版纳微型猪近交系SRY基因编码区序列克隆及生物信息学分析

目的获得版纳微型猪近交系(BMI)SRY基因编码区序列并进行分子系统进化研究。方法以看家基因GAPDH为内参,对BMI猪的SRY基因编码区序列进行PCR扩增、克隆和序列分析,并应用Lasergene、Bi-oEdit、ClustalX、MEGA等生物信息学软件同鲸鱼、海豚、鹿、绵羊、牛、海豹、马、海象、熊猫、人、驴、熊、猫、虎和美洲豹等15个物种相应SRY编码区核苷酸序列和氨基酸序列进行了比对分析,在此基础上采用NJ和ME法对其编码区氨基酸序列构建了分子系统进化树。结果 BMI猪SRY基因编码区序列长711 bp,编码236个氨基酸,GenBank登录号为GU991615。BMI猪与鲸鱼、海豚、鹿、绵羊、牛、海豹、马、海象、熊猫、人、驴、熊、猫、虎和美洲豹的SRY基因编码区核苷酸序列相似性分别为83.7%、82.8%、78.4%、78.0%、76.9%、73.3%、73.1%、73.0%、72.9%、72.7%、72.7%、72.2%、71.6%、71.3%、70.8%,相应的氨基酸序列相似性分别为72.8%、54.5%、67.3%、64.5%、61.5%、61.9%、59.5%、61.4%、62.0%、59.1%、59.0%、62.0%、59.6%、59.6%、59.2%。结论 BMI猪同鲸鱼等15个物种的SRY基因编码区核苷酸和相应氨基酸序列具有较高的保守性。NJ和ME方法聚类构建的分子系统进化树表明,BMI猪与牛、绵羊、鹿聚为一个分支,符合分类学地位,它们分别为偶蹄目下的猪科、牛科和鹿科动物。     

版纳微型猪近交系CD46基因克隆、序列及组织表达分析

根据猪NM_213888及EST序列,设计特异引物扩增BMI CD46基因,并进行克隆、测序和生物信息学分析。同时应用半定量RT-PCR技术对BMI 30个重要组织进行表达谱分析。获得了BMI CD46 1 092 bp的编码区序列（Gen Bank登录号：KJ513478）,编码363个氨基酸。分析表明,CD46蛋白质分子量（Mw）为39.60 k D,等电点（p I）为5.39,存在4个保守域和1个跨膜结构域,N端有信号肽序列;其N末端疏水,C末端亲水;亚细胞定位显示,该蛋白位于细胞周质的概率是56.7%。活性位点分析表明,BMI CD46蛋白有6类活性位点。系统进化分析表明,BMI与牛的亲缘关系最近。BMI 30种组织表达分析表明,CD46基因在十二指肠中高表达;在睾丸、胸腺、甲状腺、附睾、肺、淋巴结、空肠、回肠、结肠、小脑及舌下腺中中度表达;在颌下腺、肝、肾上腺、盲肠、直肠、食管、垂体及脑干中低表达;在心、脾、肾、肌肉、胰脏、胃、皮肤、大脑、下丘脑及脊髓中不表达。该结果为进一步研究基因功能奠定基础。     

版纳微型猪近交系GHR基因克隆及生物信息学分析

目的获得版纳微型猪近交系(BMI)生长激素受体基因(GHR)序列,通过生物信息学分析预测GHR功能并进行GHR mRNA多组织表达谱分析。方法以版纳微型猪近交系的肝脏组织为材料提取RNA,RTPCR方法扩增GHR基因编码区序列,将序列连接至pMD18-T载体进行克隆、测序和生物信息学分析;半定量PCR检测GHR mRNA在BMI不同组织中表达量的差异。结果克隆出了BMI GHR编码区序列,提交GenBank获得登录号KC999114。该基因CDS长1917 bp,编码638个氨基酸。生物信息学分析表明,与长白猪的GHR序列相比BMI存在4处氨基酸替换,分别为p.E381D、p.A409S、p.L556V和p.A580G,均发生在胞内域。GHR基因多组织表达谱分析显示:GHR mRNA几乎在各组织中均有表达,在肌肉中表达量最高,在小肠、心、肝、神经纤维、脾、卵巢中表达量较高,在肺、胃、大脑、胰和肾中的表达量较低。结论成功克隆了版纳微型猪近交系GHR全长编码区序列,进行了生物信息学功能分析和组织表达谱分析,为进一步阐明版纳微型猪近交系生长矮小机理奠定了基础。     

