实验室2种检测小儿巨细胞病毒方法的比较

比较胶体金法和实时定量PCR法对小儿巨细胞病毒IgM抗体水平检测的敏感性及准确率。收集临床上243例小儿的血液标本,分别采用实时荧光定量PCR法和胶体金法检测这243例患者外周血巨细胞病毒IgM抗体水平,并对这2种检测方法的阳性率和敏感性进行比较分析。实时荧光定量PCR法阳性率为11.93%,胶体金法为6.58%,2者差异有统计学意义(P<0.01)。在HCMV-DNA检测阳性患者中,IgM抗体阳性组HCMV-DNA拷贝数显著高于阴性组(P<0.01),比较这2种检测方法的敏感性,实时荧光定量PCR法的敏感性为72.5%,胶体金法的敏感性为40%,两者差距有统计学意义(P<0.01)。实时荧光定量PCR法与胶体金法相比,对巨细胞病毒IgM抗体检测具有较高的敏感性和准确率,值得临床推广应用。     

双标准曲线相对定量PCR试验原理与方法

实时荧光定量PCR(FQ-PCR)是一种准确有效的核酸定量分析技术,具有易操作、高通量、高敏感性、高特异性、高度自动化和低污染等优点,并随新定量PCR仪及新操作方法的发展而得到广泛应用,但是,定量PCR的高敏感性特点使得实验操作严格而繁琐。阐述了一种改进的相对定量方法——双标准曲线法的试验原理和特点,描述了定量PCR体系的优化方式,探讨了试验误差分析方法及试验操作技巧,并就试验数据的处理方法进行讨论。试验证明,双标准曲线法是一种经济、简单而准确的定量方法。     

荧光晕法在细胞染色质结构状态检测中的应用

荧光晕法是近年来发展起来的定量检测细胞染色质结构状态的方法,由于其简易、直观、灵敏、快速,已被广泛用于放射生物学及肿瘤细胞生物学研究中。我们依据文献报道建立了此法,并对其进行了改良,进一步优化了操作步骤。并用该法检测了两种相同来源(具有相似遗传背景)、具不同辐射敏感性的细胞株的染色质结构状态,发现辐射敏感株SX-9具有更松散的染色质结构,可能与两者的辐射敏感性差异有关,为研究染色质结构状态与辐射敏感性的关系提供了佐证。     

荧光晕法在细胞染色质细胞状态检测中的应用

荧光晕法是近年来发展起来的定量检测细胞染色质细胞染色质结构状态的方法,由于其简易、直观、灵敏、快速,已被广泛用于放射生物学及肿瘤细胞这研究中。我们依据文献报道建立了此法,并对其进行了改良,进一步优化了操作步骤。并用３该法检测了两种相同来源（具有相似遗传背景）、具不同辐射敏感性的细胞株的染色质结构状态,发现辐射敏感株ＳＸ－９具有更松散的染色质结构,可能与两者的辐射敏感性差异有关,为研究染色质结构状态     

实时定量聚合酶螺旋反应定量检测变形链球菌方法的建立

目的:建立实时定量检测口腔内变形链球菌的实时定量聚合酶螺旋反应(PSR)方法。方法:针对变形链球菌的gtf B基因设计4套引物,通过实时浊度法和显色法两种方法判断结果。结果:从4套引物中筛选出最佳引物,并确定最佳温度为65℃;进一步实验表明采用最佳引物能特异性地检测变形链球菌,与13种其他病原核酸无交叉反应,敏感性达10拷贝/μL。结论:建立了实时定量检测变形链球菌的PSR方法,该方法具有简单快速、特异性强、敏感性高的特点,为实时定量检测变形链球菌提供了新技术。     

实时定量RT-PCR技术及在植物基因表达分析中的应用

近年来实时定量RT-PCR（real-time quantitative RT-PCR,qPCR）由于其具有敏感性,广阔的动力学范围,可靠性的特点,成为基因表达研究的标准方法。介绍了实时定量RT-PCR的原理和实验过程中的潜在问题,并且讨论了实时定量RT-PCR在植物基因表达研究中的应用。     

