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Cell metabolism pathways involved in the pathophysiological changes of diabetic peripheral neuropathy 被引量:5
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作者 Yaowei Lv Xiangyun Yao +3 位作者 Xiao Li Yuanming Ouyang Cunyi Fan Yun Qian 《Neural Regeneration Research》 SCIE CAS CSCD 2024年第3期598-605,共8页
Diabetic peripheral neuropathy is a common complication of diabetes mellitus.Elucidating the pathophysiological metabolic mechanism impels the generation of ideal therapies.However,existing limited treatments for diab... Diabetic peripheral neuropathy is a common complication of diabetes mellitus.Elucidating the pathophysiological metabolic mechanism impels the generation of ideal therapies.However,existing limited treatments for diabetic peripheral neuropathy expose the urgent need for cell metabolism research.Given the lack of comprehensive understanding of energy metabolism changes and related signaling pathways in diabetic peripheral neuropathy,it is essential to explore energy changes and metabolic changes in diabetic peripheral neuropathy to develop suitable treatment methods.This review summarizes the pathophysiological mechanism of diabetic peripheral neuropathy from the perspective of cellular metabolism and the specific interventions for different metabolic pathways to develop effective treatment methods.Various metabolic mechanisms(e.g.,polyol,hexosamine,protein kinase C pathway)are associated with diabetic peripheral neuropathy,and researchers are looking for more effective treatments through these pathways. 展开更多
关键词 cell metabolism diabetic peripheral neuropathy peripheral nerve injury protein kinase C pathway reactive oxygen species.
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A Transcriptome Analysis of Neural Tissue of Litopenaeus vannamei After Acute Exposure to Alexandrium pacificum
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作者 YANG Huijie HUANG Xianghu +4 位作者 MA Yukun HU Zhangxi ZHANG Ning LI Changling ZHANG Yulei 《Journal of Ocean University of China》 CAS CSCD 2024年第2期529-538,共10页
Alexandrium pacificum(A.pacificum)is a typical paralytic shellfish poisonous dinoflagellate.Harmful algal blooms(HABs)caused by this species can bring serious environmental problems and economic losses to the aquacult... Alexandrium pacificum(A.pacificum)is a typical paralytic shellfish poisonous dinoflagellate.Harmful algal blooms(HABs)caused by this species can bring serious environmental problems and economic losses to the aquaculture industry.In this study,transcriptome sequencing and analyses were performed on the neural tissue of Litopenaeus vannamei(L.vannamei)after acute exposure to A.pacificum disrupted solution for 72 h,and differentially expressed genes(DEGs)were identified.The results showed that,compared with the control samples,300 DEGs were identified in the experimental group,of which 194 were up-regulated,and 106 down-regulated.The gene ontology(GO)functional enrichment analysis showed that DEGs were significantly enriched in the cortical cytoskeleton organization,troponin complex,amylo-alpha-1,6-glucosidase and thymidine phosphorylase.Kyoto encyclopedia of genes and genomes(KEGG)enrichment analysis found that DEGs were mainly enriched in the oxidative phosphorylation process,intercellular tight junctions and mitophagy.The results showed that the proteoglycans,signaling pathways,and various metabolic processes that regulate cell proliferation,differentiation,and apoptosis all played an essential role in the response of L.vannamei to A.pacificum toxins. 展开更多
关键词 Litopenaeus vannamei Alexandrium pacificum paralytic shellfish poisoning TRANSCRIPTOME NERVE
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Identification,Characterization,and Probiotic Potentials of Lactobacillus pentosus SF-1
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作者 JIAO Lin LIANG Shufei +4 位作者 CHU Ruixia WANG Wentao MAI Kangsen LIU Ming WAN Min 《Journal of Ocean University of China》 CAS CSCD 2024年第2期509-517,共9页
In recent years probiotics have been considered as a potential substitution of antibiotics to control pathogens and treat infectious diseases in aquaculture.In the present study a strain of Lactobacillus pentosus,name... In recent years probiotics have been considered as a potential substitution of antibiotics to control pathogens and treat infectious diseases in aquaculture.In the present study a strain of Lactobacillus pentosus,named as L.pentosus SF-1,was isolated from waters in aquaculture.The species identification of this strain was conducted by 16S rRNA sequence,and the physiological and biochemical characteristics of this strain were assessed.Furthermore,the virulence,antibiotic sensitivity,cell surface characteristics and acid/base-resistance of L.pentosus SF-1 were determined to evaluate the probiotic potentials of this strain.Specifically,L.pentosus SF-1 is sensitive to most common antibiotics,and no hemolysin was generated from it,indicating the safety of this strain to hosts.In addition,L.pentosus SF-1 was able to tolerate the artificial gastric juice at pH 3 for 4 h and the artificial intestinal fluid at pH 6.8 or 8.0 for 6 h.Moreover,the analysis of self-aggregation and the adhesion of L.pentosus SF-1 to organic solvents suggested a high potential of L.pentosus SF-1 to inhabit the hosts,which was confirmed by testing the colonization of L.pentosus SF-1 in germ-free zebrafish.Interestingly,L.pentosus SF-1 displayed a high bactericidal activity against several bacterial pathogens.Consistently,the incubation of L.pentosus SF-1 significantly promoted the expression of antimicrobial components in zebrafish,contributing to the protection of the fish from E.tarda infection in vivo.Taken together,the probiotic strain L.pentosus SF-1 could be applied as anti-infection reagent in aquaculture. 展开更多
