scholarly journals The TLR9 2848C/T Polymorphism Is Associated with the CMV DNAemia among HIV/CMV Co-Infected Patients

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2360
Author(s):  
Agnieszka Jabłońska ◽  
Elżbieta Jabłonowska ◽  
Mirosława Studzińska ◽  
Juliusz Kamerys ◽  
Edyta Paradowska
Keyword(s):  
Innate Immune ◽  
Wild Type ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Essential Components ◽  
Immunodeficiency Virus ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Molecular Patterns ◽  
Cmv Dnaemia

Toll-like receptors (TLRs) recognize pathogen-associated molecular patterns and are essential components of the host’s innate immune response. The aim of this study was to determine the TLR9 genotype frequency and investigate the association between TLR9 polymorphisms and cytomegalovirus (CMV) DNAemia in human immunodeficiency virus (HIV)/CMV co-infected patients. A total of 205 HIV/CMV co-infected adults were screened for the presence of the four TLR9 polymorphisms (−1237T/C, −1486T/C, 1174G/A, and 2848C/T) by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Mutation presented in at least one allele of the TLR9 2848C/T single nucleotide polymorphism (SNP) was associated with the occurrence of CMV DNAemia among HIV-infected patients with CMV co-infection (p = 0.004). The level of CMV DNA was higher in patients who were homozygous recessive or heterozygous for the 2848C/T polymorphism compared with those who had a wild-type genotype for this polymorphism (p = 0.005). Mutation detected in at least one allele of this SNP was also associated with a lower interferon type β (IFN-β) concentration (p = 0.048), while no relationships between TLR9 −1237T/C, −1486T/C, and 1174G/A SNPs and CMV DNAemia were observed. Our findings suggest that the mutation present in at least one allele of the TLR9 2848C/T SNP may be associated with the active CMV infection in HIV/CMV co-infected subjects.

scholarly journals Identifikasi Keragaman Gen DGAT1 serta Asosiasinya terhadap Karakteristik Karkas dan Sifat Perlemakan Domba

2019 ◽  
Vol 6 (2) ◽  
pp. 259
Author(s):  
Asep Gunawan ◽  
Ratna Sholatia Harahap ◽  
Kasita Listyarini ◽  
Cece Sumantri
Keyword(s):  
Polymerase Chain Reaction ◽  
Single Nucleotide Polymorphism ◽  
Fragment Length Polymorphism ◽  
Nucleotide Polymorphism ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Dgat1 Gene ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Restriction Fragment Length

ABSTRAK Karakteristik karkas dan sifat perlemakan pada daging domba dikontrol oleh banyak gen salah satunya gen DGAT1 (Diacylglycerol Acyltransferasel 1). Penelitian ini bertujuan mengidentifikasi SNP (Single Nucleotide Polymorphism) gen DGAT1 pada titik mutasi g.8539 C>T dan asosiasinya terhadap karakteristik karkas dan sifat perlemakan pada domba Indonesia. Total sampel domba yang digunakan sebanyak 150 buah terdiri dari 35 sampel domba compass agrinak (DCA), 36 sampel domba barbados cross (DBC), 41 sampel domba komposit garut (DKG), 20 sampel domba ekor gemuk (DEG), dan 18 sampel domba ekor tipis (DET). Karakteristik karkas dan sifat perlemakan diukur dari domba jantan berumur 10-12 bulan. Identifikasi keragaman DGAT1|ALuI dianalisis dengan metode PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). Hasil keragaman gen DGAT1 bersifat polimorfik dalam DET dan DEG, sedangkan DCA, DBC, dan DKG bersifat monomorfik. Dua genotipe disebut CC dan  CT ditemukan dalam DET dan DEG. Titik mutasi gen DGAT1 berasosiasi (P<0.05) dengan karakteristik karkas, yaitu bobot dan panjang karkas. Selain itu, keragaman gen DGAT1 juga berasosiasi signifikan (P<0.05) dengan asam lemak jenuh, yaitu asam stearat (C18:0) dan asam arakidat (C20:0) dan asam lemak tak jenuh tunggal, yaitu asam oleat (C18:1n9c). Gen DGAT1 memiliki kontribusi dalam karakteristik karkas dan komposisi asam lemak pada domba.Kata Kunci: domba, gen DGAT1, karakteristik karkas, PCR-RFLP, sifat perlemakan                                                              ABSTRACT            Characteristic of carcass and fatness traits of sheep is regulated by many genes such as DGAT1 (Diacylglycerol Acyltransferasel 1) gene. The research was aimed to investigate SNP (Single Nucleotide Polymorphism) of DGAT1 and its association with characteristic of carcass and fatness traits in Indonesian sheep. A total sample of sheeps used 150 rams of 10–12 months consisted 35 samples of compas agrinak sheep (CAS), 36 of barbados cross (BCS), 41 of garut composite (GCS), 20  of javanese fat tailed (JFT), and 18 of javanese thin tailed (JTT). Identification variant of DGAT1|ALuI were performed by PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). The results of polymorphism of DGAT1 were found in JTT and JFT. However, SNP of DGAT1 in CAS, BCS and GCS were monomorfic. Two genotype namely CC and CT were found in JTT and JFT populations. A SNP of the DGAT1 was associated (P<0.05) with characteristic of carcass, including weight and length of carcass. The variant of DGAT1 was associated too with saturated fatty acids (SFA) including stearic acid (C18:0) and arachidic acid (C20:0), and mono unsaturated fatty acid (MUFA) including oleic acid (C18:1n9c). The DGAT1 gene was contribute to characteristic carcass and fatty acid composition in sheep.Keywords: DGAT1 gene, characteristic carcass, fatness traits, PCR-RFLP, sheep

