Development of Species-Specific PCR Primers and Sensitive Detection of the Tylenchulus semipenetrans in China

Tylenchulus semipenetrans is the most economically important and widespread nematode pest of citrus in China.rDNA-ITS of 14 populations of T.semipenetrans which were collected from different citrus groves or Chinese fir（Cunninghamia lanceolata） plantations in China were amplified and sequenced.The species-specific primers were designed for the first time to diagnosis T.semipenetrans based on the sequences of rDNA-ITS regions of geographic population above.The primers were sensitive to amplify the expected band size（297 bp） from DNA template of a single second-stage juvenile（J2） or different life stages of T.semipenetrans.No specific band was amplified from 15 non-target nematode species which were commonly found in citrus groves.Specificity and reliability of the primers were validated by further PCR amplification of 16 extra populations of T.semipenetrans collected from 4 provinces of China.The primers successfully detected a single J2 of T.semipenetrans within a whole nematode community comprising a large numbers of non-target nematode.The developed diagnostic technique can be used for accurate identification of T.semipenetrans and also as a decision tool for nematode management for citrus or Chinese fir in China.

Expression and role of specificity protein 1 and collagenⅠin recurrent pterygial tissues

AIM:To investigate the expression profiles of the transcription factor specificity protein 1(Sp1)and collagenⅠin recurrent pterygial tissues.What is more,to compare the changes of Sp1 and collagen I among primary pterygial tissue,recurrent pterygial tissue and conjunctival tissue.METHODS:In the prospective study,we collected the pterygial tissues of 40 patients who underwent resection of primary pterygial tissue and recurrent pterygial tissue,and the conjunctival tissues of 10 patients with enucleation due to trauma.The relative expression levels of Sp1 and collagen I were analyzed by reverse transcription quantitative-polymerase chain reaction and Western blot.Paired t-test was performed to compare the Sp1 and collagen I of recurrent pterygial tissues,as well as the primary pterygial tissues and conjunctival tissues.In further,Pearson’s hypothesis testing of correlation coefficients was used to compare the correlations of Sp1 and Collagen I.RESULTS:The content of Sp1 and collagen I m RNA and protein was significantly greater in recurrent pterygial tissue than that was in primary and conjunctival tissue(P<0.05).There was a positive correlation between the m RNA and protein levels of Sp1 and collagen I in recurrent pterygial tissues(protein:r=0.913,P<0.05;m RNA:r=0.945,P<0.05).CONCLUSION:Sp1 and collagen I are expressed in normal conjunctival,primary,and recurrent pterygial tissues,but expression is significantly greater in the latter.Sp1 and collagen I may be involved in the regulation of the development of recurrent pterygium.

Species-specific COI primers for rapid identification of a globally significant invasive pest, the cassava mealybug Phenacoccus manihoti Matile-Ferrero

The globally invasive cassava mealybug Phenacoccus manihoti Matile-Ferrero is a pernicious pest of cassava,and its recent introduction into Asia has raised considerable alarm.To slow or prevent further invasion,an accurate,simple,and developmental-stage-independent detection method for P.manihoti is required.In the present study,a PCR method based on a species-specific mitochondrial DNA cytochrome oxidase I(SS-COI)marker was developed for rapid identification of P.manihoti.One pair of SS-COI primers(PMSSZW-1F and PMSSZW-1R)was designed based on sequence variations in the COI gene among P.manihoti and related mealybug species.Specificity of the primer pair was validated on 21 closely related species.Sensitivity tests were performed on four immature developmental stages and female adults.Efficacy tests demonstrated that at the relatively low concentration of(135.2±14.7)pgresuspended DNA,the specific fragment was detected in all replicates.Furthermore,the SS-COI primer pair was assayed on three populations of P.manihoti from major exporting countries of cassava.The PCR assay was proved to be a rapid,simple,and reliable molecular measure for the identification of P.manihoti.This tool will be useful for quarantine,monitoring,and management of this invasive pest.

