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Tytuł:
The mRNA sequence polymorphisms of flowering key genes in bolting sensitive or tolerant sugar beet genotypes
Autorzy:
Alimirzaee, M.
Mirzaie-Asl, A.
Abdollahi, M.R.
Kolaei, H.E.
Fasahat, P.
Powiązania:
https://bibliotekanauki.pl/articles/79841.pdf
Data publikacji:
2017
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
sugar-beet
Beta vulgaris ssp.maritima
mRNA
polymorphism
flowering
single nucleotide polymorphism
genetic control
RNA extraction
protein structure prediction
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2017, 98, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Association of XRCC6 C1310G and LIG4 T9I polymorphisms of NHEJ DNA repair pathway with risk of colorectal cancer in the Polish population
Autorzy:
Balinska, Kinga
Wilk, Damian
Filipek, Beata
Mik, Michal
Zelga, Piotr
Skubel, Pawel
Dziki, Łukasz
Dziki, Adam
Mucha, Bartosz
Kabziński, Jacek
Majsterek, Ireneusz
Powiązania:
https://bibliotekanauki.pl/articles/1391955.pdf
Data publikacji:
2019
Wydawca:
Index Copernicus International
Tematy:
Colorectal Neoplasms/genetics
DNA-Binding Proteins/genetics
Genetic Predisposition to Disease/genetics
Genotype
Polymorphism
Single Nucleotide
Opis:
Introduction: Colorectal cancer is the second most common cancer worldwide. DNA double strand breaks (DSBs) are the most dangerous lesions which can lead to carcinogenesis. Nonhomologous end joining (NHEJ) is an important pathway, that allows for recovering DNA by direct end joining. The XRCC6 and LIG4 genes encode respectively Ku70 protein and human ATP-dependent DNA ligase, which are the components of the NHEJ repair pathway. The aim of our study was to evaluate the influence of XRCC6 C1310G and LIG4 T9I genes polymorphisms on colorectal cancer risk among Polish population. Materials and method: Genotyping was performed using TaqMan probes based on analysis of PCR products amplified in Real Time PCR. The research has been carried out on the material obtained from 100 patients with colorectal cancer and 100 cancer-free individuals who were age and sex-matched as a control group. The results were developed using the chi – squer test and odds ratio (OR). Results: Odd ratio analysis indicates reduced risk of colorectal cancer for LIG4 T9I polymorphism in heterozygotus model C/T (OR= 0.2717 95% CI= 0.1247-0,5918) and homozygous model T/T (OR= 0.3593 95% CI= 0.1394-0.9266). Similar situation we observed for XRCC6 C1310G gene polymorphism, which indicated on heterozygotus variant C/G (OR= 0.1181 95% CI= 0.0145-0.964) and homozygotus variant G/G (OR= 0.0972 95% CI= 0.0097-0.9713) to decrease the risk of colorectal cancer. Conslusions: Our research revealed XRCC6 C1310G and LIG4 T9I polymorphisms are associated with diminished risk of colorectal cancer. However, to confirm obtained results, a further investigations should be carried out.
Źródło:
Polish Journal of Surgery; 2019, 91, 3; 15-20
0032-373X
2299-2847
Pojawia się w:
Polish Journal of Surgery
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Association of the DIO2 gene single nucleotide polymorphisms with recurrent depressive disorder
Autorzy:
Gałecka, Elżbieta
Talarowska, Monika
Orzechowska, Agata
Górski, Paweł
Bieńkiewicz, Małgorzata
Szemraj, Janusz
Powiązania:
https://bibliotekanauki.pl/articles/1039107.pdf
Data publikacji:
2015
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
depressive disorder
iodothyronine deiodinase type II
polymorphism
haplotype
Opis:
Genetic factors may play a role in the etiology of depressive disorder. The type 2 iodothyronine deiodinase gene (DIO2) encoding the enzyme catalyzing the conversion of T4 to T3 is suggested to play a role in the recurrent depressive disorder (rDD). The current study investigates whether a specific single nucleotide polymorphism (SNP) of the DIO2 gene, Thr92Ala (T/C); rs 225014 or ORFa-Gly3Asp (C/T); rs 12885300, correlate with the risk for recurrent depression. Genotypes for these two single nucleotide polymorphisms (SNPs) were determined in 179 patients meeting the ICD-10 criteria for rDD group and in 152 healthy individuals (control group) using a polymerase chain reaction (PCR) based method. The specific variant of the DIO2 gene, namely the CC genotype of the Thr92Ala polymorphism, was more frequently found in healthy subjects than in patients with depression, what suggests that it could potentially serve as a marker of a lower risk for recurrent depressive disorder. The distribution of four haplotypes was also significantly different between the two study groups with the TC (Thr-Gly) haplotype more frequently detected in patients with depression. In conclusion, data generated from this study suggest for the first time that DIO2 gene may play a role in the etiology of the disease, and thus should be further investigated.
