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1.
目的:通过网络药理学和分子对接技术对“蒲黄-姜黄”抗动脉粥样硬化的作用机制进行探讨。方法:基于TCMSP数据库获取“蒲黄-姜黄”的有效活性成分及靶点,通过OMIM、GeneCards、DisGeNet、DrugBank数据库挖掘动脉粥样硬化的潜在靶点,将药物与疾病靶点取交集后,利用STRING数据库进行蛋白质-蛋白质相互作用(PPI)分析,使用R语言进行基因本体(GO)功能及京都基因与基因组百科全书(KEGG)通路富集分析,最后使用PyMOL、AutoDock Vina进行分子对接。结果:共筛选出“蒲黄-姜黄”有效成分9个,与动脉粥样硬化相关靶点190个,核心靶点为转录因子激活蛋白1(JUN)、肿瘤蛋白P53(IP53)、丝裂原激活蛋白激酶1(MAPK1)、苏氨酸蛋白激酶(AKT1)等。GO功能富集分析显示生物过程有2438个、细胞组分有97个、分子功能有252个,共计2787个GO功能条目。KEGG通路富集筛选得到信号通路170条,主要涉及血脂和动脉粥样硬化、流体剪切应力和动脉粥样硬化等。分子对接显示各个成分与靶点均能较好地结合,其中AKT1靶点与这些成分的结合强度最佳。结论:“蒲黄-姜黄”可以多成分、多靶点、多通路地抗动脉粥样硬化。  相似文献   

2.
为揭示不同抗流能力的大黄鱼(Larimichthyscrocea)肌肉基因表达水平的变化,筛选抗流相关基因,解析大黄鱼抗流性状形成的分子基础,收集福建福鼎沙埕湾主养区1 000尾大黄鱼,在设计制作的抗流实验水槽中,以流速1.0m/s为筛选条件,将抗流时间>30 min的大黄鱼归为抗流组(HM组),抗流时间<5 min的大黄鱼归为非抗流组(SM组),对其肌肉进行转录组分析,并统计抗流分组后48 h内大黄鱼的累计死亡率。转录组结果显示, HM组与SM组文库共富集到1806个差异表达基因(DEGs),其中1090个上调,716个下调。GO功能注释发现显著富集的条目主要集中在肌肉收缩相关功能, KEGG富集分析发现上调的DEGs主要富集在心肌收缩、氧化磷酸化、黏着斑、ECM-受体相互作用、AGE-RAGE、MAPK、心肌细胞中的肾上腺素能等相关通路;下调的DEGs主要富集在真核生物核糖体的发生、蛋白酶体、内质网中的蛋白加工、RNA转运、泛素介导的蛋白水解信号通路等。此外,RT-qPCR结果表明,随机选取的DEGs与RNA-seq结果的表达趋势一致。48h的累计死亡率结果显示,SM组...  相似文献   

3.
目的:利用网络药理学分析技术探寻清痹汤治疗痛风性关节炎(GA)的潜在作用机制。方法:采用TCMSP平台挑选出清痹汤主要活性化合物及靶点;利用五大疾病数据库查找GA的对应靶点;借助韦恩图工具构建“药物-疾病靶点”交集图;将交集靶点导入String数据库构建蛋白互作(PPI)图;通过DAVID数据库进行基因功能GO分析、KEGG通路富集分析;依托Cytoscape 3.7.2绘制“中药-活性成分-靶点”“活性成分-交集靶点”“核心靶点-KEGG 通路”网络图。结果:清痹汤有效活性化合物共133个,潜在对应作用靶点125个;GA疾病相关靶点823个;疾病-药物共同靶点41个。通过蛋白互作网络图提示IL-6、VEGFA、CASP3、RELA、MYC、PPARG等可能是清痹汤治疗GA的核心靶基因。GO富集分析共237个,其中生物过程(BP)174条、细胞组成(CC)20条、分子功能(MF)73条。KEGG通路富集分析共73条。结论:清痹汤主要通过调节细胞增殖和凋亡、控制炎症、抑制血管生成等多途径发挥治疗GA的作用,与“多成分-多靶点-多通路”治疗疾病的特点相契合。  相似文献   

