Assessment of cytoplasmic contaminations in isolated vacuole preparations

A method for testing the purity of isolated vacuoles is proposed. Preparations of isolated vacuoles often contain “impure vacuoles,” namely, vacuoles contaminated with some cytoplasmic remnants. Such impure vacuoles are stained by the vital fluorescent dye fluorescein-diacetate. Vacuoles enclosed only by the tonoplast, “naked vacuoles,” do not stain.     

A new method for automatic metaphase finding adaptable to different chromosome preparations

A FORTRAN computer program, running on a Digital PDP 11-34 minicomputer, has been developed for use in conjunction with a Cambridge Quantimet 720 image analyzer for the investigation of metaphase preparations in routine cytogenetics. During a short initiation phase the program is adapted to the type of metaphase being analyzed. The program is fast and its performance is good, even at low microscopic magnifications. It has other uses in biology for all investigations and characterizations of small distinct elements widely spread within a preparation (e.g., autoradiography, bacteriology).     

A simple two-step, 'hit and fix' method to generate subtle mutations in BACs using short denatured PCR fragments

The bacteriophage lambda recombination system has proven to be a valuable tool for engineering bacterial artificial chromosomes (BAC). Due to its high efficiency, subtle alterations in the BACs can be generated using oligonucleotides as targeting vectors. Since no selection marker is used, recombinant clones are identified utilizing a selective PCR screening method. However, occasionally the selective PCR screening is not feasible. We describe here a two-step 'hit and fix' method that can be reliably used for generating any subtle alteration in BACs using short denatured PCR fragments as targeting vectors. In the first step of this method, 6-20 nucleotides are changed around the base where the mutation has to be generated. In the second step, these altered nucleotides are reverted to the original sequence and simultaneously a subtle alteration is introduced. Since in each step several nucleotides are changed, PCR primers specific for such alterations can be designed. This two-step method provides a simple and efficient tool for generating subtle alterations in BACs that can be very valuable for functional analysis of genes.     

Detection of mycoplasma contaminations in cell cultures by PCR analysis

Mycoplasma contamination is still one of the main problems in using cell cultures in biological and medical research and in the production of bioactive substances, because mycoplasma can alter nearly all parameters and products of the cell. They can persist undetected in the culture if no special detection methods are applied. In recent years, the PCR technology has become a commonly used method to analyze genomic DNA and the expression of genes, with both high specificity and sensitivity. This technique can be effectively employed for the detection and even the identification of mycoplasma contaminations in cell cultures applying primers complementary to the 16S rDNA region. Although this technique, once established, is characterized by simplicity and speed, PCR is still a complex process and its sensitivity and specificity can be influenced by a number of different parameters, e.g. inhibiting compounds originating from the preparation process of the DNA, RNA or cDNA, contamination of the solutions with PCR products, and the selection of a primer pair which does not cover all the mycoplasma species occurring in cell cultures. Thus, adequate controls have to be included to obtain reliable results. The present review examines the use of different primers of the 16S rDNA region including their specificity, the sensitivity applying various DNA or RNA preparation procedures, and the methods to detect finally the amplicons. In conclusion, basic nucleic acid preparation and PCR product detection methods offer a simple, fast and reliable technique for the examination of mycoplasma contaminations in cell cultures, provided that the indispensable control assays are implemented.     

A simple and loss-free method to remove TRIzol contaminations from minute RNA samples

Acid guanidium phenol preparations such as TRIzol allow the reproducible isolation of high-quality total RNA from various sources. However, if applied to minimal sample sizes, the quality parameters of the isolated RNA are often low. Here we present an approach to improve the 260/280- and 230/260-nm ratios of such preparations as well as the ratio of the 18S/28S RNA. A simple extraction with 1-butanol eliminates smearing of the 28 S RNA and restores the characteristic ultraviolet (UV) spectrum of highly purified RNA. Application of the method is demonstrated for fluorescence-activated cell sorting (FACS)-sorted cells where the population of interest is often small.     

人血基因组PCR扩增模板的制血及其保存

建立一种简单的人血基因组PCR反应扩增模板制备及其保存方法,用于α-globin基因HS40位点扩增。     

A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition

Background  

Real-time PCR analysis is a sensitive DNA quantification technique that has recently gained considerable attention in biotechnology, microbiology and molecular diagnostics. Although, the cycle-threshold (Ct) method is the present "gold standard", it is far from being a standard assay. Uniform reaction efficiency among samples is the most important assumption of this method. Nevertheless, some authors have reported that it may not be correct and a slight PCR efficiency decrease of about 4% could result in an error of up to 400% using the Ct method. This reaction efficiency decrease may be caused by inhibiting agents used during nucleic acid extraction or copurified from the biological sample.     