Źródło:
Acta Biochimica Polonica; 2015, 62, 2; 297-302
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Lack of signals of selection at candidate loci at a small geographical scale along a steep altitudinal gradient in Norway spruce (Picea abies [L.] Karst.)
Autorzy:
Hrivnak, M.
Krajmerova, D.
Gomory, D.
Powiązania:
https://bibliotekanauki.pl/articles/2117886.pdf
Data publikacji:
2019
Wydawca:
Polska Akademia Nauk. Czasopisma i Monografie PAN
Tematy:
local adaptation
single nucleotide polymorphisms
FST-outliers
spatial analysis method
Opis:
Local adaptation is a key concept in biology: shift of genetic structures of populations due to differential survival of genotypes is expected to lead to phenotypes providing an advantage in the local environment. Variation of sequences of twelve candidate genes was investigated in 13 Norway spruce (Picea abies (L.) Karst.) provenances originating from sites distributed along an altitudinal gradient from 550 to 1300 m a.s.l. Signals of selection were assessed in 103 single nucleotide polymorphisms (SNP). The Bayesian FST-outlier identification methods as implemented in the programs BayeScan and Arlequin did not identify any SNP with a clear evidence of selection. The approaches relying on SNP-climate associations (spatial analysis method based on logistic regression of allele frequencies with environmental variables, Bayesian method applied in BayEnv2) identified several relationships but none of them remained significant after correction for multiple testing. Gene flow, epigenetic inheritance and former management of the studied populations are discussed as potential reasons for this weak evidence of selec- tion signals.
Źródło:
Acta Biologica Cracoviensia. Series Botanica; 2019, 61, 1; 43-51
0001-5296
Pojawia się w:
Acta Biologica Cracoviensia. Series Botanica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Sustained virologic response and IL28B single-nucleotide polymorphisms in patients with chronic hepatitis C treated with pegylated interferon alfa and ribavirin
Autorzy:
Jabłonowska, Elżbieta
Piekarska, Anna
Koślińska-Berkan, Ewa
Omulecka, Aleksandra
Szymańska, Bożena
Wójcik, Kamila
Powiązania:
https://bibliotekanauki.pl/articles/1039705.pdf
Data publikacji:
2012
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
ribavirin
interferon
HCV
IL28B
HIV
sustained virologic response
Opis:
Introduction. Hepatitis C virus (HCV) infection is a global health problem which can lead to liver cirrhosis or hepatocellular carcinoma in one-fifth of chronically infected patients. Materials and methods. The study group consisted of 123 patients: 90 with HCV mono- and 33 with HIV/HCV co-infection, who were treated with pegylated interferon alfa (Peg-IFN-α) and ribavirin. We analyzed selected pretreatment factors: age, sex, HIV/HCV co-infection, grade of inflammation, necrotic changes and fibrosis in histological analysis of liver bioptates, HCV viral load, HCV genotypes, and single nucleotide polymorphisms (SNPs) of IL28B and tried to find out which of them influence sustained virological response (SVR). The IL28B SNP C/T (rs12979860) was analyzed using Custom® SNP Genotyping Assays (Applied Biosystems). Results. Multivariate analysis demonstrated that after adjusting for the other variables three predictors independently influence SVR, namely genotype 3 of HCV, presence of the CC genotype and age >40 years (OR respectively 15.14, 3.62, and 0.36). HCV mono-infected patients were infected with HCV genotype 3 or 4 less frequently (p=0.0001) compared to HIV/HCV co-infected individuals. In patients with HIV/HCV co-infection the CC variant occurred more frequently whereas CT was found less frequently (p=0.001, p=0.0146, respectively). In patients with HIV/HCV co-infection, 3 and 4 genotype of HCV occurred more frequently compared to patients with HCV mono-infection (p=0.0001). Conclusions. These data suggest that age, HCV genotype and IL28B polymorphism are useful for prediction of the response to treatment with Peg-IFN-α and ribavirin. The more frequent occurrence of HCV genotypes 3 or 4 in patients with HIV/HCV co-infection could be associated with the route of transmission.