关键词 Lactobacillus pentosus PROBIOTICS ANTIBIOTICS HEMOLYSIS cell surface characteristics bactericidal activity INFECTION
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Anti-infective immune functions of type Ⅳ interferon in grass carp(Ctenopharyngodon idella):A novel antibacterial and antiviral interferon in lower vertebrates
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作者 Yuchen Liu Wentao Zhu +3 位作者 Yanqi Zhang Jingjing Zhang Maolin Lv Jianguo Su 《Zoological Research》 SCIE CSCD 2024年第5期972-982,共11页
Type Ⅳ interferon(IFN-υ)is a recently discovered cytokine crucial for host defense against viral infections.However,the role and mechanisms of IFN-υin bacterial infections remain unexplored.This study investigated ... Type Ⅳ interferon(IFN-υ)is a recently discovered cytokine crucial for host defense against viral infections.However,the role and mechanisms of IFN-υin bacterial infections remain unexplored.This study investigated the antibacterial and antiviral functions and mechanisms of grass carp(Ctenopharyngodon idella)IFN-υ(CiIFN-υ)both in vivo and in vitro.The CiIFN-υgene was first identified and characterized in grass carp.Subsequently,the immune expression of CiIFN-υsignificantly increased following bacterial challenge,indicating its response to bacterial infections.The eukaryotic recombinant expression plasmid of CiIFN-υwas then constructed and transfected into fathead minnow(FHM)cells.Supernatants were collected and incubated with four bacterial strains,followed by plate spreading and colony counting.Results indicated that CiIFN-υexhibited more potent antibacterial activity against gram-negative bacteria compared to gram-positive bacteria and aggregated gram-negative bacteria but not gram-positive bacteria.In vivo experiments further confirmed the antibacterial function,showing high survival rates,low tissue edema and damage,reduced tissue bacterial load,and elevated proinflammatory response at the early stages of bacterial infection.In addition,the antiviral function of CiIFN-υwas confirmed through in vitro and in vivo experiments,including crystal violet staining,survival rates,tissue viral burden,and reverse transcription-quantitative real-time polymerase chain reaction(RT-qPCR).This study highlights the antibacterial function and preliminary mechanism of IFN-υ,demonstrating that IFN-υpossesses dual functions against bacterial and viral infections. 展开更多
关键词 Grass carp(Ctenopharyngodon idella) IFN-υ Bactericidal activity Antiviral activity Antimicrobial immunity
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Stock appraisal for Atlantic tripletail(Lobotes surinamensis;Bloch,1790)in the Bay of Bengal,Bangladesh
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作者 Suman BARUA Qun LIU +4 位作者 Ahmed Fazley RABBY MdAbdullah AL-MAMUN Xu CHEN Rokeya SULTANA Aidah BALOCH 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2024年第5期1683-1694,共12页
The Atlantic tripletail(Lobotes surinamensis)is a high revenue-generating fish species predominantly caught by mechanized artisanal fishers community and the most available member of its family in Bangladesh.This is a... The Atlantic tripletail(Lobotes surinamensis)is a high revenue-generating fish species predominantly caught by mechanized artisanal fishers community and the most available member of its family in Bangladesh.This is a ground work of fish stock assessment study in the Bay of Bengal region to explore the life history parameters and associated biomass of this species,using three length-based approaches of TropFishR,the length-based Bayesian biomass estimation(LBB),and Froese’s length based indicators(LBIs).An almost homogenous body growth pattern(b=3.07;R^(2)=0.98)was observed in the length-weight relationship of tripletail.The life history parameters for tripletail,as determined by the von Bertalanffy Growth Function(VBGF)model,were L_(∞)=113.36 cm and k=0.51/a.The length converted catch curve(LCCC)yielded an estimation of the total mortality(Z=1.77/a),with the natural mortality estimated at(M=0.53/a)and the fishing mortality estimated at(F=1.24/a).But,the ratio of mortality(F/M=0.15)by LBB captured the non-fully exploited status of biomass(B/B_(MSY)=2.1).LBI analysis indicated that the tripletail fishery’s spawning stock biomass is greater than the target and limit reference points,indicating a healthy state of biomass. 展开更多
关键词 Bay of Bengal Lobotes surinamensis TropFishR length based indicator(LBI) length-based Bayesian biomass estimation(LBB) BANGLADESH
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Characterization of Nutrients,Heavy Metals,Petroleum and Their Impact on Phytoplankton in Laizhou Bay:Implications for Environmental Management and Monitoring
