Fragment Length Polymorphism Research Articles

Development of a PCR-RFLP assay to identify Drosophila melanogaster among field-collected larvae.

The fruit fly Drosophila melanogaster is a model organism to study several aspects of metazoan biology. Most of the work has been conducted in adult fruit flies, including laboratory and field‐derived specimens, but Drosophila melanogaster larvae recently became a valuable model to better understand animal physiology, development, or host–microbe interactions. While adult flies can be easily assigned to a given Drosophila species based on morphological characteristics, such visual identification is more intricate at the larval stage. This could explain the limited number of studies focusing on larvae, especially field‐derived samples. Here, we developed a polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) assay that discriminates D. melanogaster from other ecologically relevant Drosophila species at the larval stage. The method, which targets the cytochrome oxidase I (COI) gene, was validated using laboratory‐derived larvae from seven D. melanogaster populations originating from different geographic areas as well as six Drosophila species. We further validated this PCR‐RFLP assay in a natural context, by identifying wild larvae collected in two locations in France. Notably, among all PCR‐RFLP profiles that matched the D. melanogaster species, 100% were correctly identified, as confirmed by COI sequencing. In summary, our work provides a rapid, simple, and accurate molecular tool to identify D. melanogaster from field‐collected larvae.

Evaluation of Association of Vitamin D Receptor Genetic Polymorphism with Severe Chronic Periodontitis in an Ethnic Tamilian Population.

Periodontitis is a multifactorial disease characterized by inflammatory responses to increased levels of subgingival pathogens, resulting in connective tissue destruction and alveolar bone loss. The susceptibility of an individual is determined by the complex interplay of the host, genetic, and environmental factors. Vitamin D, a secosteroid hormone, interacts with its nuclear receptor vitamin D receptor (VDR) to regulate crucial biological processes, such as bone metabolism and immune function modulation. Various studies have been conducted in different populations to analyze the association of VDR gene polymorphisms with chronic periodontitis, as these polymorphisms have been demonstrated to play vital roles in the pathogenesis of other diseases. The aim of the present study was to determine the prevalence and association of the VDR TaqI gene polymorphism with severe chronic periodontitis in an Ethnic Tamilian population. A total of 140 subjects were recruited for the study, of which 70 were diagnosed with severe chronic periodontitis and 70 had healthy gums. Each subject's medical and dental histories were taken, and periodontal examinations were performed. Genomic DNA was extracted and genotyping of the VDR gene at the TaqI site was carried out using polymerase chain reaction/restriction fragment length polymorphism. The frequencies of genotypes and alleles were analyzed between the study groups. The frequency of homozygous TT genotype was 40%, for both the severe chronic periodontitis and the healthy control groups. The distribution of heterozygous Tt genotype was 42.9% in the severe chronic periodontitis group and 47.1% in the healthy control group. The frequency of homozygous tt genotype was 17.1% in the severe chronic periodontitis group and 12.7% in the healthy control group. Although the prevalence of genotype tt and t allele was slightly increased in severe chronic periodontitis patients compared with healthy controls, the frequency of VDR genotype between the study groups was not statistically significant (p-value = 0.751). This present study performed in an Ethnic Tamilian population does not support an association between either of the TaqI alleles within the VDR gene and Severe Chronic Periodontitis.

The active participation of p22phox-214T/C in the formation of intracranial aneurysm and the suppressive potential of edaravone.

Oxidative stress reactions play an important role in the pathogenesis of intracranial aneurysm (IA). p22phox is involved in the oxidative stress reaction, and it is a critical subunit of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase. The present study investigated the association of genetic variants within the gene encoding p22phox‑214T/C with IA. The p22phox‑214T/C gene polymorphisms in 192cases of IA and 112 controls were analyzed by polymerase chain reaction‑restriction fragment length polymorphism (PCR‑RFLP). The mRNA expression of NADPH oxidase was also analyzed by RT‑PCR. The results of RT‑PCR were validated by ELISA. In a rabbit model of elastase‑induced aneurysm, we used edaravone for anti‑oxidative stress treatment to observe the curative effects. In the clinical cases, a significant difference in p22phox‑214T/C allele frequencies in the IA group was observed compared with the control group (P<0.001). The expression level of NADPH oxidase was differed significantly between the IA group and the control group. In the rabbit model of elastase‑induced aneurysm, the success rate of the aneurysmal model in the edaravone group and the wound ulcer rate were lower than those in the control group. In addition, the diameter of the aneurysm was smaller than in the edaravone group than in the control group (3.26±0.13mm vs. 3.85±0.07mm), and the expression of matrix metalloproteinase‑9 (MMP‑9) was significantly lower than that in the control group (P<0.0001). Thus, these data suggest the active participation of p22phox‑214T/C in the formation of IA and the suppressive potential of edaravone against IA formation.