Species-specific PCR-based assays for identification and detection of Botryosphaeriaceae species causing stem blight on blueberry in China

Botryosphaeriaceae species are important causal agents of blueberry stem blight worldwide. Blueberry stem blight has become an important disease, potentially affecting the quality and production of blueberries in China. It is difficult and time-consuming to identify at the species level using morphological methods. The aim of this study was to develop polymerase chain reaction（PCR） assays for the diagnosis and early detection of latent infections of blueberry stems by Botryosphaeria spp. Species-specific primers, based on the ribosomal DNA internal transcribed spacer region and β-tubulin gene, were designed and selected for use in PCR assays. Three primer pairs, Lt347-F/R for Lasiodiplodia theobromae, Np304-F/R for Neofusicoccum parvum and FaF/Bt2b for Botryosphaeria dothidea, successfully amplified specific PCR fragments of different sizes on pure cultures or from blueberry stems inoculated and naturally infected blueberry plants with three pathogens, respectively. These primers did not amplify any PCR fragments from other blueberry stem disease-associated pathogens, such as Phomopsis spp. and Pestalotiopsis spp. This PCR protocol could detect as low as 1 00 pg to 1 ng of purified fungal DNA. This PCR-based protocol could be used for the diagnosis and detection of these pathogens from pure cultures or from infected blueberry plants.

Impact of preformed donor-specific antibodies against HLA class Ⅰ on kidney graft outcomes:Comparative analysis of exclusively anti-Cw vs anti-A and/or-B antibodies

AIM To analyze the clinical impact of preformed antiH LA-Cw vs antiH LA-A and/or-B donor-specific antibodies(DSA) in kidney transplantation.METHODS Retrospective study, comparing 12 patients transplanted with DSA exclusively antiH LA-Cw with 23 patients with preformed DSA antiH LA-A and/or B.RESULTS One year after transplantation there were no differencesin terms of acute rejection between the two groups(3 and 6 cases, respectively in the DSA-Cw and the DSA-A-B groups; P = 1). At one year, eG FR was not significantly different between groups(median 59 mL /min in DSA-Cw group, compared to median 51 mL /min in DSA-A-B group, P = 0.192). Moreover, kidney graft survival was similar between groups at 5-years(100% in DSA-Cw group vs 91% in DSA-A-B group, P = 0.528). The sole independent predictor of antibody mediated rejection(AMR) incidence was DSA strength(HR = 1.07 per 1000 increase in MFI, P = 0.034). AMR was associated with shortened graft survival at 5-years, with 75% and 100% grafts surviving in patients with or without AMR, respectively(Log-rank P = 0.005).CONCLUSION Our data indicate that DSA-Cw are associated with an identical risk of AMR and impact on graft function in comparison with "classical" class I DSA.

Identification of various Biomphalaria alexandrina strains collected from five Egyptian governorates using RAPD and species-specific PCR techniques

The first generation of Biomphalaria snails collected from five Egyptian governorates (Giza, Fayoum, Kafr El-Sheikh, Ismailia and Damietta) were sub-jected to species-specific PCR assays and the results showed that snails collected from the field were B. alexandrina, and there was no evidence for the pres-ence of B. glabrata. The snails were subjected also to RAPD- PCR technique. The results showed that dif-ferent fingerprints with each B. alexandrina strain were produced with varying numbers of bands rang-ing in size from 123.6 to 796.6 bp depending on the snail strain and the primer used. Many specific bands were obtained with the four primers in each strain. Primer OPA-1 amplified the highest number of spe-cific bands (26 bands) and gave the highest poly-morphism among the primers used (100% polymor-phism). The estimated similarity coefficients among B. alexandrina strains based on the RAPD-PCR pro-files ranged from 0.56 to 0.72. The highest similarity coefficient (0.72) was recorded between the strains of Ismailia and Kafr El-Sheikh, while the lowest coeffi-cient (0.56) was reported between the strains of SPSC and Ismailia.

