Genotyping and Phylogenetic Analysis of Plasmodium vivax Circumsporozoite Protein (pvcsp) Gene of Clinical Isolates in South-Eastern Iran

2020 ◽  
Author(s):  
Soudabeh ETEMADI ◽  
Mehdi NATEGHPOUR ◽  
Afsaneh MOTEVALLI HAGHI ◽  
Hamid ESLAMI ◽  
Mehdi MOHEBALI ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Vivax ◽  
Circumsporozoite Protein ◽  
Genomic Databases ◽  
A Value ◽  
Eastern Iran ◽  
Pcr Products ◽  
Gene Polymerase Chain Reaction ◽  
Lower Variation ◽  
Polymerase Chain

Background: Circumsporozoite protein (CSP) is one of the most important surface sporozoite antigens in malaria, recently considered as a candidate for vaccination. Considering the importance of CSP, this study was conducted to investigate the polymorphism and genetic diversity of Plasmodium vivax Circumsporozoite Protein (Pvcsp) in the southeastern region of Iran during 2015-2016. Methods: To investigate polymorphism and genetic diversity, 20 blood samples were collected from patients with P. vivax, then DNA was extracted and amplified using partial sequence of CSP gene. Polymerase chain reaction (PCR) products were sequenced and compared to sequences from genomic databases using BLAST. Genetic evaluation and phylogenic analysis were performed using MEGA7 and DnaSP5 software’s on 38 sequences include 20 sequences of our study and 18 sequences of Gene Bank. Results: Eleven isolates were VK210 genotype and 9 isolates contained VK247. The result of variable segregation nucleotide site indicated that the differentiation of sequences in CSP were 25.67% in our 20 samples which are less than the 38 samples with a value of 26.67%. Comparing the ratio of dN/dS regions in the CSP gene indicates that the CSP varies more synonymously and amino acid has lower variation. Out of 38 samples, 35 unique haplotypes were identified based on 1042 nucleotide sequences in CSP, showing a variation percentage of 99.4%. Conclusion: The Tajima D analyses showed that CSP gene in P. vivax had a positive number in the total analyzed sequences, which means that the P. vivax mutations are in order to select positive evolution.

scholarly journals Genetic Characterization of Plasmodium vivax Isolates from Pakistan Using Circumsporozoite Protein (pvcsp) and Merozoite Surface Protein-1 (pvmsp-1) genes as genetic markers

2021 ◽  
Author(s):  
Zainab Bibi ◽  
Anam Fatima ◽  
Rehana Rani ◽  
Ayesha Maqbool ◽  
Samea Khan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Dynamics ◽  
Plasmodium Vivax ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Circumsporozoite Protein ◽  
Population Divergence ◽  
Large Sample Size ◽  
Merozoite Surface Protein 1 ◽  
Pcr Products

Abstract Background: Plasmodium vivax contributes to over 70% malaria burden in Pakistan, but limited data exists on various aspects including genetic diversity of the parasite as compared to other parts of the world. Since the information about the genetic diversity of P. vivax assists to understand the population dynamics of the parasite, the current study was designed to understand population divergence of Plasmodium vivax in Pakistan using circumsporozoite protein (pvcsp) and merozoite surface protein-1 (pvmsp-1) genes as molecular markers. Methods: The PCR for pvcsp and pvmsp-1 genes was carried out for 150 P. vivax isolates followed by DNA sequencing of only 35 and 30 respective amplified PCR products for both pvcsp and pvmsp-1 genes. Genetic diversity and polymorphism were analyzed using ChromasPro, ClustalW, MEGA7, DnaSP v.5 and WebLogo programs. Results: The PCR for pvcsp and pvmsp-1 genes was carried out for 150 P. vivax isolates and resulting the PCR products ranging from 900 to 1100 bp for pvcsp and ~400bp for pvmsp-1 genes, respectively. In the central-repeat region (CRR) of pvcsp gene, sequences comprised of four variable repeats of PRMs, out of which GDRADGQPA (PRM1), GDRAAGQPA (PRM2) were more extensively dispersed among the P. vivax isolates. Partial sequences (~400bp) of block 2 of pvmsp-1 gene depicted high level of diversity.Conclusion: The results revealed the polymorphism and genetic diversity especially at the CRR of pvcsp and block 2 of pvmsp-1 genes respectively. The base-line data presented here warrants future studies to investigate more into the genetic diversity of P. vivax with large sample size from across the country for better understanding of population dynamics of P. vivax that will help to control malaria at individual and community level.

