属特异性T-RFLP技术用于乳酸杆菌的群落分析

【目的】设计乳酸杆菌属特异性T-RFLP技术(末端限制性片段长度多态性分析)对14株乳酸杆菌进行分型。【方法】采用源于16S-23S rRNA基因间隔区序列的乳酸杆菌属特异性引物LAB-rev,乳酸杆菌的属特异性引物,6-FAM荧光标记后结合16S上游通用引物7f用于乳酸杆菌的PCR扩增。【结果】选取HaeⅢ和HhaⅠ进行限制性酶切,最后对酶切后的产物末端测序得到T-RFLP峰谱图,该图谱能够快速准确地对不同种的乳酸杆菌进行定性、定量的分析。【结论】实验成功搭建T-RFLP技术用于微生态环境中乳酸杆菌检测的平台,对于在功能性食品、乳酸饮料和药物对肠道微生态的影响及菌种鉴定等领域有重大意义。     

双歧杆菌属特异性定量引物的设计及验证

【目的】旨在设计一对双歧杆菌属特异性引物以检测不同样品中低丰度双歧杆菌的含量。【方法】在NCBI中下载57株双歧杆菌全基因组序列,以其共有单拷贝核心基因为目的片段设计双歧杆菌属特异性引物;并对引物进行PCR初筛和特异性复筛;之后借助ddPCR(Droplet Digital PCR,微滴式数字PCR)依次对筛选出的引物进行特异性、灵敏度和实用性验证。【结果】引物Bif-D-9特异性最好,可扩增出4株双歧杆菌而不能扩增20株非双歧杆菌中的任何一株菌;同时通过ddPCR仪定量稀释后的DNA,其扩增结果呈线性下降趋势,证明其灵敏度较好;另外,Bif-D-9结合ddPCR定量出婴儿粪便中双歧杆菌的拷贝数为71 copies/μL,母亲粪便中双歧杆菌的拷贝数为2.7 copies/μL,证明了该方法的实用性。【结论】引物Bif-D-9具有双歧杆菌属特异性,且灵敏度较高、实用性较好,适用于复杂样品中双歧杆菌属定量。     

双歧杆菌属特异性测序引物筛选及优化

【背景】目前双歧杆菌的益生功能被普遍认可,越来越多的研究开始关注肠道中双歧杆菌的生物多样性。然而双歧杆菌是肠道中的低丰度物种,现有技术尚难以深入研究其多样性。【目的】基于双歧杆菌16SrRNA基因序列筛选一对适用于分析粪便样品中低丰度双歧杆菌属多样性的特异性引物。【方法】依据已有引物的相对位置及其与双歧杆菌属16S rRNA基因序列的匹配率,将引物重组优化得到扩增片段800 bp的双歧杆菌属特异性引物;通过PCR扩增和琼脂糖凝胶电泳对引物进行实验筛选和特异性验证;以细菌通用引物(27f/1492r)为参照,通过单分子实时(Single-molecule real-time,SMRT)测序技术对不同引物的3份粪便样品中细菌的DNA扩增子进行测序,在种水平上分析比较不同引物的优劣。【结果】对文献中已有的9对双歧杆菌特异性引物进行重组并优化,其中2对引物的理论特异性较好且扩增产物大于800 bp,它们分别为Bif164-f/Pbi R2和Pbi F1/Pbi R2。PCR扩增和琼脂糖凝胶电泳实验发现,Bif164-f/Pbi R2的扩增条带明亮且无拖尾。此外,利用SMRT测序平台对引物27f/1492r和Bif164-f/Pbi R2的3份粪便样品中细菌的DNA扩增子进行测序并分析。27f/1492r扩增子的分析结果显示,3份样品依次分别含1、3、4个双歧杆菌种且双歧杆菌的平均相对含量为0.34%;而Bif164-f/Pbi R2扩增子的分析结果显示,3份样品依次分别含2、6和8个双歧杆菌种且双歧杆菌的平均相对含量为98.72%。上述结果表明,Bif164-f/Pbi R2可在种水平上特异地检出粪便中低丰度的双歧杆菌,进而实现样品中双歧杆菌的多样性分析。【结论】筛选出一对双歧杆菌特异性引物Bif164-f/PbiR2,可在种水平上分析粪便样品中低丰度双歧杆菌的生物多样性,同时也验证了理论结合实验进行引物筛选这种方法的可行性。     

双歧杆菌属天然质粒系统分类

【背景】以往双歧杆菌质粒分类学研究较少,双歧杆菌属质粒系统分类方法缺失。【目的】建立双歧杆菌属天然质粒系统分类和鉴定方法,促进质粒在双歧杆菌生物学研究中的理解和应用。【方法】利用质粒复制起始蛋白进化树和基因组共线性分析方法,对目前所有已测序的双歧杆菌属天然质粒进行系统分类研究。【结果】双歧杆菌所有已知天然质粒可以划分为6个不同类型的质粒家族和3个独特的复合质粒,家族Ⅲ和家族Ⅵ质粒可进一步划分为不同的亚型类群。家族Ⅲ质粒是双歧杆菌属天然质粒的主要类型和优势家族。家族Ⅵ质粒成员亚型分类最丰富。在质粒家族水平,2种方法的分类结果完全一致。【结论】本文揭示了所有分析质粒之间的系统分类关系,建立了双歧杆菌属天然质粒系统的分类标准、方法和体系,可为今后双歧杆菌天然质粒分类和鉴定提供重要的理论参考和分类依据。     