Źródło:
Acta Biochimica Polonica; 2012, 59, 3; 333-337
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Association between RBMS1 gene rs7593730 and BCAR1 gene rs7202877 and Type 2 diabetes mellitus in the Chinese Han population
Autorzy:
Kazakova, Elena
Chen, Meijun
Jamaspishvili, Esma
Lin, Zhang
Yu, Jingling
Sun, Lulu
Qiao, Hong
Powiązania:
https://bibliotekanauki.pl/articles/1038363.pdf
Data publikacji:
2018
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
type 2 diabetes mellitus
RBMS1 gene
BCAR1 gene
single nucleotide polymorphisms
SNPscan
Opis:
Two recent studies found that RBMS1 gene rs7593730 and BCAR1 gene rs7202877 are related to type 2 diabetes. However, the association of these loci with type 2 diabetes mellitus (T2DM) has not been examined in Chinese. We performed a replication study to investigate the association of the 2 susceptibility loci with T2DM in the Chinese population. We genotyped 1961 Chinese participants (991 with T2DM and 970 controls) for each of the 2 single nucleotide polymorphisms (SNPs) rs7593730 in RBMS1 and rs7202877 near BCAR1 using SNPscan and examined their association with T2DM using logistic regression analysis. We also analyzed the correlation of the SNP alleles and clinical phenotypes. In additive model, genotype association analysis of BCAR1 rs7202877 loci revealed that the homozygous of rs7202877 GG carriers had significantly decreased T2DM risk compared to homozygous carriers of TT (P=0.038, OR 0.44, 95% CI 0.20-0.96). In the recessive model, the GG genotype GG had significantly decreased T2DM risk compared to GT+TT (P=0.043, OR 0.67, 95% CI 0.46-0.99). Allele G was statistically significantly correlated with TC (mmol/L) (P=0.036) and LDL-C (mmol/L) (P=0.007). As for rs7593730, the carriers of CT and TT genotype had significantly decreased T2DM risk compared to the carriers of CC genotype (CT: CC P=0.038, OR 0.71, 95% CI 0.51-0.98; TT: CC P=0.010, OR 0.32, 95% CI 0.13-0.76). In a dominant model, TT+CT: CC (P=0.013, OR 0.673, 95% CI 0.49-0.92) and in a recessive model, TT: CT+CC (P=0.019, OR 0.59, 95% CI 0.39-0.92). The T allele carriers had significantly decreased T2DM risk compared to the carriers of C (P=0.002, OR 0.65, 95% CI 0.50-0.86). Allele T was statistically correlated with FINS (P=0.010). In conclusion, our study showed that RBMS1 gene rs7593730 and BCAR1 gene rs7202877 were significantly associated with type 2 diabetes in the Chinese population.
Źródło:
Acta Biochimica Polonica; 2018, 65, 3; 377-382
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The Gas6 gene rs8191974 and Ap3s2 gene rs2028299 are associated with type 2 diabetes in the northern Chinese Han population
Autorzy:
Kazakova, Elena
Zghuang, Tianwei
Li, Tingting
Fang, Qingxiao
Han, Jun
Qiao, Hong
Powiązania:
https://bibliotekanauki.pl/articles/1038636.pdf
Data publikacji:
2017
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Type 2 diabetes mellitus
Gas6 gene
Ap3s2 gene
single nucleotide polymorphisms
epidermal growth factor (EGF)-like
Opis:
Previous studies in other countries have shown that single nucleotide polymorphisms (SNPs) in the growth arrest-specific gene 6 (Gas6; rs8191974) and adapter-related protein complex 3 subunit sigma-2 (Ap3s2; rs2028299) were associated with an increasedrisk for type 2 diabetes mellitus (T2DM). However, the association of these loci with T2DM has not been examined in Chinese populations. We performed a replication study to investigate the association of these susceptibility loci with T2DM in the Chinese population.We genotyped 1968 Chinese participants (996 with T2DM and 972controls) for rs8191974 in Gas6 and rs2028299 near Ap3s2, and examined their association with T2DM using a logistic regression analysis. We also analyzed the correlation of genotypes and clinical phenotypes. The distribution of the T allele of SNP rs8191974 in the Gas6 gene was significantly different between T2DM cases and controls when compared with the C allele (P<0.05, OR: 0.80, 95% CI: 0.69-0.94). The occurrence of the CT genotype and the dominant model was also significantly less frequent in the T2DM cases vs. controls when compared with the CC genotype (CT vs. CC: P<0.05, OR: 0.75, 95% CI:0.62-0.90; TT+CT vs. CC: P<0.05, OR:0.75, 95% CI:0.63-0.90). In SNP rs2028299, the allele C showed no statistically significant differencein distribution between the control and T2DM groups when compared with allele A. However, in male populations, the dominant model was statistically more frequent when compared with genotype AA (CC+CA vs. AA: P<0.05, OR:1.29, 95% CI:1.02-1.64), and in obesity-stratified analysis, we also observed a significant difference in the distribution of the dominant model between the T2DM cases and controls in subjects with BMI≥24 kg/m2 and BMI<28kg/m2 (CC+CA vs. AA: P<0.05, OR: 6.33, 95% CI:4.17-9.61). In conclusion, our study shows that SNPsrs8191974 and rs2028299 are significantly associated with T2DM in the Chinese population.
