Polymerase Chain Reaction Primer Sets Research Articles

Development, Comparison, and Validation of Real-Time and Conventional PCR Tools for the Detection of the Fungal Pathogens Causing Brown Spot and Red Band Needle Blights of Pine

Dothistroma pini, D. septosporum, and Lecanosticta acicola are fungal pathogens that cause severe foliage diseases in conifers. All three pathogens are listed as quarantine organisms in numerous countries throughout the world and, thus, are subject to specific monitoring. Detection and identification of these pathogens still often relies on cumbersome and unsatisfactory methods that are based upon the morphological characterization of fungal fruiting bodies and conidia. In this study, we present the development of several new molecular tools that enable a rapid and specific in planta detection of each of these pathogens. Several DNA extraction procedures starting from infected needles were compared and four commercial DNA extraction kits provided DNA of satisfactory quality for amplification by polymerase chain reaction (PCR). In addition, we developed several sets of conventional PCR primers, dual-labeled probes (DLPs), and duplex-scorpion probes (DSPs), all of which targeted each pathogen. Their ability to detect the pathogens in a series of naturally infected needle samples was compared. The quadruplex DLP real-time assay proved to be more sensitive than the DSP assay and conventional PCR but the two real-time probe formats yielded identical results in the naturally infected samples. Both real-time assays proved to be significantly superior to the technique of humid chamber incubation, which often failed to produce spores for the accurate identification of the pathogens.

Detection, Distribution, and Genetic Variability of 'Candidatus Liberibacter' Species Associated with Zebra Complex Disease of Potato in North America.

The specificity and sensitivity of polymerase chain reaction (PCR) primers developed for 'Candidatus Liberibacter solanacearum' and 'Candidatus Liberibacter psyllaurous' were evaluated in conventional and real-time PCR assays. All PCR primers were specific for 'Ca. L. psyllaurous' and 'Ca. L. solanacearum' insomuch as they did not detect other prokaryotic plant pathogens that affect potato except for the putative pathogens associated with psyllid-yellows and haywire. Conventional PCR assays were capable of detecting 0.19 to 1.56 ng of total DNA per reaction, and real-time PCR was found capable of detecting 1.56 to 6.25 ng of total DNA per reaction, depending on the specific PCR primer set used. 'Ca. Liberibacter' species associated with zebra complex disease (ZC) was confirmed in plants affected by this disease throughout Texas from 2005 to 2008, in seed tubers produced in Wyoming in 2007, and in Colorado, Kansas, Nebraska, and Mexico in 2008. A multiplex PCR assay using 'Ca. L. solanacearum'-specific primers and primers specific for the β-tubulin DNA regions from potato was developed, providing possible utility of the multiplex assay for 'Ca. Liberibacter' detection in different solanaceous plant species. Preliminary studies suggest silverleaf nightshade (Solanum elaeagnifolium), wolfberry (Lycium barbarum), black nightshade (S. ptychanthum), and jalapeno pepper (Capsicum annuum) as additional solanaceous hosts for the ZC-associated bacterium. The 'Ca. Liberibacter' species detected in all samples divided into two clusters sharing similarity of 99.8% in their partial 16S rRNA gene sequences and 99.3% in their partial intergenic spacer region (ISR)-23S rRNA gene sequences. Genetic variation in the 16S rDNA region consistently matched that of the ISR-23S rDNA region. In this partial 16S-ISR-23S rDNA region, there was a total of eight single nucleotide polymorphisms among 'Ca. L. psyllaurous' and 'Ca. L. solanacearum' "strains" investigated in this study. 'Ca. L. solanacearum' and 'Ca. L. psyllaurous' were shown to be very closely related bacteria, if not the same, by successful amplification using a combination of forward primer of 'Ca. L. solanacearum' and reverse primer of 'Ca. L. psyllaurous' in ZC-affected potato samples. This finding clarifies the current taxonomic status of 'Ca. L. solanacearum' and 'Ca. L. psyllaurous'. The detection of 'Ca. L. solanacearum' from haywire-symptomatic potato samples demonstrates that this bacterium might also be associated with this disease.