The association of LRP6 rs2302685 (V1062I) polymorphism with the risk of hyperlipidemia in Iranian children and adolescents.

Wnt signaling/LRP6 plays a critical role in metabolic syndrome and atherosclerosis, and variation in this pathway may lead to hyperlipidemia, nonalcoholic fatty liver disease, and coronary artery disease. In the present study, we investigated the effect of LRP6 rs2302685 (V1062I) on hyperlipidemia in Iranian children and adolescents. The population in this study consisted of 200 children (101 boys, 99 girls) aged 9-18 years old. Total cholesterol, high-density lipoprotein (HDL), low-density lipoprotein (LDL), non-HDL cholesterol, and triglyceride levels were measured. Body composition was evaluated by the Hologic DXA system. PCR/restriction fragment length polymorphism was performed for LRP6 rs2302685 (V1062I) genotyping. Logistic regression analysis was done to find the association between LRP6 rs2302685 (V1062I) and categorized lipid parameters in the adjusted model for confounding factors (age, sex, and puberty). Individuals with the CC genotype showed significantly higher levels of cholesterol, triglycerides, LDL, and non-HDL compared to the CT and TT genotypes. In modeling analysis, for categorized lipid parameters, a significant association was found between CC versus CT, and CC versus TT in terms of cholesterol, LDL, and non-HDL. It seems that LRP6 rs2302685 (V1062I) variant carriers are associated with an increased risk of hyperlipidemia in Iranian children and adolescents.

Associations of miR‑146aC>G, miR‑149C>T, miR‑196a2C>T and miR‑499A>G polymorphisms with brain tumors.

MicroRNAs (miRNAs/miRs) are short, non‑coding RNAs that are implicated in tumorigenesis, functioning as tumor suppressors and oncogenes. However, the clinical significance of miRNA expression profiles for brain tumors remains unclear. Therefore, the present study was designed to investigate the associations between miRNA genetic variants and brain tumor risk. A total 362participants were recruited, including 179who were healthy subjects and 183who were patients with brain tumors confirmed as gliomas, meningiomas or schwannomas. This study investigated the single nucleotide polymorphisms miR‑146aC>G, miR‑149T>C, miR‑196a2T>C and miR‑499A>G by polymerase chain reaction‑restriction fragment length polymorphism. It was found that the dominant miR‑149 and CC genotypes were significantly more frequent in patients with glioma. The odds ratios for the C‑C‑C‑G, C‑T‑C‑G and G‑C‑T‑G haplotypes (miR‑146aC>G‑miR‑149T>C‑miR‑196a2T>C‑miR‑499A>G) were significantly increased in glioma, as were the odds ratios for the GCT haplotype of miR‑146aC>G, miR‑149T>C and miR‑196a2T>C, and for the C‑C‑G haplotype of miR‑149T>C, miR‑196a2T>C and miR‑499A>G. In meningioma, the odds ratios were increased in the G‑T‑C‑G haplotype of miR‑146aC>G, miR‑149T>C, miR‑196a2T>C and miR‑499A>G. The odds ratios were also increased in the G‑C‑G haplotype of miR‑146aC>G, miR‑196a2T>C and miR‑499A>G, and in the C‑C‑G haplotype of miR‑149T>C, miR‑196a2T>C and miR‑499A>G. The odds ratios for schwannoma were increased in the G‑C‑T‑G haplotype of miR‑146aC>G, miR‑149T>C, miR‑196a2T>C and miR‑499A>G, and in the C‑C‑G haplotype of miR‑149T>C, miR‑196a2T>C and miR‑499A>G. In conclusion, these results suggested that the miR‑149 polymorphism may be involved in the development of gliomas, and the C‑C‑G haplotype of miR‑149T>C, miR‑196a2T>C and miR‑499A>G showed increased odds ratios for all types of brain tumors.

