太平洋鳕IRF3 基因的克隆及绝对定量表达分析

本研究通过克隆首次得到太平洋鳕(Gadus macrocephalus)干扰素调节因子3(interferon regulatory factor 3,IRF3)的部分序列。该序列长1878 bp,包含长1377 bp的完整开放阅读框(open reading frame,ORF),编码459个氨基酸,其编码的蛋白质分子量约为51 k D。经氨基酸序列比对发现,太平洋鳕IRF3的氨基酸序列包括1个含有5个保守色氨酸残基的DNA结合域(DNA binding domain,DBD)和1个保守的C端IRF关联域(IRF association domain,IAD);系统进化树分析表明,太平洋鳕IRF3与其他物种的IRF3亲缘关系较近。应用绝对荧光定量PCR方法对IRF3在不同组织和不同日龄(days post-hatching,dph)仔鱼的表达水平进行检测,并对干扰素在仔鱼期的免疫作用进行分析。组织表达绝对定量结果显示,性腺,肝和胸腺表达量高于其他组织。不同日龄仔鱼IRF3表达量结果显示,IRF3在受精卵就已经表达,在25 dph表达量大幅提高。本研究的结果为进一步研究太平洋鳕干扰素作用机制以及其在早期发育中的作用奠定了基础。     

荧光定量PCR技术应用综述

实时荧光定量PCR技术是指在PCR反应体系中加入荧光基团,利用荧光信号积累实时监测整个PCR进程,最后通过标准曲线对未知模板进行定量分析的方法。该技术具有范围宽、敏感性高、精确度高等优点,是迄今为止定量最准确,重现性最好的定量方法,其应用领域越来越广泛。研究表明,应用实时荧光定量PCR技术,可以快速、准确、特异性地对猪链球菌2型、炭疽杆菌、空肠弯曲菌、猪繁殖与呼吸综合征病毒、弓形虫等细菌、病毒性病原及食品微生物进行检测、鉴定;可以用于食源性微生物、食品过敏源、转基因食品、乳品等检测。荧光定量PCR技术也可用于肿瘤早期诊断、分型、分期和预后判断。     

基于鞭毛蛋白基因的坚强芽孢杆菌特异性套式PCR和荧光定量PCR方法的建立

细菌鞭毛蛋白编码基因hag具两端的保守序列及中间可变区域,在细菌的分类和鉴定中可作为分子标记。本研究克隆了坚强芽孢杆菌鞭毛蛋白编码基因hag部分序列,根据所得核酸序列设计套式引物Bfho和Bfhi,进行菌株的套式PCR特异性检测。此外,采用内引物Bfhi建立坚强芽孢杆菌荧光定量PCR特异性检测方法并确定该方法的检测限,对15个模拟样品进行检测并对阳性组中坚强芽孢杆菌的含量进行定量分析。结果显示,克隆得到的坚强芽孢杆菌hag基因长为1213 bp,经比对,与枯草芽孢杆菌hag基因相似性为13%-15%。荧光定量PCR方法对坚强芽孢杆菌菌株PC004和PC024的检测限分别为17.3×103和19.7×103 CFU/ml。模拟样品检测结果显示,15个样品中检测出7个阳性,并同时定量各样品中坚强芽孢杆菌的含量。本研究建立的坚强芽孢杆菌检测方法特异性强、操作时间短、灵敏度高,可为该菌的实际检测提供技术支持。     

牡蛎中副溶血弧菌荧光定量PCR检测方法的建立及其应用

以副溶血弧菌毒素调控基因(toxin regulations,toxR)作为靶标基因,设计特异性引物及TaqMan探针,以含toxR基因的质粒为模板,建立质粒拷贝数与CT值的标准曲线,分别采用含toxR基因质粒、纯培养的副溶血弧菌和添加副溶血弧菌的牡蛎(Ostrea)模拟样品进行灵敏度试验,结果表明,其灵敏度分别为15拷贝、18 CFU/mL和180CFU/mL.同一个样品的30次重复性试验表明,试验内及试验间的变异系数分别为0.95%和1.5%.结果显示,本研究建立的副溶血弧菌荧光定量PcR检测方法特异性强、灵敏度高、重复性好,可用于牡蛎等水产品中副溶血弧菌的定量检测.     