应用实时荧光定量PCR方法定量检测双歧杆菌对Caco-2细胞的黏附

【目的】采用实时荧光定量PCR的方法定量分析黏附于Caco-2细胞的双歧杆菌,并建立一种快速有效分离黏附于细胞的细菌的方法。【方法】采用Triton X-100溶液处理黏附于Caco-2细胞上的菌体,确定获得最佳分离效果的处理时间;建立实时荧光定量PCR定量检测双歧杆菌的方法,获得标准曲线,进行特异性、灵敏度、重复性评价;应用建立的方法分析11株双歧杆菌对Caco-2细胞的黏附能力。【结果】Triton X-100处理黏附于Caco-2细胞的双歧杆菌的最佳作用时间为10 min。实时荧光定量PCR定量检测双歧杆菌的方法重复性好、特异性强、灵敏度高;起始模板浓度范围在104?108 CFU/mL之间具有良好的线形关系,相关系数>99%,在该浓度范围线性方程为：y=?3.345 2x+37.637 0。应用建立的方法定量分析双歧杆菌的黏附能力,与直接镜检法相比差异不显著(P>0.05),检测时间由48 h缩短至4 h。【结论】Triton X-100分离处理结合实时荧光定量PCR方法是一种快速、有效的检测双歧杆菌对Caco-2细胞黏附能力的方法。     

益生菌DGGE Marker的制备及验证

目的 制备指示益生菌标准菌株的DGGE marker并对其可靠性进行验证.方法 分别利用乳杆菌、双歧杆菌特异性引物和细菌V3区通用引物对选取的乳杆菌、双歧杆菌标准菌株DNA进行扩增,利用DGGE检测每个标准菌株条带位置是否与利用这些标准菌株制备的DGGE marker条带相对应.结果 DGGE图谱显示,乳杆菌和双歧杆菌特异性引物或V3区通用引物扩增后的每个标准菌株优势条带,与乳杆菌、双歧杆菌DGGE marker均有对应关系.结论 常见益生菌菌株的DGGE marker可以指示相应菌株的存在;其研制成功,可为微生物生态学中应用DGGE技术检测特定微生物种类的动态变化,提供新的思路.     

应用特异PCR快速鉴定微生物肥料中4种乳酸菌

【目的】植物乳杆菌(Lactobacillus plantarum)、鼠李糖乳杆菌(L.rhamnosus)、嗜酸乳杆菌(L.acidophilus)和德氏乳杆菌(L.delbrueckii)是微生物肥料生产中常用的乳酸菌,它们表型特征相似,若采用传统方法鉴定则费时费力,为准确、快速地鉴定这些种,建立种特异PCR方法。【方法】利用NCBI中Primer-BLAST(引物设计和特异性检验工具),以GenBank数据库中上述菌种的recA和gyrB为靶基因,设计和筛选种特异性引物从而建立相应特异PCR鉴定方法。【结果】经过乳杆菌属(Lactobacillus)、乳球菌属(Lactococcus)、片球菌属(Pediococcus)、芽孢杆菌属(Bacillus)、类芽孢杆菌属(Paenibacillus)、短芽孢杆菌属(Brevibacillus)和假单胞菌属(Pseudomonas)7个属24个种共40株标准菌株的实验验证,4个目标种分别扩增出唯一的目的产物,而其他种均无目的扩增产物。采用建立的4种特异PCR方法对产品中分离的16株乳杆菌进行鉴定,结果与16S rDNA序列分析、Biolog鉴定结果一致。【结论】建立的特异PCR鉴定方法均具有较高的种内通用性和种间特异性,可快速、准确的用于微生物制剂中植物乳杆菌、德氏乳杆菌、鼠李糖乳杆菌、嗜酸乳杆菌的检测和鉴定,具有较好的应用前景。     

胶质类芽胞杆菌PCR快速检测方法

摘要:【目的】胶质类芽胞杆菌(Paenibacillus mucilaginosus) 是微生物肥料广泛应用的功能菌种之一,筛选并鉴定其特异性引物,建立该菌种快速检测方法,对微生物肥料产品检测和评价至关重要。【方法】本文筛选了胶质类芽胞杆菌基因间的一段非编码序列作为特异性引物(orf06701-F:5'-ATGGAGGAAACATGGGGTGA-3'/orf06701-R: 5'-TCAGGAATGAAGGCCCCCTT-3'),通过PCR 反应条件/ 体系的优化、特异性及灵敏度检测,建立了胶质类芽胞杆菌     