Comparison of polymerase chain reaction primer sets for amplification of rodent Pasteurellaceae

Monitoring of rodents for Pasteurellaceae infection may be carried out by the polymerase chain reaction (PCR). We tested which of 17 rodent Pasteurellaceae strains were detected by three PCR primer sets. By phylogenetic analysis, 12 strains were assigned to the Rodent cluster and five strains to other clusters, namely the Somnus cluster, Pasteurella sensu stricto, Actinobacillus sensu stricto, the Mannheimia and Rossii cluster. A primer set developed to detect biotype Heyl [Pasteurella] pneumotropica produced amplicons from three strains and appeared specific for this taxon. A primer set developed to detect biotype Jawetz [P.] pneumotropica produced amplicons from the [P.] pneumotropica type strain and two other strains within the Rodent cluster. A primer set as described by Bootz and his co-workers (Bootz F, Kirschnek S, Nicklas W, Wyss SK, Homberger FR. Detection of Pasteurellaceae in rodents by polymerase chain reaction analysis. Lab Anim Sci 1998;48:542-6) for the detection of all Pasteurellaceae indeed detected all bacterial strains examined. Bootz's primer set should be used to monitor rodents for Pasteurellaceae infection by PCR as FELASA recommends the monitoring of rodents for all Pasteurellaceae taxa. Health monitoring reports should specify the primer set(s) used for PCR testing rodents for Pasteurellaceae infection.

Polymerase chain reaction primers miss half of rRNA microbial diversity

The rRNA approach is the principal tool to study microbial diversity, but it has important biases. These include polymerase chain reaction (PCR) primers bias, and relative inefficiency of DNA extraction techniques. Such sources of potential undersampling of microbial diversity are well known, but the scale of the undersampling has not been quantified. Using a marine tidal flat bacterial community as a model, we show that even with unlimited sampling and sequencing effort, a single combination of PCR primers/DNA extraction technique enables theoretical recovery of only half of the richness recoverable with three such combinations. This shows that different combinations of PCR primers/DNA extraction techniques recover in principle different species, as well as higher taxa. The majority of earlier estimates of microbial richness seem to be underestimates. The combined use of multiple PCR primer sets, multiple DNA extraction techniques, and deep community sequencing will minimize the biases and recover substantially more species than prior studies, but we caution that even this--yet to be used--approach may still leave an unknown number of species and higher taxa undetected.

Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

DNA-based techniques have proven useful for defining trophic links in a variety of ecosystems and recently developed sequencing technologies provide new opportunities for dietary studies. We investigated the diet of Australian fur seals (Arctocephalus pusillus doriferus) by pyrosequencing prey DNA from faeces collected at three breeding colonies across the seals' range. DNA from 270 faecal samples was amplified with four polymerase chain reaction primer sets and a blocking primer was used to limit amplification of fur seal DNA. Pooled amplicons from each colony were sequenced using the Roche GS-FLX platform, generating > 20,000 sequences. Software was developed to sort and group similar sequences. A total of 54 bony fish, 4 cartilaginous fish and 4 cephalopods were identified based on the most taxonomically informative amplicons sequenced (mitochondrial 16S). The prevalence of sequences from redbait (Emmelichthys nitidus) and jack mackerel (Trachurus declivis) confirm the importance of these species in the seals' diet. A third fish species, blue mackerel (Scomber australasicus), may be a more important prey species than previously recognised. There were major differences in the proportions of prey DNA recovered in faeces from different colonies, probably reflecting differences in prey availability. Parallel hard-part analysis identified largely the same main prey species as did the DNA-based technique, but with lower species diversity and no remains from cartilaginous prey. The pyrosequencing approach presented significantly expands the capabilities of DNA-based methods of dietary analysis and is suitable for large-scale diet investigations on a broad range of animals.

