羊流产嗜衣原体ompA基因克隆及生物信息学分析

分析羊流产嗜衣原体ompA基因结构并预测其编码蛋白的结构和功能。采用DNA Star、DNA MAN、vector NTI suite11.5序列分析软件和在线网站ExPASy分析该基因的结构和预测其编码蛋白的理化性质、亚细胞定位、一级结构修饰位点、二级结构特征及三维空间构象、潜在抗原表位等。结果显示,该基因全长1 170 bp,可编码389个氨基酸,编码蛋白理化性质较稳定,无各种亚细胞定位序列,含有多个能被其他酶修饰的位点,该蛋白以无规则卷曲为主,大部分氨基酸残基包埋在分子内部,含5个跨膜区,3个亲水性较强的抗原表位。ompA基因生物信息学分析结果为ompA蛋白功能的深入研究和新型多价疫苗的开发提供了基础数据。     

羊口疮病毒安徽株VIR基因克隆与 生物信息学分析

目的获取并分析ORFV AH-F10株VIR基因序列及预测其编码蛋白的生物信息学特点。方法利用实验室保存的羊口疮AH-F10株,设计VIR基因引物并进行PCR扩增、克隆及序列测定,同时利用生物信息学方法对其编码的蛋白的理化性质、二级结构、三级结构、信号肽、磷酸化位点、跨膜结构域以及线性细胞表位进行预测。结果 AH-F10-VIR基因长552bp,编码183个氨基酸,与Nantou株的VIR基因同源性最高,核苷酸同源性高达99.6%,氨基酸同源性为100.0%。生物信息学分析结果显示编码的蛋白相对分子量为19.88kDa,等电点为4.83,为亲水性蛋白;α-螺旋、β-转角、无规则卷曲和延伸链分别占36.07%、3.83%、43.17%和16.94%;三级结构预测显示VIR蛋白存在较多的α-螺旋与无规则卷曲,同二级结构预测结果相符;含有17个磷酸化位点,无信号肽和跨膜结构区域,有15个潜在的B细胞优势表位,4个CTL细胞表位以及5个Th细胞表位。结论成功克隆了羊口疮安徽株VIR基因并预测了VIR蛋白的生物信息学相关信息,为进一步研究VIR蛋白奠定了基础。     

兔多杀性巴氏杆菌C51-3株黏附蛋白的表达、纯化及其抗原性检测

应用PCR从兔多杀性巴氏杆菌C51-3株基因组DNA中扩增出编码36 kD黏附蛋白的cp36基因, 将其克隆到pMD18-T载体并对插入片段进行测序。以重组质粒pMD18-cp36为模板, 用PCR扩增得到编码信号肽除外的成熟黏附蛋白基因cpm36, 并克隆到原核表达质粒pQE30中, 得到重组质粒pQE30-cpm36, 转化大肠杆菌M15, 在IPTG诱导下表达融合蛋白CPM36, 经Ni2+-NTA亲和层析纯化。DNA测序结果表明cp36基因片段大小为1032 bp, 与已报道的16个血清型多杀性巴氏杆菌cp36基因的核苷酸序列比较, 同源性在76.9%~100%之间。SDS-PAGE结果显示, 表达分子量约为37 kD的带有6×His标签的CPM36蛋白, 与预期分子量相符。Western blotting结果表明, 抗重组蛋白抗体分别能与CPM36蛋白和多杀性巴氏杆菌36 kD蛋白发生特异性反应, 证明原核表达蛋白具有抗原性, 为进一步开展多杀性巴氏杆菌免疫保护性抗原的研究奠定了基础。     

金黄色葡萄球菌肠毒素A蛋白的B细胞表位的预测

目的预测金黄色葡萄球菌肠毒素A蛋白（SEA）的B细胞表位。方法以金黄色葡萄球菌合肥乳源分离株M3基因组DNA为模板,PCR扩增SEA基因并进行序列测定与分析。应用DNAstar protean软件对SEA蛋白的二级结构、柔性、亲水性、表面可能性和抗原指数等多参数进行综合分析,预测其B细胞表位。结果M3分离株的SEA基因全长774bp,编码由257个氨基酸组成的相对分子量为29．67kDa的SEA蛋白,M3分离株SEA基因与标准株的核苷酸序列与氨基酸序列同源性分别为98．7％和98．4％。SEA蛋白的优势B细胞表位位于肽链的第64—68、100～107、138—141、156—160、166～173、213～217和237～244区段。结论预测出SEA蛋白的7个优势B细胞表位,为进而克隆表达表位蛋白,制备针对SEA表位的单克隆抗体奠定了基础。     

