基于PCR-LDR平台的近交系小鼠遗传质量快速检测方法

目的建立基于PCR-LDR平台的近交系小鼠SNP快速分型方法,用于检测实验小鼠的遗传质量与品系纯度。方法利用可移植性极高的PCR-LDR技术,以常见近交系小鼠为研究对象,选取了21条染色体上的45个SNP位点,分别设计引物和探针,经过筛选和验证,建立了多重PCR-LDR(polymerase chain reaction and ligase detection reaction,PCR-LDR)分型方案。结果四组多重PCR-LDR可实现45个SNP位点的基因分型,其中43个、44个与45个SNP在样本中的检出率分别为100%、90.9%与36.4%。所有样本经分型确定为纯合体,并得到了常见近交系小鼠SNP位点信息。结论实现了常见近交系小鼠快速、高通量的基因分型,可用于遗传质量检测和品系鉴定。     

小鼠冷冻胚胎和精子SNP遗传鉴定方法的建立

目的建立小鼠冷冻胚胎和精子SNP(single nucleotide polymorphism)分型方法,用于冷冻胚胎和精子快速遗传鉴定方案。方法以中科院上海实验动物中心(国家啮齿类实验动物种子中心上海分中心)提供的小鼠冷冻胚胎和精子为样本,采用全基因组扩增技术和PCR-LDR分型技术建立小鼠冷冻物SNP遗传鉴定方法。结果全基因组扩增技术能大幅度增加冷冻胚胎样本的DNA总量;PCR-LDR分型方法适用于小鼠全基因组45个SNPs的分型;分型确定C57BL/6,BALB/c,FVB/NJ等胚胎和精子各10种近交系,SNP位点信息与测序结果一致;小鼠冷冻胚胎个数与SNPs检出个数成正比,当胚胎数达到12以上时SNP检出率100%。结论实现近交系小鼠冷冻胚胎和精子快速SNP基因分型及遗传质量鉴定。     

Establishment of the model of white blood cell membrane chromatography and screening of antagonizing TLR_4 receptor component from Atractylodes macrocephala Koidz

Inflammation is a common and fundamental patho- physiological response. The inflammatory reaction is characterized by activation of white blood cell (WBC) with an accompanying vascular reaction. Recently, it has been found that the inflammatory reaction d…     

Signal transduction pathways in guinea pig sperm

Trifluoperazine (TFP), the antagonist of calmodulin (CaM). significantly stimulated the capacitation and acrosome reaction of guinea pig spermatozoa at the concentration of 10-100μmol/L, independent of the external Ca2+. Forskolin, dbcAMP and caffeine evidently promoted the occurrence of acrosome reaction of spermatozoa at early capacitation stage (5 h) in nonsynchronous system but not in synchronous system. If the spermatozoa were capacitated for 15 h in synchronous system, the above three drugs significantly stimulated acrosome reaction in a Ca2+-independent manner. Protein kinase C activators, i.e. phorbol 12-myristate 13-acetate (PMA) and phorbol 12,13-dibutyrate (PDB) did not influence the occurrence of acrosome reaction of spermatozoa at early capacitation stage, but significantly increased the acrosome reaction rate in capacitated spermatozoa in a Ca2+-independent manner. In contrast. PKC inhibitor staurosporine significantly inhibited the occurrence of acrosome reaction.     

Influence of pigment substitution on the electrochemical properties of Rhodobacter sphaeroides 601 reaction centers

With the help of pigment substitution, self-assembled monolayer film and square wave voltammetry, the influence of pigment substitution on the electrochemical properties of Rhodobac-ter sphaeroides 601 reaction centers was investigated. Results showed that the charge separation could also be driven by externally electric field, similar to the primary photochemical reaction in purple bacterial reaction center. On the surface of Au electrode, a self-assembled monolayer film (the RC-PDDA-DMSA film) was made up of 2,3-dimercaptosuccinic acid (DMSA), poly-dimeth-yldiallylammonium chloride (PDDA) and reaction center (RC). When square wave voltammetry was used to study the RC-PDDA-DMSA film, four redox pairs in the photochemical reaction of RC were observed by changing frequency. With nonlinear fitting, the standard potential of P/P+ and the corresponding electrode reaction rate constant were determined to be 0.522 V and 13.04 S-1, respectively. It was found that the redox peak at -0.02 V changed greatly when b     