4.
为研究仿刺参昼伏夜出行为节律的内源性调控机制,需要先筛查出仿刺参是否具有能够调控生物节律的生物钟基因。本研究通过Blastp,将KEGG数据库中哺乳动物和果蝇的昼夜节律通路成员基因与仿刺参全基因组进行同源比对,筛选仿刺参基因组中的同源生物钟基因,并参考不同光照条件下仿刺参触手转录本数据,对相关基因在不同光照条件下的表达量进行初步分析。结果显示,在仿刺参全基因组中找到了绝大部分具有较好注释的同源候选生物钟基因,包括CLOCK(Circadian Locomotor Output Cycles Kaput)、BMAL1 (Brain and Muscle Arnt-Like 1)/CYC(Cycle)、TIM (timeless)等,但PER (Period)和DEC (class B basic helix-loop-helix protein 2/3)基因未能匹配到有效的同源基因;转录本的数据表明,在120 lx光照1 h与120 lx光照5 min比较组中(Lt1h:Lt5m),发现只有CLOCK基因具有显著的下调表达(log2FC=-1.1209),其他生物钟...  相似文献   

5.
目的:运用网络药理学研究青皮治疗抑郁症的作用机制。方法:采用中药系统药理学分析平台(TCMSP)检索青皮的有效成分及其作用靶点;采用OMIM、GeneCards数据库检索抑郁症的疾病靶点;应用R语言等计算软件获取青皮有效成分的作用靶点和抑郁症疾病靶点的交集基因;运用Perl软件与Cytoscape 3.7.0软件联合构建青皮-有效成分-靶点-抑郁症调控网络;使用STRING构建PPI网络;应用DAVID数据分析软件和Metascape数据库,对所筛选出的“核心基因”进行基因本体(GO)功能和京都基因与基因组百科全书(KEGG)通路富集分析,最终获得预测结果。结果:通过以上方法,获得青皮的5个有效成分,有效成分的基因靶点与抑郁症基因靶点的交集基因有30个。通过对青皮-有效成分-靶点-抑郁症调控网络的可视化分析,发现有效成分中的川陈皮素(nobiletin)所对应的交集基因最多。运用PPI网络预测到雌激素受体1(ESR1)、胱天蛋白酶3(CASP3)、过氧化物酶体增生激活受体γ(PPARG)等25个基因是青皮治疗抑郁症所干预的重要靶点。GO功能富集分析和KEGG富集分析结果显示,青皮有效成分在分子层面对抑郁症基因的干预有较好的作用。结论:青皮治疗抑郁症的机制主要是作用于ESR1、CASP3、PPARG等25个基因,并在分子层面起到改变抑郁症基因的转录翻译等作用。  相似文献   

6.
目的:通过生物信息学方法分析骨关节炎(OA)中软骨生成祖细胞(CPC)损伤的差异基因表达,并找出关键基因来预测可用于诊断或治疗CPC损伤的生物标志物及中药。方法:从GEO数据库下载CPC数据。共包含样本8 例。以R语言处理数据,得到差异表达基因。再使用DAVID数据库对差异表达基因进行基因本体(GO)功能及京都基因与基因组百科全书(KEGG)通路富集分析。对显著差异表达的前100个差异表达基因进行分析后绘制蛋白质-蛋白质相互作用(PPI)网络图。比较关键基因在OA组织及正常组织中的表达水平。筛选网络中显著模块及关键基因,最后预测作用于关键基因的中药。结果:共筛选出DEGs 1027个,其中上调基因327个,下调基因700个。DEGs 显著富集于细胞外基质(ECM)受体相互作用、金黄色葡萄球菌感染、粘着斑、人乳头瘤病毒感染、磷脂酰肌醇-3-激酶-蛋白激酶B(PI3K-Akt)信号通路、肺结核等通路。前7个关键基因为:基质金属肽酶3(MMP3)、脂多糖结合蛋白(LBP)、基质金属肽酶1(MMP1)、脂质运载蛋白(LCN2)、人血浆丝氨酸蛋白激酶(SERPINA5)、成纤维细胞生长因子23(FGF23)、颗粒酶B(GZMB)。其中MMP3和LBP为核心基因。MMP3和LBP出现显著表达,预测出治疗CPC损伤的潜在代表中药有黄芩、淫羊藿、桃仁等。结论:MMP3和LBP的显著表达有助于区分OA中的CPC,并且有望成为诊断和治疗CPC损伤的生物标志物。  相似文献   

