scholarly journals A Single-Nucleotide Polymorphism in a Methylatable Foxa2 Binding Site of the G6PC2 Promoter Is Associated With Insulin Secretion In Vivo and Increased Promoter Activity In Vitro

Diabetes ◽  
2008 ◽  
Vol 58 (2) ◽  
pp. 489-492 ◽  
Author(s):  
C. Dos Santos ◽  
P. Bougneres ◽  
D. Fradin
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Insulin Secretion ◽  
Binding Site ◽  
Promoter Activity ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Insulin Secretion In Vivo

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 A Novel Assay for Viral MicroRNA Function Identifies a Single Nucleotide Polymorphism That Affects Drosha Processing

2006 ◽  
Vol 80 (11) ◽  
pp. 5321-5326 ◽  
Author(s):  
Eva Gottwein ◽  
Xuezhong Cai ◽  
Bryan R. Cullen
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Target Genes ◽  
Human Herpesvirus ◽  
Northern Analysis ◽  
Luciferase Expression ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Stem Loop

ABSTRACT MicroRNAs (miRNAs) are a class of ∼22-nucleotide noncoding RNAs that inhibit the expression of specific target genes at the posttranscriptional level. Recently, 11 miRNAs encoded by the pathogenic human herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) were cloned from latently infected cells. While the expression of these miRNAs has been confirmed by Northern analysis, their ability to inhibit target gene expression has not been demonstrated. We have devised a novel assay for miRNA function that uses lentiviral indicator vectors carrying two perfectly complementary target sites for each given miRNA in the 3′ untranslated region of the Renilla luciferase gene. This assay allowed us to demonstrate the activity of each viral miRNA upon cotransduction of cells with the Renilla luciferase indicator vector together with a firefly luciferase control vector. In KSHV-infected BC-1 and BCBL-1 cells, but not uninfected control cells, Renilla luciferase expression was selectively reduced up to 10-fold. Interestingly, one of the viral miRNAs (miR-K5) exhibited much higher activity in BC-1 cells than in BCBL-1 cells. Sequence analysis of both viral genomes revealed a single nucleotide polymorphism in the miR-K5 precursor stem-loop, which inhibits the expression of mature miR-K5 in BCBL-1 cells. We show that the primary miR-K5 sequence present in BCBL-1 results in diminished processing by Drosha both in vivo and in vitro. This is the first report of a naturally occurring sequence polymorphism in an miRNA precursor that results in reduced processing and therefore lower levels of mature miRNA expression and function.

193 BOVINE EMBRYO GENOTYPING USING A 50K SINGLE NUCLEOTIDE POLYMORPHISM CHIP

2011 ◽  
Vol 23 (1) ◽  
pp. 197 ◽  
Author(s):  
A. D. Le Bourhis ◽  
E. Mullaart ◽  
P. Humblot ◽  
W. Coppieters ◽  
C. Ponsart
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Room Temperature ◽  
Drop Out ◽  
Bovine Embryo ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Good Efficiency ◽  
Student’S T