Źródło:
Acta Biochimica Polonica; 2017, 64, 2; 227-231
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Association between polymorphisms in CHRNA3 and PHACTR2 gene and environment and NSCLC risk in Chinese population
Autorzy:
Lou, Guangyuan
Zhang, Yongjun
Bao, Wenlong
Deng, Dehou
Powiązania:
https://bibliotekanauki.pl/articles/1039210.pdf
Data publikacji:
2014
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Non-small cell lung cancer
phosphatase and actin regulator 2 (PHACTR2)
cholinergic receptor
nicotinic
alpha 3 (CHRNA3)
single-nucleotide polymorphism
Opis:
Aims. This study aimed to investigate CHRNA3 (rs8040868) and PHACTR2 (rs9390123) single-nucleotide polymorphisms (SNPs) for association with non-small-cell lung cancer (NSCLC) risk in a Chinese population, and whether the environment affects the genetic polymorphisms. Methods. This case and control study included 500 NSCLC patients and 500 age-matched healthy controls. CHRNA3 (rs8040868) and PHACTR2 (rs9390123) SNPs were genotyped and associated for NSCLC risk by computing the odds ratio and 95% confidence interval from multivariate unconditional logistic regression analyses with adjustment of age. Results. The minor allele frequency (MAF) of CHRNA3 (rs8040868) and PHACTR2 (rs9390123) was 0.350 (C) and 0.397 (C), respectively. The frequencies of genotype and allele in CHRNA3 (rs8040868) and PHACTR2 (rs9390123) were not significantly different between the cases and controls, or between either of the subgroups. Conclusion. Although rs8040868 and rs9390123 SNPs are not associated with NSCLC risk in Chinese population, the results strongly suggest that geographical agents interact with human genetic polymorphism independent of ethnic background.
Źródło:
Acta Biochimica Polonica; 2014, 61, 4; 765-768
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
VDR gene single nucleotide polymorphisms and their association with risk of oral cavity carcinoma
Autorzy:
Małodobra-Mazur, Małgorzata
Paduch, Agnieszka
Lebioda, Arleta
Konopacka, Maria
Rogoliński, Jacek
Szymczyk, Cezary
Wierzgoń, Janusz
Maciejewski, Adam
Chmielik, Ewa
Jonkisz, Anna
Półtorak, Stanisław
Dobosz, Tadeusz
Powiązania:
https://bibliotekanauki.pl/articles/1039670.pdf
Data publikacji:
2012
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
VDR gene
SNP
oral cavity cancer
Opis:
Vitamin D3 (1,25(OH)2D3 (1,25-dihydroxyvitamin D3)) is a hormone playing a crucial role in numerous biological processes in the human body, including induction and control of cell proliferation and differentiation. Numerous data relate the vitamin D3 level with various types of cancer. It has been suggested that SNPs in the vitamin D3 receptor (VDR) gene might influence both the risk of cancer occurrence and cancer progression. The aim of this study was to search for genetic correlations between individual SNPs in the VDR gene and the risk of oral cavity carcinoma. Two SNPs were selected based on the literature and our previous results. Seventy-three patients with squamous cell carcinoma of the head and neck and one hundred control subjects were investigated. Two SNPs in the VDR gene were genotyped in minisequencing reactions followed by capillary electrophoresis. Hardy-Weinberg equilibrium (HWE), the χ2 test and logistic regression were used for statistical analysis. The SNP rs2238135 in the VDR gene displayed statistical differences in frequency between the tested groups (p=0,0007). Furthermore, the G/C genotype of the rs2238135 in the VDR gene was characterized by a 3.16 fold increased risk of oral cavity carcinoma. The obtained results provide evidence for a genetic association between rs2238135 in the VDR gene and the occurrence and risk of oral cavity cancer.