大鲵虹彩病毒TaqMan实时荧光定量PCR检测方法的建立

利用PCR技术扩增出大鲵虹彩病毒(giant salamander iridovirus, GSIV)主要衣壳蛋白(MCP)编码区长度为1 392 bp 的片段, 克隆到 pMD19-T载体上, 构建重组质粒 pMD19-T-MCP。经PCR鉴定确认正确后, 以10倍梯度稀释 pMD19-T-MCP重组质粒, 作为标准模板进行 TaqMan实时荧光定量PCR扩增, 制作标准曲线, 建立了大鲵虹彩病毒的 TaqMan实时荧光定量PCR检测方法。制作的标准曲线有极好的线性关系, 且线性范围宽, 相关系数为0.990 19。组内重复试验的CT值标准偏差为0.52%。检测结果显示, 该方法对大鲵虹彩病毒的检测有高度的特异性, 与锦鲤疱疹病毒、弗氏柠檬酸杆菌、嗜水气单胞菌以及鲤上皮瘤细胞基因组DNA之间均无交叉反应, 特异性好, 检测总DNA灵敏度为10个病毒核酸分子拷贝数, 约1.1×10-3 pg/μL病毒核酸, 较之常规PCR的敏感度高出约1 000倍。研究建立的大鲵虹彩病毒TaqMan实时荧光定量PCR方法灵敏度高、特异性强, 对大鲵虹彩病毒病的快速诊断与病毒病原定量检测有重要意义。     

虾肝肠胞虫实时荧光定量PCR检测方法的建立及应用

近年来,虾肝肠胞虫(Enterocytozoon hepatopenaei,EHP)流行区域不断扩大,已经成为我国南美白对虾(Litopenaeus vannamei)养殖重要病原之一。本研究根据Gen Bank中虾肝肠胞虫18S r RNA保守区域设计一套特异性引物和荧光探针,通过优化反应条件,建立检测EHP的TaqMan探针实时荧光定量PCR(Real-time quantitative polymerase chain reaction,qPCR)检测方法。建立的方法呈良好的线性关系(R²=0.998),灵敏度是巢式PCR的10倍。特异性试验表明：检测其他常见病原均为阴性,特异性好;重复性试验显示：批内批间变异系数均小于1.5%,重复性良好;对临床样品检测,与巢式PCR的符合率为97.81%。使用该方法对中山市、江门市和珠海市珠三角部分地区南美白对虾开展EHP流行病学调查,其中虾苗检出率为10.75%,成虾检出率为54.07%,部分区域检出率较高,要防范爆发风险。本研究建立的实时荧光定量PCR灵敏度高、特异性和重复性良好,具有较好的应用前景。     

实时荧光定量PCR技术及其在水生动物病毒病定量检测中的应用

聚合酶链式反应(Polymerase chain reaction, PCR)是美国科学家Mullis于1983年发明的一种在体外快速扩增特定基因的方法,其最早的应用报道是Saiki等[1]1985年应用于β-珠蛋白基因的扩增和镰状细胞性贫血的诊断分析.     

三倍体虹鳟实时荧光定量PCR内参基因稳定性分析

采用实时荧光定量PCR(qRT-PCR)方法比较甘油醛-3-磷酸脱氢酶(gapdh)、核糖体大亚基蛋白基因(rplp2)、真核延伸因子基因(ef1-α)、β-肌动蛋白(β-actin)和18S核糖体核酸基因(18S rRNA)等5个候选内参基因在体质量约800 g三倍体虹鳟脑、眼、鳃、皮肤、心脏、肾脏(头肾、中肾、后肾...     

实时荧光定量PCR技术及在畜牧兽医中的应用

RT-FQ-PCR技术是一种最新PCR技术,具有特异性强、灵敏度高、重复性好、定量准确、速度快、全封闭反应等优点,在畜牧兽医中已得到了广泛的应用,虽然该技术目前仍存有许多有待解决的问题,但因其所具有的独特优势,必定会在生命科学领域得到更广泛的应用。该文就RT-FQ-PCR概念、原理、方法、应用、存在问题及应用前景等作了综述。     

鳗鲡疱疹病毒SYBR Green Ⅰ实时荧光定量PCR检测方法的建立与应用

为了建立鳗鲡疱疹病毒(Anguillid herpesvirus,AngHV)的SYBR Green Ⅰ实时荧光定量PCR(qPCR)检测方法,利用PCR扩增出AngHV ORF49的序列,克隆至pET-32a载体,构建重组质粒pET-32a-ORF49,作为qPCR的标准品;根据ORF49序列设计引物,以梯度稀释的质...     

