基于DIG -化学发光法的Southern blot方法优化

目前,基于DIG-化学发光法的Southern blot技术已在生物实验室广泛应用,但在试验过程中经常会遇到背景黑、目的信号弱等问题,以致不能获得理想结果.在棉花线拉体基因组RFLP分析过程中结合前人经验对基于DIG -化学发光法的Southern blot技术在探针标记、探针浓度、探针剥高等方面进行了优化.优化后的方...     

Efficient mRNA detection from human archival paraffin-embedded tissue: An update

We recently published an in situ hybridization protocol for archival tissue using a commercial hybridization buffer. This buffer is no more available. Therefore, we have developed an improved protocol with a defined hybridization buffer.     

Cooperativity of paired oligonucleotide probes for microarray hybridization assays

Synthetic DNA probes attached to microarrays usually range in length from 25 to 70 nucleotides. There is a compromise between short probes with lower sensitivity, which can be accurately synthesized in higher yields, and long probes with greater sensitivity but lower synthesis yields. Described here are microarrays printed with spots containing a mixture of two short probes, each designed to hybridize at noncontiguous sites in the same targeted sequence. We have shown that, for a printed microarray, mixed probe spots containing a pair of 30mers show significantly greater hybridization than spots containing a single 30mer and can approach the amount of hybridization to spots containing a 60mer or a 70mer. These spots with mixed oligonucleotide probes display cooperative hybridization signals greater than those that can be achieved by either probe alone. Both the higher synthesis yields of short probes and the greater sensitivity of long oligonucleotides can be utilized. This strategy provides new design options for microarray hybridization assays to detect RNA abundance, RNA splice variants, or sequence polymorphisms.     

人βNGFDNA地高辛标记探针的制备及在小鼠颌下腺中的基因表达

本研究在国内首先制备非放射性地高辛标记的人βＮＧＦＤＮＡ（ｄｉｇ－ｈ－βＮＧＦＤＮＡ）探针,并应用原位杂交技术结合计算机图像分析,对ＮＧＦｍＲＮＡ在ＩＣＲ雄性小鼠颌下腺中的分布进行了观察。实验结果显示ＮＧＦｍＲＮＡ主要分布于颌下腺纹状管（ＳＳＴ）和颗粒曲管（ＧＣＴ）的上皮细胞,其细胞基底部胞质呈杂交反应强阳性,细胞顶部呈弱阳性,图像分析显示二者具有显著性差异。本实验制备的ｄｉｇ－ｈ－βＮＧＦＤＮＡ探针灵敏度高达０．１ｐｇ／ｍｌ,并且特异性强,分辨力高,重复性好,是研究ＮＧＦｍＲＮＡ基因表达和调控的有力工具。     

生物素标记寡核苷酸探针检测B群轮状病毒

用５′端接氨基标记法,用生物素对Ｂ群轮状病毒（ＧＢＲＶ）ＩＤＩＲ株具有群特异性的３片段基因上２３ｂｐ寡核苷酸序列进行标记,经高效薄层层析板（ＨＰＴＬＣ）纯化,制备了Ｂ群轮状病毒生物素寡核苷酸探针,探针显色灵敏度达１０Ｐｇ,与ＧＢＲＶ、ＫＢ６３株基因杂交可检测到１００ｐｇ靶序列,而与Ａ群和Ｃ群轮状病毒及无关基因均不产生杂交信号,该探针可用于Ｂ群轮状病毒的检测、鉴定,以及同群不同毒株间基因相关性研究。     

Alaskan marine mammal tissue archival project

A project to establish an archive of Alaskan marine mammal tissues was conceived in 1987 to be a part of the National Biomonitoring Specimen Bank (NBSB). Protocols and field collection of marine mammals, long-term storage, and analysis are summarized in this paper. Instrumental neutron activation analysis has been used for an initial evaluation of trace element content in samples of northern fur seal (Callorhinus ursinus) from the Pribilof Islands. The findings agree with previously observed trace element levels in northern fur seals. The archived specimens can be used in future studies when comparisons of past and present pollution levels are needed.