Źródło:
Acta Biochimica Polonica; 2012, 59, 4; 627-630
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Genetic diversity in populations of Slovak Spotted cattle based on single nucleotide polymorphisms analyses
Autorzy:
Moravčíková, Nina
Trakovická, Anna
Navrátilová, Alica
Powiązania:
https://bibliotekanauki.pl/articles/1039494.pdf
Data publikacji:
2013
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
cattle
growth hormone
leptin
leptin receptor
polymorphism
Opis:
The aim of this study was to identify SNPs in leptin (LEP), leptin receptor (LEPR) and growth hormone (GH) genes in order to analyze genetic diversity of Slovak Spotted cattle. The total numbers of blood samples were taken from 353 Slovak Spotted cows originating from four farms. Genomic DNA was isolated by phenol-chloroform extraction method and analyzed by PCR-RFLP method. After digestion with restriction, enzymes were detected in whole population of cow's alleles with frequency: LEP/Sau3AI A 0.84 and B 0.16 (±0.0152); LEPR/BseGI C 0.95 and T 0.05 (±0.0089) and GH/AluI L 0.70 and V 0.30 (±0.0188). Based on the observed vs. expected genotypes frequencies populations across loci were in Hardy-Weinberg equilibrium (P\>0.05). Predominant for SNP LEP/Sau3AI was AA genotype (0.70), for SNP LEPR/T945M CC genotype (0.91), and LL genotype (0.48) was most frequent for SNP GH/AluI. The observed heterozygosity of SNPs across populations was also transferred to the low or median polymorphic information content 0.24 (He 0.28), 0.08 (He 0.09) and 0.33 (He 0.47) for LEP, LEPR and GH genes, respectively. Within genetic variability estimating negative values of fixation indexes FIS (-0.09-0.05) and FIT (-0.07-0.03) indicating heterozygote excess were observed. The value of FST indexes (0.018-0.023) shows very low levels of genetic differentiation in allele frequencies of loci among evaluated subpopulations. The low values of genetic distances (0.0018-0.0159) indicated high genetic relatedness among animals in subpopulations caused probably by common ancestry used in breeding program at farms.
Źródło:
Acta Biochimica Polonica; 2013, 60, 4; 807-810
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
CTLA-4 polymorphisms (+49 A/G and -318 C/T) are important genetic determinants of AITD susceptibility and predisposition to high levels of thyroid autoantibodies in Polish children - preliminary study
Autorzy:
Pastuszak-Lewandoska, Dorota
Domańska, Daria
Rudzińska, Magdalena
Bossowski, Artur
Kucharska, Anna
Sewerynek, Ewa
Czarnecka, Karolina
Migdalska-Sęk, Monika
Czarnocka, Barbara
Powiązania:
https://bibliotekanauki.pl/articles/1039459.pdf
Data publikacji:
2013
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
Graves' disease
Hashimoto's thyroiditis
autoimmune thyroid disease
CTLA-4
single nucleotide polymorphism
TAb production
Opis:
Autoimmune thyroid diseases (AITDs), including Hashimoto' s thyroiditis (HT) and Graves' disease (GD), are related to environmental and genetic factors. We analyzed the association of cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) gene two polymorphisms (+49 A/G, -318 C/T) with HT and GD development in Polish children, and correlated both polymorphisms with the production of thyroid autoantibodies (TPOAb and TgAb). The study involved 49 AITD patients (age 10-19) with HT (n=25) or GD (n=24) and 69 healthy controls. SNP genotyping was performed using genomic DNA and TaqMan® probes. The obtained results indicated that CTLA-4 +49 GG genotype was significantly more frequent in both HT and GD patients, whereas the AA genotype was more common in controls. CTLA-4-318 CT genotype was significantly more frequent in AITD, and the CC genotype more often occurred in controls. Significantly higher median TPOAb and TgAb values were associated with G allele in HT, and with T allele in GD patients. Concluding, both studied polymorphisms seem to be important genetic determinants of the risk of HT and GD, and appear to be associated with a predisposition to high levels of TAbs and clinical AITD. The obtained results give more information on the distribution of the CTLA-4 polymorphism in Polish AITD children, and further support the proposal that the CTLA-4 gene plays an important role in a TAb production.