牦牛HORMAD1基因的克隆及生物信息学分析

利用分子克隆技术获得了牦牛HORMAD1基因编码区序列,并采用生物信息学方法对该基因及其编码蛋白的基本理化性质、疏水性、信号肽、二级结构等方面进行了预测和分析.结果表明,牦牛HORMAD1基因包含一个长度为1 182 bp的开放阅读框,编码393个氨基酸;其编码蛋白属于亲水性蛋白,无明显的信号肽,含有很多个磷酸化位点.二级结构主要以无规则卷曲和α螺旋为主.HORMAD1基因编码产物氨基酸邻接系统树表明,牦牛HORMAD1与黄牛、马和猪等物种的HORMAD1氨基酸遗传距离较近,具有高度相似性.     

猪细小病毒自然弱毒N株VP2基因的克隆、测序及生物信息学分析

本研究对猪细小病毒(porcine parvovirus,PPV)自然弱毒N株(PPV-N)VP2基因进行克隆、测序并利用生物信息学技术分析PPV-NVP2蛋白基因的同源性、遗传进化、密码子偏爱性、糖基化位点、磷酸化位点、B细胞抗原表位及其二、三级结构。结果表明:成功扩增出包含VP2基因完整目的片段(1901bp),构建了VP2基因的克隆重组质粒pMD18-T-VP2,测序获取VP2基因序列(1740bp)并将该序列登录到GenBank(HM355807)。PPVVP2基因属高度保守的基因;PPV-N株与PPV弱毒代表毒株NADL-2株亲缘性近,推测PPV-N株属于弱毒株;PPV-N株VP2基因氨基酸密码子偏爱以A结尾的密码子;PPV-N株VP2蛋白可能存在7个糖基化位点,其丝氨酸、苏氨酸和酪氨酸可能分别有9、7、8个磷酸化位点,可能存在24个B细胞抗原表位;PPV-N株VP2蛋白二级结构预测,α-螺旋占11.74%,β-折叠占22.97%,无规则卷曲占65.28%,而三维结构预测VP2蛋白主要以无规则卷曲为主,存在多个螺旋和折叠区域。本研究结果为进一步阐释PPV-N株自然弱毒的分子机理提供依据,并为PPV分子诊断试剂及基因工程疫苗研究等提供有益借鉴。     

奶牛妊娠相关糖蛋白BoPAG16的表达及其结构功能预测

[目的]为了获得奶牛妊娠相关糖蛋白16(bovin pregnancy associated glycoproteins 16,BoPAG16),并对该蛋白进行结构和功能分析。[方法]从荷斯坦奶牛胎盘子叶中扩增BoPAG16基因,并用构建真核表达载体pcDNA3.1-Flag-BoPAG16,转染至293F细胞中,用SDS-PAGE和Western Blotting检测表达效果,用Flag-tag亲和层析柱纯化蛋白,并对BoPAG16基因编码的蛋白进行结构和功能预测分析。[结果]BoPAG16基因在293F细胞中成功表达,大小为56 kDa,纯化后纯度达到92%。预测BoPAG16蛋白N端15个氨基酸为信号肽,6个糖基化位点和13个B细胞抗原表位。[结论]成功表达并纯化奶牛妊娠相关糖蛋白BoPAG16,BoPAG16蛋白有6个糖基化位点和13个B细胞抗原表位。     