逆转录-聚合酶螺旋反应检测结核分枝杆菌的应用

目的:建立并应用逆转录-聚合酶螺旋反应(RT-PSR)快速检测结核分枝杆菌(MTB)。方法:针对结核分枝杆菌16S rRNA基因设计特异性引物,通过反应条件的优化初步建立结核分枝杆菌的RT-PSR扩增方法;随后,用2株结核分枝杆菌和11株其他致病菌进行RT-PSR、RT-LAMP和荧光定量PCR法的特异性与敏感性试验;利用RT-PSR法、罗氏培养法、RT-LAMP法和荧光定量PCR法对83名结核病患者的痰液标本进行诊断对比。结果:成功建立并优化了MTB的RT-PSR检测方法,与RT-LAMP法相比,两者特异性均为100%;RT-PSR法的检测灵敏性为1 CFU/mL,为荧光定量PCR法的10倍,且检测下限可达0.1 pg/μL;临床患者痰液样本检测结果表明,与罗氏培养法相比,RT-PSR法和RT-LAMP法的阳性率分别为98.80%(P0.05)和96.39%(P0.05),差异均具有统计学意义。结论:与传统检测法相比,RT-PSR法对于诊断临床样本中的MTB具有良好的特异性和敏感性,适合基层医疗单位防治MTB的推广和应用。     

化学发光法在梅毒实验诊断中的应用价值

目的:探讨化学发光法在梅毒实验诊断中的应用价值。方法:采用化学发光法、RPR法、TPPA法分别检测150例梅毒患者及125例非梅毒患者血清。结果:化学发光法、RPR法、TPPA法对150例梅毒血清标本和125例非梅毒血清标本对照组的敏感性分别为98.0%、75.3%和97.3%,特异性分别为98.3%、81.6%和97.5%。化学发光法、TPPA法敏感性和特异性明显高于RPR法,差异有统计学意义(P<0.05);化学发光法和TPPA法相比,敏感性和特异性差别不大,差异没有统计学意义(P>0.05);联合3种方法检测,梅毒诊断阳性率可提高到100%。结论:梅毒的化学发光检测法具有极高的敏感性和特异性,是一种自动化、定量检测方法,能够用于梅毒的准确诊断和疗效观察,与传统方法联检可防止误诊、漏诊,具有较大的临床应用价值。     

布鲁氏菌荧光定量PCR检测分析

本研究为探析荧光定量PCR检测布鲁氏菌的临床价值,通过研究PCR法的重复性和敏感性,建立了布鲁氏菌采用复合探针荧光定量PCR检测的方法,对布鲁氏菌病进行诊断和筛选。表明复合探针荧光定量PCR检测布鲁氏菌具有较高的特异性为100%。同时,在5次重复实验中,阴性和阳性质控品的检测CV值均小于5%。说明采用复合探针荧光定量PCR法检测布鲁氏菌具有较高的准确性,有助于诊断和筛选布鲁氏菌病,具有一定的推广应用价值。     

应用鞣化载体酶联金葡菌A蛋白的“ELISA”法检测抗核抗体的研究

本文报告用鞣化载体酶联 A 蛋白的“ELISA”法检测 DNA 抗体的研究。以OD 值492nm>0.14为阳性,对60例正常人和104例自身免疫病、心血管病及非免疫性疾病患者的1:25倍稀释血清进行了检测。上述同样标本也用免疫荧光法检测进行比较。酶标法阳性率为69.1%,荧光法阳性率为47.6%,提示酶标法比荧光法有较高的敏感性。本文也对其影响因素进行了探讨。结果显示该法对检测抗核抗体是一种简便、快速、特异、敏感的方法,其 OD 值的测定又具有定性与定量的双重     

A fast atom bombardment-mass spectrometric method to quantitate lysophosphatidylserine in rat brain

A method to quantitate lysophosphatidylserine by fast atom bombardment-mass spectrometry using 1-hexa-decanoyl-sn-glycero-3-phospho-L-serine as internal standard is described. The standard curve is linear with a correlation coefficient r2 = 0.999 from 10 to 1000 ng. This curve has been used to quantitate LPS in rat brain using phosphorus assay as a test control. We found 475 +/- 70 ng of LPS in 1 mg of tissue (n = 3). This method presents advantages due to its sensitivity and its capability to give molecular information of the unmodified compound.     