Genetic comparison of experimental farmed strains and wild Icelandic populations of Atlantic cod (Gadus morhua L.)

Microsatellite DNA loci and the Pantophysin locus (Pan I) were used to investigate levels of genetic diversity within farmed strains of Atlantic cod Gadus morhua and to compare them with the wild source population. A total of 282 farmed samples originating from a spawning ground off the south-west coast of Iceland were sampled in the years 2002 and 2003, and 258 wild cod were collected at the same spawning ground in the same years. The farmed strains exhibited a lower mean number of alleles and allelic diversity than the wild samples at the microsatellite loci. Significant differences were observed between wild and farmed samples both in allele and genotype frequencies at the Pan I locus. We argue that the genetic divergence of wild and farmed samples of Atlantic cod may be due to a small number of effective founding breeders contributing to the genetic variation of the farmed strains, inducing a reduction in allelic diversity. We discuss the potential effect of breeding practices on the genetic diversity of Atlantic cod.     

Growth variation and fin damage in Atlantic cod (Gadus morhua L.) fed at graded levels of feed restriction

Atlantic cod (initial weight 55, 250 and 450 g) were deprived of feed for 1 month or fed one of two diets differing in crude protein and lipid levels at rations corresponding to about 25, 50, 75 or 130% of group satiation for two months. The fish were individually weighed at the start, mid and end of the experiment and growth variation and fin damage were registered. The fin damage patterns differed between size groups; 55 g cod had most wounds on the dorsal fins whereas the pectoral fins were the most damaged in the 250 g fish. The incidence of damage in these groups was high and increased significantly when feeding was restricted. In the 450 g cod there was little fin damage and the incidence did not seem to depend on diet treatment.In the 55 and 250 g cod groups, fast growing fish had lower incidence of fin damage than fish that grew slowly, suggesting that the fish that received most aggression were prevented from feeding. However, a similar trend was registered in non-fed fish, showing that the recipients of aggression also suffered other disadvantages.The variation in individual growth rates increased when feeding was restricted and the distribution was differently skewed depending on feeding level. The data provide evidence that competition is an important factor limiting growth of individual cod held in groups in culture.     

Histopathology and a real-time PCR assay for detection of Bonamia ostreae in Ostrea edulis cultured in western Canada

Bonamia ostreae is an intracellular haplosporidian parasite in European flat oysters Ostrea edulis that occurs on both coasts of the United States and causes significant mortality in Europe. Canada was considered free of B. ostreae until 2004, when it was first detected in O. edulis obtained for laboratory study from a western Canadian oyster farm. Bonamia ostreae was confirmed in O. edulis at the index farm in November 2004 using histopathology, conventional polymerase chain reaction (PCR) assays, restriction fragment length polymorphism (RFLP) analysis, and sequencing of the PCR product. Archived samples of European flat oysters obtained from the index farm between 1999 and 2004 (n = 343) were re-examined and all samples collected before 2003 (n = 306) were confirmed negative for B. ostreae by histopathology (n = 306) and PCR (n = 62). In archived samples from 2003, B. ostreae was detected in 3 of 37 O. edulis by histopathology (n = 2) and/or PCR (n = 2). Also, records indicate that B. ostreae was not detected in O. edulis (n = 348) from five other locations in western Canada between 1986 and 2000. To better understand the distribution and prevalence of B. ostreae in western Canada, 607 oysters from the index farm and 2 additional farms were sampled in the summer of 2005. All 3 farms had been stocked with O. edulis spat from the State of Washington, USA, where B. ostreae is endemic. Samples were analyzed by histopathology and a new real-time PCR that amplifies a 68-bp target DNA fragment. B. ostreae was detected in all three locations, with prevalence ranging from 0.5 to 11.1%. Diagnostic sensitivity of the real-time PCR method was consistently greater than histopathology. Also, preliminary evidence supports the conclusion that real-time PCR on paraffin sections is more sensitive than histopathology; B. ostreae DNA was confirmed in 4 oysters by real-time PCR on paraffin-embedded tissues (and independently confirmed on unfixed tissues) that was not detected by histopathology. As a result of these findings, O. edulis spat are no longer allowed to be imported from endemic areas into Canada.     