版纳微型猪近交系AQP3克隆、序列分析及组织表达

目的 克隆版纳微型猪近交系aquaporin 3(AQP3)基因,并利用生物信息学方法分析其序列特征,研究其在猪各组织中的表达情况.方法 从版纳微型猪近交系脾脏中提取总RNA,利用RT-PCR方法扩增猪AQP3编码区序列,将纯化的片段与pMD18-T载体连接,转化宿主菌DH 5α,筛选阳性克隆进行测序.并采用半定量RT...     

版纳微型猪近交系TNF-α基因mRNA实时荧光定量PCR检测方法的建立

目的快速、灵敏、可靠的检测与临床多种疾病密切相关的重要基因TNF-α的表达情况,构建TNF-α基因及内参GAPDH基因荧光定量PCR质粒标准品。方法利用版纳微型猪近交系4～6月龄猪建立动物模型,提取皮肤创面总RNA,设计特异引物,进行RT-PCR扩增。纯化目的片段与pMD18-T载体连接,转化宿主菌DH5α,提取重组质粒DNA,并经酶切、PCR和测序鉴定,计算重组质粒原液拷贝数浓度并制备梯度浓度标准品,进行实时荧光定量PCR,生成标准曲线。结果建立的TNF-α基因和GAPDH内参基因mRNA表达实时荧光定量PCR检测方法灵敏度分别可达103和105拷贝,线性范围分别为103～109和105～109拷贝,阈值循环数(Ct)与PCR体系中起始模板量的对数值之间存在的线性关系R2分别为0.993和0.999,扩增效率E分别为111.073%和95.948%。结论成功的构建了版纳微型猪近交系TNF-α基因质粒标准品和标准曲线,并用内参基因GAPDH进行校正,此方法可为探讨TNF-α基因在临床多种疾病中所发挥的分子机理奠定基础。     

版纳小耳猪近交系5家系35个微卫星座位的遗传分析

利用35个微卫星座位对版纳小耳猪近交系5个家系进行了遗传检测。统计各家系的等位基因组成,计算各家系的平均基因纯合率,利用基因频率计算出各家系的平均杂合度及品系间的遗传距离,并进行系统聚类。结果表明各家系的平均基因纯合度均较高,其151家系达到88.79％;PIC（多态信息含量）和平均杂合度均较普通商品猪低;各家系等位基因组成差别较大;各家系间亲缘关系与其近交过程一致,据此认为版纳小耳猪近交系5家系均具有较高的近交程度;其基因多态性和遗传多样性较普通商品猪低;各家系均已构成独立遗传群体。     

版纳微型猪近交系 GHR 基因克隆及生物信息学分析简

目的 获得版纳微型猪近交系（BMI）生长激素受体基因（GHR）序列,通过生物信息学分析预测GHR功能并进行GHR mRNA多组织表达谱分析.方法 以版纳微型猪近交系的肝脏组织为材料提取RNA,RT-PCR方法扩增GHR基因编码区序列,将序列连接至pMD18-T载体进行克隆、测序和生物信息学分析;半定量PCR检测GHR mRNA在BMI不同组织中表达量的差异.结果克隆出了BMI GHR 编码区序列,提交GenBank获得登录号KC999114.该基因CDS长1917 bp,编码638个氨基酸.生物信息学分析表明,与长白猪的GHR序列相比BMI存在4处氨基酸替换,分别为p.E381D、p.A409S、p.L556V和p.A580G,均发生在胞内域.GHR基因多组织表达谱分析显示：GHR mRNA几乎在各组织中均有表达,在肌肉中表达量最高,在小肠、心、肝、神经纤维、脾、卵巢中表达量较高,在肺、胃、大脑、胰和肾中的表达量较低.结论 成功克隆了版纳微型猪近交系GHR全长编码区序列,进行了生物信息学功能分析和组织表达谱分析,为进一步阐明版纳微型猪近交系生长矮小机理奠定了基础.     