scholarly journals Genetic Characterization of Plasmodium vivax Isolates from Pakistan Using Circumsporozoite Protein (PvCSP) and Merozoite Surface Protein-1 (PvMSP-1) genes as genetic markers 

2021 ◽  
Author(s):  
Zainab Bibi ◽  
Anam Fatima ◽  
Rehana Rani ◽  
Ayesha Maqbool ◽  
Samea Khan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Vivax ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Circumsporozoite Protein ◽  
Effective Vaccine ◽  
Population Divergence ◽  
Large Sample Size ◽  
Base Line ◽  
Merozoite Surface Protein 1

Abstract Background: Plasmodium vivax contributes to over 70% malaria burden in Pakistan, but limited data exists on various aspects including genetic diversity of the parasite as compared to other parts of the world. Since the information about the genetic diversity of P. vivax assists to understand the population dynamics of the parasite, the current study was designed to understand population divergence of Plasmodium vivax in Pakistan using circumsporozoite protein (PvCSP) and merozoite surface protein-1 (PvMSP-1) genes as molecular markers. Methods: PvCSP and PvMSP-1 specific PCR and DNA sequencing were carried out for 150 blood samples collected from Islamabad and Rawalpindi, Pakistan. Genetic diversity and polymorphism was analyzed using ChromasPro, ClustalW, MEGA7, DnaSP v.5 and WebLogo programs. Results: The PCR for PvCSP and PvMSP-1 genes was carried out for 150 P. vivax isolates and resulting the PCR products ranging from 900 to 1100 bp for PvCSP and ~400bp for PvMSP-1 genes respectively. Majority (93%; 141/150) of the P. vivax isolates were of VK210 variant and only 9 isolates were found to be of VK247 variant based on PvCSP gene. Out of the numerous peptide repeat motifs (PRMs) detected, GDRADGQPA (PRM1) and GDRAAGQPA (PRM2) were more extensively dispersed among the P. vivax isolates. Partial sequences (~400bp) at the N-terminal of PvMSP-1 gene depicted high level of diversity.Conclusion: High levels of genetic diversity based on PvCSP and PvMSP-1 genes was observed in the isolated samples from the study area. Parasite typing is essential in predicting pattern of antigenic variations and drug resistance and for effective vaccine designing and development which can further assist in evaluating measures for malaria control at individual and community level. The base-line data presented here warrants future studies to investigate more into the genetic diversity of P. vivax with large sample size from across the country for better understanding of the transmission patterns of vivax malaria.

scholarly journals Genetic Characterization of Plasmodium vivax Isolates from Pakistan Using Circumsporozoite Protein (PvCSP) and Merozoite Surface Protein-1 (PvMSP-1) Genes as Genetic Markers

2020 ◽  
Author(s):  
Zainab Bibi ◽  
Anam Fatima ◽  
Rehana Rani ◽  
Ayesha Maqbool ◽  
Samea Khan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Vivax ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Circumsporozoite Protein ◽  
Population Divergence ◽  
Large Sample Size ◽  
Base Line ◽  
Variant Type ◽  
High Level