黄海大头鳕0龄幼体分布及其与环境因子的关系

大头鳕是广泛分布于太平洋北部沿岸海域的重要经济和生态种,研究其幼体的生物学特性和分布有助于了解大头鳕的种群动态。本实验根据2016年6月、8月、10月、12月在黄海进行的渔业资源和环境调查数据,研究了黄海大头鳕种群幼体的生长规律;并运用广义可加模型(GAM)方法,分析了该海域大头鳕幼体分布及其与环境因子的关系。结果显示,黄海大头鳕幼体为正异速增长,体质量增长较快,b值为3.316 1。黄海大头鳕0龄幼体主要在底层盐度31.7~33.3、底层水温6.6~12.1°C、深度35.8~87.2 m、底质为细粉砂或黏土质软泥底质的海域中生活。研究表明,大头鳕幼体分布的季节变化与黄海冷水团的季节演变过程具有同步性。对大头鳕幼体密度有显著影响的环境因子依次为底层水温、底质、底层盐度,而深度对大头鳕幼体密度的影响不显著。     

Digestive capacity, intestinal morphology, and microflora of 1-year and 2-year old Atlantic cod (Gadus morhua) fed standard or bioprocessed soybean meal

The objectives of this work were to evaluate how dietary soybean meal (SBM) or a soy meal made by bioprocessing the SBM (BPSBM) to remove anti-nutritional factors affected hydrolytic capacity, amino acid absorption, intestinal morphology, and microflora along the intestinal tract of Atlantic cod at two life stages. Three fish meal based standard cod diets were formulated to contain no soy (FM control), 25% SBM, or 22% BPSBM. Prior to sampling the diets were fed to duplicate groups of 0.5 kg (1-year old) and 1.7 kg (2-year old) cod for a period of 3 months, and the groups reached 0.9 and 2.5 kg, respectively. Digesta was then sampled from different intestinal sections for analyses of trypsin and amylase activity as well as absorption of amino acids, nitrogen, and sulphur. Gastrointestinal sections were sampled for measurements of relative weight (kg^− 1 body weight), and tissues from these sections were sampled for analyses of brush border enzyme (alkaline phosphatase (ALP), leucine aminopeptidase (LAP), and maltase) activity and histological examination. Microflora was sampled from both digesta and the intestinal wall. The SBM diet stimulated relative growth of all gastrointestinal sections except the distal intestine in both age classes. Relative growth of the pyloric intestine was also stimulated by BPSBM. The pyloric caeca and the upper mid intestine were found to be the major sites for enzymatic hydrolysis of protein and starch and for amino acid absorption. Dietary SBM and BPSBM did not alter the activity of trypsin and LAP, but the activity of these enzymes in the proximal intestine was affected by age, being higher in 1-year old than in 2-year old cod. The rate of amino acid, nitrogen, and sulphur absorption along the gastrointestinal tract was not affected by SBM, but was slowed by BPSBM. Dietary SBM or BPSBM did not alter the morphology of the intestinal mucosa in any sections of the cod intestine. The distal-most structure of the intestine, a compartment with inlet and outlet (anus) valves, showed very high microbial colonisation in the mucosal brush border. Inclusion of SBM in the diet changed the intestinal microflora, increasing the population level of transient bacteria in the pyloric and mid intestine, but reducing the population level of adherent bacteria throughout the intestine. To conclude, Atlantic cod appeared to have a robust and flexible digestive system able to adjust to high dietary levels of soy protein meals.     

黄颡鱼IgM基因的个体发生和抗体的代间传递

为了解黄颡鱼IgM基因表达的个体发生和IgM抗体代间传递机制,实验利用Real-time PCR和ELISA等技术研究了黄颡鱼IgM重链基因在卵巢、胚胎和仔鱼的表达变化,以及黄颡鱼IgM抗体在卵巢、胚胎和仔鱼中的含量变化。结果显示,黄颡鱼3~7 d仔鱼中,没有检测到IgM mRNA;14 d仔鱼IgM基因开始表达。用细菌免疫亲鱼后,对仔鱼IgM mRNA表达没有影响。黄颡鱼IgM抗体在卵巢、胚胎和仔鱼中都有分布,且呈现下降趋势,至9 d仔鱼中抗体水平最低(是卵抗体含量的0.31倍)。14 d仔鱼中IgM抗体水平上升(是9 d仔鱼抗体含量的1.6倍)。用细菌免疫亲鱼后,能显著提高胚胎、仔鱼中的IgM抗体水平,在卵中抗体含量提高了2.3倍,9 d仔鱼中提高了1.8倍。研究表明,黄颡鱼IgM抗体可以在母本和后代之间传递,早期仔鱼IgM抗体主要来自于亲本;因此,免疫亲鱼能显著增加子代的抗体水平。     