7.
泥蚶(Tegillarcagranosa)是一种比较特别的具有较强耐低氧能力的贝类,但目前其耐低氧分子调控机理尚不知。为探究泥蚶耐受低氧的分子调控机理,本研究对低氧胁迫下的泥蚶(Tegillarca granosa)血细胞转录组中富集的信号通路及生物学过程进行分析,并初步筛选分析耐低氧基因。对低氧(DO=0.5 mg/L)胁迫6、24、72、120 h的泥蚶血细胞进行转录组测序(RNA-seq)并开展生物信息学分析,筛选出差异基因集,并对胁迫72、120 h的DEGs进行GO富集分析、KEGG通路分析,采用qPCR方法检测7个DEGs的表达量并与转录组比较。结果显示从6 h开始到120 h的4个时间点的DEGs数量呈增多的趋势, GO功能分析主要富集在JUN激酶活性的负调控、蛋白质水解的负调控及免疫系统进程等主动抗凋亡、抗逆进程; KEGG通路分析主要富集在胰岛素及胰腺分泌的信号通路、HIF-1通路、钙信号相关通路和细胞凋亡相关通路。qPCR检测结果显示, 7个基因的表达上调/下调趋势与转录组测序一致,证实了转录组测序结果的可靠性。本研究推测胰腺分泌信号通路、钙信号通路及凋亡通路在泥蚶...  相似文献   

8.
目的:运用网络药理学和分子对接技术探讨罗汉果治疗糖尿病的作用机制。方法:通过TCMSP平台和Swiss Target Prediction数据库筛选出罗汉果的活性成分及其靶点;利用GeneCard、TTD、OMIM数据库筛选出糖尿病潜在靶点;采用Cytoscape 3.7.2软件构建药物-活性成分-疾病-靶点的可视化网络;通过STRING数据库对关键靶点构建蛋白质-蛋白质相互作用(PPI)网络;利用Metascape数据库进行基因本体(GO)功能以及京都基因与基因组百科全书(KEGG)通路富集分析;利用Autodock4和Pymol软件对关键活性成分和关键靶点进行分子对接分析和可视化。结果:筛选出有效成分18种,糖尿病靶点146个。GO功能富集分析得到GO条目572条,KEGG通路富集分析得到信号通路167条。分子对接结果显示β-谷甾醇、山柰酚、罗汉果醇等关键活性成分与原癌基因酪氨酸蛋白激酶(SRC)等关键靶点的亲和力较高。结论:罗汉果通过多靶点、多通路发挥抗糖尿病的作用,其关键活性成分通过与SRC、丝氨酸/苏氨酸蛋白激酶1(AKT1)、丝裂原活化蛋白激酶3(MAPK-3)等靶点调节晚期糖基化终末产物-糖基化终末产物受体(AGE-RAGE)、缺氧诱导因子1(HIF-1)、磷脂酰肌醇-3-激酶/蛋白激酶(PI3K-Akt)等信号通路起到治疗糖尿病的作用。  相似文献   

9.
目的:运用网络药理学方法探讨八珍汤抗疲劳的药理机制,为八珍汤抗疲劳的临床应用提供理论依据。方法:筛选八珍汤药物的活性成分及靶点,查找疲劳相关基因,确定八珍汤抗疲劳靶点,进行基因本体(GO)功能和京都基因与基因组百科全书(KEGG)通路富集分析,将预测靶点最多的活性成分与蛋白质-蛋白质相互作用(PPI)网络中节点最大的靶点进行分子对接。结果:共筛选出143个有效活性成分,作用于133个疲劳靶点,八珍汤抗疲劳的核心基因主要有白细胞介素-1β(IL-1β)、趋化因子8(CXCL8)等47个。中药-疾病靶点涉及的GO功能分析中,生物过程主要集中在对无机物的反应、脂多糖的反应、炎症反应等;分子功能主要集中在激酶结合、DNA 结合转录因子结合、蛋白质结构域特异性结合等;细胞组分主要集中在膜筏、细胞周期蛋白依赖性蛋白激酶全酶复合物、囊腔等。KEGG通路富集分析主要富集在包括癌症通路、糖尿病并发症晚期糖基化终产物及其受体信号通路、白细胞介素-17(IL-17)信号通路等。分子对接结果显示槲皮素、山柰酚、甘草酮a和β谷甾醇与核心靶点结合性较好,结合能均<0 kcal/mol。结论:八珍汤抗疲劳的机制是多靶点、多通路的,为后续的基础研究提供了思路,并为临床运用八珍汤抗疲劳提供了理论支持。  相似文献   

