institute of Fujian Xiamen 361000China

Acanthopagrus latus is an essential aquaculture species on the south coast of ***,there is a lack of systematic breeding of ***,which considerably limits the sustainable development of *** a result,genetic improvements are urgently needed to breed new strains of *** with rapid growth and strong resistance to *** selective breeding,it is necessary to estimate the genetic parameters of the target trait,which in turn depends on an accurate disentangled pedigree for the selective ***,it is necessary to establish the parentage assignment technique for *** this study,95 individuals selected from their parents and their 14 families were used as experimental *** were developed by genome resequencing,and highly polymorphic SNPs were screened on the basis of optimized filtering parameters.A total of 14392738 SNPs were discovered and 205 SNPs were selected for parentage assignment using the CERVUS *** the model where the gender of the parents is known,the assignment success rate is 98.61%for the male parent,97.22%for the female parent,and 95.83%for the parent *** the model where the gender of the parents is unknown,the assignment success rate is 100%for a single parent and 90.28%for the parent *** results of this study were expected to serve as a reference for the breeding of new varieties of ***.

关键词： Acanthopagrus latus parentage assignment SNP Genome re-sequencing

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