A new set of PCR assays for the identification of multiple human adenovirus species in environmental samples

To assess human adenovirus (HAdV) diversity in environmental samples based on sequence comparisons of hexon gene fragments amplified using newly designed HAdV-specific polymerase chain reaction (PCR) assays. Six PCR primer sets were designed based on 56 aligned hexon sequences from NCBI GenBank to amplify different hexon gene sections (241-349 bp) of the six HAdV species. The amplified hexon genes from wastewater samples were cloned, sequenced, and compared with those in publicly accessible databases (i.e. NCBI GenBank) by using the Blast program. A total of 46 analysed positive clones were affiliated to five HAdV serotypes, i.e. 1, 2, 12, 31 and 41. Similarities between the cloned and database hexon sequences ranged from 95.9 to 100% (with an average of 98.1 +/- 1.0%). The designed primers showed higher amplification efficiencies when compared with the existing assays. Using the new assays, HAdV species A, C, and F (serotypes 1, 2, 12, 31 and 41 in particular) were identified in the studied municipal wastewater. The six PCR primer sets developed in this study can be used to efficiently amplify hexon gene fragments in HAdV. Multiple HAdV serotypes identified in the municipal wastewater provide new information about HAdV diversity in environmental samples.

Effect of HIV viral load, CD4 cell count and antiretroviral therapy on human papillomavirus prevalence in urine samples of HIV-infected men

HIV-infected patients are at increased risk for persistent human papillomavirus (HPV) infection, the major cause of anogenital cancer. The present study describes the HPV prevalence in urine samples of 243 HIV-infected men and a control group of 231 men. HPV DNA was amplified by the SPF10 polymerase chain reaction primer set. The overall HPV prevalence in HIV-infected men was 27.5% compared with 12.6% in controls (P < 0.01). Infections with high-risk and multiple HPV genotypes were present in both groups. Differences were not statistically significant. A multivariate logistic regression model showed a decreased HPV prevalence associated with use of a nucleoside and a non-nucleoside reverse transcriptase inhibitor combination (P = 0.03). A trend was observed towards a higher HPV prevalence and a lower CD4 cell count. Further prospective studies are needed to determine the role of HPV DNA testing in urine in future screening programmes for anal cancer in men.

Multiplex real-time polymerase chain reaction for rapid detection of β-lactamase–negative, ampicillin-resistant Haemophilus influenzae

We evaluated a multiplex real-time quantitative polymerase chain reaction (PCR) method for quantification of Haemophilus influenzae and rapid detection of β-lactam–resistant strains. We designed 5 PCR primer sets to simultaneously detect the β-lactam–resistant genes and quantify the pathogen. To demonstrate the validity of this assay, we used 191 clinical isolates, including 141 H. influenzae strains, and 100 purulent sputum samples, including 30 samples from which H. influenzae had been isolated. This assay showed 92.9% sensitivity and 91.8% specificity for detecting β-lactam–resistant genes, relative to the conventional phenotypic method, and this assay correlated well with conventional quantitative culture counts. By using this assay, we could quantify H. influenzae and identify β-lactam susceptibility in only 3 h and with only one tube. This method will be helpful for the rapid detection of H. influenzae infections and the selection of appropriate antibiotics.

Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach

We have constructed a large fosmid library from a mesophilic anaerobic digester and explored its 16S rDNA diversity using a high-density filter DNA–DNA hybridization procedure. We identified a group of 16S rDNA sequences forming a new bacterial lineage named WWE3 (Waste Water of Evry 3). Only one sequence from the public databases shares a sequence identity above 80% with the WWE3 group which hence cannot be affiliated to any known or candidate prokaryotic division. Despite representing a non-negligible fraction (5% of the 16S rDNA sequences) of the bacterial population of this digester, the WWE3 bacteria could not have been retrieved using the conventional 16S rDNA amplification procedure due to their unusual 16S rDNA gene sequence. WWE3 bacteria were detected by polymerase chain reaction (PCR) in various environments (anaerobic digesters, swine lagoon slurries and freshwater biofilms) using newly designed specific PCR primer sets. Fluorescence in situ hybridization (FISH) analysis of sludge samples showed that WWE3 microorganisms are oval-shaped and located deep inside sludge flocs. Detailed phylogenetic analysis showed that WWE3 bacteria form a distinct monophyletic group deeply branching apart from all known bacterial divisions. A new bacterial candidate division status is proposed for this group.

Sequence length polymorphisms within primate amelogenin and amelogenin‐like genes: usefulness in sex determination

Sequence length polymorphisms between the amelogenin (AMELX) and the amelogenin-like (AMELY) genes both within and between several mammalian species have been identified and utilized for sex determination, species identification, and to elucidate evolutionary relationships. Sex determination via polymerase chain reaction (PCR) assays of the AMELX and AMELY genes has been successful in greater apes, prosimians, and two species of old world monkeys. To date, no sex determination PCR assay using AMELX and AMELY has been developed for new world monkeys. In this study, we present partial AMELX and AMELY sequences for five old world monkey species (Mandrillus sphinx, Macaca nemestrina, Macaca fuscata, Macaca mulatta, and Macaca fascicularis) along with primer sets that can be used for sex determination of these five species. In addition, we compare the sequences we generated with other primate AMELX and AMELY sequences available on GenBank and discuss sequence length polymorphisms and their usefulness in sex determination within primates. The mandrill and four species of macaque all share two similar deletion regions with each other, the human, and the chimpanzee in the region sequenced. These two deletion regions are 176-181 and 8 nucleotides in length. In analyzing existing primate sequences on GenBank, we also discovered that a separate six-nucleotide polymorphism located approximately 300 nucleotides upstream of the 177 nucleotide polymorphism in sequences of humans and chimps was also present in two species of new world monkeys (Saimiri boliviensis and Saimiri sciureus). We designed primers that incorporate this polymorphism, creating the first AMELX and AMELY PCR primer set that has been used successfully to generate two bands in a new world monkey species.

Development and Optimization of a Real-Time Detection Assay for Xanthomonas fragariae in Strawberry Crown Tissue with Receiver Operating Characteristic Curve Analysis

Angular leaf spot of strawberry is caused by the bacterium Xanthomonas fragariae. The disease is transmitted primarily through systemically infected nursery stock. This creates problems for nurseries wishing to export plants to Europe because of quarantine restrictions. Currently, field inspections for symptoms are used to certify plants free of X. fragariae, but visual inspection is not useful for detecting plants infected systemically. To detect systemic infections, polymerase chain reaction (PCR) is the desired tool because of its sensitivity, specificity, and ease of use. In this study, we developed three sets of real-time PCR primers and probes and determined optimal reaction conditions for use of these primers for the detection of the bacterium X. fragariae in strawberry crown tissue. Real time detection proved to be both more sensitive and specific than standard PCR. Moreover, the detection of X. fragariae in crown tissue extract was possible with real-time PCR but not with standard PCR which is a significant improvement over standard PCR. The information on sensitivity and specificity of the primer sets was used to evaluate the performance of these primers with receiver operating characteristic (ROC) curve analysis under different tolerances. The results of this analysis can be used to provide guidance on threshold selection to manage disease below unacceptable levels. The results of this research may be useful to regulators and inspectors who must certify that plants meet European and Mediterranean Plant Protection Organization standards.