Abstract Background Plasmodium vivax contribute over 70% malaria burden in Pakistan. Limited data exist on various aspects including genetic diversity of the parasite as compared to other parts of the world. The information about extent of genetic diversity assists to understand the transmission patterns of the parasite in human host. The current study was designed to understand population divergence of Plasmodium vivax in Pakistan using circumsporozoite protein and merozoite surface protein-I genes as molecular markers.Methods PvCSP and PvMSP-1 specific PCR and DNA sequencing were carried out for 150 blood samples collected from Islamabad and Rawalpindi, Pakistan. Genetic diversity was analysed using ChromasPro, ClustalW, MEGA7 and DnaSP v.5 programs.Results The PCR for PvCSP and PvMSP-1 genes was carried out for 150 P. vivax isolates resulting the PCR products ranging from 900 to 1100 bp for PvCSP gene and ~ 400 bp for PvMSP-1 gene. Majority (93%; 121/150) of the P. vivax isolates were of VK210 variant type and only 9 isolates were found of VK247 variant type based on PvCSP gene. Out of the numerous peptide repeat motifs (PRMs) detected, GDRADGQPA (PRM1) and GDRAAGQPA (PRM2) were more extensively dispersed among the P. vivax isolates. Partial sequences (~ 400 bp) at the N-terminal of PvMSP-1 gene depicted high level of diversity.Conclusion High-level genetic diversity based on PvCSP and PvMSP-1 genes was observed in clinical isolated in the study area. Parasite typing is essential in predicting pattern of antigenic variations, drug resistance and for effective drug and vaccine designing and development which can further evaluate for malaria control and eradication at individual and community level. The base-line data presented here warrant future studies to investigate more into the genetic diversity of P. vivax with large sample size from across the country for better understanding of the vivax malaria transmission patterns.

scholarly journals Genetic Diversity of Elaeagnus angustifolia L. (Elaeagnaceae) Populations in İzmir (Turkey)

2021 ◽  
Vol 78 (1) ◽  
pp. 35
Author(s):  
Erengül SOFYALIOĞLU ◽  
Emre SEVİNDİK ◽  
Hüseyin UYSAL
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Uv Light ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Genetic Distances ◽  
Elaeagnus Angustifolia ◽  
A Value ◽  
Pcr Products ◽  
Issr Primers

This study was performed out genetic diversity of some Elaeagnus angustifolia L. populations growing in İzmir province by using ISSR markers. In the study, PCR was performed using 15 ISSR primers. PCR products were run in agarose gel and visualized under UV light. Amplified products were scored as follows. A total of 46 bands were produced from 15 ISSR primers, of which 27 were polymorphic. The proportion of polymorphic bands was evaluated as approximately 58.7%. Genetic distances between phylogenetic trees and genotypes were calculated using the PAUP program. The phylogenetic tree consists of two large clades. The longest distance between populations was between Gümüldür-Özdere and Çeşme-Alaçatı population with a value of 0.50, while the closest distance was between Çeşme-Ayayorgi and Konak-Hatay populations with a value of 0.06. The results show that ISSR markers are useful tools for determining genetic relationships between E. angustifolia populations

Investigation of the relationship between CE cyst characteristics and genetic diversity of Echinococcus granulosus sensu lato in humans from Turkey

Parasitology ◽  
2020 ◽  
Vol 147 (14) ◽  
pp. 1712-1717
Author(s):  
Serra Örsten ◽  
Türkmen Çiftçi ◽  
Aynur Azizova ◽  
Gökhan Yüce ◽  
Aycan Uysal ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Echinococcus Granulosus ◽  
Rural Areas ◽  
Sensu Stricto ◽  
Genetic Identification ◽  
Cyst Volume ◽  
Gene Polymerase Chain Reaction ◽  
Polymerase Chain ◽  
The Relationship ◽  
Echinococcus Granulosus Sensu Lato

AbstractCystic echinococcosis (CE) is one of the most common zoonotic diseases worldwide, particularly in rural areas. This study aimed at the identification of the genotype/species belonging to Echinococcus granulosus sensu lato (s.l.) specimens in retrieved percutaneously from the human host and to investigate their relationship with cyst characteristics. The genetic identification of cyst material was performed by mt-CO1 gene polymerase chain reaction, and confirmed via sequencing. A total of 110 CE cysts were identified as E. granulosus s.l. In detail, 104 belonged to E. granulosus sensu stricto (G1 and G3) and six isolates were in the E. canadensis cluster (G6/7). All clusters were tested for the relationship between demographics, cyst features and genetic diversity. The relationship between genetic variation and certain clinical characteristics such as cyst volume and location were statistically significant for G6/7 cluster. Further studies are required with a larger sample set to investigate the relationship between the genetic variability of E. granulosus s.l. and cyst features.

