多等位基因PCR-SSO反相杂交法及其在HLA-DR_4亚型结构分析中的应用

本文介绍一种适合于多等位基因定型和结构分析的反相顺序特异性寡核苷酸探针杂交方法。将化学合成的多种探针分别经脱氧核苷末端转移酶(TdT)催化,于3′端加上100个以上碱基的Poly(dT)尾,然后将各探针分别以斑点固定于同一张尼龙膜上。用PCR法对该基因位点进行扩增,扩增的同时加入α-~(32)P-dCTP以直接参入放射标记,然后将PCR产物与膜固定探针杂交,以四甲基氯化铵根据探针长度统一洗涤温度。该方法克服了以往对同一份样品进行多个等位基因检测时需要进行多次探针标记和杂交的缺点。我们用该方法对中国人群MHC-Ⅱ类DR4多等位基因进行了研究。     

Typing of methicillin-resistant Staphylococcus aureus with IS256

A simple one-step procedure is described for specifically amplifying and labelling insertion element IS256 which is associated with the gentamicin-resistance transposon Tn4001. The product has been used to probe DNA digests of methicillin-resistant Staphylococcus aureus. The resulting restriction fragment length polymorphisms were found to be able to distinguish isolates which were indistinguishable by other typing methods. The probe also hybridised with methicillin-resistant Staphylococcus aureus which were isolated before the emergence of gentamicin resistance, demonstrating its usefulness in typing species other than those that are gentamicin-resistant.     

New Labelling Technology for Molecular Probes Applied to the Ligation Detection Reaction–Universal Array System

The ligation detection reaction (LDR) associated with universal arrays (UA) uses a fluorescently labelled probe (DP) and a Zip Code-extended probe to detect single nucleotide polymorphisms in DNA target sequences. When used for genotyping, the LDR-UA technique uses two DPs, each specific to an allele and labelled with a different fluorophore. The fluorescent signals are processed to calculate the genotype. The uneven decay of fluorophores due to ageing and freezing/thawing cycles and the consequent unequal fluoresce level can lead to erroneous genotype calls. To circumvent this problem, an indirect labelling strategy was developed based on the substitution of the fluorophore with allele-specific 22 bp universal labelling sequences (ULS). Labelling is achieved with fluorescently labelled oligos complementary to the ULS (cULS). The strategy improved the uniformity in probe labelling, and generated results comparable to those using direct-labelled probes, as shown by genotyping 22 polymorphic sites in 70 samples with both strategies. This method can be easily implemented in the routine screening with LDR-UA or other techniques. Moreover, the approach results in a significant cost reduction over traditional direct labelling, and offers the possibility to interchange fluorophores and to increase the fluorescent signal by using multiple-labelled cULS.     

Rapid methods of detecting the target molecule in immunohistology using a bioluminescence probe

We demonstrate a novel rapid direct detection method for immunohistochemistry, using a bioluminescent probe. An anti‐CEA antibody‐fused far‐red bioluminescent protein can monitor the accumulation of this type of probe in tumour tissues. The bimodal spectrum (λ_max = 460 and 675 nm) of this bioluminescent probe is extremely stable under different conditions of pH and ion concentration. The sensitivity of our bioluminescent labelling was at the same level of enzymatic labelling, e.g. peroxidase, as an indirect system. Our novel technique is simple and can shorten the pretreatment time of paraffin sections to around 30 min. The utility of our bioluminescent labelling covers all imaging in vitro, in vivo and ex vivo, suggesting that our antibody‐fused bioluminescent probe has the potential to detect tumour antigens with a high sensitivity in routine immune histological examinations. Copyright © 2012 John Wiley & Sons, Ltd.     

Evaluation of non-radioactive labelling and detection of deoxyribonucleic acids: Part one: chemiluminescent methods

The growth of analytical methods for the detection of nucleic acid from various biological samples reflects recent advances in biotechnology development especially in the areas of genetic, infections and cancer diagnosis. The target DNA is detected by hybridization techniques derived from Southern's blotting. However such assays, based on the use of ³²P labelled DNA probes, bring with them the associated problems of handling radioactive materials. In order to overcome these difficulties, a number of chemiluminescent detection methods have recently been developed.These new, alternative probe labelling procedures and chemiluminescent detection methods are easy to use in routine assays performed in research laboratories as well as for medical applications, and can reach the level of sensitivity found in classical radiolabelling techniques.The techniques investigated include peroxydase, biotin 16-dUTP or digoxigenin 11-dUTP probe labelling. The target DNAs are transferred onto nitrocellulose or nylon membranes and further fixed by heat or UV crosslinking. Specific hybridization on the target DNA is finally revealed by the use of chemiluminescent substrates. For all these techniques the detection limit is 10 aM (attomol) of a 561 bp target DNA. However for the probes labelled with peroxydase and with digoxigenin the detection limit drops to 1.0 aM of the target DNA. In the present paper we shall compare several of these DNA labelling and detection procedures and show that the detection threshold can vary by as much as a factor of 20 from method to method. This is the first time that various chemiluminescent methods for label and detection of DNA are compared and evaluated in order to determine the best protocol.     