scholarly journals Association Study between BGLAP Gene HindIII Polymorphism and Type 2 Diabetes Mellitus Development in Ukrainian Population

2019 ◽  
Vol 2019 ◽  
pp. 1-7
Author(s):  
Yaroslav D. Chumachenko ◽  
Viktoriia Yu. Harbuzova ◽  
Alexander V. Ataman
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Single Nucleotide Polymorphism ◽  
Type 2 Diabetes Mellitus ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Hindiii Polymorphism ◽  
Polymerase Chain

Type 2 diabetes mellitus (T2DM) belongs to the diseases with hereditary predisposition, so both environmental and genetic factors contribute to its development. Recent studies have demonstrated that the skeleton realizes systemic regulation of energy metabolism through the secretion of osteocalcin (OCN). Thus, the association analysis between HindIII single nucleotide polymorphism of OCN gene (BGLAP) promoter region and T2DM development in Ukrainian population was carried out. 153 individuals diagnosed with T2DM and 311 control individuals were enrolled in the study. The genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The lack of association between BGLAP HindIII single nucleotide polymorphism (SNP) and T2DM development among Ukrainians was found. Further studies with extended groups of comparison are needed to confirm the obtained results.

Effects of prolactin receptor genotype on the litter size of Mangalica

2011 ◽  
Vol 59 (2) ◽  
pp. 269-277 ◽  
Author(s):  
Károly Tempfli ◽  
Gergely Farkas ◽  
Zsolt Simon ◽  
Ágnes Bali Papp
Keyword(s):  
Litter Size ◽  
Fragment Length Polymorphism ◽  
Prolactin Receptor ◽  
Hair Follicles ◽  
Nucleotide Polymorphism ◽  
Allelic Discrimination ◽  
Single Nucleotide ◽  
Breed Group ◽  
Pcr Rflp ◽  
Polymerase Chain

The aim of this study was to detect different alleles of the prolactin receptor (PRLR) gene and to examine their effects on the litter size of the indigenous Hungarian pig, the Mangalica. G1789A single nucleotide polymorphism (SNP) was investigated as a candidate for litter size. Samples from 80 purebred Mangalica sows and data of their 335 litters were provided by Olmos & Tóth Ltd. Hair follicles were used to isolate the required DNA. Allelic discrimination was performed by means of the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method using the AluI restriction enzyme and agarose gel electrophoresis. In the population examined, the A allele was found to be preferable in the Mangalica breed group. The most advantageous AA genotype was the least prevalent (8.75%), while the frequencies of AB and BB were 40% and 51.25%, respectively. Remarkably, the average number of piglets born alive per litter was 1.11 ± 0.39 higher in sows with AA as compared to those with BB genotype. By raising the frequency of the AA genotype, the litter size is likely to increase. However, the effect of PRLR genotypes can differ among pig breeds and even lines. Further studies may be required to observe and estimate possible pleiotropic effects of this polymorphism on other traits.

scholarly journals Genotype TNF-α(-308) and Silicosis on Factory Workers in Vietnam in 2020

2021 ◽  
Vol 1 (2) ◽  
Author(s):  
Viet NGUYEN ◽  
Thi Thu Huyen NGUYEN ◽  
Xuan Dat DAO ◽  
Xuan Quy VU ◽  
Thi Quan PHAM ◽  
...  
Keyword(s):  
Average Concentration ◽  
Control Group ◽  
Case Group ◽  
Nucleotide Polymorphism ◽  
Factory Workers ◽  
Single Nucleotide ◽  
Tnf Α ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Study Participants