ПОЛИМОРФИЗМЫ ГЕНОВ СОМАТОТРОПИНОВОГО КАСКАДА, АССОЦИИРОВАННЫЕ С МЯСНОЙ ПРОДУКТИВНОСТЬЮ КОРОВ КАЗАХСКОЙ БЕЛОГОЛОВОЙ ПОРОДЫ

The aim of the research was to establish the genotype asssociation of the polymorphisms bPit-1-HinfI, bGH-AluI and bGHR-SspI with the beef productivity of Kazakh white-headed cattle. The material of the studies was the blood of farm animals. Blood samples and boning data were provided by LP «Zhanabek» and LP «Karaman-K», Kostanay region. The animal genotypes were determined by polymerase chain re-action-restriction fragment length polymorphism. Statistical processing of the results of genotyping and zoo-technical data was carried out using the programs Statistica 6.0 and Microsoft Excel. Evaluation of geno-types with meat productivity was carried out according to the live weight index, and indices characterizing the physique of animals were also analyzed. The results of the studies showed that the genotype bPit-1-HinFIAA of the pituitary transcription factor-1 gene was positively associated with the stretch sign at the age of 24 months. Thus, the index of the stretch index in cows with the genotype bPit-1-HinFIAA is 132.768 (126.667; 137.500), while this indicator for cows with genotypes bPit-1-HinFIAB and bPit-1-HinFIBB is 127.966 (120.833; 137.705 ) and 119.643 (117.544; 124.074) The polymorphism bIGF-1-SnaBI is associ-ated with the sign of live weight at the age of 12, 18, 24 months (the highest value is the genotype bIGF-1-SnaBIAB and bIGF-1-SnaBIAA, the smallest is the genotype bIGF-1-SnaBIBB). Thus, the genotype bPit-1-HinFIAA can be recommended as a genetic marker for the increased meat productivity of cattle of Kazakh white-headed breed. The genotype bIGF-1-SnaBIBB is a marker of reduced meat productivity of cattle. Working with polymorphism bIGF-1-SnaBI, as with a genetic marker, should not be based on selection on a preferred genotype, but on elimination of the negative genotype bIGF-1-SnaBIBB

Single Nucleotide Polymorphisms in Key One-Carbon Metabolism Genes and Their Association with Blood Folate and Homocysteine Levels in a Chinese Population in Yunnan.

One-carbon metabolism (OCM) is essential for DNA synthesis and methylation. Single nucleotide polymorphisms (SNPs) within OCM genes may affect folic acid (FA) metabolism, disrupt homocysteine (Hcy) homeostasis, and increase the risk of disease. This study investigated the relationship between SNPs in key OCM genes and their association with blood FA and Hcy levels in a healthy population in Yunnan, China. Six SNPs within five key OCM genes (MTHFR C677T, MTHFR A1298C, MS A2756G, MTRR A66G, CBS T833C, and SHMT C1420T) were genotyped in 300 healthy volunteers (148 males and 152 females) using polymerase chain reaction/restriction fragment length polymorphism. Blood folate [serum FA (SFA) and red blood cell folate (RBC FA)] and Hcy levels were determined by chemiluminescence immunoassays and enzymatic assays. Subjects with the MTHFR 677TT genotype had significantly higher Hcy levels and RBC FA concentrations compared with those harboring the MTHFR 677CC/CT genotypes (p < 0.01). Both Hcy and blood FA concentrations were also increased in subjects with MS 2756AA, as well as those within CBS 833TT, when compared with those with MS 2756AG/GG (p < 0.05) and CBS 833TC/CC (p < 0.05) genotypes, respectively. Subjects harboring the combined genotype of MTHFR 677TT and MS 2756AA had a higher Hcy concentration than those carrying other MTHFR and MS combinations (p = 0.002). Similarly, subjects harboring the combination of CBS 833TT with MTHFR 677TT had higher Hcy concentrations than those harboring other CBS and MTHFR combinations (p = 0.011). The genotypes involving the MTHFR C677T, MS A2756G, and CBS T833C polymorphisms, including combinations of these genotypes, were the most important factors associated with blood FA and Hcy levels of the investigated SNPs in the OCM genes.