10.
目的:通过网络药理学方法探析板蓝根-山豆根-白茅根治疗银屑病的作用机制。方法:应用 TCMSP 平台检索板蓝根-山豆根-白茅根的化学成分,利用GeneCards等数据库检索银屑病的相关靶点基因,将药物靶点与疾病靶点取交集绘制韦恩图。运用Cytoscape 3.8.2软件构建药物-成分-靶点网络图,构建蛋白质-蛋白质相互作用(PPI)网络图,对交集靶点进行基因本体(GO)功能和京都基因与基因组百科全书(KEGG)通路富集分析。结果:共获有效成分52种,如β-谷甾醇、槲皮素、山柰酚等;与银屑病相关靶点90个,其中白细胞介素-6、肿瘤坏死因子、肿瘤蛋白p53、白细胞介素-1β、活化蛋白-1等为核心基因;GO功能富集分析中共确定了614条GO条目,其中生物过程480条、细胞组分52条、分子功能82条;KEGG富集分析中共确定了102条通路,涉及多种癌症通路、肝炎、磷脂酰肌醇3-激酶(PI3K)-丝氨酸-苏氨酸-激酶(Akt)信号、肿瘤坏死因子信号、丝裂原活化蛋白激酶等信号通路。结论:板蓝根-山豆根-白茅根可通过多种活性成分、多个靶点、多条通路抑制炎症因子的表达及角质细胞增殖、分化而发挥治疗作用。  相似文献   

11.
The food sources of aquacultured Apostichopus japonicus and the trophic levels of organisms in a sea cucumber(A. japonicus) and prawn(Penaeus japonica) polyculture system in a saltwater pond in Zhuanghe, Liaoning Province were examined using carbon and nitrogen stable isotopes. Across organisms, δ13C ranged from(–25.47±0.20)‰ to(–16.48±0.17)‰(mean±SD), and δ15N ranged from(4.23±0.49)‰ to(12.44±0.09)‰. The δ13C and δ15N contents of A. japonicus, P. japonica and Fenneropenaeus chinensis were comparatively higher than those of other organisms. Values of δ13C and δ15N revealed that P. japonica, Hemigrapsus sanguineus and Neomysis japonica comprised the largest component of the diet of A. japonicus. The mean trophic level of the organisms in this saltwater pond polyculture system was(2.75±0.08). P. japonica, A. japonicus, F. chinensis,Synechogobius hasta and Neomysis japonica were in the 3rd trophic level(2–3); jellyfish, H. sanguineus and zooplankton were in the 2nd trophic level(1–2); and Enteromorpha prolifera, benthic microalgae, periphyton and suspended matter primarily consisting of phytoplankton, bacteria and humus were in the primary trophic level(0–1).  相似文献   