     

应用多重标记引物增强寡核苷酸芯片的荧光信号强度

寡核苷酸芯片技术是一种高通量发掘和采集生物信息的强大技术平台,目前已广泛应用于生物科学领域 . 为改善寡核苷酸芯片的分析性能,对影响芯片杂交结果的因素,如片基表面的化学处理、探针的长度、间隔臂的长度、杂交条件等,进行了深入的研究和优化 . 对寡核苷酸芯片而言,仍有待解决的问题是如何产生更强的荧光信号来改善其检测灵敏度 . 利用两种类型的多个荧光分子标记的引物,来增强二维寡核苷酸芯片平面上的荧光信号强度 . 两种引物分别命名为：多标记线性引物和多标记分支引物 . 通过增加标记在目标 DNA 片段上的荧光分子数,可以显著增强寡核苷酸芯片上相应捕获探针的信号强度 . 实验表明,使用多标记引物能将所用的寡核苷酸微阵列的检测限 ( 以能够检测的最低模板量计算 ) 降低至单荧光标记引物的 1/100 以下,多重标记技术是一种有效增强微型化探针矩阵检测灵敏度的信号放大方法 .     

Detection of bladder cancer by multitarget multicolour FISH: comparative analysis on archival cytology and paraffin-embedded tissue

Detection of bladder cancer by multitarget multicolour FISH: comparative analysis on archival cytology and paraffin-embedded tissue We have evaluated the possibility of using the same specimen for both cytological diagnosis and multitarget multicolour FISH (MtMcFISH) analysis in order to determine whether the routinely processed specimens used for diagnosis were also suitable for this ancillary procedure. For this purpose 18 positive samples (11 voided urine and seven bladder washings) were selected, together with a representative section of the corresponding immediately previous or subsequent histological specimens. Two negative cytology slides were added as negative controls. FISH analysis revealed a normal pattern for each probe in the two negative controls and an abnormal pattern in the 18 positive cases. In the latter the same FISH alterations were found in the cytology samples and in the corresponding histological sections, and superimposable cytological/histological features were observed in two cases where two different histology samples were analyzed. The results clearly show that MtMcFISH may be successfully applied to destained routinely processed cytology slides.     

Study of the quality of aminated substrates used for hybridization analysis

A set of methods for analysis of the quality of aminated substrates that could be a basis for the large-scale manufacturing of biological microchips is suggested. The analysis includes the determination of the number of amino groups, their availability for the immobilization of phosphorylated oligonucleotides, and the characterization of surface properties of the substrates in respect to the nonspecific sorption of reagents during hybridization. A simple procedure was suggested for determination of the density/number of amino groups. It is based on the use of dimethoxytrityl chloride with the subsequent spectrophotometric determination of dimethoxytrityl cation. The availability of amino groups was estimated by covalent attachment of an oligonucleotide probe containing a fluorescently labeled group to the aminated surface and the subsequent comparison of the intensity of fluorescing zones formed on the chip. The sorption properties of the surface were investigated with the help of a model hybridization reaction. A comparative analysis of aminated glasses manufactured by various firms and in our laboratory showed that the glasses with the amino group density from 0.7 to 2.0 groups/nm² prepared by our procedure have the best properties for the hybridization analysis.     

Evaluation of hybridization conditions for spotted oligonucleotide-based DNA microarrays

We compared different hybridization conditions of oligonucleotide-based DNA microarray to acquire optimized and reliable microarray data. Several parameters were evaluated at different hybridization conditions, including signal-to-background (S:B) ratios, signal dynamic range, usable spots, and reproducibility. Statistical analysis showed that better results were obtained when spotted, presynthesized long oligonucleotide arrays were blocked with succinic anhydride and hybridized at 42°C in the presence of 50% formamide.     

An optimized protocol for rapid and sensitive application of southern (Northern) hybridization by using fluorescein labeling and detecting system

An optimized complete protocol that produces consistent Southern hybridization results (RFLP) for as many as 240 samples in 36 h is presented. Signals can be detected from 0.1 g genomic DNA. The protocol can be adapted to Northern hybridization by using 0.05 M NaOH as transfer buffer in a downward blotting method. Probes can be removed in stripping solution containing 2–5 mM EDTA. The protocol using this system has many advantages over the conventional radioactive method as safety, rapidness, sensitivity, and signal quality.     

