A High-Resolution Melting Analysis with an Unlabeled Probe for CRISPR/Cas9-Induced ZBED6 Knockout Pigs Detection

Background The zinc finger BED-type containing 6 knockout (ZBED6-KO) pigs were created to improve economic traits by increasing the expression of insulin-like growth factor 2. They were generated by CRISPR/CRISPR-associated protein 9 (Cas9) technology and a single-base deletion of ZBED6 was found. An efficient and rapid method was needed to detect this type of pig. Objective This study aimed to develop a high-resolution melting (HRM) method to detect ZBED6-KO pigs. Methods An unlabeled probe and two primers were designed to develop HRM method. The limit of detection, specificity and accuracy of established method were tested by the constructed plasmid and DNA extracts of tissue specimens. Results The limit of detection by established method was 102 copies/µL. The HRM method with an unlabeled probe showed good specificity and high accuracy. Conclusions The established HRM analysis with an unlabeled probe showed it to be a highly effective, rapid and reliable to distinguish ZBED6-KO pigs with wild-type pigs. Highlights It is the first time that HRM analysis with an unlabeled probe has been used in the detection of genome editing pigs by the CRISPR/Cas9 technology.

An unlabeled probe based real time PCR and modified semi nested PCR as molecular tools for analysis of chloroquine resistant in Plasmodium vivax isolates from Afghanistan

Background: Plasmodium vivax isolate resistance to Chloroquine (CQ) has been reported from many endemic regions in the world. P. vivax is responsible for 95% of malaria cases in Afghanistan and CQ is the first-line treatment given for treatment of vivax malaria. The pvmdr-1 and pvcrt-o (K10 insertion) genes are the possible markers for CQ-resistance P. vivax isolates. There have been no studies done on the presence or absence of molecular markers for CQ-resistance P. vivax in Afghanistan. The present work aimed to evaluate the frequency of mutations in the pvmdr-1 and K10 insertion in the pvcrt-o genes of P. vivax.Methods: P. vivax isolates were collected from Laghman, Baghlan and Khost provinces. For investigation of polymorphisms of desired regions in pvmdr-1 and pvcrt-o genes, sequencing was applied on the PCR products. A new asymmetric qPCR and melting analysis assay based on unlabeled probe developed for scanning of K10 insertion in pvcrt-o gene. Results: The analysis of sequencing data of the pvmdr-1 gene showed wild type Y976 and K997 and mutant M958 and L1076 in 33 isolates from three provinces and submitted in GenBank (accession number MK419882-MK419914)Of 36 samples that evaluated for K10 insertion in pvcrt-o, 2/18(11%), 0/10(0%) and 0/8(0%) isolates from Laghman, Baghlan and Khost province possessed K10 insertion, respectively, that confirmed by either sequencing and unlabeled probes and submitted in GenBank (accession number MK292011-MK292046).Conclusion: Two samples with K10 insertion and 33 samples with pvmdr1 polymorphism, indicating on the possibility of CQ resistance P. vivax populations in Afghanistan. Furthermore, unlabeled probes are simple and inexpensive alternative tools for screening of P. vivax mutations.

An unlabeled probe based real time PCR and modified semi nested PCR as molecular tools for analysis of chloroquine resistant in Plasmodium vivax isolates from Afghanistan

Background: Plasmodium vivax isolate resistance to Chloroquine (CQ) has been reported from many endemic regions in the world. P. vivax is responsible for 95% of malaria cases in Afghanistan and CQ is the first-line treatment given for treatment of vivax malaria. The pvmdr-1 and pvcrt-o (K10 insertion) genes are the possible markers for CQ-resistance P. vivax isolates. There have been no studies done on the presence or absence of molecular markers for CQ-resistance P. vivax in Afghanistan. In the present work, we aimed to evaluate the frequency of mutations in the pvmdr-1 and K10 insertion in the pvcrt-o genes of P. vivax.Methods: P. vivax isolates were collected from Laghman, Baghlan and Khost provinces. For investigation of polymorphisms of desired regions in pvmdr-1 and pvcrt-o genes, sequencing was applied on the PCR products. We developed a new asymmetric qPCR and melting analysis assay based on unlabeled probe for scanning of K10 insertion in pvcrt-o gene. Results: The analysis of sequencing data of the pvmdr-1 gene showed wild type Y976 and K997 and mutant M958 and L1076 in 33 isolates from three provinces and submitted in GenBank (accession number MK419882-MK419914)Of 36 samples that evaluated for K10 insertion in pvcrt-o, 2/18(11%), 0/10(0%) and 0/8(0%) isolates from Laghman, Baghlan and Khost province possessed K10 insertion, respectively, that confirmed by either sequencing and unlabeled probes and submitted in GenBank (accession number MK292011-MK292046).Conclusion: Two samples with K10 insertion and 33 samples with pvmdr1 polymorphism, indicating on the possibility of CQ resistance P. vivax populations in Afghanistan. Furthermore, unlabeled probes are simple and inexpensive alternative tools for screening of P. vivax mutations.

An unlabeled probe based real time PCR and modified semi nested PCR as molecular tools for analysis of chloroquine resistant in Plasmodium vivax isolates from Afghanistan

Background: Chloroquine (CQ) resistance Plasmodium vivax isolates have been reported from many endemic regions in the world. P. vivax has been reported to be about 95% of the whole malaria in Afghanistan and CQ is prescribing in the first-line treatment of vivax malaria. The pvmdr-1 and pvcrt-o (K10 insertion) genes are the possible markers of CQ-resistance P. vivax isolates. There have been no studies done on the prevalence of molecular markers of CQ-resistance P. vivax in Afghanistan. In the present work, we aimed to evaluate the prevalence of mutations in the pvmdr-1 and K10 insertion in the pvcrt-o genes of P. vivax.Methods: P. vivax isolates were collected from Laghman, Baghlan and Khost provinces. For investigation of polymorphisms of desired regions in pvmdr-1 and pvcrt-o genes, sequencing was applied on the PCR products. We developed a new asymmetric qPCR and melting analysis assay based on unlabeled probe for scanning of K10 insertion in pvcrt-o gene.Results: The analysis of sequencing data of the pvmdr-1 gene showed wild type Y976 and K997 and mutant M958 and L1076 in 33 isolates from three provinces and submitted in GenBank (accession number MK419882-MK419914)Of 36 samples that evaluated for K10 insertion in pvcrt-o, 2/18(11%), 0/10(0%) and 0/8(0%) isolates from Laghman, Baghlan and Khost province possessed K10 insertion, respectively, that confirmed by either sequencing and unlabeled probes and submitted in GenBank (accession number MK292011-MK292046).Conclusion: The existence of 2 samples with K10 insertion and 33 samples with pvmdr1 polymorphism indicating on CQ resistance P. vivax populations in Afghanistan. This can lead to spreading of resistant strains in the society. Furthermore, unlabeled probes are simple and inexpensive alternative tools for screening of P. vivax mutations.