Genotyping the bovine kappa-casein locus using polymerase chain reaction]

Polymerase chain reaction (PCR) was used for detecting kappa-casein (kappa-casein) genotype in the synthetic breed (Jersey x Black and White x Holstein-Friesian) dairy cattle. The amplified 228 bp fragment includes a region, where relevant mutations lead to both the appearance of different kappa-casein alleles associated with amino acid substitutions and the appearance of new TaqI and HindIII restriction sites in ae-casein B gene. The specificity of the kappa-casein gene fragment amplification was supported by restriction analysis and Southern blot hybridization. Digestion of amplified fragment with endonucleases PstI, HindIII and/or TaqI allows detection of AA-, AB- and BB genotypes of kappa-casein. A total of 32 animals with known (18 samples) and unknown (14 samples) kappa-casein phenotypes were tested using PCR and blot hybridization. In all known cases the detected genotype confirmed the phenotype. Frequencies of the B allele and of the AB genotype in the breeding population are rather high (53.1 +/- 8.8 and 43.7%, respectively). The possibility of effective use of the PCR analysis for genotyping kappa-casein locus in bulls and their offspring has been shown. The advantages of the PCR method in large breeding programs and linkage analysis have been discussed.     

B-cell-negative severe combined immunodeficiency associated with a common γ chain mutation

Severe combined immunodeficiency (SCID) is caused by a variety of underlying defects. Approximately 40% of cases are thought to be of the X-linked type (SCIDX1), which is phenotypically characterised by the absence, or very low numbers, of T cells, but normal or even high B cell numbers. The gene responsible for SCIDX1 is that coding for the common γ chain (γ_c), a component of multiple cytokine receptors. Mutations in this gene have been demonstrated in a large number of boys affected by typical SCIDX1. We describe a sporadic case of a boy who had SCID with absent B cells and absent T cells, but in whom a mutation in the γ_c gene has been demonstrated. In the absence of a typical X-linked pedigree, the phenotype in this boy suggested an autosomal recessive form of SCID and the family would usually have been counselled accordingly. This family raises the question of the true frequency of SCIDX1 amongst sporadic male cases of SCID and highlights the need to screen these boys for γ chain mutations. Received: 4 December 1996     

鲍曼不动杆菌IRS-PCR基因分型研究

目的 用低频限制性位点聚合酶链反应(IRS-PCR)对鲍曼不动杆菌进行基因分型,分析基因型与鲍曼不动杆菌耐药谱的关系,并初步探讨其在分子流行病学中的作用.方法 随机收集2008年8月至2009年8月临床分离的73株鲍曼不动杆菌,采用K-B法进行药物敏感试验确定鲍曼不动杆菌耐药谱;同时利用IRS-PCR对此73株鲍曼不动杆菌进行基因分型;并分析IRS-PCR分型与鲍曼不动耐药谱的关系;结合IRS-PCR分型结果与73株鲍曼不动杆菌感染病例的临床资料,分析在此时间段鲍曼不动杆菌在我院流行感染的情况.结果 药物敏感试验将73株鲍曼不动杆菌菌株分为A1(19株全耐药型)和A2 ～ A31(54株耐药谱型)31个药敏谱.IRS-PCR法将其分为A～W共23个基因型,其中A、C、B、D和E型为5种优势菌株,分别为14、11、10、8和6株.对比研究发现A1型菌株(15/19)主要集中在基因型A、C、D内,而基因型B包含A15型耐药菌株9株(69.2％),基因型E包含A3型耐药菌株3株(42.9％).A基因型在院内特别是ICU中心引起2次爆发流行,而C和D型主要在呼吸内科引起感染.结论 IRS-PCR基因分型与药敏分型有较高的一致性,且IRS-PCR基因分型在早期发现和预防感染暴发流行方面优于药敏分型.     

Apolipoprotein E genotyping using the polymerase chain reaction and allele-specific oligonucleotide primers

A method for apolipoprotein (apo) E genotyping was developed using the polymerase chain reaction (PCR) with allele-specific oligonucleotide primers (ASP). Synthetic oligonucleotides with base-pair mismatches at the 3' terminus were used as primers to amplify the apoE gene in subjects previously phenotyped using isoelectric focusing (IEF). Complementary primer-allele combinations were specifically amplified by PCR, together with a control pair of primers specific to the human prothrombin gene. Identification of genotype by PCR using ASP was consistent with the phenotypes that were determined by IEF for 14 healthy normolipidemic subjects. These results were achieved using DNA isolated from buccal epithelial cells obtained from a mouthwash or DNA extracted from leukocytes. Genotype identification required analysis of the PCR products on an ethidium-stained agarose gel, yielding results 3 h after DNA extraction. In comparison with other current methods, PCR using ASP is suggested as a rapid and simple noninvasive technique for determining population apoE allelic distribution.     