A much better replacement of the Michaelis—Menten equation and its application

Michaelis-Menten equation is a basic equation of enzyme kinetics and gives acceptable approximations of real chemical reaction processes.Analyzing the derivation of this equation yields the fact that its good performance of approximating real reaction processes is due to Michaelis-Menten curve(8).This curve is derived from Quasi-Steady-State Assumption(QSSA),which has been proved always true and called Quasi-Steady-State Law by Banghe Li et al.[Quasi-steady state laws in enzyme kinetics,J.Phys.Chem.A 112(11)(2008)2311-2321].Here,we found a polynomial equation with total degree of four A(S,E)= 0(14),which gives more accurate approximation of the reaction process in two aspects:during the quasi-steady-state of the reaction,Michaelis-Menten curve approximates the reaction well,while our equation A(S,E)= 0 gives better approximation;near the end of the reaction,our equation approaches the end of the reaction with a tangent line the same to that of the reaction process trajectory simulated by mass action,while MicheielisMenten curve does not.In addition,our equation A(S,E)= 0 differs to Michaelis-Menten curve less than the order of 1/S^3 as S approaches +∞.By considering the above merits of A(S,E)= 0,we suggest it as a replacement of Michaelis-Menten curve.Intuitively,this new equation is more complex and harder to understand.But,just because of its complexity,it provides more information about the rate constants than Michaelis-Menten curve does.Finally,we get a better replacement of the Michaelis-Menten equation by combing 4(S,E)= 0 and the equation dP/dt = k2C(t).     

Replacement of bacteriopheophytin in reaction centers fromRhodobacter sphaeroides RS601 with plant pheophytin

In the presence of acetone and an excess of exogenous plant pheophytins, bacterio-pheophytins in the reaction centers from Rhodobacter sphaeroides RS601 were replaced by pheophytins at sites HA and HB, when incubated at 43.5℃ for more than 15 min. The substitution of bacteriopheophytins in the reaction centers was 50% and 71% with incubation of 15 and 60 min, respectively. In the absorption spectra of pheophytin-replaced reaction centers (Phe RCs), bands assigned to the transition moments Qx (537 nm) and QY (758 nm) of bacteriopheophytin disappeared, and three distinct bands assigned to the transition moments Qx (509/542 nm) and QY (674 nm) of pheophytin appeared instead. Compared to that of the control reaction centers, the photochemical activities of Phe RCs are 78% and 71% of control, with the incubation time of 15 and 60 min. Differences might exist between the redox properties of Phe RC and of native reaction centers, but the substitution is significant, and the new system is available for further     

实时定量PCR发展概述

实时定量聚合酶链反应(real-time quantitative polymerase chain reaction,简称qPCR)是一种通过荧光信号对PCR进程进行实时监测,并对未知模板进行定量分析的一种核酸定量技术,该技术在临床诊断和生命科学等多领域发挥着重要的作用。现就生物制品领域有着重要应用价值的中介探针聚合酶链反应(mediator probe polymerase chain reaction,MP PCR)和数字聚合酶链反应(digital polymerase chain reaction,dPCR)新技术加以介绍,同时也对qPCR技术中的关键因素(如参考基因选择和核酸质量评价)以及qPCR最低限度标准(minimum information for the publication of real-time quantitative PCR,MIQE)指南作一概述。     

Approximate analytical solution of fractional order biochemical reaction model and its stability analysis

Approximate analytical solution of the system of coupled nonlinear Ordinary Differential Equations (ODEs) of a biochemical reaction model is much relevant due to its practical significance to biochemists.In this paper,an effective and powerful mathematical technique,viz.fractional homotopy analysis transform method (FHATM),is employed to get the numerical solutions of biochemical reaction model with time fractional derivatives.The adopted scheme is the beautiful copulation of homotopy analysis technique and Laplace transform algorithm.This paper shows that the adopted scheme is quite easy as well as computationally attractive in the context of a solution procedure.The Caputo-type fractional derivatives are considered in the present paper.Approximate results of the probability density functions of the time fractional biochemical reaction model are computed for miscellaneous fractional Brownian motions as well as for classical motion and are presented graphically.The time fractional biochemical reaction model with respect to stability analysis for various values of fractional order q is also analyzed.In the context of stability discussion,we have used the fractional Routh-Hurwitz stability criterion to establish the local stability of the biochemical reaction model of fractional order.     