版纳微型猪近交系TDRP1基因克隆、鉴定及mRNA的组织表达特性

目的克隆版纳微型猪近交系（BMI）不育和可育公猪TDRP1基因,分析其序列及mRNA表达水平上的差异,预测其蛋白质功能,并检测该基因在可育公猪中的组织表达分布情况。方法以猪NM_001198925序列为模板,设计特异引物,采用RT-PCR方法结合测序获得TDRP1的c DNA序列并进行生物信息学分析;采用半定量PCR方法检测TDRP1在不育和可育公猪睾丸中的表达规律,分析该基因在可育公猪17种组织中的表达特征。结果获得了BMI TDRP1基因的编码区序列（Gen Bank登录号：KJ186786）,生物信息学分析表明其编码186个氨基酸,蛋白质相对分子质量（Mw）为20.49×10^3,等电点（p I）为5.86,无信号肽,有94.1%的概率位于细胞核,含有1个亮氨酸富集的核输出信号。不同物种的氨基酸序列比对表明猪TDRP1与人、恒河猴、小鼠和大鼠等哺乳动物的TDRP1相似性在73%-83.2%之间,其中与人、恒河猴的相似性较高。mRNA表达分析表明,TDRP1在BMI不育和可育公猪睾丸间表达水平差异无显著,在精囊腺和前列腺中高表达,在睾丸和小脑中中度表达,在大脑和肾脏中低表达,在其余组织中不表达。结论成功克隆了BMI TDRP1基因的全长编码区序列并发现了BMI特有的2个SNP位点;TDRP1基因在BMI不育和可育公猪间序列完全一致,睾丸mRNA表达水平差异无显著性,多组织转录谱分析表明该基因存在明显的组织差异表达现象,在精囊腺和前列腺中有较高表达量,为深入研究TDRP1基因在精子发生方面的作用奠定了基础。     

版纳小型猪近交系内分泌器官的解剖观察

猪在生理、解剖、组织、免疫及营养代谢等方面与人类有很多相似之处,已被应用于生物学及医学研究的各个领域。近年来随着异种器官移植研究的深入,猪成了人最理想的异种器官供给［１］。版纳小型猪近交系［２］目前已进入１８世代,近交系数达９７．８％,是目前最理想的人类异种器官供体［２］和最理想的实验用小型猪之一［３,４］。但缺乏翔实的解剖学资料。本实验对版纳小型猪近交系的内分泌器官进行了解剖观察,以期提供版纳小型猪近交系内分泌器官的解剖学资料。１　　材料和方法１．１　　材料　　选取中国版纳小型猪近交系５头,１…     

Characterization and evolution of major histocompatibility complex class II genes in the aye-aye, Daubentonia madagascariensis

Major histocompatibility complex genes (Mhc-DQB and Mhc-DRB) were sequenced in seven aye-ayes (Daubentonia madagascariecsis), which is an endemic and endangered species in Madagascar. An aye-aye from a north-eastern population showed genetic relatedness to individuals of a north-western population and had a somewhat different repertoire from another north-eastern individual. These observations suggest that the extent of genetic variation in Mhc genes is not excessively small in the aye-aye in spite of recent rapid destruction of their habitat by human activities. In light of Mhc gene evolution, trans-species and allelic polymorphisms can be estimated to have been retained for more than 50 Ma (million years) based on the time scale of lemur evolution.     