Construction of Agropyrum intermedium 2Ai-2 Chromosome DNA Library and Cloning of Species-Specific DNA Sequences

The univalent from the meiosis-metaphase spreads of F1 (Z2× wheat variety Wan7107) wasidentified to be Agropyrum intermedium 2Ai-2 chromosome by GISH. The 2Ai-2 chromosomes weremicroisolated and collected. After two rounds of PCR amplification, the PCR products wereranged from 150-3 000 bp,with predominant fragments at about 200-2 000 bp. Using Ag.intermedium genomic DNA as a probe, Southern blotting analysis confirmed the products originatedfrom Ag. intermedium genome. The products were purified, ligated to pUC18 and then transformedinto competence E.coli DH5αto produce a 2Ai-2 chromosome DNA library. The microcloningexperiments produced approximately 5 ×105 clones, the size range of the cloned inserts was 200-1 500 bp, with an average of 580 bp. Using Ag.intermedium genomic DNA as a probe, dot blottingresults showed that 56% clones are unique/low copy sequences, 44% are repetitive sequences inthe library. Four Ag. intermedium clones were screened from the library by RFLP, and threeclones(Mag065, Mag088, Mag139)belong to low/single sequences, one clone(Mag104)was repetitivesequence, and GISH results indicated that Mag104 was Ag.intermedium species-specific repetitiveDNA sequence.

Comparative transcriptomes reveal the disjunction adaptive strategy of Thuja species in East Asia and North America

The genus Thuja is ideal for investigating the genetic basis of the East Asia-North America disjunction.The biogeographical background of the genus is debatable and an adaptive strategy is lacking.Through the analysis and mining of comparative transcriptomes,species differentiation and positively selected genes(PSGs)were identified to provide information for understanding the environmental adaptation strategies of the genus Thuja.De novo assembly yielded 44,397-74,252 unigenes of the five Thuja species with contig N50length ranging from 1,559 to 1,724 bp.Annotations revealed a similar distribution of functional categories among them.Based on the phylogenetic trees constructed using the transcriptome data,T.sutchuenensis was divided first,followed by T.plicata and T.occidentalis.The final differentiation of T.koraiensis and T.standishii formed a clade.Enrichment analysis indicated that the PSGs of the North American Thuja species were involved in plant hormone signal transduction and carbon fixation of photosynthetic organisms pathways.The PSGs of East Asian Thuja were related to phenolic,alkaloid,and terpenoid synthesis,important stress-resistant genes and could increase plant resistance to external environmental stresses.This study discovered numerous aroma synthetic-related PSGs including terpene synthase(TPS)genes and lipid phosphate phosphatase 2(LPP2),associated with the synthetic aroma of T.sutchuenensis.Physiological indicators,such as the contents of soluble sugars,total chlorophyll,total phenolics,and total flavonoids were determined,which are consistent with the PSGs enrichment pathways associated with adaptive strategies in the five Thuja species.The results of this study provide an important basis for future studies on conservation genetics.

Allele-specific expression and alternative splicing in horse×donkey and cattle×yak hybrids

Divergence of gene expression and alter native splicing is a crucial driving force in the evolution of species;to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expressi on (ASE) and allele-specific alter native splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interferenee of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horsex don key (mule/hi nny) and cattlexyak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, IncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptati on. In con clusi on, our study dem on strated that explorati on of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.

Species composition,distribution patterns and ecological functions of biological soil crusts in the Gurbantunggut Desert

As one of the most important biological factors that maintain the stability of the largest fixed and semi-fixed desert in China,the Gurbantunggut Desert,the biological soil crusts (BSCs) develop well and play critical ecological roles in the desert ecosystem. In this paper,we briefly summarize our research findings since 2002 including species composition,distribution pattern and ecological functions of BSCs in the desert. Our results indicate abundant species diversity of BSCs in the Gurbantunggut Desert in comparison to other deserts in China. At the scales of sand dune or whole desert,the distribution patterns of BSCs are location-specific. The existence of BSCs in this desert could:(1) accelerate the formation of desert soil and the weathering of minerals; (2) accumulate organic matter in surface soil through related species in soil crusts; (3) enhance the abilities of sand surface to resist wind erosion; (4) influence seed germination of vascular plants; and (5) enhance the production of dew deposition on sandy soil surface.