Time-Dependent Alterations of Select Genes in Streptozotocin-Induced Diabetic Rat Bladder

To investigate time-course changes in the expression of select genes and extracellular matrix proteins in the bladder of rats with streptozotocin-induced diabetes, so as to examine the mechanisms underlying changes in mechanical properties of the bladder due to diabetic cystopathy. Female Sprague-Dawley rats were injected with streptozotocin (65 mg/kg). Rats that were fed with 5% sucrose in drinking water served as diuretic controls, in addition to normal control rats. At the end of 2, 4, and 8 weeks, total ribonucleic acid (RNA) isolated from the detrusor layer of the bladders was reverse transcribed, and then complementary deoxyribonucleic acid was amplified with polymerase chain reaction primer sets for type I collagen, type III collagen, tropoelastin, and transforming growth factor beta 1 (TGF-beta-1). Collagen and elastin contents of the bladders were quantified with commercially available assays. Both diabetic and diuretic rat bladders exhibited significantly (P <0.05) lower expression of type I collagen and TGF-beta-1 messenger RNA (mRNA) compared with normal controls at all time points tested. In contrast, downregulation of type III collagen mRNA expression in both diabetic and diuretic groups was seen at 4 and 8 weeks. Furthermore, tropoelastin mRNA expression in the diabetic rat bladders was, compared with normal and diuretic rats, significantly (P <0.05) greater at 2 weeks. Both diabetic and diuretic rat bladders exhibited significantly (P <0.05) decreased collagen and increased elastin protein content at 2 and 8 weeks. The results of the present study suggest that increases in compliance of the bladders in diabetic cystopathy result not only from diuresis-driven reduction of collagen synthesis but also from increased elastin synthesis.

Evaluation of the PCR method for identification of Bifidobacterium species

Bifidobacterium species are known for their beneficial effects on health and their wide use as probiotics. Although various polymerase chain reaction (PCR) methods for the identification of Bifidobacterium species have been published, the reliability of these methods remains open to question. In this study, we evaluated 37 previously reported PCR primer sets designed to amplify 16S rDNA, 23S rDNA, intergenic spacer regions, or repetitive DNA sequences of various Bifidobacterium species. Ten of 37 experimental primer sets showed specificity for B. adolescentis, B. angulatum, B. pseudocatenulatum, B. breve, B. bifidum, B. longum, B. longum biovar infantis and B. dentium. The results suggest that published Bifidobacterium primer sets should be re-evaluated for both reproducibility and specificity for the identification of Bifidobacterium species using PCR. Improvement of existing PCR methods will be needed to facilitate identification of other Bifidobacterium strains, such as B. animalis, B. catenulatum, B. thermophilum and B. subtile.

Transfusion‐transmitted virus DNA in serum, tear and aqueous humour of patients undergoing cataract operation

Transfusion-transmitted virus (TTV) is a novel non-enveloped, single-stranded DNA virus with unclear pathogenesis throughout the world. Many studies were conducted to determine this virus in various body fluids and different primer sets have been tested for accurate diagnosis. This study aimed to collect data on the prevalence of TTV in serum, tear and aqueous humour of patients undergoing planned cataract surgery and to determine efficacy of three different polymerase chain reaction (PCR) techniques. A total of 72 specimens (24 each of serum, tear and aqueous humour specimens) were collected from 24 patients (11 male and 13 female) having age-related cataract. The patients did not have any other ocular pathology. TTV DNA was investigated by three different PCR methods: a seminested PCR performed with Okamato's primers, a one-step PCR performed with degenerative Takashi's primers and a commercial real-time PCR system. TTV DNA was detected in 20 (83.3%) of the 24 serum specimens by the one-step PCR and real-time PCR system. However, seminested PCR yielded a positivity rate of 25%. TTV DNA positivities of the one-step PCR and the real-time PCR system were 33.3% and 66.6% of the 24 tear specimens, respectively. Seminested PCR did not yield positive result in these specimens. From aqueous humour specimens, TTV DNA was detected in 3 (12.5%) of the 24 specimens only by the real-time PCR. TTV DNA positivity of seminested PCR was significantly low in all specimens. TTV DNA was detected in serum, tear and aqueous humour of patients undergoing cataract surgery, supporting the idea that this virus can be detected almost all of the body fluids but at different rates under various PCR conditions and primer sets. Using commercial real-time PCR significantly increased the TTV DNA positivity.