猪肌生成抑制素基因去信号肽蛋白二级构预测和B细胞表位分析

目的预测猪肌生成抑制素去信号肽蛋白的二级结构和B细胞优势抗原表位,为生产该蛋白的单克隆抗体、建立噬菌体抗体库、研制针对该基因的表位多肽疫苗、表位核酸疫苗等奠定基础。方法根据猪肌生成抑制素去信号肽蛋白氨基酸序列,应用7种参数和方法分析预测二级结构和抗原表位,包括Garnier-Robson、Chou-Fasman、Karplus-Schulz、Kyte-Doolittle、Emini、Jameson-Wolf及吴氏综合预测方法。结果MSTN去信号肽蛋白存在多个潜在的抗原表位位点,其中B细胞抗原优势表位可能在1-11、41-55、57-64、62-90、99-104、138-144、193-200、202-212、235-243区段或其附近,此结果将为进一步鉴定和合成多肽疫苗和表位核酸疫苗制备抗猪MSTN蛋白抗体提供依据,并为研究MSTN结构和功能奠定基础。     

结核分枝杆菌Rv0081基因编码蛋白的生物信息学分析

运用生物信息学分析软件预测结核分枝杆菌（Mycobacterium tuberculosis, Mtb）Rv0081蛋白的生物学特征及筛选潜在的优势抗原表位。 从NCBI数据库获取Mtb Rv0081蛋白的氨基酸序列，利用生物信息学分析软件ProtParam、ProtScale及TMPRED分析Rv0081蛋白的理化性质及亲疏水性；TMHMM、SignalP-5.0 Server预测蛋白的跨膜区及信号肽；NetNGlyc-1.0 Server、NetPhos 3.1 Server分别预测蛋白的糖基化位点及磷酸化位点；STRING预测能与Rv0081相互作用的蛋白；分别运用SOPMA、SWISS-MODEL预测蛋白的二、三级结构；综合运用softberry、WoLF PSORT预测蛋白的亚细胞定位；运用DNAStar预测蛋白的B细胞抗原表位；综合运用SYFPEITHI、NetCTL 1.2 Server、Net MHC pan 4.1 server预测蛋白的CTL细胞抗原表位；综合运用SYFPEITHI、Net MHCII pan 4.0 server预测蛋白的Th细胞抗原表位。 结果表明，Rv0081蛋白由114个氨基酸组成，相对分子质量为12 356.32，亚细胞定位于细胞质中，为稳定的疏水性蛋白，无跨膜区和信号肽，含有1个糖基化位点及9个磷酸化位点；二级结构主要由α-螺旋和无规则卷曲构成，结构较松散；与hycE、hycP、Rv0088、Rv0083、hycD、hycQ、Rv0082、devR、Rv0080及Rv0079蛋白存在相互作用关系；综合分析各软件预测结果筛选出6个优势B细胞抗原表位、6个优势CTL细胞抗原表位及7个优势Th细胞抗原表位。Mtb Rv0081蛋白具有较多潜在的候选B、T细胞抗原表位，可作为研发新型结核疫苗的候选抗原。     

绿脓杆菌外膜蛋白OprF的生物信息学分析

[目的]利用生物信息学方法预测绿脓杆菌外膜蛋白OprF的理化性质、高级结构和细胞表位。[方法]采用在线软件预测OprF蛋白的理化性质;Signal P 4.1软件预测OprF信号肽序列;利用TMHMM软件预测ACFA蛋白跨膜结构;SOPMA服务器预测蛋白的二级结构;Swiss-Model程序预测OprF三维结构;综合ABCpred与Bepi Pred方案预测OprF的B细胞表位;运用神经网络法预测OprF的CTL表位;使用MHC-Ⅱ类分子结合肽程序预测OprF的Th细胞表位。[结果]OprF为亲水性蛋白;1~24位氨基酸为信号肽序列;存在多个酶切位点;无跨膜结构并定位于细胞膜外;二级结构中含无规则卷曲34.36%、α-螺旋31.90%、β-转角11.66%、β-片层22.09%;并可能存在3个B细胞表位、2个CTL表位、4个Th细胞表位。[结论]系统分析了OprF蛋白的理化性质、信号肽、跨膜结构、二级与三级结构,以及B、T细胞抗原表位。     