Population genetic structure of the Culex pipiens (Diptera: Culicidae) complex, vectors of West Nile virus, in five habitats

BackgroundThe Culex pipiens complex consists of several morphologically similar, closely related species. In the United States, Cx. pipiens L. is distributed North of 39° latitude, while Cx. quinquefasciatus Say occurs South of 36° latitude; a hybrid zone occurs between these two latitudes including in the Central Valley of California. Members of the Cx. pipiens complex and their hybrids are vectors for West Nile virus (WNv). Hybrid offspring of Cx. pipiens and Cx. quinquefasciatus have been found to have enhanced transmission rates of WNv over those of pure populations of each species. We investigated whether hybrids of Cx. pipiens and Cx. quinquefasciatus occurred more frequently in any of five habitats which were dairies, rural, suburban, and urban areas, and wetlands. In addition, the proportion of alleles unique to Cx. quinquefasciatus and Cx. pipiens found in each habitat-associated population were determined.MethodsAmplified fragment length polymorphism (AFLP) markers were used to compare the population structure of the Cx. pipiens complex from each habitat to geographically distant populations considered pure Cx. pipiens and Cx. quinquefasciatus. Structure analyses were used to assign individuals to either Cx. pipiens, Cx. quinquefasciatus, or hybrids of the Cx. pipiens complex. The ancestry of hybrids (F1, F2, or backcrossed) in relation to the two parent populations was estimated for each Central Valley population. Loci unique to the pure Cx. pipiens population and the pure Cx. quinquefasciatus population were determined. The proportion of loci unique to Cx. pipiens and Cx. quinquefasciatus populations were subsequently determined for each population from the five Merced habitats and from the Oroville California population. The unique loci found in Merced populations and not in Cx. pipiens or Cx. quinquefasciatus were also determined. A principal components analysis was run, as was an analysis to determine loci under putative selection.ResultsThe Structure Harvester analysis found K = 3, and the Culex pipiens complex mosquitoes formed a genetic cluster distinct from Cx. quinquefasciatus and Cx. pipiens. Individuals collected from each habitat were nearly all hybrids. However, Cx. pipiens complex collected near dairies had more individuals categorized as Cx. pipiens than collections from the other habitats. None of the mosquitoes collected in Merced or Oroville were considered pure Cx. quinquefasciatus. Significant genetic divergence was detected among the Cx. pipiens complex from the five habitats in Merced; Cx. pipiens complex mosquitoes from dairies were divergent from the urban and suburban populations. New Hybrids analysis found that individuals from all five Merced habitat-associated populations and the population from Oroville were primarily categorized as hybrids backcrossed to the Cx. pipiens population. Finally, all five habitat-associated populations shared more alleles with Cx. pipiens than with Cx. quinquefasciatus, even though the pure Cx. quinquefasciatus population was more geographically proximate to Merced. Results from the principal component analysis, and the occurrence of several unique loci in Merced populations, suggest that Cx. pipiens molestus may also occur in the habitats sampled.ConclusionsNearly all mosquitoes in the five habitats in Merced in the Central Valley of California area were hybrids of Cx. pipiens and Cx. quinquefasciatus, consisting of hybrids backcrossed to Cx. pipiens. Habitat-associated mosquitoes collected near dairies had more individuals consisting of pure Cx. pipiens, and no mosquitoes from Merced or Oroville CA classified as pure Cx. quinquefasciatus. The genetic distances among Cx. pipiens and Cx. quinquefasciatus, and hybrid populations agree with previous studies using other molecular markers. Cx. pipiens hybrids in Merced shared more alleles with Cx. pipiens than Cx. quinquefasciatus which was unexpected, since Merced is geographically closer to the northern limit of Cx. quinquefasciatus distribution. Culex pipiens molestus may occur in more habitats in the Central Valley than previously suspected, which warrants further investigation. Future studies could investigate the vector competence of hybrids backcrossed to either Cx. pipiens or Cx. quinquefasciatus parent for their ability to transmit West Nile virus.

The relationship between L-leucine-7-amido-4-methyl coumarin 1 gene polymorphism and susceptibility to the chronic hepatitis B virus infection in an Iranian population.

Background:Lamnin has important effects on human immunity system. The current study aimed to assess the role of L-leucine-7-amido-4-methyl coumarin 1 gene polymorphisms on hepatitis B virus (HBV) susceptibility.Materials and Methods:The rs20558, rs20563, rs10911193, rs10911251, and rs1413390 polymorphisms were analyzed using polymerase chain reaction (PCR) and PCR-reaction–restriction fragment-length polymorphism and amplification-refractory mutation system-PCR using three different groups including chronic HBV-infected patients, HBV patients who were resolved their infection spontaneously and healthy volunteers. Laminin concentrations were also measured in the blood of these individuals.Results:People with rs20558C, rs20563G, and rs10911193T alleles have an increased risk of HBV infection. Moreover, we found that CGTAT haplotype was more frequent in chronically infected people who could affect the mechanism of disease. Furthermore, there was a significant relationship between laminin concentration and rs20558, rs20563, and rs10911193 genotypes in patients.Conclusion:According to the statistical analysis, rs20558, rs20563, rs10911193 polymorphisms probably, related to the chronic HBV infection. In addition, no association of the rs10911251, rs1413390 single nucleotide polymorphisms with the disease was found.