Morphological and Phylogenetic Studies of a Copepod Species, Irodes parupenei Ho and Lin (2007), Infecting Parupeneus rubescens in Saudi Arabia

Dammam City is one of the gorgeous coastal areas in the Arabian Gulf of Saudi Arabia.The present study aimed to ex-amine one of the copepod species infecting the rosy goatfish that represents a highly consumed fish species by the local population in the Arabian Gulf.The copepod species isolated from the infected fish specimens belong to the family Taeniacanthidae and was iden-tified as Irodes parupenei Ho and Lin(2007),primarily based on its morphological,morphometric,and ultrastructural characteris-tics,especially the structures of the dorsal cephalic area,segmentation of the first antenna,the absence of the maxilliped claw in the fe-male specimens,and the setation and spinulation of the legs 2-4 for the adult females are of great significance in the taxonomic iden-tification.The 18S rRNA gene sequence was analyzed to ensure the precise identity and exact taxonomic status of the copepod species.The result showed that this copepod species belong to Taenicanthidae and closely related to Irodes sauridi(gb|JF781550.1)in the same taxon.More details on the specificity of the goatfish for Irodes species and identifying these parasitic taxa using molecular analysis are given in the present study.

Allometric prediction of above-ground biomass of eleven woody tree species in the Sudanian savanna-woodland of West Africa

Allometric models are necessary for estimating biomass in terrestrial ecosystems. Generalized allometric relationship exists for many tropical trees, but species- and region-specific models are often lacking. We developed species-specific allometric models to predict aboveground biomass for 11 native tree species of the Sudanian savanna- woodlands. Diameters at the base and at breast height, with species means ranging respectively from 11 to 28 cm and 9 to 19 cm, and the height of the trees were used as predictor variables. Sampled trees spanned a wide range of sizes including the largest sizes these species can reach. As a response variable, the biomass of the trees was obtained through destructive sampling of 4 754 trees during wood harvesting. We used a stepwise multiple regression analysis with backward elimination procedure to develop models separately predicting, total biomass of the trees, stem biomass, and biomass of branches and twigs. All species- specific regression models relating biomass with measured tree dimen- sions were highly significant （p 〈 0.001）. The biomass of branches and twigs was less predictable compared to stem biomass and total biomass, although their models required fewer predictors and predictor interac- tions. The best-fit equations for total above-ground biomass and stem biomass bad R2 〉 0.70, except for the Acacia species; for branches including twig biomass, R2-values varied from 0.749 for Anogeissus leiocarpa to 0.183 for Acacia macrostachya. The use of these equations in estimating available biomass will avoid destructive sampling, and aid in planning for sustainable use of these species.

重大检疫性害虫玉米根萤叶甲的种特异性SS-CO Ⅰ快速检测技术研究

玉米根萤叶甲在欧洲和美国是一种严重为害玉米的入侵性害虫,传播速度快,侵入我国的可能性极高。本文针对其难以快速准确进行形态鉴别的问题,以玉米根萤叶甲为研究对象,以其他9种/生物型叶甲总科常见害虫为参照,采用基于COⅠ基因的种特异性PCR方法(species-specific COⅠ, SS-COⅠ),研究其快速分子检测鉴定技术。通过提取10种/生物型叶甲DNA和通用型引物扩增测序,获得其基因片段的碱基序列,并比对分析设计1对玉米根萤叶甲特异性引物(DvvZCE1/DvvZCF1),其扩增片段为462 bp。种特异性检验结果显示,该对引物只对玉米根萤叶甲的COⅠ基因具有扩增能力,对其他常见叶甲类害虫,包括玉米双斑长跗萤叶甲、榆黄毛萤叶甲、黄曲条跳甲、油菜蚤跳甲、黄点直缘跳甲、莲草直胸跳甲、枸杞负泥虫以及褐足角胸叶甲的棕黄型和蓝绿型没有扩增能力,该对引物不仅对成虫有很好的扩增效果,对单粒卵、2龄幼虫以及成虫残体(包括触角、头部、胸部、腹部、前足、后足)也具有同样的扩增效果,其最低检出阈值为102.73 pg/μL(相当于1/122 880头雌性成虫)。玉米根萤叶甲特异性SS-COⅠ检测技术在其口岸检疫,以及有效阻截中具有重要意义。