12.
As a major aldehyde pollutant widely existing in industry and our daily life, acetaldehyde is more and more harmful to human health. As characteristic habitat niche, bacteria from deep sea environments are abundant and distinctive in heredity, physiology and ecological functions. Thus, the development of acetaldehyde-degrading bacteria from deep sea provides a new method to harness acetaldehyde pollutant. Firstly, in this study,acetaldehyde-degrading bacteria in the deep sea water of the West Pacific Ocean were enriched in situ and in the laboratory respectively, and then the diversity of uncultured bacteria was studied by using 16 S r RNA genes. Then acetaldehyde-degrading strains were isolated from two samples, including enrichment in situ and enrichment in laboratory samples of deep sea water from the West Pacific Ocean using acetaldehyde as the sole carbon source,and then the ability of acetaldehyde degradation was detected. Our results showed that the main uncultured bacteria of two samples with different enrichment approaches were similar, including Proteobacteria,Actinobacteria, Firmicutes, Cyanobacteria, but the structure of bacterial community were significant different.Four subgroups, α, γ, δ and ε, were found in Proteobacteria group. The γ-Proteobacteria was dominant(63.5%clones in laboratory enriched sample, 75% clones in situ enriched sample). The species belonged to γ-Proteobacteria and their proportion was nearly identical between the two enrichment samples, and Vibrio was the predominant genus(45% in laboratory enriched sample, 48.5% in situ enriched sample), followed by Halomonas(9% in situ enriched sample) and Streptococcus(6% in laboratory enriched sample). A total of 12 acetaldehyde-degrading strains were isolated from the two samples, which belonged to Vibrio, Halomonas,Pseudoalteromonas, Pseudomonas and Bacillus of γ-Proteobacteria. Strains ACH-L-5, ACH-L-8 and ACH-S-12,belonging to Vibrio and Halomonas, have strong ability of acetaldehyde degradation, which could tolerate 1.5 g/L acetaldehyde and degrade 350 mg/L acetaldehyde within 24 hours. Our results indicated that bacteria of γ-Proteobacteria may play an important role in carbon cycle of deep sea environments, especial the bacteria belonging to Vibrio and Halomonas and these strains was suggested for their potentials in government of aldehyde pollutants.  相似文献   

13.
A small armed dinoflagellate bloomed in the aquaculture ponds off the coast of Liaodong Bay, Bohai Sea of China,resulting in heavy mortalities of the cultured prawns(Penaeus japonicus) and larvae of Chinese mitten handed crabs(Eriocheir sinensis). The bloom-forming species was successfully isolated, and cellular morphology of the specimen was consequently investigated through light, fluorescent and electron microscopy. The small((14.4±1.6) μm in length) ellipsoid cells show typical Heterocapsa thecal plate arrangement(Po, cp, 5′, 3 a, 7′′, 6 c,5 s, 5′′′, 2′′′′). The episome is evidently bigger than the hyposome. One to three spherical pyrenoids are located above or beside the large elongated nucleus. The body scale is characterized by a triangle basal plate with one central upright and nine peripheral spines. Above all, Heterocapsa bohaiensis could be distinguished from other Heterocapsa species by the combination of the cell size, morphology, cellular structure and body scale. Sequence analyses of both ITS and LSU regions reveal the significant genetic divergence between H. bohaiensis and other established species in this genus, further supporting novelty of this species. Noticeably, different sample treatment methods resulted in morphological variation of the apical pore complex(APC) of H. bohaiensis, which needs to be taken into account in future study.  相似文献   

14.
腹壁纤毛虫是一种附着在浮游动物上的原生生物,尤其是附着在桡足类和甲壳类上的。而缘毛虫是可以以自由或寄生的形式在世界各沿海地区和港湾处被发现。本研究首次对东印度洋表层至200 m深海域的缘毛类纤毛虫以及其水平分布展开了研究。根据纤毛虫的形态、纤毛结构和茎的形态等的特征,在2014年4月10日至5月13日东印度洋航次的浮游生物拖网样品中鉴定出了五种富腹纤毛虫,海洋钟形虫Vorticella oceanica、交替聚缩虫Zoothamnium alternans、阿拉聚缩虫Zoothamnium alrasheidi、远洋聚缩虫Zoothamnium pelagicum和海洋聚缩虫Zoothamnium marinum。并通过光显微镜和扫描显微镜拍摄的照片,说明了其形态、尺寸和特征。研究结果表明,海洋钟形虫和远洋聚缩虫的分布与硅藻(如,密聚角毛藻Chaetoceros coarctatus)和桡足类(如,短角长腹剑水蚤Oithona brevicornis)等寄主有关,也包括甲藻(如,三角角藻Ceraitum tripose)周围的一些个体。这些附着纤毛虫的分布在东印度洋海域东南区以海洋钟形虫、远洋聚缩虫和海洋聚缩虫为主,而在孟加拉湾北部则有大量的阿拉聚缩虫。这种分布的变化可能是与寄主的分布有关,如桡足类(短角长腹剑水蚤)和硅藻(密聚角毛藻)的分布影响。  相似文献   

