scholarly journals Analysis of Single-Nucleotide Polymorphisms in the crt-o and mdr1 Genes of Plasmodium vivax among Chloroquine-Resistant Isolates from the Brazilian Amazon Region

2009 ◽  
Vol 53 (8) ◽  
pp. 3561-3564 ◽  
Author(s):  
Pamela Orjuela-Sánchez ◽  
Franklin Simões de Santana Filho ◽  
Ariane Machado-Lima ◽  
Yonne Francis Chehuan ◽  
Mônica Regina Farias Costa ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Plasmodium Vivax ◽  
Brazilian Amazon ◽  
Chloroquine Resistance ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Noncoding Sequences ◽  
Brazilian Amazon Region ◽  
Virulent Phenotype

ABSTRACT Plasmodium vivax parasites with chloroquine resistance (CQR) are already circulating in the Brazilian Amazon. Complete single-nucleotide polymorphism (SNP) analyses of coding and noncoding sequences of the pvmdr1 and pvcrt-o genes revealed no associations with CQR, even if some mutations had not been randomly selected. In addition, striking differences in the topologies and numbers of SNPs in these transporter genes between P. vivax and P. falciparum reinforce the idea that mechanisms other than mutations may explain this virulent phenotype in P. vivax.

Single Nucleotide Polymorphism Analysis of Pvmdr-1 in Plasmodium Vivax Isolated From Military Personnel of Republic of Korea in 2016 and 2017

2021 ◽  
Author(s):  
Jin-Jong Bong ◽  
Wonsig Lee ◽  
Qu-Ehn Park ◽  
Kyung Tae Noh
Keyword(s):  
Plasmodium Vivax ◽  
Chloroquine Resistance ◽  
Republic Of Korea ◽  
Multi Drug Resistance ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Malaria Chemoprophylaxis ◽  
Resistance Protein

Abstract Background: Malaria chemoprophylaxis using chloroquine and primaquine has been administered to resident soldiers in the 3rd Army of Republic of Korea (ROK) to prevent malaria infection since the year 1997. Due to mass chemoprophylaxis against malaria, concern exists about occurrence of chloroquine resistance. Herein, we investigated the single nucleotide polymorphisms (SNPs) of the Plasmodium vivax multi-drug resistance protein-1 (Pvmdr-1) gene to monitor the risk of chloroquine resistance.Methods: To evaluate the risk of malaria chemoprophylaxis, SNPs of the Pvmdr-1 gene were analysed in 73 soldiers of the 3rd Army of ROK diagnosed with infection by Plasmodium vivax. Results: Quintuple mutations (G698S, L845F, M908L, T958M, and F1076L) were detected in 73 soldiers. Mutation in the Y541C position was detected in soldiers at a frequency of 1.3% (1/73). In addition, silent mutations were detected at positions 44K, 493L, 529T, and 1233E. Based on these SNPs, Pvmdr-1 sequences of ROK were classified into 6 haplotypes. Phylogenetic analysis showed that the neighbourhood of the 6 haplotypes were Chaina_NB-16 and Papua New Guinea-PNG58 (Figure 1).Conclusions: Genetic- or phenotypic-based chloroquine resistance was not observed. However, various SNPs including a newly identified non-synonymous mutation (Y541C) have been introduced into Plasmodium vivax malaria endemic areas in ROK. Thus, to prevent the emergence of chloroquine resistance, continuous surveillance for SNPs of Pvmdr-1 related with chloroquine resistance is essential in the malaria chemoprophylaxis-executed regions of ROK.

scholarly journals Single-Nucleotide-Polymorphism-Specific PCR for Quantification and Discrimination of Chlamydia pneumoniae Genotypes by Use of a “Locked” Nucleic Acid

2006 ◽  
Vol 72 (5) ◽  
pp. 3785-3787 ◽  
Author(s):  
Jan Rupp ◽  
Werner Solbach ◽  
Jens Gieffers
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Chlamydia Pneumoniae ◽  
Locked Nucleic Acid ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Intraspecies Diversity

ABSTRACT Single-nucleotide polymorphisms (SNPs) are targets to discriminate intraspecies diversity of bacteria and to correlate a genotype with a potential pathotype. Quantification of polygenotypic populations supports this task for in vitro and in vivo applications. We present a novel assay capable of quantifying mixtures of two genotypes differing by only one SNP.

scholarly journals Quantitative Analysis of Single-Nucleotide Polymorphism for Rapid Detection of TR34/L98H- and TR46/Y121F/T289A-Positive Aspergillus fumigatus Isolates Obtained from Patients in Iran from 2010 to 2014

2015 ◽  
Vol 60 (1) ◽  
pp. 387-392 ◽  
Author(s):  
Faezeh Mohammadi ◽  
Seyed Jamal Hashemi ◽  
Jan Zoll ◽  
Willem J. G. Melchers ◽  
Haleh Rafati ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Quantitative Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Aspergillus Fumigatus ◽  
Tandem Repeat ◽  
Promoter Region ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type