灵长类主要组织相容性复合体Ⅰ类基因进化概述

主要组织相容性复合体(MHC)是和免疫反应直接相关的基因群。MHCⅠ类分子的多态性和病原体的多变性相对应,它是个体在重大传染疾病中存活下来的重要依据。在灵长类动物进化过程中,由于分化时间的差异和生存压力的不同,造成了各物种MHCⅠ类基因不同的存在状态,使它们的MHCⅠ类基因在基因数量和基因功能上有所差异,同时还产生了物种特异性基因。文章描述了灵长类MHCⅠ类基因的总体变化特征,并着重讨论了6个典型MHCⅠ类基因在各典型灵长类物种中的特点及关联性。

着丝粒特异性蛋白CENP-Ⅰ的原核表达、纯化及抗体制备

用RT-PCR的方法从Hela细胞总RNA中获得编码CENP-Ⅰ蛋白第1-293位氨基酸的CENP-ⅠcDNA序列,采用基因体外重组法将其克隆到原核表达载体pET-32a(+)内;将重组质粒转化到大肠杆菌BL21(DE3)中,用IPTG诱导表达、Ni2+-NTA亲和层析纯化获得高纯度的重组蛋白质;用纯化的蛋白质免疫家兔制备抗血清,琼脂糖免疫双扩法和Western blot鉴定得到高效价的特异性抗CENP-Ⅰ抗体.

虎制品的SYB RGreen Ⅰ实时荧光PCR特异性鉴定

针对虎线粒体细胞色素b(Cyt b)基因设计特异性引物,建立并优化SYBR GreenⅠ实时荧光PCR检测鉴定体系。利用该体系分别对从虎(东北虎、孟加拉虎、印支虎)和狮、豹、熊等13种非虎哺乳动物的肌肉、血液、毛发和肉骨粉中提取的DNA进行鉴定分析。结果表明:虎血液、毛发和肌肉DNA样本均出现特异性的实时扩增曲线,平均熔解温度在(83.8±0.1)℃。狮、豹、熊等13种非虎哺乳动物DNA样本的检测结果均为阴性。检测灵敏度可达到在骨粉中检出质量分数为0.05%的虎源性成分。SYBR GreenⅠ实时定量PCR方法具有方便、经济、灵敏度高和重复性好等特性,可用于虎制品的检测鉴定。

重大潜在入侵害虫番茄潜叶蛾的SS-COⅠ快速检测技术

【背景】番茄潜叶蛾是源自南美洲的一种最具毁灭性的世界性入侵害虫,其适生区范围广,且与其他潜叶类昆虫难以准确、快速识别。【方法】以田间常见的其他6种潜叶类害虫为对照,采用基于mtDNA COⅠ基因的种特异性SS-COⅠ方法,研究番茄潜叶蛾快速分子检测技术。【结果】种特异性检测结果显示,SS-COⅠ引物只对番茄潜叶蛾mtDNA具有扩增能力,对美洲斑潜蝇、南美斑潜蝇、三叶草斑潜蝇、葱斑潜蝇、豌豆潜叶蝇、桃潜叶蛾等其他潜叶类害虫不具有扩增效果。该引物不仅对成虫和单粒卵具有很好的扩增效能,对单根触角、头部、胸部、腹部以及翅和足等成虫残体亦具有同样的扩增能力,其最低检出阈值为312.5pg·μL-1。【结论与意义】该方法在有效防范番茄潜叶蛾侵入我国,保障农业生产安全和生态环境安全中意义重大。