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作者 WANG Kai ZHAO Linlin +3 位作者 ZHU Yugui YANG Liqiang WANG Yunfeng HONG Xuguang 《Journal of Ocean University of China》 SCIE CAS CSCD 2024年第3期822-834,共13页
The Laizhou Bay(LB)represents a substantial ecological area that is vulnerable to human activities and confronts diverse environmental challenges.This study provides a comprehensive characterization of nutrients,petro... The Laizhou Bay(LB)represents a substantial ecological area that is vulnerable to human activities and confronts diverse environmental challenges.This study provides a comprehensive characterization of nutrients,petroleum,heavy metals,and phytoplankton community structure across seven distinct areas in LB.The results indicate relatively high concentrations of NO_(2)-N,SiO_(4)-Si,and NO_(3)-N in the Southwest Laizhou Bay(SWLB)and Huanghe River Estuary(HRE).In contrast,the East Laizhou bay(ELB)and the North of Huanghe River Estuary(NHRE)exhibit the highest concentrations of heavy metals(As,Cr and Hg).The areas with high phytoplankton density and community diversity are mainly located in the SWLB.After adjusting for basic environmental factors,phytoplankton density and Margalef richness index D are significantly associated with nutrients(NO_(3)-N,NO_(2)-N,NH_(4)-N,SiO_(4)-Si),and heavy metal(Cr)concentrations.We highlight that,in addition to Xiaoqinghe River,nutrients brought by the Mihe River in the SWLB and heavy metal(Cr)pollution in the ELB resulting from industrial and mining activities along the coast significantly influence phytoplankton growth and community structure.Therefore,it is recommended that more monitoring and management efforts be focused on these regions in the future. 展开更多
关键词 Huanghe River Estuary Laizhou Bay NUTRIENTS heavy metals PHYTOPLANKTON BIODIVERSITY
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Temporal variations of food web in a marine bay ecosystem based on LIM-MCMC model
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作者 Pengcheng Li Hu Zhang +4 位作者 Chongliang Zhang Binduo Xu Yupeng Ji Yiping Ren Ying Xue 《Acta Oceanologica Sinica》 SCIE CAS CSCD 2024年第8期79-88,共10页
Climate change has led to significant fluctuations in marine ecosystems,including alterations in the structure and function of food webs and ecosystem status.Coastal ecosystems are critical to the functioning of the e... Climate change has led to significant fluctuations in marine ecosystems,including alterations in the structure and function of food webs and ecosystem status.Coastal ecosystems are critical to the functioning of the earth’s lifesupporting systems.However,temporal variations in most of these ecosystems have remained unclear so far.In this study,we employed a linear inverse model with Markov Chain Monte Carlo(LIM-MCMC)combined with ecological network analysis to reveal the temporal variations of the food web in Haizhou Bay of China.Food webs were constructed based on diet composition data in this ecosystem during the year of 2011 and 2018.Results indicated that there were obvious temporal variations in the composition of food webs in autumn of 2011 and 2018.The number of prey and predators for most species in food web decreased in 2018 compared with 2011,especially for Trichiurus lepturus,zooplankton,Amblychaeturichthys hexanema,and Loligo sp.Ecological network analysis showed that the complexity of food web structure could be reflected by comprehensive analysis of compartmentalized indicators.Haizhou Bay ecosystem was more mature and stable in 2011,while the ecosystem’s self-sustainability and recovery from disturbances were accelerated from 2011 to 2018.These findings contribute to our understanding of the dynamics of marine ecosystems and highlight the importance of comprehensive analysis of marine food webs.This work provides a framework for assessing and comparing temporal variations in marine ecosystems,which provides essential information and scientific guidance for the Ecosystem-based Fisheries Management. 展开更多
关键词 LIM-MCMC ecological network analysis marine ecosystem food web
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Impacts of Aggregation Methods and Trophospecies Number on the Structure and Function of Marine Food Webs
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作者 LI Pengcheng ZHANG Chongliang +4 位作者 XU Binduo JI Yupeng LI Fan REN Yiping XUE Ying 《Journal of Ocean University of China》 CAS CSCD 2024年第1期190-198,共9页
Aggregation of species with similar ecological properties is one of the effective methods to simplify food web researches.However,species aggregation will affect not only the complexity of modeling process but also th... Aggregation of species with similar ecological properties is one of the effective methods to simplify food web researches.However,species aggregation will affect not only the complexity of modeling process but also the accuracy of models’outputs.Selection of aggregation methods and the number of trophospecies are the keys to study the simplification of food web.In 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)model.Impacts of aggregation methods and trophospecies number on food webs were evaluated based on the robustness and unitless of ecological net-work indices.Results showed that aggregation method of SEA performed better than the other two methods in estimating food web structure and function indices.The 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 flow.According 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 indices.Therefore,trade-off between simplifying food webs and reflecting the status of ecosystem should be con-sidered in food web studies.These findings highlight the importance of aggregation methods and trophospecies number in the analy-sis of food web simplification.This 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. 展开更多