Characterization ofBacillusandPseudomonasstrains with suppressive traits isolated from tomato hydroponic-slow filtration unit

Bacillus and Pseudomonas spp. are known to be involved in plant pathogenic fungi elimination during the slow filtration process used in tomato soilless cultures. We isolated 6-8 strains of both Bacillus and Pseudomonas from the top, middle, and bottom sections of filters and identified them after 16S rDNA sequencing. Four Pseudomonas strains were identified as Pseudomonas fulva, 5 as Pseudomonas plecoglossicida, and 12 as Pseudomonas putida. The use of specific oligonucleotide polymerase chain reaction primer sets designed from gyrB gene sequences additionally permitted the identification of 17 Bacillus cereus and 3 Bacillus thuringiensis strains. Ribotyping with EcoRI pointed out an important polymorphism within Bacillus and Pseudomonas strains. Molecular characterization did not reveal a correlation between the location of isolates within the filter (top, middle, or bottom) and bacterial identification or riboclusters. Functional aspects assessed by community-level physiological profiling showed marked phenotypic differences between Pseudomonas communities isolated from the top and bottom filter layers; differences were lower between Bacillus communities of different layers and far less noticeable between mixed communities of Bacillus and Pseudomonas. These strains were tested for several suppressive activities. Conversely to most Bacillus, the majority of Pseudomonas strains were auxin producers and promoted the growth of tomato plantlet roots. On the other hand, only Bacillus strains displayed antagonistic activities by inhibiting the growth of pathogenic fungi frequently detected in soilless cultures. Siderophores were produced by nearly all bacteria, but at higher amounts by Pseudomonas than Bacillus strains. The biocontrol agent potentiality of certain strains to optimize the slow filtration process and to promote the suppressive potential of nutrient solution is discussed.

Comparison of Molecular Procedures for Detection and Identification of Guignardia citricarpa and G. mangiferae.

Citrus black spot, caused by Guignardia citricarpa, is a serious fruit spot disease and is widely distributed in Asia, southern Africa, and South America, but does not occur in North America or the Mediterranean region. A nonpathogenic species, G. mangiferae, is cosmopolitan with a wide host range and can colonize citrus fruit and leaves saprophytically. Detection and identification of Guignardia spp. on citrus fruit is necessary for epidemiological, management, and regulatory purposes. In this study, we compared published and unpublished polymerase chain reaction primer sets for their specificity and sensitivity in the detection and differentiation of the two Guignardia spp. All primers evaluated successfully identified the two species using purified DNA from fungal cultures or mycelia as source materials. However, some primer sets were not highly effective in detecting G. citricarpa when DNA was extracted directly from single characteristic black spot lesions on fruit. Thus, new primer pairs for both species were designed from the internal transcribed spacer region that were highly sensitive and specific for detection of G. citricarpa using DNA recovered from single lesions on fruit by a rapid DNA extraction procedure.

A Soybean Transcript Map: Gene Distribution, Haplotype and Single-Nucleotide Polymorphism Analysis