Źródło:
Acta Biochimica Polonica; 2013, 60, 4; 641-646
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Sampling Properties of Estimators of Nucleotide Diversity at Discovered snp Sites
Autorzy:
Renwick, A.
Bonnen, P. E.
Trikka, D.
Nelson, D. L.
Chakraborty, R.
Kimmel, M.
Powiązania:
https://bibliotekanauki.pl/articles/908150.pdf
Data publikacji:
2003
Wydawca:
Uniwersytet Zielonogórski. Oficyna Wydawnicza
Tematy:
genetyka
statystyka
single nucleotide polymorphisms
ascertainment bias
nucleotide diversity
molecular evolution
Opis:
SNP sites are generally discovered by sequencing regions of the human genome in a limited number of individuals. This may leave SNP sites present in the region, but containing rare mutant nucleotides, undetected. Consequently, estimates of nucleotide diversity obtained from assays of detected SNP sites are biased. In this research we present a statistical model of the SNP discovery process, which is used to evaluate the extent of this bias. This model involves the symmetric Beta distribution of variant frequencies at SNP sites, with an additional probability that there is no SNP at any given site. Under this model of allele frequency distributions at SNP sites, we show that nucleotide diversity is always underestimated. However, the extent of bias does not seem to exceed 10-15% for the analyzed data. We find that our model of allele frequency distributions at SNP sites is consistent with SNP statistics derived based on new SNP data at ATM, BLM, RQL and WRN gene regions. The application of the theory to these new SNP data as well as to the literature data at the LPL gene region indicates that in spite of ascertainment biases, the observed differences of nucleotide diversity across these gene regions are real. This provides interesting evidence concerning the heterogeneity of the rates of nucleotide substitution across the genome.
Źródło:
International Journal of Applied Mathematics and Computer Science; 2003, 13, 3; 385-394
1641-876X
2083-8492
Pojawia się w:
International Journal of Applied Mathematics and Computer Science
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Hepatocyte nuclear factor 4 alpha P2 promoter variants associate with insulin resistance
Autorzy:
Saif-Ali, Riyadh
Harun, Roslan
Al-Jassabi, S.
Wan Ngah, Wan
Powiązania:
https://bibliotekanauki.pl/articles/1039910.pdf
Data publikacji:
2011
Wydawca:
Polskie Towarzystwo Biochemiczne
Tematy:
insulin resistance
HNF4 alpha
single nucleotide polymorphisms
haplotypes
Opis:
This study aimed to investigate the associations of hepatocyte nuclear factor 4 (HNF4) alpha single nucleotide polymorphisms (SNPs) and haplotype with insulin resistance and metabolic syndrome parameters. Nine SNPs spanning the HNF4 alpha P2 promoter (rs4810424, rs1884613 and rs1884614) and coding region (rs2144908, rs6031551, rs6031552, rs1885088, rs1028583 and rs3818247) were genotyped in 160 subjects without diabetes or metabolic syndrome. The HNF4 alpha P2 promoter SNPs rs4810424, rs1884613 and rs1884614 were associated with insulin resistance (p = 0.017; 0.037; 0.024) and body mass index (BMI) (p = 0.03; 0.035; 0.039). The intron 1D SNP rs2144908 was associated with high-density lipoprotein cholesterol (HDLc) (p = 0.020) and the intron 9 SNP rs3818247 showed association with systolic (p = 0.02) and diastolic (p = 0.034) blood pressure. HNF4 alpha common haplotype CCCGTC associated with higher insulin resistance (p = 0.022), fasting blood glucose (FBG) (p = 0.035) and lower HDLc (p = 0.001). In conclusion, subjects with HNF4 alpha P2 variants and haplotypes have been shown to have a higher insulin resistance and are therefore at a higher risk for developing type 2 diabetes mellitus.