分子信标-实时 PCR法快速检测双歧杆菌的研究

为建立双歧制品中双歧杆菌快速、敏感、特异的检测方法,根据双歧杆菌16SrRNA/16SrDNA基因设计合成了双歧杆菌属特异性引物和分子信标探针,建立了快速检测双歧杆菌的分子信标-实时PCR检测方法,并对反应条件进行优化。检测方法重复性好,批内和批间变异系数均小于5%;特异性强,扩增曲线呈现明显的S型,无非特异性扩增;灵敏度高,是普通PCR的100倍,对纯双歧杆菌DNA的检出限为5.7fg/PCR反应体系,纯双歧杆菌菌液的检出限为2×103CFU/mL;线形范围宽,起始模板数在2×108CFU/mL～2×104CFU/mL之间具有良好的线性关系,相关系数大于97%。该方法具有灵敏、特异、简便和快速的特点,可用于对双歧杆菌原位菌数的定量检测。     

双歧杆菌的分类学研究与新进展

双歧杆菌作为一种重要的益生菌,被广泛应用在乳制品和微生态制剂生产中。本文围绕双歧杆菌在《伯杰氏系统细菌学手册》中的演化历史、最新分类,以及其多相分类法的应用进行了阐述,并对近年来双歧杆菌属的新种做了详细的介绍。     

Recent advances in the study of Kaposi's sarcoma-associated herpesvirus replication and pathogenesis

It has now been over twenty years since a novel herpesviral genome was identified in Kaposi's sarcoma biopsies. Since then, the cumulative research effort by molecular biologists, virologists, clinicians, and epidemiologists alike has led to the extensive characterization of this tumor virus, Kaposi's sarcoma-associated herpesvirus(KSHV; also known as human herpesvirus 8(HHV-8)), and its associated diseases. Here we review the current knowledge of KSHV biology and pathogenesis, with a particular emphasis on new and exciting advances in the field of epigenetics. We also discuss the development and practicality of various cell culture and animal model systems to study KSHV replication and pathogenesis.     

A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus (2019-nCoV) Potentially Related to Viral Transmissibility

正Dear Editor,In December 2019, a novel human coronavirus caused an epidemic of severe pneumonia(Coronavirus Disease 2019,COVID-19) in Wuhan, Hubei, China(Wu et al. 2020; Zhu et al. 2020). So far, this virus has spread to all areas of China and even to other countries. The epidemic has caused 67,102 confirmed infections with 1526 fatal cases     

Curcuminoids as inhibitors of thioredoxin reductase: A receptor based pharmacophore study with distance mapping of the active site

Curcumin is the yellow pigment of turmeric that interacts irreversibly forming an adduct with thioredoxin reductase (TrxR), an enzyme responsible for redox control of cell and defence against oxidative stress. Docking at both the active sites of TrxR was performed to compare the potency of three naturally occurring curcuminoids, namely curcumin, demethoxy curcumin and bis-demethoxy curcumin. Results show that active sites of TrxR occur at the junction of E and F chains. Volume and area of both cavities is predicted. It has been concluded by distance mapping of the most active conformations that Se atom of catalytic residue SeCYS498, is at a distance of 3.56 from C13 of demethoxy curcumin at the E chain active site, whereas C13 carbon atom forms adduct with Se atom of SeCys 498. We report that at least one methoxy group in curcuminoids is necessary for interation with catalytic residues of thioredoxin. Pharmacophore of both active sites of the TrxR receptor for curcumin and demethoxy curcumin molecules has been drawn and proposed for design and synthesis of most probable potent antiproliferative synthetic drugs.     

The structure, reproduction and taxonomy of Vidalia and Osmundaria (Rhodophyta, Rhodomelaceae)

Comprises species occurring mostly in subtidal habitats in tropical, subtropical and warm-temperate areas of the world. An analysis of the type species, V. spiralis (Sonder) Lamouroux ex J. Agardh, a species from Australia, establishes basic characters for distinguishing species in the genus. These characters are (1) branching patterns of thalli, (2) flat blades that may be spiralled on their axis, (3) width of the blade, (4) primary or secondary derivation of sterile and fertile branchlets and (5) position of sterile and fertile branchlets on the thalli. Application of the latter two characters provides an important basic method for separation of species into three major groups. Osmundaria , a genus known only in southern Australia, was studied in relation to Vidalia , and its separation from the Vidalia assemblage is not accepted. Species of Vidalia therefore are transferred to the older genus name, Osmundaria. Two new species, Osmundaria papenfussii and Osmundaria oliveae are described from Natal. Confusion in the usage of the epithet, Vidalia fimbriala Brown ex Turner has been clarified, and Vidalia gregaria Falkenberg, described as an epiphyte on Osmundaria pro/ifera Lamouroux, is revealed to be young branches of the host, Osmundaria prolifera.     

New or rare chromosome counts in Artemisia L. (Asteraceae, Anthemideae) and related genera from Kazakhstan

Fifteen chromosome counts of six Artemisia taxa and one species of each of the genera Brachanthemum, Hippolytia, Kaschgaria, Lepidolopsis and Turaniphytum are reported from Kazakhstan. Three of them are new reports, two are not consistent with previous counts and the remainder are confirmations of very scarce (one to four) earlier records. All the populations studied have the same basic chromosome number, x = 9, with ploidy levels ranging from 2x to 6x. Some correlations between ploidy level, morphological characters and distribution are noted.