Changes in the rRNA levels of specific microbial groups in activated sludge during sample handling and storage

AIMS: To quantitatively analyse the changes in group-specific rRNA levels in activated sludge as a function of sample handling and storage procedure. METHODS AND RESULTS: Quantitative membrane hybridizations with (32)P-labelled oligonucleotide probes were used to analyse the effects of different sample handling and storage conditions on the relative rRNA levels of the alpha, beta, and gamma-Proteobacteria, the Cytophaga-Flavobacteria group, and the mycolic acid-containing actinomycetes in activated sludge. Group-specific rRNA levels, expressed as percentages of total 16S rRNA detected with a universal probe, in samples maintained at room temperature significantly changed after 48 h. Group-specific rRNA levels in samples treated with chloramphenicol showed significant change after 72 h. CONCLUSIONS: Sample storage at room temperature is a viable option if freezing or analysis can be performed within 24 h, while treatment with chlorampenicol can extend that time to at least 48 h. SIGNIFICANCE AND IMPACT OF THE STUDY: Handling, shipping, and storage of environmental samples under several conditions may result in inaccurate determination of the microbial populations in microbial ecology studies.     

情感性障碍的遗传异质性研究啊

对10省市的548例情感性障碍患者进行了遗传异质性的分析。结果表明,抑郁症在发病年龄上存在异质性,提示抑郁症可能存在着早发和晚发二类亚型。又经亲属相关性的分析,表明抑郁症或单次躁狂发作均与双相情感性障碍之间存在着遗传异质性,支持了Lconhard（1959）（3）将该症区分为单相型和双相型观点。     

肽核酸相关技术在杂交检测中的应用

肽核酸是一种寡核苷酸的类似物,它是由丹麦哥本哈根大学的Ｎｉｅｌｓｅｎ、Ｅｇｈｏｌｍ等人首先发明合成的。肽核酸与传统的寡核苷酸相比,骨架结构发生了根要变化。肽核酸的电中性骨架有许多ＤＮＡ所不具备的性质,例舅高灵敏度、高特异性、非盐依赖性等,从而使它成为一种优良的寡核苷酸的取代物,尤其是杂交检测领域。     

Novel isosteric, isopolar phosphonate analogs of oligonucleotides: preparation and properties

A synthetic approach leading to novel-type modified oligothymidylates containing an isosteric, isopolar, enzyme-stable C3'-O-P-CH(2)-O-C4' phosphonate alternative to phosphodiester internucleotide bond was elaborated. The suitable monomers were prepared from 4'-phosphonomethoxy derivatives of alpha-L-threo and beta-D-erythro-2',5'-dideoxythymidine, which were considered interesting as structurally related to nucleoside 5'-monophosphates. The phosphotriester method was applied to the automated synthesis of both homooligomeric phosphonate 15-mer chains and alternating phosphonate-phosphate constructs. The fully modified homooligomers did not hybridize while homooligomers with alternating sequences containing alpha-L-threo-configured units (but not beta-D-erythro-) showed a significant decrease in T(m) values in comparison with natural dT(15). For a comparative study, phosphodiester 4'-CH(3)-substituted oligothymidylate was synthesized and physical studies (NMR, CD, MDS modeling) were undertaken to shed more light on the changes in conformational behavior arising from the chosen structural alterations.     

The quenching of electrochemiluminescence upon oligonucleotide hybridization.