基于COⅠ基因的厦门海域鱼类DNA条形码鉴定

为研究DNA条形码技术在厦门海域鱼类分类鉴定中的可行性,随机选取了厦门海域23种鱼类样品进行COⅠ基因扩增,结果共获取23条序列,平均长度为656 bp,序列中T、C、G、A碱基的平均含量分别为:29.40%、28.10%、18.40%、24.10%.样品种内、种间、科内和目内的遗传距离(K2P)分别为:0.21%,20.50%、24.47%和25.62%,遗传距离随着分类阶元的提高而增大,种间遗传距离明显大于种内遗传距离.所选厦门海域鱼类样品仅蓝圆鯵鉴定到圆鯵属,未能鉴定到种,其余22种全部鉴定到种,表明COⅠ基因序列可以作为鱼类分类鉴定的有效DNA条形码.

血清胃蛋白酶原Ⅰ、Ⅱ及其比值诊断效能评价

目的以血清胃蛋白酶原Ⅰ(PGⅠ)、Ⅱ(PGⅡ)及其PGⅠ/PGⅡ比值(PGR)作为筛查慢性萎缩性胃炎和胃癌前期病变指标,评价其诊断效能。方法收集经胃镜排除胃肿瘤的患者474例,进一步将受检者分为轻度非萎缩性胃炎组(对照组,n=164)、萎缩性胃炎组(n=162)和萎缩性胃炎伴肠上皮化生(简称肠化)组(n=148)。以乳胶增强免疫比浊法定量检测血清PGⅠ和PGⅡ,计算PGR,通过受试者工作特征曲线(ROC)评价PGⅠ、PGⅡ和PGR的诊断价值。结果萎缩性胃炎组和萎缩性胃炎伴肠化组PGⅠ、PGⅡ和PGR较对照组显著降低(P<0.01)。PGⅠ、PGⅡ和PGR诊断萎缩性胃炎,其ROC曲线下面积(AUCROC)分别为0.679、0.593和0.622,最佳临界值分别为71.8、9.1和8.12,灵敏度分别为66.1%、54.3%和77.2%,特异度分别为61.0%、61.6%和43.9%;诊断萎缩性胃炎伴肠化AUCROC分别为0.787、0.583和0.836,最佳临界值分别为59.4、9.8和6.76,灵敏度分别为64.9%、58.8%和81.8%,特异度分别为78.1%、55.5%和77.4%。PGⅠ和PGR平行联合,灵敏度为93.6%、特异度为60.4%;PGⅠ和PGR序列联合,灵敏度为53%、特异度为95%。结论 PGⅠ和PGR作为监测胃黏膜状态的指标,联合运用能提高诊断效率;当PGⅠ和PGR同时小于最佳临界值时可预测萎缩性胃炎伴肠化。

MT01对牙龈卟啉单胞菌感染成骨细胞MG63中Ⅰ型胶原mRNA表达的促进作用及其意义

目的:检测单链寡脱氧核苷酸MT01作用下牙龈卟啉单胞菌(Pg)感染成骨细胞MG63中Ⅰ型胶原(ColⅠ)mRNA表达水平,探讨MT01对感染状态下成骨细胞成骨向分化的影响。方法:体外培养的MG63细胞分为空白对照组、MT01组、Pg组和MT01+Pg组。按分组情况进行相应处理,加入MT01(质量浓度1mg·L-1),以1mg·L-1PBS作对照共孵育3h后,以100∶1的感染复数(MOI)加入Pg悬液共培养。4组细胞分别孵育2、4、6、8、12和24h后采用RT-PCR法检测MG63细胞中ColⅠmRNA表达水平。结果:与空白对照组比较,MT01和MT01+Pg组MG63细胞中ColⅠmRNA表达水平在2和4h时无明显变化(P>0.05),8、12和24h时MT01组细胞中ColⅠmRNA表达水平明显升高(P<0.05或P<0.01);与Pg组比较,2和4h时MT01+Pg组细胞中ColⅠmRNA呈低表达,6、8、12和24h时ColⅠmRNA表达水平升高(P<0.05或P<0.01)。结论:MT01上调感染状态下MG63细胞中ColⅠmRNA的表达水平,MT01可促进感染状态下成骨细胞成骨向分化。