Detection of somatic mosaicism in humans using polymerase chain reaction with random primers

Using the method PCR amplification with random primers, DNA samples from human embryonic organs and tissues were examined. Among 27 oligonucleotide primers tested, 10 primers, producing stable, well-reproducible profiles of amplification products, were chosen for further analysis. With the help of two primers (447 and R45), the differences in RAPD PCR profiles obtained from the tissues of one embryo, were revealed. These differences were associated with the change of mobility, or with the fragment gain/loss in the RAPD profile, and could be caused either by genomic rearrangements, or mutations involving the regions of the DNA-primer pairing. Different epigenetic factors, like methylation, can also play the role in this process.     

Alumorphs--human DNA polymorphisms detected by polymerase chain reaction using Alu-specific primers

The simultaneous analysis of multiple loci could substantially increase the efficiency of mapping studies. Toward this goal, we used the polymerase chain reaction to amplify multiple DNA fragments originating from dispersed genomic segments that are flanked by Alu repeats. Analysis of different human DNA samples revealed numerous amplification products distinguishable by size, some of which vary between individuals. A family study demonstrated that these polymorphic fragments are inherited in a Mendelian fashion. Because of the ubiquitous distribution of Alu repeats, these markers, called "alumorphs," could be useful for linkage mapping of the human genome. A major advantage of alumorphs is that no prior knowledge of DNA sequence of marker loci is required. This approach may find general application for any genome where interspersed repetitive sequences are found.     

Detection of somatic mosaicism in humans using polymerase chain reaction with random primers

Using the method PCR amplification with random primers, DNA samples from human embryonic organs and tissues were examined. Among 27 oligonucleotide primers tested, 10 primers, producing stable, well-reproducible profiles of amplification products, were chosen for further analysis. With the help of two primers (447 and R45), the differences in RAPD PCR profiles obtained from the tissues of one embryo, were revealed. These differences were associated with the change of mobility, or with the fragment gain/loss in the RAPD profile, and could be caused either by genomic rearrangements, or mutations involving the regions of the DNA-primer pairing. Different epigenetic factors, like methylation, can also play the role in this process.     

Leishmania (Viannia) braziliensis: New primers for identification using polymerase chain reaction

The objective of this study was to develop specific primers for Leishmania (Viannia) braziliensis species identification using PCR. The designed primers (LBF1 and LBR1) were evaluated for sensitivity and specificity using various L. (V.) braziliensis serodemes and various Leishmania species and also using Trypanosoma cruzi. A specific fragment of 536 bp was detected from 50 ng of DNA in a crude extract derived from L. (V.) braziliensis. The DNA fragment was not detected when DNA from other Leishmania species or from T. cruzi was used as template in the PCR. Furthermore, when tested with DNA from cutaneous leishmaniasis the designed primers and reaction gave positive results. Taking into consideration that the primers LBF1 and LBR1 could specifically identify L. (V.) braziliensis, they could be considered for use in L. (V.) braziliensis diagnosis and epidemiological studies.     

Differentiation of Trichinella genotypes by polymerase chain reaction using sequence-specific primers.

A method was developed to identify species and genotypes within the genus Trichinella using polymerase chain reaction (PCR) and specific primers. Enzymatic amplification of 2 partially conserved and repetitive genomic DNA sequences that have been shown to be variable in length within the different Trichinella genotypes form the basis of this test. Within these regions of the genome, 4 sets of primers were evaluated from which 2 were chosen for their ability to differentiate among the genotypes under stringent primer annealing conditions while maintaining high yields of amplification product. Differences in the size of PCR products from multiple isolates of each genotype indicate sufficient variation to identify 7 of the 8 parasite groups within this genus. One primer set can differentiate among some genotypes working from a single larva. Identification of Trichinella genotypes will assist in distinguishing between sylvatic and synanthropic life cycles. Such information will be critical in tracing sources of trichinellosis by easily and unambiguously identifying likely host reservoirs and will provide valuable information for instituting methods of control.     

Deletion mutagenesis in M13 by polymerase chain reaction using universal sequencing primers

A simple procedure is described for the efficient deletion of large DNA sequences. The method involves a combination of oligonucleotide-directed mutagenesis in bacteriophage M13 and amplification of the mutagenized product by polymerase chain reaction. In contrast to other protocols employing polymerase chain reaction, synthesis of only one specific primer is required. The efficiency of heteroduplex formation between mutagenic primers directing large deletions and single-stranded template is discussed.     

Comparison of different primers for rapid detection of Vibrio parahaemolyticus using the polymerase chain reaction

AIMS: The aim of this study was to compare different primers for rapid and effective detection of Vibrio parahaemolyticus by polymerase chain reaction (PCR). METHODS AND RESULTS: A total of four pairs of primers, three previously published and one based on a newly developed V. parahaemolyticus metalloprotease (vpm) gene, have been assayed for PCR detection of V. parahaemolyticus. They have been tested for specificity and sensitivity on a total of 101 strains including reference and environment isolates belonging to V. parahaemolyticus and other species in Vibrio. Of the four sets of primers tested, the one designed on the basis of the metalloprotease gene (675 bp) gave optimal results with bacterial strains examined as they only amplified the specific fragment in strains that had been genetically and biochemically assessed as V. parahaemolyticus and the limit of detection was 4 pg of purified target DNA. CONCLUSIONS: The primers designed on the metalloprotease gene gave optimal results for specific, sensitive and rapid detection of V. parahaemolyticus by PCR. SIGNIFICANCE AND IMPACT OF THE STUDY: PCR amplification with the optimal primer set VPM1/VPM2 could facilitate the rapid diagnosis and surveillance of potentially pathogenic strains of V. parahaemolyticus and reduce food-borne illness.     