scholarly journals AuNPs-Based Colorimetric Assay for Identification of Chicken Tissues in Meat and Meat Products

2015 ◽  
Vol 2015 ◽  
pp. 1-6
Author(s):  
Hejing Han ◽  
Wen Yi ◽  
Dongjun Hou ◽  
Tingting Huang ◽  
Zhihui Hao
Keyword(s):  
Target Gene ◽  
Colorimetric Assay ◽  
Meat Products ◽  
Chain Reaction ◽  
Chicken Tissues ◽  
Pcr Products ◽  
Gene Polymerase Chain Reaction ◽  
D Loop ◽  
Polymerase Chain

A simple colorimetric assay was developed to identify chicken tissues in meat and meat products by utilizing thiol-labeled primers and unmodified gold nanoparticles (AuNPs). Primers were designed based on the chicken-specific mitochondrial D-loop gene. Polymerase chain reaction (PCR) is applied to amplify the target gene, and the PCR products labeled with thiol at one end were obtained. Following the mixing of AuNPs with the PCR products, the thiol binds to the surface of AuNPs, resulting in the formation of GNP-PCR products. The resultant PCR products had abundant negative charges, which made AuNPs maintain dispersion under the role of electrostatic repulsion. As a result, in the presence of PCR products, AuNPs remained red in the presence of salt. In the absence of PCR products, the color of AuNPs changed from red to blue; therefore, the method described here could be exploited for the verification of chicken tissues with high accuracy.

Genetic diversity analysis of diazotrophs in the rice rhizosphere

2007 ◽  
Vol 4 (3) ◽  
pp. 253-258 ◽  
Author(s):  
Chen Bin ◽  
Zheng Si-Ping ◽  
Zhou Li-Juan ◽  
Lin Zhi-Min ◽  
Song Ya-Na ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Fragment Length Polymorphism ◽  
Rhizospheric Soil ◽  
Chain Reaction ◽  
Rice Roots ◽  
Rice Rhizosphere ◽  
Pcr Rflp ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Diazotrophic Community

SUMMARYThe genetic diversity of dinitrogen-fixing bacteria associated with rice (Oryza sativa) was assessed by a polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) approach on thenifHgene amplified directly from DNA extracted from washed rice roots and rhizospheric soil. Restriction digestion with the enzymesMnlI andHaeIII was performed to characterize 54 clonednifHPCR products. RFLP profiles were clustered and analysed with the UPGMA program. Eight pairs of similar RFLP patterns (similarity>50%) and two pairs of homologous RFLP patterns (100% identity) were found from the washed roots and the rhizospheric soil, respectively. Three specific diazotrophic patterns were found from rhizospheric soil and rice roots. The analyses have revealed the presence of differentnifHtypes, which appear to be significant components of the diazotrophic community in paddy fields, indicating that some of the diazotrophs may colonize the inside and the surface of the rice roots.

scholarly journals Optimasi Konsentrasi DNA dan MgCl2 pada Reaksi Polymerase Chain Reaction-Random Amplified Polymorphic DNA untuk Analisis Keragaman Genetik Tanaman Faloak (Sterculia quadrifida R.Br) (Optimization of DNA and MgCl2 Concentrations in Polymerase Chain Reacti

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Uslan Uslan ◽  
Made Pharmawati
Keyword(s):  
Genetic Diversity ◽  
Polymerase Chain Reaction ◽  
Random Amplified Polymorphic Dna ◽  
Optimum Conditions ◽  
Chain Reaction ◽  
Dna Templates ◽  
Clear Band ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Pcr Conditions