An efficient method for the physical mapping of transgenes in barley using in situ hybridization.

The genetic transformation of crops by particle bombardment and Agrobacterium tumefaciens systems have the potential to complement conventional plant breeding programmes. However, before deployment, transgenic plants need to be characterized in detail, and physical mapping is an integral part of this process. Therefore, it is important to have a highly efficient method for transgene detection by fluorescence in situ hybridization (FISH). This study describes a new approach, which provides efficient control of probe length and labelling, both of which play an important role in in situ hybridization of transgenes. The approach is based on reducing the size of the plasmid prior to labelling by nick translation, rather than using the whole or linearized plasmid, or varying the amounts of DNaseI in the nick translation mixture. This provided much more efficient labelling of the probe, which yielded optimal hybridization. minimal fluorescent background, and accurate physical location of the transgene.     

The use of a ribosomal RNA targeted oligonucleotide probe for fluorescent labelling of viable Cryptosporidiumparvum oocysts

A fluorescence in situ hybridization (FISH) technique has been developed for the fluorescent labelling of Cryptosporidium parvum oocysts in water samples. The FISH technique employs a fluorescently labelled oligonucleotide probe (Cry1 probe) targeting a specific sequence in the 18S ribosomal RNA (rRNA) of C. parvum. Hybridization with the Cry1 probe resulted in fluorescence of sporozoites within oocysts that were capable of excystation, while oocysts that were dead prior to fixation did not fluoresce. Correlation of the FISH method with viability as measured by in vitro excystation was statistically highly significant, with a calculated correlation coefficient of 0·998. Examination of sequence data for Cryptosporidium spp. other than C. parvum suggests that the Cry1 probe is C. parvum -specific. In addition, 19 isolates of C. parvum were tested, and all fluoresced after hybridization with the Cry1 probe. Conversely, isolates of C. baileyi and C. muris were tested and found not to fluoresce after hybridization with the Cry1 probe. The fluorescence of FISH-stained oocysts was not bright enough to enable detection of oocysts in environmental water concentrates containing autofluorescent algae and mineral particles. However, in combination with immunofluorescence staining, FISH enabled species-specific detection and viability determination of C. parvum oocysts in water samples.     

生物素肼化学标记和DIG标记cDNA探针检测柑桔裂皮病类病毒

分别用生物素肼化学标记和ＤＩＧ标记我国柑桔裂皮病类病毒（ＣＥＶｄ）全长克隆ｃＤＮＡ,用以上探讨对不同来源的的核酸样品进行斑点杂交。两种探针可检出病柑桔总核酸的最低含量久为４００ｎｇ／斑点和８０ｎｇ／斑点;生物素肼标记ＣＥＶｄ－ＤＮＡ探讨针,可检出ＣＥＶｄ－ｃＤＮＡ的最低含量约为１０ｐｇ／斑点,研制的ＣＥＶｄ检测试剂盒能检测出发病和隐性带毒苗木中的ＣＥＶｄ,灵敏、特异、简便、快速。试剂盒已使用于检测     

3′-末端标记法制备乙型肝炎病毒(HBV)直接重复序列(DR)的生物素化的寡核苷酸探针

本文首次报告用3’—末端核苷酸转移酶将生物素—11—dUTP标记到人工合成的21寡核苷酸上,该d(NMP)_(21)与HBV DNA长链缺口区附近的序列互补,并含HBV DNA的直接重复序列(Direct Repeat)。本文对其标记条件、检出方法进行观察比较,找出合适的条件,制成的生物素化d(NMP)_(21)探针可与标准的HBVDNA进行杂交,检测敏感度为25pg。用这种探针可以从乙型肝炎病人血清中检出HBV DNA。     

Direct labelling of BAC-DNA by rolling-circle amplification

Efficient amplification and labelling of probes are crucial for successful sequence detection by fluorescent in situ hybridization (FISH). In particular, chromosome painting to visualize chromosome segments or entire chromosomes by FISH requires large amounts of probes derived from extended templates. There are a number of techniques for probe labelling. The most widespread is nick translation, based on the replicational incorporation of modified nucleotides. Here we demonstrate successful rolling-circle amplification (RCA) of very low amounts of long circular template sequences (single bacterial artificial chromosomes (BACs) or pools of BACs). The amplicons were suitable for labelling by nick translation and subsequent FISH. A novel achievement is the use of RCA for simultaneous amplification and labelling of single BACs or BAC pools in a labour- and cost-effective manner.     