Outer membrane protein H for protective immunity against Pasteurella multocida

Pasteurella multocida, a Gram-negative facultative anaerobic bacterium, is a causative animal pathogen in porcine atrophic rhinitis and avian fowl cholera. For the development of recombinant subunit vaccine against P. multocida, we cloned and analyzed the gene for outer membrane protein H (ompH) from a native strain of Pasteurella multocida in Korea. The OmpH had significant similarity in both primary and secondary structure with those of other serotypes. The full-length, and three short fragments of ompH were expressed in E. coli and the recombinant OmpH proteins were purified, respectively. The recombinant OmpH proteins were antigenic and detectable with antisera produced by either immunization of commercial vaccine for respiratory disease or formalin-killed cell. Antibodies raised against the full-length OmpH provided strong protection against P. multocida, however, three short fragments of recombinant OmpHs, respectively, showed slightly lower protection in mice challenge. The recombinant OmpH might be a useful vaccine candidate antigen for P. multocida.     

Cloning and characterization of the major outer membrane protein gene (ompH) of Pasteurella multocida X-73.

The major outer membrane protein (OmpH) of Pasteurella multocida X-73 was purified by selective extraction with detergents, followed by size exclusion chromatography. The planar lipid bilayer assay showed that OmpH has pore-forming function. The average single channel conductance in 1.0 M KCl was 0.62 nS. The gene (ompH) encoding OmpH has been isolated and sequenced by construction of a genomic library and PCR techniques. The coding region of this gene is 1,059 bp long. The predicted primary protein is composed of 353 amino acids, with a 20-amino-acid signal peptide. The mature protein is composed of 333 amino acids with a molecular mass of 36.665 kDa. The ompH gene encoding mature protein has been expressed in Escherichia coli by using a regulatable expression system. The ompH gene was distributed among 15 P. multocida serotypes and strain CU. Protection studies showed that OmpH was able to induce homologous protection in chickens. These findings demonstrate that OmpH is a protective outer membrane porin of strain X-73 and is conserved among P. multocida somatic serotypes.     

Safety and efficacy of a streptomycin dependent live Pasteurella multocida vaccine in rabbits

The safety of and protection provided by a streptomycin dependent live Pasteurella multocida (serotype 12:A) vaccine was evaluated in New Zealand white rabbits. The vaccine strain was isolated from two of twelve rabbits 24 hours after intranasal administration. Streptomycin independent P. multocida isolates were not recovered for 4 weeks after vaccination, indicating a lack of reversion to the wild type. Thirty days after a single intranasal administration of vaccine, eight rabbits were challenged with either P. multocida serotype 3:A or serotype 12:A. Eight non-vaccinated rabbits were challenged in the same manner. Vaccinated rabbits challenged with serotype 12:A had nasal infections for only 2 weeks following challenge. Vaccinated rabbits challenged with serotype 3:A developed chronic nasal infections but were protected from severe disease. Immunoglobulin A or G antibodies against P. multocida were not detected after vaccination in nasal lavages or sera using an enzyme-linked immunosorbent assay. However, both antibodies increased following challenge with either serotype 3:A or serotype 12:A. These studies indicated that the streptomycin dependent pasteurella strain colonized rabbits briefly and was genetically stable in vivo. The results in challenged rabbits suggest that the vaccine provided protection against chronic infection by a homologous pasteurella serotype and protection against severe disease by a heterologous pasteurella serotype.     

Screening and Molecular Cloning of a Protective Antigen from the Midgut of Haemaphysalis longicornis

Vaccination is considered a promising alternative for controlling tick infestations. Haemaphysalis longicornis midgut proteins separated by SDS-PAGE and transferred to polyvinylidene difluoride (PVDF) membrane were screened for protective value against bites. The western blot demonstrated the immunogenicity of 92 kDa protein (P92). The analysis of the P92 amino acid sequence by LC-MS/MS indicated that it was a H. longicornis paramyosin (Hl-Pmy). The full lenghth cDNA of Hl-Pmy was obtained by rapid amplification of cDNA ends (RACE) which consisted of 2,783 bp with a 161 bp 3'' untranslated region. Sequence alignment of tick paramyosin (Pmy) showed that Hl-Pmy shared a high level of conservation among ticks. Comparison with the protective epitope sequence of other invertebrate Pmy, it was calculated that the protective epitope of Hl-Pmy was a peptide (LEEAEGSSETVVEMNKKRDTE) named LEE, which was close to the N-terminal of Hl-Pmy protein. The secondary structure analysis suggested that LEE had non-helical segments within an α-helical structure. These results provide the basis for developing a vaccine against biting H. longicornis ticks.     