Many genomic assays rely on a distance-dependent interaction between luminescent labels, such as luminescence quenching or resonance energy transfer. We studied the interaction between electrochemically excited Ru(bpy)(3) (2+) and Cy5 in a hybridization assay on a chip. The 3' end of an oligonucleotide was labelled with Ru(bpy)(3) (2+) and the 5' end of a complementary strand with Cy5. Upon the hybridization, the electrochemiluminescence (ECL) of Ru(bpy)(3) (2+) was efficiently quenched by Cy5 with a sensitivity down to 30 nmol/L of the Cy5-labelled complementary strand. The quenching efficiency is calculated to be 78%. A similar phenomenon was observed in a comparative study using laser-excitation of Ru(bpy)(3) (2+). The hybridization with the non-labelled complementary or labelled non-complementary strand did not change the intensity of the ECL signal. Resonance energy transfer, electron transfer and static quenching mechanisms are discussed. Our results suggest that static quenching and/or electron transfer are the most likely quenching mechanisms.     

Organometallic Intermediates in the Synthesis of Nucleoside Analogs

Abstract

The common nucleosides, modified or derivatized in some way at the heterocyclic ring carbons, include examples of structures which a r e useful as biological probes and chemotherapeutic agents. Like previous authors, we will use the term “nucleoside analog” for structures related to one of the common naturally occurring nucleosides. Nucleosicle analogs can be derivatives which differ by such minor modification as replacement of hydrogen by a single atom or derivatives which are grossly modified at both the carbohydrate and the base. Examples of the former include 5-fluoro-2′-deoxyuridine, an inhibitor of thymidylate synthetase as its 5′-phosphate, and 5′-iodo-2′-deoxyuridine, a clinically useful antiviral agent. Larger groups have frequently been linked to nucleoside as probes for enzymatic processes. Side chains in “nonrestricted positions” may be used to carry spectroscopic or chemically reactive probes, or provide the means to attach a molecule to an affinity column. Ultimately with positions of bulk tolerance defined, it may be possible to design “active site directed irreversible enzyme inhibitors” as defined by B.R. Baker. Nucleoside structures in which a side chain is attached at a pyrimidine or purine carbon will undoubtedly, in some instances be the most appropriate structure. Yet, these have typically been more difficult to synthesize than analogs with side chains attached to heteroatoms.     

Analysis of bacterial community structure in bulk soil by in situ hybridization

In situ hybridization with rRNA-targeted, fluorescent (Cy3-labeled) oligonucleotide probes was used to analyze bacterial community structure in ethanol- or paraformaldehyde-fixed bulk soil after homogenization of soil samples in 0.1% pyrophosphate by mild ultrasonic treatment. In ethanol-fixed samples 37 ± 7%, and in paraformaldehyde 41 ± 8% of the 4′, 6-diamidino-2-phenylindole(DAPI)-stained cells were detected with the bacterial probe Eub338. The yield could not be increased by enzymatic and/or chemical pretreatments known to enhance the permeability of bacterial cells for probes. However, during storage in ethanol for 7 months, the detectability of bacteria increased in both ethanol- and paraformaldehyde-fixed samples to up to 47 ± 8% due to an increase in the detection yield of members of the α-subdivision of Proteobacteria from 2 ± 1% to 10 ± 3%. Approximately half of the bacteria detected by probe Eub338 could be affiliated to major phylogenetic groups such as the α-, β-, γ-, and δ-subdivisions of Proteobacteria, gram-positive bacteria with a high G+C DNA content, bacteria of the Cytophaga-Flavobacterium cluster of the CFB phylum, and the planctomycetes. The analysis revealed that bacteria of the α- and δ-subdivision of Proteobacteria and the planctomycetes were predominant. Here, members of the α-subdivision of Proteobacteria accounted for approximately 10 ± 3% of DAPI-stained cells, which corresponded to 44 ± 16 × 10⁸ cells (g soil, dry wt.)^–1, while members of the δ-subdivision of Proteobacteria made up 4 ± 2% of DAPI-stained cells [17 ± 9 × 10⁸ cells (g soil, dry wt.)^–1]. A large population of bacteria in bulk soil was represented by the planctomycetes, which accounted for 7 ± 3% of DAPI-stained cells [32 ± 12 × 10⁸ cells (g soil, dry wt.)^–1]. The detection of planctomycetes in soil confirms previous reports on the occurrence of planctomycetes in soil and indicates a yet unknown ecological significance of this group, which to date has never been isolated from terrestrial environments. Received: 29 March 1997 / Accepted: 28 May 1997