The studFigy aims to determine the TNF-α single-nucleotide polymorphism TNF-α (-308) andassess the association of TNF-a(-308) SNP with the risk of silicosis among workers directly exposed tosilica dust in Vietnam. A study was undertaken among 78 cases with silicosis and 103 controls withoutsilicosis in Vietnam. Blood samples were collected for genomic DNA extraction from each subject. Thephenotyping of TNF-α(-308) was performed using polymerase chain reaction‐based restriction fragmentlength polymorphism (PCR‐RFLP) and dye termination sequencing. Results: The average exposure timeof the case group was slightly higher than that of the control group (12.46 ± 6.732 years vs. 12.09 ± 7.854years). The majority of genotypes in both silicosis and non-silicosis was GG. When analyzing theconcentration of TNF-α in the study participants' blood, it is shown that the average concentration of TNF-α in the case group was higher than that in the control group. The genotype AG in the case group was1.368 times higher than that in the control group. The percentage of all A alleles in the case group withsilicosis was 1.342 times higher than the control group without the disease, similar to previous studies.Conclusion: The majority of genotypes in both groups was GG. The average concentration of TNF-α inblood, genotype AG, and the percentage of all A alleles in the case group was higher than that in thecontrol group.

Comparison of SNP-Based Detection Assays for Food Analysis: Coffee Authentication

2014 ◽  
Vol 97 (4) ◽  
pp. 1114-1120 ◽  
Author(s):  
Stelios Spaniolas ◽  
Christos Bazakos ◽  
Gregory A Tucker ◽  
Malcolm J Bennett
Keyword(s):  
Detection Methods ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Advantages And Disadvantages ◽  
Coffee Beans ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Analytical Approaches ◽  
Rflp Assay ◽  
Food Model

Abstract Recently, DNA-based authentication methods were developed to serve as complementary approaches to analytical chemistry techniques. The single nucleotide polymorphism (SNP)-based reaction chemistries, when combined with the existing detection methods, could result in numerous analytical approaches, all with particular advantages and disadvantages. The dual aim of this study was (a) to develop SNP-based analytical assays such as the single-base primer extension (SNaPShotTM) and pyrosequencing in order to differentiate Arabica and Robusta varieties for the authentication of coffee beans and (b) to compare the performances of SNaPshot, pyrosequencing and the previously developed polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using an Agilent 2100 Bioanalyzer on the basis of linearity (R2) and LOD, expressed as percentage of the adulterant species, using green coffee beans (Arabica and Robusta) as a food model. The results showed that SNaPshot analysis exhibited the best LOD, whereas pyrosequencing revealed the best linearity (R2 = 0.997). The PCR-RFLP assay using the Agilent 2100 Bioanalyzer could prove to be a very useful method for a laboratory that lacks sequencing facilities but it can be used only if a SNP creates/deletes a restriction site.

scholarly journals The Relationship Between the PPARδ-87T>C Polymorphism and Colorectal Cancer Risk in a Chinese Han Population

2020 ◽  
Author(s):  
ZongGuang Zhou ◽  
Bo Dong ◽  
Lie Yang ◽  
Bin Zhou ◽  
Dan Zhang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Fragment Length Polymorphism ◽  
Clinicopathological Parameters ◽  
Nucleotide Polymorphism ◽  
Chain Reaction ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Han Population ◽  
Pcr Rflp ◽  
Polymerase Chain

Abstract BackgroundPeroxisome proliferator-activated receptor-β/δ (PPARβ/δ) is a transcription factor that has the potential to be associated with the development of colorectal cancer (CRC). However, the exact role of PPARδ in the context of CRC development remains to be clarified. This present study was thus designed to understand the association between CRC risk and the PPARδ-87T>C single nucleotide polymorphism (SNP) in a western Chinese Han population. MethodsThe PPARδ-87T>C (rs2016520) polymorphism was analyzed via the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach in 410 CRC patients and 496 frequency-matched healthy controls via a case-control study design. Relationships between PPARδ-87T>C polymorphisms and clinicopathological parameters were assessed using Pearson chi-squared tests or Fisher's exact test, Odds ratios (ORs) and 95% confidence intervals (CIs) were used to evaluate the association between the PPARδ-87T>C SNP and CRC risk. ResultsWe observed significant differences in genotypic frequencies when comparing CRC patients (TT 62%, TC 32%, and CC 6.1%) and controls (TT 65.5%, TC 32,3%, and CC 22%). In addition, PPARδ-87T>C genotype was associated with tumor differentiation (P=0.033), but was unrelated to clinicopathological parameters in CRC patients. An unconditioned logistic regression model analysis revealed that individuals harboring the homozygous CC genotype exhibited an elevated CRC risk relative to those harboring the TT genotype (OR=2.931,95% CI =1.41- 6.08; P=0.004).ConclusionsOur findings indicate that the homozygous PPARδ-87T>C CC genotype is associated with an elevated CRC risk as compared to the homozygous TT genotype, indicating that PPARδ-87T>C polymorphisms have the potential to serve as a marker for CRC risk. Keywords PPARδ, Colorectal cancer (CRC), Single nucleotide polymorphism (SNP), Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)

scholarly journals Polymorphism of DTNBP1 Gene P 1635 (Rs3213207) In Schizophrenic Javanese, Indonesia

