Touchdown thermocycling program enables a robust single nucleotide polymorphism typing method based on allele-specific real-time polymerase chain reaction

High-resolution melting analysis identifies reservoir hosts of zoonotic Leishmania parasites in Tunisia

BACKGROUND

Leishmaniasis is endemic in Tunisia and presents with different clinical forms, caused by the species Leishmania infantum, Leishmania major, and Leishmania tropica. The life cycle of Leishmania is complex and involves several phlebotomine sand fly vectors and mammalian reservoir hosts. The aim of this work is the development and evaluation of a high-resolution melting PCR (PCR-HRM) tool to detect and identify Leishmania parasites in wild and domestic hosts, constituting confirmed (dogs and Meriones rodents) or potential (hedgehogs) reservoirs in Tunisia.

METHODS

Using in vitro-cultured Leishmania isolates, PCR-HRM reactions were developed targeting the 7SL RNA and HSP70 genes. Animals were captured or sampled in El Kef Governorate, North West Tunisia. DNA was extracted from the liver, spleen, kidney, and heart from hedgehogs (Atelerix algirus) (n = 3) and rodents (Meriones shawi) (n = 7) and from whole blood of dogs (n = 12) that did not present any symptoms of canine leishmaniasis. In total, 52 DNA samples were processed by PCR-HRM using both pairs of primers.

RESULTS

The results showed melting curves enabling discrimination of the three Leishmania species present in Tunisia, and were further confirmed by Sanger sequencing. Application of PCR-HRM assays on reservoir host samples showed that overall among the examined samples, 45 were positive, while seven were negative, with no Leishmania infection. Meriones shawi were found infected with L. major, while dogs were infected with L. infantum. However, co-infections with L. major/L. infantum species were detected in four Meriones specimens and in all tested hedgehogs. In addition, multiple infections with the three Leishmania species were found in one hedgehog specimen. Sequence analyses of PCR-HRM products corroborated the Leishmania species found in analyzed samples.

CONCLUSIONS

The results of PCR-HRM assays applied to field specimens further support the possibility of hedgehogs as reservoir hosts of Leishmania. In addition, we showed their usefulness in the diagnosis of canine leishmaniasis, specifically in asymptomatic dogs, which will ensure a better evaluation of infection extent, thus improving elaboration of control programs. This PCR-HRM method is a robust and reliable tool for molecular detection and identification of Leishmania and can be easily implemented in epidemiological surveys in endemic regions.

Allele-specific real-time polymerase chain reaction as a tool for urate transporter 1 mutation detection

Allele-specific polymerase chain reaction (ASPCR) method has long been applied for the detection of nucleotide variations and genotyping, which are detected by the presence or absence of DNA amplification PCR products. Recently, Real-Time PCR genotyping has fast developed and offered a rapid method of detecting mutations without the need of gel electrophoresis as with ASPCR. Here, we describe an easy and rapid touchdown real-time PCR method for the detection of nucleotide variations. Using our method we successfully detect two main mutations in human urate transporter 1 (SLC22A12), W258X and R90H, and validate the results. The method can potentially be applied to genotype of various other nucleotide variations.

Association between single nucleotide polymorphisms of the estrogen receptor 1 and receptor activator of nuclear factor kappa B ligand genes and bone mineral density in postmenopausal Taiwanese

OBJECTIVE

To investigate the relationship between single nucleotide polymorphisms (SNPs) of the genes encoding the estrogen receptor 1 (ESR1) and the receptor activator of nuclear factor kappa B ligand (RANKL) and bone mineral density (BMD) in postmenopausal Taiwanese.

MATERIALS AND METHODS

Five ESR1 SNPs and three RANKL SNPs in 467 women were genotyped. Results of genotyping were correlated with BMD that had been adjusted for body mass index (BMI), age, and years after menopause.

RESULTS

Those with the ESR1 Crs1884054 allele were found to have a lower BMD at LS2-4/Lateral view (p = 0.005 and permutated p = 0.046), and those with the ESR1 haplotype Trs2234693-Ars922996 had a higher risk for low BMD also at LS2-4/Lat (OR = 1.8, 95% CI = 1.1-2.9). In addition, women without the RANKL haplotype Grs2148072-Crs2200287-Grs922996 had a higher risk for low BMD at LS1-4/AP (OR = 2.09, 95% CI = 1.21 ∼ 3.64). Stratification analyses revealed that those with ESR1 AArs1884054 and RANKL Ars2148072 (p = 0.032) or RANKL Trs2200287 (p = 0.007) had a lower BMD at LS1-4/AP.

CONCLUSION

Genotypes of these SNPs of ESR1 and RANKL may help us predict the osteoporosis risk in menopausal women.

Simple and rapid detection method for the mutations in SLC22A12 that cause hypouricemia by allele-specific real-time polymerase chain reaction

BACKGROUND

Hypouricemia is a disorder that serum urate level is less than 2.0 mg/dl, and relatively common in the Japanese population, where the main genetic cause of hypouricemia is W258X and R90H mutations in human urate trasnsporter 1(SLC22A12). Small scale screening has relied on time-consuming traditional ways like polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Therefore, it is beneficial that we have an easy and rapid detection method for these mutations.

METHODS

In this report, we established a touchdown allele-specific real-time polymerase chain reaction (ASPCR) assay for detecting W258X and R90H mutations in SLC22A12, respectively.

RESULTS

Quantifiable discrimination was successfully achieved by ∆Ct value. Furthermore, we conducted W258X and R90H screening against 120 control genome sets, whereby frequency was 2.92% for W258X, and not detected for R90H, respectively.

CONCLUSIONS

The two mutations, W258X and R90H in SLC22A12 were successfully genotyped by an easy and rapid ASPCR assay.

Allele-specific PCR in SNP genotyping

The increasing need for large-scale genotyping applications of single nucleotide polymorphisms (SNPs) in model and nonmodel organisms requires the development of low-cost technologies accessible to minimally equipped laboratories. The method presented here allows efficient discrimination of SNPs by allele-specific PCR in a single reaction with standard PCR conditions. A common reverse primer and two forward allele-specific primers with different tails amplify two allele-specific PCR products of different lengths, which are further separated by agarose gel electrophoresis. PCR specificity is improved by the introduction of a destabilizing mismatch within the 30 end of the allele-specific primers. This is a simple and inexpensive method for SNP detection that does not require PCR optimization.

Touchdown PCR for increased specificity and sensitivity in PCR amplification

Touchdown (TD) PCR offers a simple and rapid means to optimize PCRs, increasing specificity, sensitivity and yield, without the need for lengthy optimizations and/or the redesigning of primers. TD-PCR employs an initial annealing temperature above the projected melting temperature (T(m)) of the primers being used, then progressively transitions to a lower, more permissive annealing temperature over the course of successive cycles. Any difference in T(m) between correct and incorrect annealing will produce an exponential advantage of twofold per cycle. TD-PCR has found wide applicability in standard PCR protocols, including reverse transcriptase-dependent PCR, as well as in the generation of cDNA libraries and single nucleotide polymorphism screening. TD-PCR is particularly useful for templates that are difficult to amplify but can also be standardly used to enhance specificity and product formation. The procedure takes between 90 and 120 min, depending on the template length.