高通量飞行时间质谱基因分型方法的研究

为了考察飞行时间质谱基因分型方法 (MALDI-TOF) 的位点分型成功率和分型结果质量的关系,分析了 96 个 SNPs 位点的近 10 000 个基因分型数据 (用 MALDI-TOF “4 重”实验方法检测 ). 结果显示,位点分型成功率和分型结果的质量显著正相关 . 分型成功率低于 82% 的 SNP 位点,其高质量结果占的比例开始逐渐降低 . 提示 82% 的分型成功率可以作为衡量分型结果质量的数据点 . 为了进一步提高通量并降低成本,在 MALDI-TOF “ 4 重”实验方法的基础上,发展了两种“准 8 重”实验方法 . 用新的实验方法检测了 95 个样本的 32 个 SNPs 位点 . 结果显示“混合准 8 重”实验方法与“ 4 重”实验方法相比无显著差异,而“复点准 8 重”的结果差于“ 4 重”分型方法 .     

Multiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method

We describe a convenient, cost-effective and flexible medium-throughput single nucleotide polymorphism (SNP) genotyping method, Multiplex SNP-SCALE, which enables the simultaneous amplification by polymerase chain reaction (PCR) of up to 25 (or potentially more) loci followed by electrophoresis in an automated DNA sequencer. We extended the original SNP-SCALE method to include (i) use of a commercial multiplex PCR kit, (ii) a four-dye system, (iii) much-reduced (2-μL) reaction volumes, (iv) drying down of template DNA before PCR, (v) use of pig-tailed primers, (vi) a PCR product weighting system, (vii) a standard optimized touchdown PCR thermocycling programme, and (viii) software (SNP-SCALE Primer Designer) that automatically designs suitable SNP-SCALE primers for a batch of loci. This new protocol was validated for different types of SNPs. The method is cost- and time-effective for medium-scale evolutionary and ecological projects involving 10s to 100s of loci.     

Characterization of 19 single nucleotide polymorphism markers for coho salmon

We report 39 single nucleotide polymorphisms (SNPs) observed in 23 nuclear DNA sequences in coho salmon Oncorhynchus kisutch. High‐throughput genotyping assays based on the 5′‐nuclease reaction were developed for 17 of these nuclear SNPs and for two previously published mitochondrial DNA SNPs. Minor allele frequency differences (Δq) among collections were between 5.2% and 51.2%, resulting in per locus F_ST estimates of 0.00–0.24 with an average of 0.09.     

应用FP-TDI技术进行高通量单核苷酸多态分型

FP-TDI (fluorescence polarization template-directed dye-terminator incorporation）是一种操作简单、实验投入少、适于高通量反应的单核苷酸多态等位基因分型技术.使用两种评价分型图像质量的数值指标,可以有效地对分型结果进行评价,使该技术得到了改进.在此基础上优化了实验条件,并应用该技术,对人类基因组3号染色体上随机选取的337个单核苷酸多态性位点进行了高通量分型,反应的一次成功率达到59.94%.     

三色荧光技术在SNP检测中的应用

利用三色荧光标记的A、C、T双脱氧核苷酸单碱基延伸的方法结合编码寡核苷酸芯片技术检测单核苷酸多态性 (SNP)的基因型。以beta地中海贫血样本基因 (HBB基因 )突变作为模型的研究结果显示该方法能同时对多位点的SNP进行检测。     

Evaluation of genotyping concordance for commercial bovine SNP arrays using quality‐assurance samples

SNP arrays are widely used in genetic research and agricultural genomics applications, and the quality of SNP genotyping data is of paramount importance. In the present study, SNP genotyping concordance and discordance were evaluated for commercial bovine SNP arrays based on two types of quality assurance (QA) samples provided by Neogen GeneSeek. The genotyping discordance rates (GDRs) between chips were on average between 0.06% and 0.37% based on the QA type I data and between 0.05% and 0.15% based on the QA type II data. The average genotyping error rate (GER) pertaining to single SNP chips, based on the QA type II data, varied between 0.02% and 0.08% per SNP and between 0.01% and 0.06% per sample. These results indicate that genotyping concordance rate was high (i.e. from 99.63% to 99.99%). Nevertheless, mitochondrial and Y chromosome SNPs had considerably elevated GDRs and GERs compared to the SNPs on the 29 autosomes and X chromosome. The majority of genotyping errors resulted from single allotyping errors, which also included the opposite instances for allele ‘dropout’ (i.e. from AB to AA or BB). Simultaneous allotyping errors on both alleles (e.g. mistaking AA for BB or vice versa) were relatively rare. Finally, a list of SNPs with a GER greater than 1% is provided. Interpretation of association effects of these SNPs, for example in genome‐wide association studies, needs to be taken with caution. The genotyping concordance information needs to be considered in the optimal design of future bovine SNP arrays.     