TTX-sensitive Na(+) and nifedipine-sensitive Ca(2+) channels in rat vas deferens smooth muscle cells.

The inward currents in single smooth muscle cells (SMC) isolated from epididymal part of rat vas deferens have been studied using whole-cell patch-clamp method. Depolarising steps from holding potential -90 mV evoked inward current with fast and slow components. The component with slow activation possessed voltage-dependent and pharmacological properties characteristic for Ca(2+) current carried through L-type calcium channels (I(Ca)). The fast component of inward current was activated at around -40 mV, reached its peak at 0 mV, and disappeared upon removal of Na ions from bath solution. This current was blocked in dose-dependent manner by tetrodotoxin (TTX) with an apparent dissociation constant of 6.7 nM. On the basis of voltage-dependent characteristics, TTX sensitivity of fast component of inward current and its disappearance in Na-free solution it is suggested that this current is TTX-sensitive depolarisation activated sodium current (I(Na)). Cell dialysis with a pipette solution containing no macroergic compounds resulted in significant inhibition of I(Ca) (depression of peak I(Ca) by about 81% was observed by 13 min of dialysis), while I(Na) remained unaffected during 50 min of dialysis. These data draw first evidence for the existence of TTX-sensitive Na(+) current in single SMC isolated from rat vas deferens. These Na(+) channels do not appear to be regulated by a phosphorylation process under resting conditions.     

生化快速检测技术诊断需氧菌阴道炎的临床评价

目的 探讨生化快速检测法在诊断需氧菌阴道炎中的临床价值.方法 分别使用镜检法和生化快速检测法对320例疑似需氧菌阴道炎患者的阴道分泌物进行检查.结果 在320例就诊者中,生化快速检测法检出阳性患者286例,镜检法检出阳性患者283例.两种方法的符合率为96.56％[ (279+ 30)/320],二者呈高度一致性( Kappa=0.823,P＜0.05).以镜检法为诊断标准,生化快速检测法的敏感度为98.59％( 279/283)、特异度为81.08％(30/37)、阳性预测值为97.55％(279/286)、阴性预测值为88.24％(30/34).结论 生化快速检测法对需氧菌阴道炎的诊断具有较高的敏感度和特异度,值得临床推广使用.     

Accelerated Profile HMM Searches

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the "multiple segment Viterbi" (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call "sparse rescaling". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.     

Improved Coomassie Blue Dye-Based Fast Staining Protocol for Proteins Separated by SDS-PAGE

The time required to visualize proteins using Coomassie Blue dye has been significantly reduced with the introduction of fast staining protocols based on staining with a Coomassie Blue dye solution at boiling temperatures. However, fast stainings suffer from high gel backgrounds, reducing the signal-to-noise ratio and limiting the number of detectable spots in the case of 2D SDS-PAGE. The aim of this work was to eliminate the high gel background, and thus improve fast staining protocols based on Coomassie Blue dye. We show that merely replacing water with a 4 mM EDTA washing solution at boiling temperatures, results in a transparent gel background within 50 to 60 minutes of destaining. Moreover, when a combination of imidazole-zinc reverse staining and Coomassie Blue-based fast staining is used the sensitivity is improved significantly; nanogram amounts of proteins can be detected using 1D SDS-PAGE, and about 30% to 60% more spots can be detected with 2D SDS-PAGE in plasma, platelet, and rat brain tissue samples. This work represents an optimized fast staining protocol with improved sensitivity, requiring between 60 to 75 minutes to complete protein visualization.     

Kinetic analysis of the metal binding mechanism of Escherichia coli manganese superoxide dismutase

The acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (MnSOD). In this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of Escherichia coli MnSOD in vitro, permitting a detailed kinetic characterization of the uptake mechanism. Apo-MnSOD metallation kinetics are "gated", zero order in metal ion for both the native Mn2+ and a nonnative metal ion (Co2+) used as a spectroscopic probe to provide greater sensitivity to metal binding. Cobalt-binding time courses measured over a range of temperatures (35-50 degrees C) reveal two exponential kinetic processes (fast and slow phases) associated with metal binding. The amplitude of the fast phase increases rapidly as the temperature is raised, reflecting the fraction of Apo-MnSOD in an "open" conformation, and its temperature dependence allows thermodynamic parameters to be estimated for the "closed" to "open" conformational transition. The sensitivity of the metallated protein to exogenously added chelator decreases progressively with time, consistent with annealing of an initially formed metalloprotein complex (k anneal = 0.4 min(-1)). A domain-separation mechanism is proposed for metal uptake by apo-MnSOD.     