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The composition, structure, and distribution of flora and fauna on hydraulic facilities in the cooling system of the Vladivostok combined heat and power plant-2 were studied in summer and autumn of 2001. Cluster analysis was applied to differentiate Balanus rostratus, Mytilus trossulus, Jassa marmorata, Crassostrea gigas + Balanus rostratus, Modiolus modiolus + Pachycheles stevensii, Hydroides ezoensis, and Amphibalanus improvisus communities. The groups of fouling organisms found on the studied objects were shown to be assigned both to “physically controlled” and “biologically balanced” benthic communities. This study stresses the high similarity between the fouling communities of anthropogenic substrata and natural intertidal and subtidal benthic communities from adjacent areas of Peter the Great Bay.  相似文献   

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The biomass and size fraction of phytoplankton in terms of chlorophyll a(Chl a) was measured during four cruises conducted in April, July, October 2013 and January 2014 in mariculture area, the Sanggou Bay, China.Results show that total Chl a levels in the surface seawater of the Sanggou Bay generally range from 0.10 to 20.46μg/L, with an average value of 2.13 μg/L. Nano-phytoplankton was the most important size-fraction and accounted for about 65.1% of total Chl a. In order to evaluate the importance of the "protozoan trophic link" for energy transfer from the microbial loop to filter-feeding feeders, Zhikong scallop Chlamys farreri was then offered a natural planktonic community as potential prey. Results show that scallops obtained carbon source from natural plankton with the rate of 11 033.05 μg/(g·d). Protists(nanoflagellates and ciliates) were the dominant source of carbon retained by scallop(48.78%). The microbial loop provided 58.45% of the carbon source for farmed scallops. These results indicate that the microbial loop represent a valuable trophic resource in mariculture system of the Sanggou Bay.  相似文献   

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Sea cucumber, Apostichopus japonicus(Selenka), is a commercially important marine species in China. Among the differently colored varieties sold in China, white and purple sea cucumbers have the greatest appeal to consumers. Identification of the pigments that may contribute to the formation of different color morphs of sea cucumbers will provide a scientific basis for improving the cultivability of desirable color morphs. In this study,sea cucumbers were divided into four categories according to their body color: white, light green, dark green, and purple. The pigment composition and contents in the four groups were analyzed by high performance liquid chromatography(HPLC). The results show that the pigment contents differed significantly among the white, lightgreen, dark-green, and purple sea cucumbers, and there were fewer types of pigments in white sea cucumber than in the other color morphs. The only pigments detected in white sea cucumbers were guanine and pteroic acid.Guanine and pteroic acid are structural colors, and they were also detected in light-green, dark-green, and purple sea cucumbers. Every pigment detected, except for pteroic acid, was present at a higher concentration in purple morphs than in the other color morphs. The biological color pigments melanin, astaxanthin, β-carotene, and lutein were detected in light-green, dark-green, and purple sea cucumbers. While progesterone and lycopene,which are also biological color pigments, were not detected in any of the color morphs. Melanin was the major pigment contributing to body color, and its concentration increased with deepening color of the sea cucumber body. Transmission electron microscopy analyses revealed that white sea cucumbers had the fewest epidermal melanocytes in the body wall, and their melanocytes contained fewer melanosomes as well as non-pigmented pre-melanosomes. Sea cucumbers with deeper body colors contained more melanin granules. In the body wall of dark-green and purple sea cucumbers, melanin granules were secreted out of the cell. The results of this study provide evidence for the main factors responsible for differences in coloration among white, light-green, darkgreen, and purple sea cucumbers, and also provide the foundation for further research on the formation of body color in sea cucumber, A. japonicus.  相似文献   

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车轮虫是一类主要寄生于贝类和鱼类体表的缘毛类纤毛虫原生动物。本文对分别寄生于海洋贝类--虾夷扇贝Mizuhopecten yessoensis,半咸水鱼类--鲻鱼Mugil cephalus和双色鳗鲡Anguilla bicolor bicolor,以及淡水鱼类--光唇鱼Acrossocheilus fasciatus鳃表和体表的虾夷扇贝车轮虫Trichodina pectenis,亚卓车轮虫T.jadranica,急尖车轮虫T.acuta和喙状车轮虫T.rostrata,进行了详细的分类学研究。本文第一次报道了虾夷扇贝车轮虫的活体和蛋白银染色后特征,该虫体也是国内新记录种。其它三个车轮虫物种感染的鱼类,均属新纪录宿主。同时,也报道了这四种车轮虫对宿主的感染率和感染强度。  相似文献   

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