ABSTRACTWe employed an endpoint genotyping method to update the prevalence rate of positivity for the TR34/L98H mutation (a 34-bp tandem repeat mutation in the promoter region of thecyp51Agene in combination with a substitution at codon L98) and the TR46/Y121F/T289A mutation (a 46-bp tandem repeat mutation in the promoter region of thecyp51Agene in combination with substitutions at codons Y121 and T289) among clinicalAspergillus fumigatusisolates obtained from different regions of Iran over a recent 5-year period (2010 to 2014). The antifungal activities of itraconazole, voriconazole, and posaconazole against 172 clinicalA. fumigatusisolates were investigated using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) broth microdilution method. For the isolates with an azole resistance phenotype, thecyp51Agene and its promoter were amplified and sequenced. In addition, using a LightCycler 480 real-time PCR system, a novel endpoint genotyping analysis method targeting single-nucleotide polymorphisms was evaluated to detect the L98H and Y121F mutations in thecyp51Agene of all isolates. Of the 172A. fumigatusisolates tested, the MIC values of itraconazole (≥16 mg/liter) and voriconazole (>4 mg/liter) were high for 6 (3.5%). Quantitative analysis of single-nucleotide polymorphisms showed the TR34/L98H mutation in thecyp51Agenes of six isolates. No isolates harboring the TR46/Y121F/T289A mutation were detected. DNA sequencing of thecyp51Agene confirmed the results of the novel endpoint genotyping method. By microsatellite typing, all of the azole-resistant isolates had genotypes different from those previously recovered from Iran and from the Dutch TR34/L98H controls. In conclusion, there was not a significant increase in the prevalence of azole-resistantA. fumigatusisolates harboring the TR34/L98H resistance mechanism among isolates recovered over a recent 5-year period (2010 to 2014) in Iran. A quantitative assay detecting a single-nucleotide polymorphism in thecyp51Agene ofA. fumigatusis a reliable tool for the rapid screening and monitoring of TR34/L98H- and TR46/Y121F/T289A-positive isolates and can easily be incorporated into clinical mycology algorithms.

NIASGBsnp: integration of single nucleotide polymorphism data of rice (Oryzasativa L.) genetic resources

2013 ◽  
Vol 11 (3) ◽  
pp. 221-224
Author(s):  
Masaru Takeya ◽  
Fukuhiro Yamasaki ◽  
Sachiko Hattori ◽  
Kaworu Ebana
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Plant Pathology ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Resources ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Snp Data ◽  
Polymorphism Data

The NIASGBsnp system manages data on single nucleotide polymorphisms (SNPs) of rice (Oryzasativa L.) genetic resources in the National Institute of Agrobiological Science (NIAS) Genebank. NIASGBsnp currently holds data on 768 SNP markers for 301 rice accessions and plans to add the SNP data of active rice accessions in the NIAS Genebank. It can show differences between accessions by graphical genotyping. Passport, characteristics and evaluation data of accessions can be retrieved to allow phenotype to be associated with genotype. NIASGBsnp will support various research purposes such as genomic selection and plant pathology research.

scholarly journals THE EFFECT OF SINGLE NUCLEOTIDE POLYMORPHISM (SNP) IN GLIOBLASTOMA MULTIFORME

2021 ◽  
Author(s):  
Asmita Ghosh ◽  
Dattatreya Mukherjee ◽  
Parth Patel ◽  
Debraj Mukhopadhyay
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Glioblastoma Multiforme ◽  
Association Studies ◽  
Disease Onset ◽  
Genetic Alterations ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Single nucleotide polymorphism is a genetic substitution of a base pair at a single position of the genome. SNPs are a common phenomenon and influence mRNA expression. Half of the SNPs occur in the non-coding region with 25% being mis-sense mutation and 25% being silent mutations. SNPs belong to the last generation of molecular markers which is identified through SNP mapping. SNPs are extensively studied to distinguish genetic expression and protein synthesis. These genetic differences are a major source of diseases in humans like cancers. One of the most common types of cancer of the brain is the Glioblastoma Multiforme that accounts for more than 80% of the malignant primary brain tumors (PBT). Researchers have found out a potential role of various SNPs in the genome to have a strong relation with Glioma formation and proliferation. Most SNPs are either not discovered, or their biological mechanisms are unknown, making it difficult to link putative associations with disease onset. The given review aims to identify some of the most common SNPs associated with GBM and classify the genetic basis along with future prospects. These SNPs are pioneer in Genome Wide Association studies to help in cancer research and identification of specific genetic alterations liked to GBM. Single Nucleotide Polymorphisms in a gene can be used as genetic biomarkers to aid better understanding of the mechanism of cancer formation, its aetiology, progression and metastatic behaviour.

scholarly journals TNF-α -308G/A polymorphism and susceptibility to tuberculosis in Azeri population of Iran

Genetika ◽  
2016 ◽  
Vol 48 (3) ◽  
pp. 819-826 ◽  
Author(s):  
Sajjad Ghorghanlu ◽  
Mohammad Asgharzadeh ◽  
Hossein Samadi-Kafil ◽  
Fatemeh Khaki-Khatibi ◽  
Jalil Rashedi ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Tuberculosis Patient ◽  
P Value ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Tuberculosis Patients ◽  
Specific Pcr ◽  
Allele Specific ◽  
And Function