Ammonium formate, a compound for sensitive EPR dosimetry

Alanine EPR dosimetry has been applied successfully when measuring intermediate and high radiation doses. Although the performance of alanine dosimetry is being improved, the sensitivity of the material is too low for a fast and simple low- dose determination. Here we present the results using ammonium formate as an EPR dosimeter material. Ammonium formate is seven times more sensitive than alanine, using spectrometer settings optimized for the latter. Deuterated ammonium formate is found to be more than eight times more sensitive than alanine. Analysis of signal stability with time shows that the ammonium formate signal is stable by 5 min after irradiation and that no change in signal intensity is found during 8 days. The atomic composition of ammonium formate is closer to that of tissue than alanine, and thus the energy dependence is smaller than that of alanine at photon energies below 200 keV. Power saturation studies indicate that the energy transfer between the spins and the lattice is fast in ammonium formate, which gives the possibility of using high microwave power without saturation to further increase the sensitivity. These results suggest that ammonium formate has some important properties required of an EPR dosimeter for applications in dosimetry in the dose range typical for radiation therapy.     

Quantitative analysis of gene expression with an improved green fluorescent protein. p6.

The fast and easy in vivo detection predestines the green fluorescent protein (GFP) for its use as a reporter to quantify promoter activities. We have increased the sensitivity of GFP detection 320-fold compared to the wild-type by constructing gfp+, which contains mutations improving the folding efficiency and the fluorescence yield of GFP+. Twelve expression levels were measured using fusions of the gfp+ and lacZ genes with the tetA promoter in Escherichia coli. The agreement of GFP+ fluorescence with beta-galactosidase activities was excellent, demonstrating that the gfp+ gene can be used to accurately quantify gene expression in vivo. However, expression of the gfp+ gene from the stronger hsp60 promoter revealed that high cellular concentrations of GFP+ caused an inner filter effect reducing the fluorescence by 50%, thus underestimating promoter activity. This effect is probably due to the higher absorbance of cells containing GFP+. Thus promoters with activities differing by about two orders of magnitude can be correctly quantified using the gfp+ gene. Possibilities of using GFP variants beyond this range are discussed.     

An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis

MOTIVATION: Structural templates consisting of a few atoms in a specific geometric conformation provide a powerful tool for studying the relationship between protein structure and function. Current methods for template searching constrain template syntax and semantics by their design. Hence there is a need for a more flexible core algorithm upon which to build more sophisticated tools. Statistical analysis of structural similarity is still in its infancy when compared with its analogue in sequence alignment. In the context of template matching, there is an urgent need for normalization of scores so that results from templates with differing sensitivity may be compared directly. RESULTS: We introduce Jess, a fast and flexible algorithm for searching protein structures for small groups of atoms under arbitrary constraints on geometry and chemistry. We apply the algorithm to a set of manually derived enzyme active site templates, and derive an empirical measure for estimating the relative significance of hits encountered using differing templates.     

Nonprolyl cis peptide bonds in unfolded proteins cause complex folding kinetics

Folding of tendamistat, an inhibitor of alpha-amylase, is a fast two-state process accompanied by two minor slow reactions, which were assigned to prolyl isomerization. In a proline-free variant, 5% of the molecules still fold slowly with a rate constant of 2.5 s(-1). This reaction is caused by a slow equilibrium between two populations of unfolded molecules. The time constant for this equilibration process, its sensitivity to LiCl and its temperature dependence identify it as a cis-trans isomerization of nonprolyl peptide bonds. Although nonprolyl peptide bonds have the cis conformation populating only approximately 0.15% in unfolded proteins, their large number generates a significant fraction of slow-folding molecules. This emphasizes that heterogeneous populations in an unfolded protein can induce complex folding kinetics on various time scales.