Multiplex automated primer extension analysis: simultaneous genotyping of several polymorphisms.

Accurate and fast genotyping of single nucleotide polymorphisms (SNPs) is of significant scientific importance for linkage and association studies. We report here an automated fluorescent method we call multiplex automated primer extension analysis (MAPA) that can accurately genotype multiple known SNPs simultaneously. This is achieved by substantially improving a commercially available protocol (SNaPshot). This protocol relies on the extension of a primer that ends one nucleotide 5'of a given SNP with fluorescent dideoxy-NTPs (minisequencing), followed by analysis on an ABI PRisMS 377 Semi-Automated DNA Sequencer Our modification works by multiplexing the initial reaction that produces the DNA template for primer extension and/or multiplexing several primers (corresponding to several SNPs) in the same primer extension reaction. Then, we run each multiplexed reaction on a single gel lane. We demonstrate that MAPA can be used to genotype up to four SNPs simultaneously, even in compound heterozygote samples, with complete accuracy (based on concordance with sequencing results). We also show that primer design, unlike the DNA template purification method, can significantly affect genotyping accuracy, and we suggest useful guidelines for quick optimization.     

Genotyping of single nucleotide polymorphisms using base-quenched probe: A method does not invariably depend on the deoxyguanosine nucleotide

Most available methods for detecting single nucleotide polymorphisms (SNPs) are based principally on the system that can produce an increased fluorescence signal during hybridization. In the current study, we demonstrate a method of base-quenched probe for polymerase chain reaction (PCR) genotyping that requires only a pair of primers and one fluorescent probe and does not invariably depend on the deoxyguanosine nucleotide. This method further exploits the phenomenon of fluorescence quenching of fluorescent-labeled probe during hybridization to its complementary target gene’s sequence. 6-Carboxyfluorescein (FAM) can be directly conjugated to a base of either adenine (A), thymine (T), cytosine (C), or guanine (G), referred to as A-, T-, C-, or G-quenched probe, respectively, at either the 5′ or 3′ end. For describing the method in detail, we chose apolipoprotein M (apoM) as a target gene in the current study. DNA sequencing analyses validated that all four types of base-quenched probes could provide unbiased genotyping results (K = 1, P = 0.000), although the maximum speed of fluorescence increase, max(dF/dT), when using the G-quenched probe method, was approximately twofold lower than the others (P < 0.0001). Moreover, we applied this method to detect another seven SNPs in the genomes of phospholipase A2, monocyte chemoattractant protein 1 (MCP1), and l-ficolin, further confirming our method. It is concluded that this method is precise, simple, and economic as well as suitable for large-scale genotyping studies.     

SNiPORK - a microarray of SNPs in candidate genes potentially associated with pork yield and quality - development and validation in commercial breeds

SNiPORK is an oligonucleotide microarray based on the arrayed primer extension (APEX) technique, allowing genotyping of single nucleotide polymorphisms (SNPs) in genes of interest for pork yield and quality traits. APEX consists of a sequencing reaction primed by an oligonucleotide anchored with its 5' end to a glass slide and terminating one nucleotide before the polymorphic site. Extension with one fluorescently labeled dideoxynucleotide complementary to the template reveals the polymorphism. Ninety SNPs were selected from those associated directly or potentially with pork traits. Of the 90 SNPs, 5 did not produce a positive signal. For 85 SNPs, 100% repeatiblity was proved by double genotyping of 13 randomly chosen boars. In addition, the accuracy of genotyping was verified in 2 sib-families by a Mendelian inheritance of 49-50 homozygous genotypes from sire to sons. Three genotype discrepancies were found (97% accuracy rate). All inaccurities were confirmed by an alternative method (sequencing and PCR-RFLP assays). Moreover, the exclusion power of the chip was evalueted by an SNP inheritance analysis of unrelated boars within each sib-family. In the validation step, 88 boars (13 Pietrain, 31 Landrace, 16 Large White, 8 Duroc, 7 Hampshire x Pietrain crosses, and 13 other hybrid lines) were screened to validate SNPs. Among the 85 selected SNPs, 12 were found to be monoallelic, the rest showing at least two genotypes for the entire population under study. The primary application of the SNiPORK chip is the simultaneous genotyping of dozens of SNPs to study gene interaction and consequently better understand the genetic background of pork yield and quality. The chip may prospectively be used for evolutionary studies, evaluation of genetic distances between wild and domestic pig breeds, traceability tests, as well as the starting point for developing a platform for identification and paternity analysis.