Single nucleotide polymorphisms (SNPs) in cytokine genes may alter the level and function of secreted cytokine; therefore, SNPs can influence the immune response. The aim of the present study was to determine the association of TNF-? -308G/A single nucleotide polymorphism in tuberculosis patients in the Azeri population of Iran. The TNF-308G/A single nucleotide polymorphism in the promoter region was genotyped by using the allele-specific PCR method in 200 healthy controls and 124 tuberculosis patients. The distribution of allele frequencies for TNF-? -308G/A polymorphism between control and tuberculosis patient groups was not significant (P-value = 0.058, OR = 1.5). Furthermore, no statistically significant association was found between TNF-? -308G/A genotype and resistance/susceptibility to TB (P-value = 0.102). Our results suggest that TNF-? -308G/A polymorphism has no measurable effect on the development of tuberculosis in Azeri population of Iran.

scholarly journals Single-Nucleotide Polymorphism and Copy Number Variation of the Multidrug Resistance-1 Locus of Plasmodium vivax: Local and Global Patterns

2012 ◽  
Vol 87 (5) ◽  
pp. 813-821 ◽  
Author(s):  
Rosa del Carmen Miluska Vargas-Rodríguez ◽  
Maria José Menezes ◽  
Pamela Orjuela-Sánchez ◽  
Marcelo U. Ferreira ◽  
Melissa da Silva Bastos
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Multidrug Resistance ◽  
Copy Number Variation ◽  
Plasmodium Vivax ◽  
Copy Number ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Number Variation ◽  
Global Patterns

scholarly journals The Fibroblast of the Relationship Between FGFR2 Gene Rs2981582 Polymorphism and Breast Cancer Risk

2021 ◽  
Vol 24 (1) ◽  
pp. 122-135
Author(s):  
Ahmad Hamta‌ ◽  
◽  
Sahar Adl ◽  
Keyword(s):  
Breast Cancer ◽  
Single Nucleotide Polymorphism ◽  
Single Nucleotide Polymorphisms ◽  
Growth Factor Receptor ◽  
Tyrosine Kinase Receptor ◽  
Cancer Type ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Fgfr2 Gene

Background and Aim: Breast cancer is the most common cancer type and the leading cause of cancer-induced deaths in women, worldwide. The Fibroblast Growth Factor Receptor 2 (FGFR2) is a tyrosine kinase receptor that plays an essential role in the growth, invasion, movement, and angiogenesis of tumor cells. Several single nucleotide polymorphisms have been found in the intron 2 of the FGFR2 gene, i.e., associated with a high risk of breast cancer. Genetic variation in this receptor is a new risk factor for breast cancer. The current study aimed to evaluate the association of single-nucleotide polymorphism rs2981582C/T in women with breast cancer. Methods & Materials: In total, 80 women with breast cancer and 80 healthy women (controls) were selected from Markazi Province, Iran to participate in this research. Polymorphism rs2981582 was analyzed to investigate its association with breast cancer. DNA extraction from blood samples was performed using a kit. The presence of these single-nucleotide polymorphisms was determined by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR - RFLP). Statistical analyses were performed by SPSS using Chi-squared test at P≤0.05. Ethical Considerations: This study was approved by the Ethics Committee of the Arak University (Code: IR.ARAKMU.REC.1395.28). Results: Significant differences were observed in the frequency of rs2981582 polymorphism in the FGFR2 gene between the control and patient groups (P=0.000). In the patient group, the TT genotype was significantly associated with the risk of breast cancer (P=0.001; OR=3.566). On the other hand, allele C indicated a protective role against the disease (P=0.000). Conclusion: The obtained data revealed a significant relationship between rs2981582 C/T polymorphism and the risk of breast cancer; thus, this single-nucleotide polymorphism could be used as a biomarker to predict breast cancer.

scholarly journals Novel Multiplex Single Nucleotide Polymorphism-Based Method for Identifying Epidemic Clones of Listeria monocytogenes

2011 ◽  
Vol 77 (17) ◽  
pp. 6290-6294 ◽  
Author(s):  
Sara Lomonaco ◽  
Stephen J. Knabel ◽  
Alessandra Dalmasso ◽  
Tiziana Civera ◽  
Maria Teresa Bottero
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Listeria Monocytogenes ◽  
Single Nucleotide Polymorphisms ◽  
High Throughput ◽  
High Throughput Screening ◽  
Virulence Genes ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type

ABSTRACTA novel primer extension-based, multiplex minisequencing assay targeting six highly informative single nucleotide polymorphisms (SNPs) in four virulence genes correctly identified and differentiated all four epidemic clones (ECs) ofListeria monocytogenesand 9 other strains initially misclassified as non-ECs. This assay allows rapid, accurate, and high-throughput screening for all known ECs ofL. monocytogenes.

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