关键词 LIM-MCMC model species aggregation trophospecies number aggregation methods food web indices
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Effects of nutrient limitations on the sinking velocity of Thalassiosira weissflogii
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作者 Jie Zhu Qiang Hao +2 位作者 Wei Zhang Yingying Ma Jiangning Zeng 《Acta Oceanologica Sinica》 SCIE CAS CSCD 2024年第6期163-172,共10页
The sinking of diatoms is critic al to the formation of oceanic biological pumps and coastal hypoxic zones.However,little is known about the effects of different nutrient restrictions on diatom sinking.In this study,w... The sinking of diatoms is critic al to the formation of oceanic biological pumps and coastal hypoxic zones.However,little is known about the effects of different nutrient restrictions on diatom sinking.In this study,we measured the sinking velocity(SV) of Thalassiosira weissflogii using a new phytoplankton video observation instrument and analyzed major biochemical components under varying nutrient conditions.Our results showed that the SV of T.weissflogii under different nutrient limitation conditions varied substantially.The highest SV of(1.77±0.02) m/d was obtained under nitrate limitation,signific antly surpassing that under phosphate limitation at(0.98±0.13) m/d.As the nutrient limitation was released,the SV steadily decreased to(0.32±0.03) m/d and(0.15±0.05) m/d,respectively.Notably;under conditions with limited nitrate and phosphate concentrations,the SV values of T.weissflogii significantly positively correlated with the lipid content(P <0.001),with R^(2) values of 0.86 and 0.69,respectively.The change of the phytoplankton SV was primarily related to the intracellular compo sition,which is controlled by nutrient conditions but did not significantly correlate with transparent extracellular polymer and biosilica contents.The results of this study help to understand the regulation of the vertical sinking process of diatoms by nutrient restriction and provide new insights into phytoplankton dynamics and their relationship with the marine nutrient structure. 展开更多
关键词 nutrient limitation Thalassiosira weissflogii sinking velocity biochemical component lipid content
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foxl2l is a germ cell-intrinsic gatekeeper of oogenesis in zebrafish
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作者 Zhiqin Ren Ding Ye +5 位作者 Naike Su Chaofan Wang Lijia He Houpeng Wang Mudan He Yonghua Sun 《Zoological Research》 SCIE CSCD 2024年第5期1116-1130,共15页
Zebrafish serve as a valuable model organism for studying germ cell biology and reproductive processes.The AB strain of zebrafish is proposed to exhibit a polygenic sex determination system,where most males initially ... Zebrafish serve as a valuable model organism for studying germ cell biology and reproductive processes.The AB strain of zebrafish is proposed to exhibit a polygenic sex determination system,where most males initially develop juvenile ovaries before committing to male fate.In species with chromosomal sex determination,gonadal somatic cells are recognized as key determinants of germ cell fate.Notably,the loss of germ cells in zebrafish leads to masculinization,implying that germ cells harbor an intrinsic feminization signal.However,the specific signal triggering oogenesis in zebrafish remains unclear.In the present study,we identified foxl2l as an oocyte progenitor-specific gene essential for initiating oogenesis in germ cells.Results showed that foxl2l-knockout zebrafish bypassed the juvenile ovary stage and exclusively developed into fertile males.Further analysis revealed that loss of foxl2l hindered the initiation of oocyte-specific meiosis and prevented entry into oogenesis,leading to premature spermatogenesis during early gonadal development.Furthermore,while mutation of the pro-male gene dmrt1 led to fertile female differentiation,simultaneous disruption of foxl2l in dmrt1 mutants completely blocked oogenesis,with a large proportion of germ cells arrested as germline stem cells,highlighting the crucial role of foxl2l in oogenesis.Overall,this study highlights the unique function of foxl2l as a germ cell-intrinsic gatekeeper of oogenesis in zebrafish. 展开更多
关键词 foxl2l DMRT1 OOGENESIS Sex determination MEIOSIS
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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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作者 Yue Yu Shi-Ming Wan +7 位作者 Cheng-You Huang Shuang-Meng Zhang Ai-Li Sun Jun-Qi Liu Shun-Yao Li Yong-Fu Zhu Shu-Xin Gu Ze-Xia Gao 《Zoological Research》 SCIE CSCD 2024年第3期491-505,共15页