Genomic tools are now available for most livestock species and are used routinely for marker-assisted selection (MAS) and genomic selection (GS) in cattle. Recently, multiple-marker detection has been achieved from biopsies of preimplantation stage embryos, thus allowing embryos to be selected before transfer (Le Bourhis et al. 2009 Reprod. Fertil. Dev. 21, 192 abst). This strategy provides the opportunity to estimate some traits of particular interest, the presence of genetic abnormalities, or both. The present work aimed to assess the efficiency of MAS/GS evaluation from biopsied bovine embryos by using the bovine 50K single nucleotide polymorphism (SNP) Illumina chip. A biopsy of 5 to 10 cells was obtained under laboratory conditions, using a microblade under a stereomicroscope, from 29 in vitro-cultured morulae and blastocysts. Biopsies were transferred individually as dry samples in tubes and sent frozen (n = 13) or at room temperature (n = 16) to the genotyping laboratory. The genomic DNA of each biopsy was amplified using a whole-genome amplification (WGA) kit according to the manufacturer’s instructions (Qiagen REPLI-g® Mini Kit, Qiagen, Valencia, CA). Following WGA, DNA concentration was determined by using PicoGreen. For subsequent genotyping, a custom CRV 50K Illumina chip was used. Call rates were calculated from 50 905 SNP. Percentage of allele drop-out (%ADO), which was estimated from the number of heterozygous markers [%ADO = (calculated hetero – observed hetero)/calculated hetero]. Parentage error was estimated from 12 embryos by using the genotypes of the parents of the embryos. Both groups of transport conditions were compared using Student’s t-test. Results are presented as mean ± SEM. A greater quantity of DNA was obtained after amplification of biopsies that were sent frozen to the laboratory when compared with those at room temperature (P < 0.05). However, the SNP call rate, %ADO, and parentage error did not differ between groups. These results indicate that genotyping from embryo biopsies following WGA can be achieved with good efficiency when using high-density marker chips. To validate the use of MAS/GS from early embryos in breeding schemes, a larger number of in vivo embryos are currently genotyped under field conditions. This will allow the reliability of this method to be assessed and the correlation between embryo and calf genetic evaluation to be quantified with the current WGA efficiency. Table 1.Amount of DNA after WGA and genotyping results

scholarly journals A miRNA Binding Site Single-Nucleotide Polymorphism in the 3′-UTR Region of the IL23R Gene Is Associated with Breast Cancer

PLoS ONE ◽  
2012 ◽  
Vol 7 (12) ◽  
pp. e49823 ◽  
Author(s):  
Lihong Wang ◽  
Wei Liu ◽  
Wei Jiang ◽  
Jing Lin ◽  
Yongdong Jiang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Single Nucleotide Polymorphism ◽  
Binding Site ◽  
Mirna Binding Site ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals A Novel Single-Nucleotide Polymorphism Loop Mediated Isothermal Amplification Assay for Detection of Artemisinin-Resistant Plasmodium falciparum Malaria

2018 ◽  
Vol 5 (4) ◽  
Author(s):  
Abu Naser Mohon ◽  
Didier Menard ◽  
Mohammad Shafiul Alam ◽  
Kevin Perera ◽  
Dylan R Pillai
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Dynamic Range ◽  
Developed Countries ◽  
Isothermal Amplification ◽  
Test Method ◽  
Nucleotide Polymorphism ◽  
In Vitro Susceptibility ◽  
Single Nucleotide ◽  
Loop Mediated Isothermal Amplification

Abstract Background Artemisinin-resistant malaria (ARM) remains a significant threat to malaria elimination. In the Greater Mekong subregion, the prevalence of ARM in certain regions has reached greater than 90%. Artemisinin-resistant malaria is clinically identified by delayed parasite clearance and has been associated with mutations in the propeller domain of the kelch 13 gene. C580Y is the most prevalent mutation. The detection of ARM currently relies on labor-intensive and time-consuming methods such as clinical phenotyping or in vitro susceptibility testing. Methods We developed a novel single-nucleotide polymorphism loop mediated isothermal amplification (SNP-LAMP) test method for the detection of the C580Y mutation using a novel primer design strategy. Results The SNP-LAMP was 90.0% sensitive (95% confidence interval [CI], 66.9–98.3) and 91.9% specific (95% CI, 82.6–96.7) without knowledge of the parasite load and was 100% sensitive (95% CI, 79.9–100) and 97.3% specific (95% CI, 89.7–99.5) when the parasitemia was within the assay dynamic range. Tests with potential application near-to-patient such as SNP-LAMP may be deployed in low- and middle-income and developed countries. Conclusions Single-nucleotide polymorphism LAMP can serve as a surveillance tool and guide treatment algorithms for ARM in a clinically relevant time frame, prevent unnecessary use of additional drugs that may drive additional resistance, and avoid longer treatment regimens that cause toxicity for the patient.

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