实用WSSV定量检测方法的建立及其应用于脊尾白虾病毒感染规律的研究

为优化当前白斑综合征病毒( WSSV)定量检测方法,实验结合当前WSSV诊断与定量方法应用的实际,试图通过设计两对普通PCR引物来建立一种实用的WSSV绝对定量方法,并利用此方法进一步探明WSSV在脊尾白虾体内的增殖规律及致病性.首先根据WSSV的囊膜蛋白VP28基因序列设计了两对特异引物(F1,R1)和(RF2,RR2),分别用于标准品质粒的构建和扩增子的扩增,以开展SYBR Green染料法定量检测WSSV的研究;随后利用该定量检测方法分析了WSSV在脊尾白虾体内的组织分布及感染规律.研究结果显示:(1)以定量引物RF2和RR2建立的SYBR Green绝对定量检测方法具有敏感度高、特异性强、定量范围广且准确等特点;(2)WSSV能感染脊尾白虾鳃、肝胰腺、肌肉、头胸甲下结缔组织、胃及肠等组织,其中头胸甲下结缔组织病毒含量最高(1.1×107 copies/μg),其次是鳃组织(4.1×106copies/μg);正常脊尾白虾感染WSSV,首先经过一个约48 h潜伏期,而后开始大量增殖并造成部分虾死亡,死亡率约为20％.     

Susceptibility by amberjack (Seriola dumerili), yellowtail (S. quinqueradiata) and Japanese flounder (Paralichthys olivaceus) to Neobenedenia girellae (Monogenea) infection and their acquired protection

This study investigated: 1) susceptibility differences to infection by Neobenedenia girellae (Capsalidae) between amberjack Seriola dumerili (Carangidae), yellowtail S. quinqueradiata and Japanese flounder Paralichthys olivaceus (Paralichthyidae); 2) growth and egg production of N. girellae on each fish species; 3) acquired protection of each fish species against this parasite. The number of N. girellae on S. dumerili was significantly higher than on S. quinqueradiata and P. olivaceus when these fishes were exposed to oncomiracidia in the same aquarium. Neobenedenia girellae growth on S. dumerili was fastest and, thus the number of eggs laid by parasites on S. dumerili was greater than on the other two species. Seriola dumerili and P. olivaceus, which were previously infected with N. girellae and treated by freshwater bath, acquired partial protection against re-infection by N. girellae. The relative re-infection of three S. dumerili individuals out of eleven individuals was markedly low compared with the initial infection, and the relative initial infection and re-infection on two P. olivaceus out of eleven individuals was markedly low. The results of this study could be useful to control N. girellae infections when cultivating S. dumerili, S. quinqueradiata and P. olivaceus.     

凡纳滨对虾AP-1基因的克隆和表达特征分析

为了探讨凡纳滨对虾转录因子AP-1在病毒引发的免疫应答过程中的潜在作用,实验根据前期的转录组和表达谱结果提示信息,首次克隆了凡纳滨对虾AP-1基因(LvAP-1,GenBank注册号:KF999956),利用在线软件进行了生物信息学分析,运用半定量的方法进行了组织表达分析,并利用实时荧光定量PCR(qPCR)技术分析了该基因在白斑杆状病毒(WSSV)侵染过程中的表达变化特征。结果显示,AP-1基因ORF区全长882 bp,编码293个氨基酸。预测分析显示该基因编码的蛋白质含有1个Jun结构域和1个高度保守的亮氨酸拉链结构域(bZIP),其中Jun结构域在非脊椎动物中保守性不高。组织表达分析表明,该基因在凡纳滨对虾各组织中广泛表达,其中在血细胞中表达量最高。在WSSV感染早期(0.5 hpi),该基因表达没有显著改变,感染后5 h(5 hpi),AP-1基因开始显著上调表达,在人工感染后24 h,该基因的表达量达到最高(P0.01)。研究表明,该基因在一定程度上参与了凡纳滨对虾体内由WSSV引发的先天免疫应答过程,为进一步研究LvAP-1在对虾应答病毒侵染过程中的功能和作用机制奠定了基础。