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 potential.However,the species faces c... 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 potential.However,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 prematurity.In 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 C.nasus.Genotyping of the female population based on whole-genome resequencing yielded 2120695 high-quality SNPs,39 of which were suggestively associated with ovarian development.Of note,a significant SNP peak on LG21 containing 30 suggestively associated SNPs was identified,with cpne5a determined as the causal gene of the peak.Therefore,single-marker and haplotype association analyses were performed on cpne5a,revealing four genetic markers(P<0.05)and seven haplotypes(r2>0.9)significantly associated with the phenotype.Comparative 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 sizes.Integrating 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 development.The 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 C.nasus strains exhibiting population-synchronous ovarian development in the future. 展开更多
关键词 Coilia nasus GWAS TRANSCRIPTOME Ovarian development SNP
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High-quality Development Path of Graduate Education in Aquaculture Discipline:A Case Study of Guangdong Ocean University
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作者 Huanying PANG Miao XIE +2 位作者 Shuanghu CAI Yucong HUANG Jichang JIAN 《Asian Agricultural Research》 2024年第9期41-44,共4页
Aquaculture is a discipline system that focuses on exploring the growth,development,reproduction,aquaculture,and resources of aquatic animals and plants,and their complex relationships.Under the tide of the"high-... Aquaculture is a discipline system that focuses on exploring the growth,development,reproduction,aquaculture,and resources of aquatic animals and plants,and their complex relationships.Under the tide of the"high-quality development"strategy,the aquaculture discipline is also facing new opportunities and challenges for transformation,upgrading,and deepening development.Therefore,exploring and practicing an effective path for the high-quality development of graduate education in aquaculture is not only the key to promoting the transformation of graduate education in aquaculture from scale expansion to quality improvement,but also has immeasurable value for implementing the strategy on developing a quality workforce and the strategy of scientific and technological powerhouse.The high-quality development of graduate education in aquaculture can be promoted from the following aspects:optimizing and improving the construction of the graduate education system,focusing on enhancing the quality of high-level talent cultivation,strengthening the overall strength of the graduate supervisor team,actively promoting the adjustment and upgrading of the disciplinary and professional structure,strengthening the construction of resource platforms and deepening the implementation of collaborative education mechanisms,and continuously expanding and deepening the new pattern of international exchange and cooperation.Through the comprehensive promotion of the above paths,the aim is to fully build a model for the improvement and governance of graduate education quality. 展开更多
关键词 AQUACULTURE GRADUATE EDUCATION HIGH-QUALITY development
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DNA barcoding of fishes from Zhoushan coastal waters using mitochondrial COI and 12S rRNA genes 被引量:1
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作者 Yehui WANG Na SONG +3 位作者 Shude LIU Zhi CHEN Anle XU Tianxiang GAO 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2023年第5期1997-2009,共13页
Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan c... Accurate species identification is a key component of biodiversity research.DNA barcoding is an effective molecular method used for fish species identification.We aimed to study the DNA barcoding of fish in Zhoushan coastal waters,explore the differences and applicability of two gene fragments(12S rRNA and COI)of DNA barcoding in fish species identification,and established a comprehensive fish barcoding reference database.Two hundred and eighty-seven captured fish samples from Zhoushan coastal waters were identified using morphological characteristics and DNA barcoding.A total of 26412S rRNA sequences(belonging to eight orders,31 families,55 genera,and 66 species)and 188 COI sequences(belonging to seven orders,30 families,48 genera,and 58 species)were obtained.The lengths of the 12S rRNA sequences ranged from 165 to 178 bp,and the guanine-cytosine(GC)content was 45.37%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.10%and 26.66%,respectively.The length of the COI sequence ranged 574–655 bp,and the content of GC was 45.97%.The average 12S rRNA interspecific and intraspecific genetic distances(K2P)were 0.16%and 27.45%,respectively.The minimum interspecific genetic distances of 12S rRNA and COI(1.23%and 1.86%)were both greater than their maximum intraspecific genetic distances(2.42%and 8.66%).Three molecular analyses(NJ tree,ABGD,and GMYC)were performed to accurately identify and delineate species.Clustering errors occurred when the 12S rRNA sequences were delimited using the NJ tree method,and the delimitation results of ABGD and GMYC are consistent with the final species identification results.Our results demonstrate that DNA barcoding based on 12S rRNA and COI can be used as an effective tool for fish species identification,and 12S rRNA has good application prospects in the environmental DNA(eDNA)metabarcoding of marine fish. 展开更多