Characterization of the peptide-binding specificity of the chimpanzee class I alleles A*0301 and A*0401 using a combinatorial peptide library

Chimpanzees represent important models for studying several human pathogens. In the present study, we utilized a combinatorial peptide library to characterize the binding specificities of the chimpanzee class I molecules Patr A 0301 and A 0401, both of which are present in about 17% of chimpanzees. Patr A 0301 was found to recognize peptides using the canonical position 2/C-terminus spacing, with the small residues S, T, and A being the most preferred in position 2, and the positively charged residues R and K preferred at the C terminus. Patr A 0401 was found to recognize a more complex motif where the C terminus and then the residue in positions 1 and/or 5 are the primary anchors. Like A 0301, the C-terminal preference of A 0401 is for positively charged residues. At positions 1 and 5, positively charged and large residues are the most preferred, respectively. Coefficient values derived from the combinatorial library proved to be an efficient means for predicting A 0301 and A 0401 binders. The present data provide detailed information to facilitate the identification of potential T cell epitopes recognized in the context of two common chimpanzee class I alleles, and further validate the combinatorial library approach as an efficient method to characterize class I binding specificities.     

Cloning and sequencing of the porcine lactoferrin cDNA

cDNA clones encoding the entire porcine lactoferrin protein were isolated and sequenced. The porcine lactoferrin cDNA sequence presented here is 2259bp in length and encodes a leader peptide of 19 amino acids and a mature protein of 684 amino acids. Comparisons with other lactoferrins indicate a single glycosylation site. The iron- and anion-binding sites, and the cysteine residues involved in disulphide bonds, are conserved between the lactoferrin proteins.     

Cloning and sequencing of the porcine K-casein cDNA

cDNA clones encoding porcine kappa-casein were isolated and sequenced. The porcine kappa-casein cDNA is 851 bp in length and encodes a preprotein of 188 amino acids.     

麋鹿血液cDNA文库的构建

为分离出MHCⅠ、Ⅱ基因,利用TRIzol 试剂从麋鹿血液组织中提取总RNA,经mRNA 纯化试剂盒纯化后,根据Stratagene 公司的cDNA 文库构建系统构建了麋鹿血液组织的cDNA 文库。初始文库滴度为1.96 ×106 pfu/ ml,总库容为1.96 ×106 个独立克隆;cDNA 插入片段平均长度约为1.0 kb;重组率为95.6 % 。文库各项指标均达标准经典cDNA 文库的基本要求。利用本实验室设计的可扩增MHCⅡ类DQA 基因第二外显子的引物检测扩增后的文库,得到了特异性非常好的目标条带,说明本文所建文库可以用于麋鹿MHC 相关基因的分离。     

Characterization of major histocompatibility complex-associated peptides from a small volume of whole blood

Class I major histocompatibility complex (MHC) presents intracellular-derived peptides on the majority of cells within the human body. Intracellular proteins are degraded into peptides of 8-11 amino acids, allowing them to fit into the groove of an empty MHC class I molecule. Detection of MHC-associated peptides can be challenging with the major difficulty being the ability to obtain peptides in adequate concentration. Published protocols require a large sample size that is unrealistic for a clinically available sample. Based on calculations, it should be possible to characterize MHC-associated peptides from cells obtained from 30 ml of whole blood. A citric acid wash of whole platelets was implemented to release the peptides with sample cleanup by reversed-phase high-performance liquid chromatography on a peptide trap. Peptides were analyzed by liquid chromatography tandem mass spectrometry. Four peptides were identified from an individual's platelets. The binding motifs of the peptides were consistent with the published MHC binding motif of the individual. Since red blood cells do not express MHC, they were used as a negative control. Using citric acid wash of whole cells and a peptide trap, the more abundant MHC-associated peptides can be identified. This report demonstrates the identification of peptides from a sample volume compatible with reasonable clinical availability.