Źródło:
Acta Biochimica Polonica; 2011, 58, 2; 179-186
0001-527X
Pojawia się w:
Acta Biochimica Polonica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Lack of association between single nucleotide polymorphisms of CPA4, LEP and AKR1B1 genes located at the long arm of chromosome 7 (7q31-q35) and chronic kidney disease occurrence and progression
Brak związku między polimorfi zmami pojedynczego nukleotydu genów CPA4, LEP oraz AKR1B1 zlokalizowanych na długim ramieniu chromosomu 7 (7q31-q35) a występowaniem i progresją przewlekłej choroby nerek
Autorzy:
Śnit, Mirosław
Gumprecht, Janusz
Trautsolt, Wanda
Nabrdalik, Katarzyna
Grzeszczak, Władysław
Powiązania:
https://bibliotekanauki.pl/articles/1038646.pdf
Data publikacji:
2012
Wydawca:
Śląski Uniwersytet Medyczny w Katowicach
Tematy:
chronic kidney disease
gene polymorphism
tdt
snp
przewlekła choroba nerek
polimorfi zm genowy
polimorfi zm pojedynczego nukleotydu
(snp)
Opis:
BACKGROUND The aim of the study was to investigate the infl uence of single nucleotide polymorphisms (SNPs) of carboxypeptidase A4, CPA4, leptin, LEP and aldo-keto reductase family 1, AKR1B1 genes located at the long arm of chromosome 7 (7q31-q35) on development and progression of chronic kidney disease (CKD). MATERIAL AND METHODS There was an association study by PCR-RFLP method of following SNPs in parent-off spring trios performed: G934T of CPA4 gene, A19G of LEP gene and C-106T of AKR1B gene. 471 subjects, 157 patients with CKD and 314 their biological parents were examined. The patients were divided into 3 groups: diabetic nephropathy due to type 1 diabetes (n = 34), chronic primary glomerulonephritis (n = 70) and chronic inter- stitial nephritis (n = 53). The mode of alleles transmission was determined using the transmission disequilibrium test (TDT). RESULTS There was no association of studied SNPs and CKD occurrence or pro- gression rate of renal function loss. Transmission of alleles of investigated SNPs did not diff er signifi cantly: G934T of CPA4 gene: P = 0.61 in whole group of CKD patients, p = 0.66 in GN group, p = 0.70 – IN group and p = 0.61 in DN one; A19G of LEP gene: p = 0.58, 0.71, 0.78 and 0.49, respectively; C-106T of ALDR1 gene: p = 0.31, 0.47, 0.12 and 0.38, respectively. No impact of examined polymorphisms on the rate of progression of renal function loss was observed. CONCLUSIONS The results, obtained in the study, suggest that the investigated SNPs: G934T of CPA4 gene, A19G of LEP gene and C-106T of AKR1B gene may not play a major role in the development and progression of chronic nephropathies.
WSTĘP Celem badań było zbadanie wpływu polimorfi zmów pojedynczego nukleotydu (SNPs) genów karboksypepsydazy A4, CPA4, leptyny, LEP i reduktazy aldozy, AKR1B1, znajdujących się na długim ramieniu chromosomu 7 (7q31-q35) na rozwój i progresję przewlekłej choroby nerek (PChN). MATERIAŁ I METODY Wykorzystując metodę PCR-RFLP przebadano następujące polimorfizmy: G934T CPA4 genu, A19G LEP i C-106T genu AKR1B. Badaniami objęto 471 osoby: 157 z PChN i 314 ich biologicznych rodziców. Pacjentów podzielono na 3 grupy: z nefropatią cukrzycową w przebiegu cukrzycy typu 1 (DN, n = 34), z przewlekłym pierwotnym kłębuszkowym zapaleniem nerek (GN, n = 70) oraz z przewlekłym śródmiąższowym zapaleniem nerek (IN, n = 53). Tryb przekazywania alleli został oceniony testem nierównowagi przekazywania (Transmission-Disequilibrium Test, TDT). WYNIKI Częstość przekazywania alleli analizowanych SNPs nie odbiegała znacząco od oczekiwanej: G934T CPA4: p = 0,61 w całej grupie badanej, p = 0,66 w grupie GN, p = 0,70 – w grupie IN oraz p = 0,61 w grupie DN; A19G LEP: p = 0,58; 0,71; 0,78 i 0,49, odpowiednio; C-106T genu ALDR1: p = 0,31; 0,47; 0,12 i 0,38, odpowiednio. Nie zaobserwowano żadnego wpływu badanych polimorfi zmów na szybkość utraty funkcji nerek. WNIOSKI Uzyskane w badaniu wyniki wskazują, że badane SNPs: G934T genu CPA4, A19G LEP i C-106T genu AKR1B nie odgrywają istotnej roli w rozwoju i progresji przewlekłych nefropatii.