关键词 DNA barcoding cytochrome c oxidase subunit I(COI) 12S rRNA fish identification species delimitation Zhoushan coastal waters
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Performances of Clustering Methods Considering Data Transformation and Sample Size: An Evaluation with Fisheries Survey Data
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作者 WO Jia ZHANG Chongliang +2 位作者 XU Binduo XUE Ying REN Yiping 《Journal of Ocean University of China》 SCIE CAS CSCD 2020年第3期659-668,共10页
Clustering is a group of unsupervised statistical techniques commonly used in many disciplines. Considering their applications to fish abundance data, many technical details need to be considered to ensure reasonable ... Clustering is a group of unsupervised statistical techniques commonly used in many disciplines. Considering their applications to fish abundance data, many technical details need to be considered to ensure reasonable interpretation. However, the reliability and stability of the clustering methods have rarely been studied in the contexts of fisheries. This study presents an intensive evaluation of three common clustering methods, including hierarchical clustering(HC), K-means(KM), and expectation-maximization(EM) methods, based on fish community surveys in the coastal waters of Shandong, China. We evaluated the performances of these three methods considering different numbers of clusters, data size, and data transformation approaches, focusing on the consistency validation using the index of average proportion of non-overlap(APN). The results indicate that the three methods tend to be inconsistent in the optimal number of clusters. EM showed relatively better performances to avoid unbalanced classification, whereas HC and KM provided more stable clustering results. Data transformation including scaling, square-root, and log-transformation had substantial influences on the clustering results, especially for KM. Moreover, transformation also influenced clustering stability, wherein scaling tended to provide a stable solution at the same number of clusters. The APN values indicated improved stability with increasing data size, and the effect leveled off over 70 samples in general and most quickly in EM. We conclude that the best clustering method can be chosen depending on the aim of the study and the number of clusters. In general, KM is relatively robust in our tests. We also provide recommendations for future application of clustering analyses. This study is helpful to ensure the credibility of the application and interpretation of clustering methods. 展开更多
关键词 hierarchical cluster K-means cluster expectation-maximization cluster optimal number of clusters stability data transformation
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Intercross population study reveals that co-mutation of mitfa genes in two subgenomes induces red skin color in common carp(Cyprinus carpio wuyuanensis) 被引量:1
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作者 Bi-Jun Li Lin Chen +10 位作者 Meng-Zhen Yan Xiao-Qing Zou Yu-Lin Bai Ya-Guo Xue Zhou Jiang Bao-Hua Chen Cheng-Yu Li Qian He Jian-Xin Feng Tao Zhou Peng Xu 《Zoological Research》 SCIE CAS CSCD 2023年第2期276-286,共11页
Common carp are among the oldest domesticated fish in the world.As such,there are many food and ornamental carp strains with abundant phenotypic variations due to natural and artificial selection.Hebao red carp(HB,Cyp... Common carp are among the oldest domesticated fish in the world.As such,there are many food and ornamental carp strains with abundant phenotypic variations due to natural and artificial selection.Hebao red carp(HB,Cyprinus carpio wuyuanensis),an indigenous strain in China,is renowned for its unique body morphology and reddish skin.To reveal the genetic basis underlying the distinct skin color of HB,we constructed an improved highfidelity(HiFi) HB genome with good contiguity,completeness,and correctness.Genome structure comparison was conducted between HB and a representative wild strain,Yellow River carp(YR,C.carpio haematopterus),to identify structural variants and genes under positive selection.Signatures of artificial selection during domestication were identified in HB and YR populations,while phenotype mapping was performed in a segregating population generated by HB×YR crosses.Body color in HB was associated with regions with fixed mutations.The simultaneous mutation and superposition of a pair of homologous genes(mitfa) in chromosomes A06 and B06 conferred the reddish color in domesticated HB.Transcriptome analysis of common carp with different alleles of the mitfa mutation confirmed that gene duplication can buffer the deleterious effects of mutation in allotetraploids.This study provides new insights into genotype-phenotype associations in allotetraploid species and lays a foundation for future breeding of common carp. 展开更多
关键词 Cyprinus carpio Artificial selection COLORATION mitfa Structural variant
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Evaluation of Reference Genes for Quantitative Real-Time PCR Analysis in Manila Clam Ruditapes philippinarum Under Hypoxic Stress 被引量:1
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作者 JING Hao ZHOU Liqing +4 位作者 GONG Miao TU Kang LIU Zhihong WU Biao SUN Xiujun 《Journal of Ocean University of China》 SCIE CAS CSCD 2023年第4期1059-1067,共9页