The first genetic transcript map of the soybean genome was created by mapping one SNP in each of 1141 genes in one or more of three recombinant inbred line mapping populations, thus providing a picture of the distribution of genic sequences across the mapped portion of the genome. Single-nucleotide polymorphisms (SNPs) were discovered via the resequencing of sequence-tagged sites (STSs) developed from expressed sequence tag (EST) sequence. From an initial set of 9459 polymerase chain reaction primer sets designed to a diverse set of genes, 4240 STSs were amplified and sequenced in each of six diverse soybean genotypes. In the resulting 2.44 Mbp of aligned sequence, a total of 5551 SNPs were discovered, including 4712 single-base changes and 839 indels for an average nucleotide diversity of Theta= 0.000997. The analysis of the observed genetic distances between adjacent genes vs. the theoretical distribution based upon the assumption of a random distribution of genes across the 20 soybean linkage groups clearly indicated that genes were clustered. Of the 1141 genes, 291 mapped to 72 of the 112 gaps of 5-10 cM in the preexisting simple sequence repeat (SSR)-based map, while 111 genes mapped in 19 of the 26 gaps >10 cM. The addition of 1141 sequence-based genic markers to the soybean genome map will provide an important resource to soybean geneticists for quantitative trait locus discovery and map-based cloning, as well as to soybean breeders who increasingly depend upon marker-assisted selection in cultivar improvement.

Quantification of anaerobic ammonium-oxidizing bacteria in enrichment cultures by real-time PCR

The anaerobic ammonium-oxidizing (ANAMMOX) bacteria were enriched from a rotating disk reactor (RDR) biofilm in semi-batch cultures. Based on fluorescence in situ hybridization (FISH) analysis, this enrichment led to a relative population size of 36% ANAMMOX bacteria. Phylogenetic analysis revealed that all the detected clones were related to the previously reported ANAMMOX bacteria, Candidatus Brocadia anammoxidans (AF375994), with 92% sequence similarity. Furthermore, we successfully developed a real-time polymerase chain reaction (PCR) assay to quantify populations of ANAMMOX bacteria in the enrichment cultures. For this real-time PCR assay, PCR primer sets targeting 16S ribosomal RNA genes of ANAMMOX bacteria were designed and used. The quantification range of this assay was 6 orders of magnitude, from 8.9×10 1 to 8.9×10 6 copies per PCR, corresponding to the detection limit of 3.6×10 3 target copies mL −1. A significant correlation was found between the increase in copy numbers of 16S rRNA gene of ANAMMOX bacteria and the increase in nitrogen removal rates in the enrichment cultures. Quantifying ANAMMOX bacterial populations in the enrichment culture made it possible to estimate the doubling time of the enriched ANAMMOX bacteria to be 3.6 to 5.4 days. The real-time PCR assay gave comparable population sizes in the enrichment cultures with the FISH results. These results suggest that the real-time PCR assay developed in this study is useful and reliable for quantifying the populations of ANAMMOX bacteria in environmental and engineering samples.

Z-Chromosome Specific Primers for Chicken-Quail Hybrid Blastoderm

A polymerase chain reaction (PCR) primer set for a chicken pkci gene on the Z-chromosome, chPKCI, amplified a 329 bp fragment of genomic DNA in chickens but not quail. Likewise, a PCR primer set for the quail pkci gene on the Z-chromosome, quPKCI, amplified a 95 bp fragment of genomic DNA in quail but not chickens. These chicken and quail primers validly identified chicken-quail hybrids derived from Z-chromosome carrying sperm of chicken and the hybrid derived from Z-chromosome carrying oocyte of quail, respectively.

Detection of Type 1 Fimbrial Genes in Fish Pathogenic and Non-pathogenic Edwardsiella tarda Strains by PCR

Presence of fimbrial genes among fish pathogenic and non-pathogenic strains of Edwardsiella tarda was investigated by polymerase chain reaction (PCR). Four primer sets for PCR were designed to detect the four genes (etfA, etfB, etfC, etfD) of the type 1 fimbrial gene cluster of E. tarda. All the four genes were successfully amplified with the four primer sets in all the pathogenic strains. On the other hand, any of etfA, etfB and etfC were not detected in 13 of 14 non-pathogenic strains. The results suggest that fimbriae play a role in the pathogenicity of E. tarda and that detection of etfA, etfB and etfC by PCR is useful to distinguish between pathogenic and non-pathogenic strains of E. tarda.