Źródło:
Annales Academiae Medicae Silesiensis; 2012, 66, 2; 27-33
1734-025X
Pojawia się w:
Annales Academiae Medicae Silesiensis
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Zastosowanie technik genotypowania TaqMan® oraz tetra-primer ARMS-PCR do identyfikacji polimorfizmów punktowych zasocjowanych z genetycznymi determinantami kształtu korzenia marchwi
The use of TaqMan® and tetra-primer ARMS-PCR genotyping techniques for identification of single nucleotide polymorphisms associated with genetic determinants of root shape of carrot
Autorzy:
Stelmach, Katarzyna
Macko-Podgórni, Alicja
Barański, Rafał
Grzebelus, Dariusz
Powiązania:
https://bibliotekanauki.pl/articles/2199330.pdf
Data publikacji:
2018-08-29
Wydawca:
Instytut Hodowli i Aklimatyzacji Roślin
Tematy:
ARMS-PCR
GWAS
marchew
MLM
polimorfizm pojedynczego nukleotydu
sondy TaqMan®
carrot
MLN
Opis:
W ostatnich dwóch dekadach zaobserwowano znaczący wzrost tempa rozwoju zróżnicowanych systemów markerów molekularnych oraz odpowiadających im zaawansowanych platform detekcyjnych. Markery oparte na polimorfizmach pojedynczego nukleotydu (SNP), ze względu na częstość ich występowania w genomach bardzo szybko zyskały uznanie w badaniach z zakresu hodowli molekularnej roślin. Wśród najczęściej wykorzystywanych technik genotypowania polimorfizmów pojedynczego nukleotydu znajdują się sondy TaqMan®, mikromacierze DNA, oraz technologia genotypowania przez sekwencjonowanie (GBS). W celu obniżenia kosztów genotypowania opracowano również techniki oparte na standardowej reakcji łańcuchowej polimerazy z zastosowaniem zmodyfikowanych starterów, między innymi technikę tetra-primer ARMS-PCR. W niniejszej pracy zidentyfikowano pięć markerów SNP zasocjowanych z genetycznymi determinantami kształtu korzenia spichrzowego marchwi oraz dokonano ich przekształcenia do markerów wykrywalnych przy zastosowaniu technologii TaqMan® oraz tetra-primer ARMS-PCR. Przydatność wymienionych technik zweryfikowano poprzez genotypowanie 40 wybranych odmian populacyjnych marchwi typu zachodniego. Przeanalizowano zbieżność wyników identyfikacji genotypów otrzymanych przy zastosowaniu wyżej wymienionych technik oraz metody referencyjnej GBS. Techniki te oceniono pod kątem możliwości wykorzystania ich do opracowania wiarygodnych markerów specyficznych zasocjowanych z genetycznymi determinantami kształtu korzenia marchwi.
Over the last two decades a significant increase has been observed in the pace of development of diverse systems of molecular markers and the corresponding advanced detection platforms. Owing to their ubiquity in genomes, markers based on single nucleotide polymorphism (SNP) promptly gained recognition within research on molecular breeding of plants. Amongst the most widely used genotyping techniques of a single nucleotide polymorphisms are the TaqMan® probes, DNA micro-arrays and the genotyping-by-sequencing (GBS) technology. Techniques based on standard polymerase chain reaction with the use of modified primers, including the tetra-primer ARMS-PCR technique, have also been devised with in order to decrease the costs of genotyping. The current work identifies five SNP markers associated with genetic determinants of the shape of carrot taproot and converts them into markers detectable by the TaqMan® and tetra-primer ARMS-PCR technologies. The usefulness of the above techniques has been verified by genotyping 40 selected cultivars of Western-type carrot. The present authors have also analysed the convergence of the results obtained through the mentioned techniques and a GBS reference method. The techniques have been evaluated in terms of their usefulness for designing reliable specific markers associated with genetic determinants of the shape of the carrot root.
Źródło:
Biuletyn Instytutu Hodowli i Aklimatyzacji Roślin; 2017, 282; 99-121
0373-7837
2657-8913
Pojawia się w:
Biuletyn Instytutu Hodowli i Aklimatyzacji Roślin
Dostawca treści:
Biblioteka Nauki
Artykuł
Wyświetlanie 1-15 z 20

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