Quantitative analysis of polymerase chain reaction (PCR) products using primers labeled with biotin and a fluorescent dye

PCR primers covalently labeled with biotin and a fluorescent dye allow immobilization and separation of the products which can be quantitatively analyzed subsequently. The procedure we have developed circumvents electrophoretic separation and radioactive labeling. Exact quantitative analysis of reaction products is feasible during the logarithmic phase of amplification when Taq polymerase is not limiting, as it is during the plateau phase of the reaction. With appropriate standardization the procedure can be used for routine diagnostic purposes.     

Detection of DNA polymorphisms in predatory coccinellids using polymerase chain reaction and arbitrary primers (RAPD-PCR)

DNA polymorphisms were identified in some Coccinellid predators that are being tested as biological control agents against aphids and other insects in North America. The technique employs a variation of the Polymerase Chain Reaction (PCR), called RAPD-PCR, that uses single arbitrarily selected primers to amplify a random group of genomic sequences. Using this technique it was possible to distinguish among laboratory reared colonies of diverse geographic origin. Several colonies each, of three species were examined (Coccinella septempunctata, Hippodamia variegata, andPropylea quatuordecimpunctata). It was also possible to distinguishC. septempunctata from a closely related speciesC. transversoguttata biinterrupta. The technique promises to be a very useful source of markers for maintaining colonies and tracking genes in biological control projects and in identifying species and immature stages of insects.     

Typing of toxic strains of Clostridium difficile using DNA fingerprints generated with arbitrary polymerase chain reaction primers

Clostridium difficile is the causative agent for pseudomembranous colitis in humans. Toxic strains of C. difficile produce two toxins, toxin A and toxin B. A reliable and definitive method of typing the toxic strains of C. difficile is needed since nosocomial cross infection is a primary concern in hospitals and other health care facilities. A method for typing toxic strains of Clostridium difficile using arbitrary polymerase chain reaction (PCR) primers is presented in this study. The C. difficile strains were initially characterized for the toxin A genetic determinant using specific PCR primers which differentiate toxin positive from toxin negative strains. These toxic strains were then PCR typed using six arbitrary primers which generated DNA patterns that were unique for all toxic strains examined. The use of this typing scheme in clinical applications is discussed.     

Monomorphic species specific DNA, detected by polymerase chain reaction with random primers

Intra- and interspecific variability of total DNA isolated from haploid megagametophytes of coniferous species was examined using polymerase chain reaction with random primers. Based on this technique, one can with certainty detect heterozygosity at gene loci carrying null alleles and thus reveal cryptic intraspecific genetic variation. Large population samples were used. Along with random amplified polymorphic DNA, i.e., widely known fragments (amplicons) polymorphic within a species, we found invariant loci lacking individual or geographic variability but differentiating species within genera and other taxa. This DNA was termed RAMD (random amplified monomorphic DNA) to distinguish it from polymorphic DNA. Our findings suggest that genetic monomorphism of species and the dual structure of the eukaryotic genome can be detected at the DNA level as was previously shown for protein gene markers.     

Cross-species amplification of glutamine synthetase cDNA by polymerase chain reaction with degenerate primers

We have developed and optimized a consistent polymerase chain reaction (PCR)-based strategy to quickly obtain specific sequence information on novel plant glutamine synthetase (GS, EC 6.3.1.2) cDNAs. Two sets of degenerate primer pairs were designed to discriminate regions conserved in either any kind of GS messenger or exclusively in those for the chloroplastic GS. Novel GS cDNA sequences were successfully amplified from total RNA obtained from 14 different monocotyledonous and dicotyledonous plants. The procedure, coupled with a further restriction analysis, allowed us to uncover the presence of GS cDNA polymorphism, which most likely stems from the different GS gene family members within a single species. Contrary to previously reported strategies in other systems, GS cDNA oligonucleotide primers were designed keeping the degeneracy level to a minimum, together with a high melting temperature. This approach proved to be particularly effective, generating high yields of the expected products without requiring extra nested amplification steps or time-consuming optimization steps for each species GS cDNA amplification. Different clones containing sequence information from either the coding or the 3'-untranslated regions were further sequenced and characterized, confirming the high sequence identity and size uniformity the of GS cDNAs across higher plant species. Therefore, this approach is proposed as a stand-alone procedure to quickly determine the sequence of unknown GS cDNAs, as well as to speed up and complement classical molecular cloning methodologies.