A new technique to prevent self-ligation of DNA

The most widely used technique for preventing self-ligation (self-circularization and concatenation) of DNA is dephosphorylation of the 5'-end, which stops DNA ligase from catalyzing the formation of phosphodiester bonds between the 3'-hydroxyl and 5'-phosphate residues at the DNA ends. The 5'-dephosphorylation technique cannot be applied to both DNA species to be ligated and thus, the untreated DNA species remains capable of self-ligation. To prevent this self-ligation, we replaced the 2'-deoxyribose at the 3'-end of the untreated DNA species with a 2',3'-dideoxyribose. Self-ligation was prevented at the replaced 3'-end, while the 5'-phosphate remaining at the 5'-end permitted ligation with the 3'-hydroxyl end of the 5'-dephosphorylated DNA strand. We successfully applied this 3'-replacement technique to gene cloning, adapter-mediated polymerase chain reaction and messenger RNA fingerprinting. The 3'-replacement technique is simple and not restricted by sequence or conformation of the DNA termini and is thus applicable to a wide variety of methods involving ligation.     

A new approach to enhance PCR specificity

A new approach to enhanced specificity and product yield of polymerase chain reaction is proposed. It is based on control of DNA polymerase activity during PCR by changing the magnesium ion concentration, which depends on the temperature of the reaction mixture. A slightly soluble magnesium salt, magnesium oxalate, whose solubility depends on temperature, was used as a source of magnesium ions. During PCR, magnesium oxalate was maintained at saturating concentration by the presence of an insoluble excess of this salt, and the concentration of magnesium ions depended on the salt solubility: binding of magnesium ions at lower temperatures and their release at higher temperatures was shown to affect the DNA polymerase activity and to favor the specific PCR amplification of the target DNA fragment.     

实现PCR热启动的一种简便实验室技术

将Taq酶加入热的低熔点琼脂糖凝胶中,趁热将液态的凝胶加入扩增管底部,待凝胶冷却凝固后,Toq酶便得以包埋。扩增过程中只有当温度升高至70℃以上时,凝胶才能融化释放Taq酶,从而实现PCR过程中的热启动。这一方法简单方便、节约经费,是一种值得在实验室大力推广的实用技术。     

A simple two-step, ‘hit and fix’ method to generate subtle mutations in BACs using short denatured PCR fragments

The bacteriophage lambda recombination system has proven to be a valuable tool for engineering bacterial artificial chromosomes (BAC). Due to its high efficiency, subtle alterations in the BACs can be generated using oligonucleotides as targeting vectors. Since no selection marker is used, recombinant clones are identified utilizing a selective PCR screening method. However, occasionally the selective PCR screening is not feasible. We describe here a two-step ‘hit and fix’ method that can be reliably used for generating any subtle alteration in BACs using short denatured PCR fragments as targeting vectors. In the first step of this method, 6–20 nucleotides are changed around the base where the mutation has to be generated. In the second step, these altered nucleotides are reverted to the original sequence and simultaneously a subtle alteration is introduced. Since in each step several nucleotides are changed, PCR primers specific for such alterations can be designed. This two-step method provides a simple and efficient tool for generating subtle alterations in BACs that can be very valuable for functional analysis of genes.     

A FRET-based method to study protein thiol oxidation in histological preparations

Cysteine residues in proteins have important biological roles. For example, disulfide bonds are important structural elements; additionally, reversible oxidation of thiols to disulfides functions as a molecular switch and constitutes an early response to oxidative damage. Because organs are heterogeneous structures composed of diverse cell types, there is a compelling need for a histological approach to investigate thiol oxidation in situ in order to address the role of specific cell types in oxidative imbalance. Here we describe a fluorescence technique-which can be used in association with standard immunological staining procedures-to detect variations in disulfides in histological preparations. Moreover, by monitoring the fluorescence resonance energy transfer (FRET) between a labeled specific primary antibody and the thiol probe described here, this method can detect thiol oxidation in candidate proteins of interest. When applied to an animal model of Parkinson's disease, our technique demonstrated that thiol oxidation occurs selectively in the dopaminergic neurons of the substantia nigra, the same neurons that are lost selectively in the disease. In summary, this technique provides a new, powerful tool for providing further understanding of oxidative imbalance, a phenomenon common to many diseases.