Abstrak Faloak  merupakan tanaman yang tumbuh di lahan kritis. Sebagai upaya mendukung pemuliaan dan konservasi tanaman faloak diperlukan informasi keragaman genetiknya. Salah satu metode analisis keragaman genetik adalah menggunakan penanda DNA yang berbasis PCR. Untuk itu diperlukan kondisi PCR (Polymerase Chain Reaction) yang tepat sehingga diperoleh hasil yang dapat dianalisis lebih lanjut. Penelitian ini bertujuan menentukan kondisi optimum PCR-RAPD (Polymerase Chain Reaction-Random Amplified Polymorphic DNA) tanaman faloak. Ekstraksi DNA dilakukan dengan metode CTAB. Optimasi dilakukan dengan menggunakan beberapa konsentrasi DNA cetakan dan MgCl2. Kondisi optimum PCR-RAPD tanaman faloak yang menghasilkan pita produk PCR yang jelas diperoleh  menggunakan 50 ng/ul DNA, 3 mM MgCl2 serta jumlah siklus termal 45 x. Kata kunci : PCR-RAPD, optimasi, tanaman faloak Abstract Faloak is a plant that grows on critical lands. In an effort to support breeding and conservation of faloak, information about its genetic diversity is required. One of the methods of genetic diversity analysis is using PCR-based DNA markers. For that purpose, proper PCR conditions is needed in order to obtain results that can be further analyzed. This study aimed to determine the optimum conditions for PCR-RAPD of faloak plants. DNA extraction was conducted using CTAB. Optimization was done by using several concentrations of DNA templates and MgCl2. The optimum conditions of PCR-RAPD of faloak plants that produce clear band of PCR products were obtained using 50 ng/ ul DNA, 3 mM MgCl2 and 45x thermal cycles Keywords : PCR-RAPD, optimization, faloak plant

scholarly journals Genetic characterization of Plasmodium vivax isolates from Pakistan using circumsporozoite protein (pvcsp) and merozoite surface protein-1 (pvmsp-1) genes as genetic markers

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Zainab Bibi ◽  
Anam Fatima ◽  
Rehana Rani ◽  
Ayesha Maqbool ◽  
Samea Khan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Dynamics ◽  
Plasmodium Vivax ◽  
Surface Protein ◽  
Merozoite Surface Protein ◽  
Circumsporozoite Protein ◽  
Population Divergence ◽  
Large Sample Size ◽  
Base Line ◽  
Merozoite Surface Protein 1

Abstract Background Plasmodium vivax contributes to over 70% malaria burden in Pakistan, but limited data exists on various aspects including genetic diversity of the parasite as compared to other parts of the world. Since the information about the genetic diversity of P. vivax assists to understand the population dynamics of the parasite, the current study was designed to understand population divergence of P. vivax in Pakistan using circumsporozoite protein (pvcsp) and merozoite surface protein-1 (pvmsp-1) genes as molecular markers. Methods The PCR for pvcsp and pvmsp-1 genes was carried out for 150 P. vivax isolates, followed by DNA sequencing of 35 and 30, respectively. Genetic diversity and polymorphism were analysed using ChromasPro, ClustalW, MEGA7, DnaSP v.5 and WebLogo programs. Results The PCR for pvcsp and pvmsp-1 genes was carried out for 150 P. vivax isolates and resulting the PCR products of 1100 bp for pvcsp and ~ 400 bp for pvmsp-1 genes, respectively. In the central-repeat region (CRR) of pvcsp gene, sequences comprised of four variable repeats of PRMs, out of which GDRADGQPA (PRM1), GDRAAGQPA (PRM2) were more extensively dispersed among the P. vivax isolates. Partial sequences (~ 400 bp) of block 2 of pvmsp-1 gene depicted high level of diversity. Conclusion The results revealed the polymorphism and genetic diversity especially at the CRR of pvcsp and block 2 of pvmsp-1 genes, respectively. The base-line data presented here warrants future studies to investigate more into the genetic diversity of P. vivax with large sample size from across the country for better understanding of population dynamics of P. vivax that will help to control malaria at individual and community level.

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