Characterization and SNP variation analysis of a HSP70 gene from miiuy croaker and its expression as related to bacterial challenge and heat shock

Heat shock proteins (HSPs) play crucial roles in the immune response of vertebrates. In order to study immune defense mechanism of heat shock protein gene in miiuy croaker (Miichthys miiuy), a cDNA encoding heat shock protein 70 (designated Mimi-HSP70) gene was cloned from miiuy croaker. The cDNA was 2195?bp in length, consisting of an open reading frame (ORF) of 1917?bp encoding a polypeptide of 638 amino acids with estimated molecular mass of 70.3?kDa and theoretical isoelectric point of 5.55. Genomic DNA structure analysis revealed that the Mimi-HSP70 gene contain no introns in coding region and four SNPs with 373?C/T, 789?G/A, 1005?C/T, and 1185?G/A were detected by direct sequencing of 20 samples from six different populations. BLAST analysis, structure comparison and phylogenetic analysis indicated that Mimi-HSP70 should be an inducible cytosolic member of the HSP70 family. The deduced amino acid sequence of Mimi-HSP70 had 82.4%-92.2% identity with those of vertebrate. A real-time quantitative RT-PCR demonstrated that the HSP70 gene was ubiquitously expressed in ten normal tissues. Under different temperature shock stress, the expression of Mimi-HSP70 gene in miiuy croaker increased at first and then decreased with the rise of temperature, finally, reached a maximum level in liver, spleen and kidney tissues. Infection of miiuy croaker with Vibrio anguillarum resulted in significant changes expression of Mimi-HSP70 gene in the immune-related tissues. These results indicated that expression analysis of Mimi-HSP70 gene provide theoretical basis to further study the mechanism of anti-adverseness in the miiuy croaker.     

Polymorphism and natural selection of antigen B1 of <Emphasis Type="Italic">Echinococcus granulosus</Emphasis> isolated from different host assemblages in India

Antigen B (AgB) is an excretory–secretory product of larval stage of Echinococcus granulosus. This antigen is abundantly secreted by larval stage of the worm. AgB is encoded by a multigene family and is suggested to be involved in evasion of host immune system. During the present study a total of 110 animal isolates of E. granulosus has been screened by mutation scan screening. A total of 14 conformers were detected on the basis of single strand banding profile of 129 bp fragment of AgB1 subunit. Analysis of sequence information of 14 conformers could cluster the isolates into two different group viz. buffalo–cattle and sheep–goat cluster. Conceptual amino acid sequence information of two clusters could be differentiated in terms of MHCII binding propensity of agretope and B-cell epitope region. This type of analysis of clustering of animal isolates on the basis of binding propensity towards different MHC antigens and B-cell linear epitope is the example of its own kind. Positive Tajima’s D value indicated that, AgB1 is under balancing selection pressure which might be considered as heterogeneous selection pressure exerted by the host.     

禽巴氏杆菌C48-3株成熟黏附蛋白基因cpm39的克隆及序列分析

目的：对禽巴氏杆菌C48-3躺株编码成熟黏附蛋白的基因cpm39进行克隆和序列分析。方法：通过PCR从禽巴氏杆菌C448-3。基因组DNA中扩增出cpm39基因,克隆到pMD18-T载体中,转化大肠杆菌DH5d,并对目的基因进行核苷酸序列测定;用Clustal X和Mega 2．1软件将测定的序列与GenBank中已登录的16种血清型巴氏杆菌株核苷酸序列进行同源性分析。结果：测序结果表明cpm39基因大小为1002bp,与已知的16个血清型巴氏杆菌cpm39基因核苷酸序列的同源性为81．5％～100％。结论：克隆得到禽巴氏杆菌C。躺株编码成熟黏附蛋白的cpm39基因,该基因在不同血清型巴氏杆菌中具有很高的同源性,该蛋白可以作为研制预防巴氏杆菌病亚单位疫苗的候选抗原。     