Quantitative real-time PCR(qRT-PCR)has been widely used for gene expression analysis,and selection of reference genes is a key point to obtain accurate results.To find out optimal reference genes for qRT-PCR in Manila... Quantitative real-time PCR(qRT-PCR)has been widely used for gene expression analysis,and selection of reference genes is a key point to obtain accurate results.To find out optimal reference genes for qRT-PCR in Manila clam Ruditapes philippinarum in response to hypoxia,different tissues were used and compared to evaluate the stability of candidate reference genes under low oxygen stress(DO 0.5mgL^(−1) and DO 2.0mgL^(−1))and normal condition(DO 7.5mgL^(−1)).Seven candidate reference genes were selected to evaluate the stability of their expression levels.The reference genes were evaluated by Delta Ct,BestKeeper,NormFinder and geNorm,and then screened by RefFinder calculation.Under hypoxic stress of 0.5mgL^(−1),the most suitable reference gene for gill and hepatopancreas was RPL31,and the optimal reference genes for axe foot and adductor muscle were TUB and HIS,respectively.For hypoxic stress of 2.0mgL^(−1),the most stable reference gene for gill and hepatopancreas was RPL31,and the optimal reference genes for axe foot and adductor muscle were RPS23 and EF1A,respectively.At the normal condition,HIS and EF1A were identified as the optimal internal reference genes in gill and hepatopancreas respectively,and GFRP2 was the best internal reference gene for axe foot and adductor muscle.The present findings will provide important basis for the selection of reference genes for qRT-PCR analysis of gene expression level in bivalves under hypoxic stress,which might be helpful for the analysis of other molluscs too. 展开更多
关键词 CLAM reference gene HYPOXIA quantitative real-time PCR
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OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data 被引量:1
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作者 Ben-Ben Miao Wei Dong +4 位作者 Yi-Xin Gu Zhao-Fang Han Xuan Luo Cai-Huan Ke Wei-Wei You 《Horticulture Research》 SCIE CSCD 2023年第11期13-26,共14页
With the advancements in high-throughput sequencing technologies such as Illumina,PacBio,and 10X Genomics platforms,and gas/liquid chromatography-mass spectrometry,large volumes of biological data in multiple formats ... With the advancements in high-throughput sequencing technologies such as Illumina,PacBio,and 10X Genomics platforms,and gas/liquid chromatography-mass spectrometry,large volumes of biological data in multiple formats can now be obtained through multi-omics analysis.Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems;however,it is challenging for most experimental biologists to analyse data using command-line interfaces,coding,and scripting.Based on experience with multi-omics,we have developed OmicsSuite,a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization.The suite has 175 sub-applications in 12 categories,including Sequence,Statistics,Algorithm,Genomics,Transcriptomics,Enrichment,Proteomics,Metabolomics,Clinical,Microorganism,Single Cell,and Table Operation.We created the user interface with Sequence View,Table View,and intelligent components based on JavaFX and the popular Shiny framework.The multi-omics analysis functions were developed based on BioJava and 300+packages provided by the R CRAN and Bioconductor communities,and it encompasses over 3000 adjustable parameter interfaces.OmicsSuite can directly read multi-omics raw data in FastA,FastQ,Mutation Annotation Format,mzML,Matrix,and HDF5 formats,and the programs emphasize data transfer directions and pipeline analysis functions.OmicsSuite can produce pre-publication images and tables,allowing users to focus on biological aspects.OmicsSuite offersmulti-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in plants.It enables researchers to freely explore the molecular information contained in multi-omics big data(Source:https://github.com/OmicsSuite/,Website:https://omicssuite.github.io,v1.3.9). 展开更多
关键词 BREAKTHROUGH TABLES SEEKING
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Training Mode of Aquaculture Professionals in Local Applied Marine Colleges and Universities
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作者 Qingbo QIU Youming LI Xiaomei LI 《Asian Agricultural Research》 2022年第8期55-59,共5页
In the training of aquaculture professionals,there are problems such as unreasonable structure of teachers,unclear understanding of aquaculture by parents and students,poor practical ability of students,lack of grass-... In the training of aquaculture professionals,there are problems such as unreasonable structure of teachers,unclear understanding of aquaculture by parents and students,poor practical ability of students,lack of grass-roots aquaculture talents,and imperfect multi-party cooperation training mechanism.In view of the above situation,the training mode of applied talents in aquaculture needs to be reformed and innovated.In this paper,some measures to establish the training mode of aquaculture professionals were proposed,including strengthening students’correct understanding of the major,improving the curriculum system for cultivating applied talents,establishing a training model for practical teaching,improving the practical ability of teachers,increasing the provision of high-quality educational resources,and adopting school-enterprise cooperation,so as to cultivate high-quality and high-tech aquatic talents under the training mechanism of applied talents. 展开更多