Detection of nerve growth factor and its mRNA by separate and combined immunohistochemistry andin situ hybridization in mouse salivary glands

Summary Intense labelling of secretory cells in the male mouse submandibular gland was observed afterin situ hybridization using mouse nerve growth factor (NGF) cDNA probes. Under the same conditions, sparse less intensely labelled cells were also found in the sublingual gland. Hybridization to a chicken NGF cDNA probe gave weak labelling on the glands in accordance with a weak cross-hybridization between mouse NGF mRNA and chicken NGF cDNA probes, whereas no labelling was seen using pUC9 DNA as a hybridization probe. A combination ofin situ hybridization and immunohistochemistry was also carried out on the same sections of submandibular gland. A good correlation was seen between actively synthesizing and intensely immunoreactive cells in the gland. The technique described here allows the detection of individual cells synthesizing relatively low levels of NGF. The combination ofin situ hybridization and immunocytochemistry on the same section should be particularly useful in cases where NGF is transported away from its site of synthesis.     

Labelling of histone H5 and its interaction with DNA. 1. Histone H5 labelling with fluorescein isothiocyanate

Histone H5 has been labelled with fluorescein isothiocyanate (FITC) with particular attention to the reaction conditions (pH, reaction time and input FITC/H5 molar ratio) and to the complete elimination of non-covalently bound dye. We preferred to use reaction conditions which yielded non-specific uniform labelling rather than specific alpha-NH2 terminal labelling, in order to obtain higher sensitivity in further studies dealing with the detection of perturbation at the binding sites of H5 on DNA. FITC-labelled H5 was further characterized by absorption and circular dichroism spectroscopy, and the fluorescein probe titrated in the 4-8 pH range. The structural integrity of H5 was found to be preserved after labelling. The positive electrostatic potential of the environment in which the FITC probe is embedded in the arginine/lysine-rich tails of H5 is believed to be responsible for the drop of pK of 1 unit found for H5-FITC as compared to free FITC. For the globular part of H5, the pK of covalently-bound FITC was only slightly lowered; this is a consequence of the much lower content in positively-charged amino-acid side chains in this region.     

An Integrated Tool to Study MHC Region: Accurate SNV Detection and HLA Genes Typing in Human MHC Region Using Targeted High-Throughput Sequencing

The major histocompatibility complex (MHC) is one of the most variable and gene-dense regions of the human genome. Most studies of the MHC, and associated regions, focus on minor variants and HLA typing, many of which have been demonstrated to be associated with human disease susceptibility and metabolic pathways. However, the detection of variants in the MHC region, and diagnostic HLA typing, still lacks a coherent, standardized, cost effective and high coverage protocol of clinical quality and reliability. In this paper, we presented such a method for the accurate detection of minor variants and HLA types in the human MHC region, using high-throughput, high-coverage sequencing of target regions. A probe set was designed to template upon the 8 annotated human MHC haplotypes, and to encompass the 5 megabases (Mb) of the extended MHC region. We deployed our probes upon three, genetically diverse human samples for probe set evaluation, and sequencing data show that ∼97% of the MHC region, and over 99% of the genes in MHC region, are covered with sufficient depth and good evenness. 98% of genotypes called by this capture sequencing prove consistent with established HapMap genotypes. We have concurrently developed a one-step pipeline for calling any HLA type referenced in the IMGT/HLA database from this target capture sequencing data, which shows over 96% typing accuracy when deployed at 4 digital resolution. This cost-effective and highly accurate approach for variant detection and HLA typing in the MHC region may lend further insight into immune-mediated diseases studies, and may find clinical utility in transplantation medicine research. This one-step pipeline is released for general evaluation and use by the scientific community.     

A fluorescence-based method for the detection of adhesive properties of lactic acid bacteria to Caco-2 cells

AIMS: The ability of probiotic micro-organisms to adhere to the intestinal surface is regarded as a substantial advantage in terms of bacteria persistence in the gastrointestinal tract. The aim of the present study was the development of a method based on fluorescent staining of bacteria and subsequent spectrofluorimetric detection to quantify the adhesion of several strains of Lactobacillus and Bifidobacterium to Caco-2 cells. METHODS AND RESULTS: Lactic acid bacteria strains were subjected to fluorescent staining using the viable probe carboxyfluorescein diacetate and subsequently incubated on Caco-2 monolayers. The adhesion of the micro-organisms was determined by spectrofluorimetry following the lysis of the attached bacterial cells and expressed as adhesion percentage. The values obtained for the micro-organisms tested ranged from 4% for Bifidobacterium infantis Bi1 to 10% for a Bifidobacterium mixture containing three different strains. CONCLUSIONS: In the present study we successfully applied fluorescent labelling and fluorimetric detection to investigate the adhesive properties of some Lactobacillus and Bifidobacterium strains and a Bifidobacterium mixture to Caco-2 cells. SIGNIFICANCE AND IMPACT OF THE STUDY: The results proved that fluorescent labelling is suitable for adhesion studies and provides a reliable and safer alternative to radioactive labelling.     