Pathogen proteins eliciting antibodies do not share epitopes with host proteins: a bioinformatics approach

The best way to prevent diseases caused by pathogens is by the use of vaccines. The advent of genomics enables genome-wide searches of new vaccine candidates, called reverse vaccinology. The most common strategy to apply reverse vaccinology is by designing subunit recombinant vaccines, which usually generate an humoral immune response due to B-cell epitopes in proteins. A major problem for this strategy is the identification of protective immunogenic proteins from the surfome of the pathogen. Epitope mimicry may lead to auto-immune phenomena related to several human diseases. A sequence-based computational analysis has been carried out applying the BLASTP algorithm. Therefore, two huge databases have been created, one with the most complete and current linear B-cell epitopes, and the other one with the surface-protein sequences of the main human respiratory bacterial pathogens. We found that none of the 7353 linear B-cell epitopes analysed shares any sequence identity region with human proteins capable of generating antibodies, and that only 1% of the 2175 exposed proteins analysed contain a stretch of shared sequence with the human proteome. These findings suggest the existence of a mechanism to avoid autoimmunity. We also propose a strategy for corroborating or warning about the viability of a protein linear B-cell epitope as a putative vaccine candidate in a reverse vaccinology study; so, epitopes without any sequence identity with human proteins should be very good vaccine candidates, and the other way around.     

A novel strategy of epitope design in Neisseria gonorrhoeae

In spite of genome sequences of both human and N. gonorrhoeae in hand, vaccine for gonorrhea is yet not available. Due to availability of several host and pathogen genomes and numerous tools for in silico prediction of effective B-cell and T-cell epitopes; recent trend of vaccine designing has been shifted to peptide or epitope based vaccines that are more specific, safe, and easy to produce. In order to design and develop such a peptide vaccine against the pathogen, we adopted a novel computational approache based on sequence, structure, QSAR, and simulation methods along with fold level analysis to predict potential antigenic B-cell epitope derived T-cell epitopes from four vaccine targets of N. gonorrhoeae previously identified by us [Barh and Kumar (2009) In Silico Biology 9, 1-7]. Four epitopes, one from each protein, have been designed in such a way that each epitope is highly likely to bind maximum number of HLA molecules (comprising of both the MHC-I and II) and interacts with most frequent HLA alleles (A*0201, A*0204, B*2705, DRB1*0101, and DRB1*0401) in human population. Therefore our selected epitopes are highly potential to induce both the B-cell and T-cell mediated immune responses. Of course, these selected epitopes require further experimental validation.     

Functional and Immunological Relevance of Anaplasma marginale Major Surface Protein 1a Sequence and Structural Analysis

Bovine anaplasmosis is caused by cattle infection with the tick-borne bacterium, Anaplasma marginale. The major surface protein 1a (MSP1a) has been used as a genetic marker for identifying A. marginale strains based on N-terminal tandem repeats and a 5′-UTR microsatellite located in the msp1a gene. The MSP1a tandem repeats contain immune relevant elements and functional domains that bind to bovine erythrocytes and tick cells, thus providing information about the evolution of host-pathogen and vector-pathogen interactions. Here we propose one nomenclature for A. marginale strain classification based on MSP1a. All tandem repeats among A. marginale strains were classified and the amino acid variability/frequency in each position was determined. The sequence variation at immunodominant B cell epitopes was determined and the secondary (2D) structure of the tandem repeats was modeled. A total of 224 different strains of A. marginale were classified, showing 11 genotypes based on the 5′-UTR microsatellite and 193 different tandem repeats with high amino acid variability per position. Our results showed phylogenetic correlation between MSP1a sequence, secondary structure, B-cell epitope composition and tick transmissibility of A. marginale strains. The analysis of MSP1a sequences provides relevant information about the biology of A. marginale to design vaccines with a cross-protective capacity based on MSP1a B-cell epitopes.