2019 ◽  
Vol 18 (4) ◽  
pp. 703-705
Author(s):  
EM Sutrisna ◽  
Ratna Yuliani
Keyword(s):  
Medical Science ◽  
P Value ◽  
Genotype Distribution ◽  
Healthy Controls ◽  
Wild Type ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Exact Test ◽  
Pcr Products ◽  
Polymerase Chain

Background: Many putative genes were predicted as risk factors of schizophrenia. One of these genes is DTNBP1 gene. One of single nucleotide polymorphism (SNPs) of DTNBP1 gene is P1635 (rs3213207). Objective: This study aimed to find out the association between DTNBP1 gene, P1635 (rs3213207), and risk of schizophrenia. Methods: DNA was isolated from blood of 25 schizophrenia patients and 25 healthy controls. DNA was applied to restriction fragment length polymorphism polymerase chain reaction (RFLP PCR). PCR products were digested by BSr1 enzyme. Results: The results show that there are 24 AA genotype (wild type) from 25 Javanese schizophrenia patients and 1 GG homozygote, while all 25 of controls are AA genotype (wild type). The p value of Fisher’s exact test is 0,500. Conclusion: There is no significant differences of genotype distribution of SNP P 1635(rs3213207) between schizophrenia patients and healthy controls in Javanese population Bangladesh Journal of Medical Science Vol.18(4) 2019 p.703-705

An association of the MCP-1 and CCR2 single nucleotide polymorphisms with colorectal cancer prevalence

2017 ◽  
Vol 89 (5) ◽  
pp. 1-5 ◽  
Author(s):  
Anna Walczak ◽  
Karolina Przybyłowska-Sygut ◽  
Andrzej Sygut ◽  
Adrianna Cieślak ◽  
Michał Mik ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Fragment Length Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Cancer Prevalence ◽  
Pcr Rflp ◽  
Study Support ◽  
Polymorphic Variants ◽  
Polymerase Chain

The aim of the study: We evaluated the connection between the presence of the -2518 A/G MCP-1 as well as 190 G/A CCR2 polymorphic variants and colorectal cancer (CRC) occurrence. Material and methods: Study group consisted of subjects with different stages of CRC as well as healthy controls. Genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Results: W observed an association between the colorectal cancer and the GG genotype of the -2518 A/G MCP-1 single nucleotide polymorphism. No statistically significant correlation was found between CRC and the 190 G/A CCR2 polymorphism. Conclusion: The results of this study support the hypothesis that polymorphism in the MCP-1 gene may contribute to the etiology of colorectal cancer.

scholarly journals Association study of the BDNF gene polymorphism (G196A) with overweight/obesity among women from Northwest of Iran

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Haneieh Honarmand ◽  
Mortaza Bonyadi ◽  
Abbas Rafat ◽  
Reza Mahdavi ◽  
Fereshteh Aliasghari
Keyword(s):  
Analysis Of Covariance ◽  
Healthy Controls ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Logistic Regression Models ◽  
Molecular Alterations ◽  
Pcr Rflp ◽  
Obesity Trait ◽  
Northwest Of Iran ◽  
Polymerase Chain

Abstract Background Obesity is a health problem defined by surplus body fat accumulation and is one of the leading causes of morbidity and mortality. Earlier studies indicated the influence of brain-derived neurotrophic factor (BDNF) molecular alterations in the development of obesity. One of these variations is the G196A single nucleotide polymorphism (Val66Met; SNP rs6265), which impairs intracellular trafficking and reduces the secretion of BDNF. In this study, we evaluated the possible association of G196A polymorphism of the BDNF gene with body mass index (BMI) among women from the Iranian Azeri Turkish ethnic group. Four hundred eighty-four women including 343 women with obesity or overweight and 141 age-sex and ethnically matched healthy controls were genotyped for G196A SNP of BDNF gene by applying polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) method. The association of this polymorphism with BMI was evaluated using analysis of covariance (ANCOVA), and the comparison of alleles and genotypes frequencies between patients (obese and/or overweight participants) and healthy controls was carried out using logistic regression models. Results Individuals carrying Met-Met genotype have a significantly lower mean of BMI in comparison to those carrying non-Met/Met polymorphisms (P = 0.0138). Conclusions In this study, the association of the Val66Met polymorphism of the BDNF gene with BMI as an obesity trait has been confirmed among the women from the Northwest of Iran.

Sign in / Sign up

Export Citation Format

Share Document