Amplification of the in situ hybridization signal by silver postintensification: the biotin-dUTP-streptavidin-peroxidase diaminobenzidine-silver-gold detection system

Summary Frozen and vibratome sections from the adrenal gland of the rat were hybridized in situ using a biotinylated oligonucleotide probe specific for tyrosine hydroxylase (TH) messenger ribonucleic acid (mRNA). Hybridization was detected using the streptavidin-peroxidase-diaminobenzidine (DAB) system in combination with silver-gold postintensification. The signal appeared as a black coloration and was localized to the cytoplasm of catecholamine-synthesizing chromaffin cells in the adrenal medulla. This coloration was due to the deposition of the silver-gold intensified DAB chromogen onto the probe hybridized to mRNA in carrier organelles. Compared with the conventional peroxidase-DAB labelling, the silver-gold amplified version was more sensitive in detecting TH mRNA. Using this modification, we were able to adapt the procedure to electron microscopy, thereby further localizing the hybridized signal to ribosomes. Because this hybridization detection system produces grains, not just color, this method has the potential for measurement of changes in mRNA levels at the ultrastructural level.     

Highly sensitive and fast detection of Phoma tracheiphila by polymerase chain reaction

Summary A new method for the diagnosis of the plant pathogenic fungus Phoma tracheiphila has been developed. The method takes advantage of the enzymatic amplification of a specific 102 bp-long target sequence of fungal DNA by the polymerase chain reaction (PCR) using Thermus aquaticus DNA polymerase. The amplified DNA was characterized by agarose-gel electrophoresis, molecular hybridization using a synthetic oligonucleotide probe and direct sequencing. The application of the new method makes possible fast and direct detection of the pathogen in lignified plant tissues, a goal not previously achieved when a cloned probe and a dot-blot test were employed. In addition the PCR test can be used to advantage as a particularly simple and fast way of typing fungal isolates. This is achieved by submitting to DNA amplification crude homogenates of fungal mycelium and analysing the amplified DNA on an agarose mini-gel.Offprint requests to: F. Rollo     

Interaction of the fluorescent probe 1,6-diphenyl-1,3,5-hexatriene with biomembranes

The relationship between the conditions of membrane labelling by the fluorescent probe 1,6-diphenyl-1,3,5-hexatriene (DPH) and its fluorescence parameters was investigated. In the labelling solutions prepared by the usual method, the presence of DPH microcrystals was revealed which led to the lower resultant fluorescence anisotropy values. Lower labelling efficiency was observed with DPH solutions in tetrahydrofuran when compared with solutions in acetone. Modifications of the labelling procedure are proposed which give better reproducibility of the results. There modified method involves the preparation of a 2 X 10(-4) mol. 1(-1) DPH stock solution in acetone, a 100-fold dilution in an appropriate buffer, subsequent bubbling through with nitrogen for 30 min and mixing the resulting solution with cell/membrane suspension in a 1:1 (v/v) ratio. Changes in intensity, anisotropy and spectra of DPH fluorescence in the course of membrane labelling were studied. A two-stage model of the incorporation of DPH into membranes was proposed, according to which DPH molecules first quickly adhere to the membrane surface and then are slowly translocated to the apolar regions of the membrane.     

Labelling of Histone H5 and Its Interaction with DNA. 1. Histone H5 Labelling with Fluorescein Isothiocyanate

Abstract

Histone H5 has been labelled with fluorescein isothiocyanate (FITC) with particular attention to the reaction conditions (pH, reaction time and input FITC/H5 molar ratio) and to the complete elimination of non-covalently bound dye. We preferred to use reaction conditions which yielded non-specific uniform labelling rather than specific α-NH₂ terminal labelling, in order to obtain higher sensitivity in further studies dealing with the detection of perturbation at the binding sites of H5 on DNA.

FTTC-labelled H5 was further characterized by absorption and circular dichroism spectroscopy, and the fluorescein probe titrated in the 4–8 pH range. The structural integrity of H5 was found to be preserved after labelling. The positive electrostatic potential of the environment in which the FITC probe is embedded in the arginine/lysine-rich tails of H5 is believed to be responsible for the drop of pK of 1 unit found for H5-FITC as compared to free FITC. For the globular part of H5, the pK of covalently-bound UTC was only slightly lowered; this is a consequence of the much lower content in positively-charged amino-acid side chains in this region.