关键词 TRANSFORMATION Marine colleges and universities AQUACULTURE Talents TRAINING Model
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Effect of ChREBP on carbohydrate feeding regulation in mandarin fish Siniperca chuatsi
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作者 Jun YANG Yulan KUANG +7 位作者 Xufang LIANG Wenjing CAI Jing XU Junjie GAO Junran WEI Shan HE Zengqiang YIN Jinshui LIANG 《Journal of Oceanology and Limnology》 SCIE CAS CSCD 2023年第5期1988-1996,共9页
Carnivorous fish have poor tolerance to carbohydrate in feed and low utilization rate of carbohydrate.Therefore,the balance of carbohydrate and lipids in the nutrient metabolism of carnivorous fish,the ef fective conv... Carnivorous fish have poor tolerance to carbohydrate in feed and low utilization rate of carbohydrate.Therefore,the balance of carbohydrate and lipids in the nutrient metabolism of carnivorous fish,the ef fective conversion and utilization of carbohydrate and lipids,and the feedback regulation of feeding are the key links for the e fficient utilization of carnivorous fish feed.Carbohydrate response element binding protein(ChREBP)is a new transcription factor found in recent years in the glucose signaling pathway,and can also participate in feeding regulation.We performed in-vivo and in-vitro experiments to reveal the role of ChREBP in the glucose metabolism and feeding in mandarin fish.The mRNA expression of ChREBP and appetite regulatory factors were measured after intraperitoneal injection of glucose in mandarin fish Siniperca chuatsi and cotransfection with glucose and glucose+siRNA in the hypothalamic cells in mandarin fish.The results reveal that at hour 2 and 4 post intraperitoneal injection with 1 mg/g BW glucose,the blood glucose level of the mandarin fish increased significantly,but food intake decreased significantly,and it also displayed a significantly increased ChREBP mRNA expression levels in liver.At hour 4 post injection,hypothalamic ChREBP mRNA level was significantly increased,whereas the mRNA expression levels of appetite genes neuropeptide Y(npy)and agouti-related peptide(AgRP)were decreased significantly.When the glucose concentration was 40 mmol/L,the expression level of ChREBP mRNA in mandarin fish hypothalamic cells was significantly up-regulated,but the expression level of appetite gene npy mRNA was down-regulated.When siRNA and glucose were co-transfected into mandarin fish brain cells,the expression level of chrebp mRNA was significantly decreased,and the appetite gene npy mRNA was significantly increased.The results indicated that glucose regulated food intake through the modulation of appetite gene npy by ChREBP. 展开更多
关键词 Siniperca chuatsi mandarin fish carbohydrate response element binding protein(ChREBP) GLUCOSE ingestion RNA interference
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Effects of Dietary Vitamin D_(3)on Growth Performance,Immune Status,and Calcium and Phosphorus Metabolism in Litopenaeus vannamei Under Different Salinity Conditions
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作者 LIU Miao ZHANG Hui +5 位作者 SHAO Rui ZHOU Xueqi ZHOU Qicun MAI Kangsen AI Qinghui WAN Min 《Journal of Ocean University of China》 SCIE CAS CSCD 2023年第4期1023-1033,共11页
Vitamin D_(3)(VD_(3)) plays a vital role in various physiological processes in addition to its role in regulating the homeostasis of calcium and phosphorus.The present study was conducted to investigate the effects of... Vitamin D_(3)(VD_(3)) plays a vital role in various physiological processes in addition to its role in regulating the homeostasis of calcium and phosphorus.The present study was conducted to investigate the effects of dietary VD_(3) on growth performance,immune status and the metabolism of calcium and phosphorus in Litopenaeus vannamei under the optimal salinity(25)and high salinity(35)conditions.Shrimp(2.1 g±0.1 g)were fed with experimental diets containing 0,1500,6000 and 12000IUkg^(−1)VD_(3) for 30 days under two salinity conditions respectively.The results showed that the growth performance and intestinal health were reduced,while oxidative stress was induced in the shrimp cultured at salinity 35 compared to those in the shrimp cultured at salinity 25.Interestingly,dietary supplementation of 1500 IU kg^(−1)VD_(3) at salinity 35 promoted the growth performance,improved the intestinal health,and enhanced the antioxidant capacity and non-specific immunity in shrimp.In addition,the content of inorganic phosphorus in shrimp serum was affected by dietary VD_(3) independent of salinity.In contrast,the expressions of calcium transport-related genes,including calmodulin and Ca2+-ATPase,were regulated by salinity,instead of dietary VD_(3).In conclusion,an appropriate supplementation of dietary VD_(3) under high-salt condition can promote the growth,alleviate intestinal inflammation,enhance antioxidant capacity and immunity,and contribute to phosphorus metabolism in L.vannamei. 展开更多
关键词 vitamin D_(3) Penaeus vannamei SALINITY antioxidant capacity IMMUNITY metabolism intestinal health
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