Significant Association of the MDM2 T309G Polymorphism with Breast Cancer Risk in a Turkish Population

Background:Breast cancer is a leading cause of death in women worldwide. Genetic polymorphisms have been reported to be important etiological factors. Murine double minute 2 (MDM2) T309G interacts with p53 and mutations in p53 are present in approximately 50% of all cancers. However, it has been reported that effect of the polymorphism on breast cancer risk may vary in different populations. Here, we therefore investigated whether there is an association between MDM2 T309G (rs2279744) polymorphism and breast cancer in a Turkish population.Materials and Methods:We analysed 110 patients with breast cancer and 138 matched? controls. For genotyping, polymerase chain reaction and restriction length fragment polymorphism methods were used.Results:A significant difference was observed between case and control groups with regard to the distribution of the MDM2 T309G polymorphism (p<0.05). There was a significantly higher frequency of the TT genotype in the control group (p=0.028; OR, 2.42; 95% CI, 1.09-5.37). However, we did not find any relationships among tumor grade and metastasis status and this polymorphism.Conclusion:This study indicates that the MDM2 T309G polymorphism GG genotype and the TG+GG combination may be risk factors for breast cancer in our Turkish population.

Long-term dynamics of the bacterial community in a Swedish full-scale wastewater treatment plant

ABSTRACTThe operational efficiency of activated sludge wastewater treatment plants depends to a large extent on the microbial community structure of the activated sludge. The aims of this paper are to describe the composition of the bacterial community in a Swedish full-scale activated sludge wastewater treatment plant, to describe the dynamics of the community and to elucidate possible causes for bacterial community composition changes. The bacterial community composition in the activated sludge was described using 16S rRNA gene libraries and monitored for 15 months by a terminal restriction fragment (T-RF) length polymorphism (T-RFLP) analysis of the 16S rRNA gene. Despite variable environmental conditions, a large fraction of the observed T-RFs were present at all times, making up at least 50% in all samples, possibly representing a relatively stable core fraction of the bacterial community. However, the proportions of the different T-RFs in this fraction as well as the T-RFs in the more variable fraction showed a significant variation over time and temperature. The difference in community composition between summer and winter coincided with observed differences in floc structure. These observations suggest a relationship between floc properties and bacterial community composition, although additional experiments are required to determine causality.

TNFα gene polymorphism in steroid resistant nephrotic syndrome

Cytokines play a main role as progressive factors in nephrotic syndrome (NS). Tumor necrosis factor alpha (TNFα) produced by activated macrophages is often accompanied by pro inflammatory properties. Some cytokine gene polymorphisms like TNFα have associated with various inflammatory diseases as glomerulonephritis. The aim of the current work was to investigate the serum level of TNFα and the association between TNFα G308A polymorphism and the response to steroid therapy in nephrotic syndrome. This study was conducted on 250 subjects, 100 healthy children, 50 steroid sensitive nephrotic syndrome (SSNS), and 100 steroid resistant nephrotic syndrome patients (SRNS). Serum concentration of TNFα was measured by enzyme-linked immunosorbent assay (ELISA) technique and TNFα-G308A gene polymorphism was estimated by polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP). Serum concentrations of TNFα significantly increased in SRNS cases when compared to SSNS subgroups. TNF GA, AA, GA + AA genotypes and A allele showed significant association with risk of NS development within healthy control subjects. TNFα-G308A genotypes and alleles did not differ significantly between SSNS and SRNS groups.

CYP2B6 Haplotype Predicts Efavirenz Plasma Concentration in Black South African HIV-1-Infected Children: A Longitudinal Pediatric Pharmacogenomic Study.

South Africa has the highest burden of the human immunodeficiency virus (HIV) infection globally. Efavirenz (EFV), a frequently used drug against HIV infection, displays a relationship between drug concentration and pharmacodynamics effects clinically. However, haplotype-based genetic variation in drug metabolism in a pediatric sample has been little considered in a longitudinal long-term context. CYP2B6 plays a key role in variation of EFV plasma concentration through altered drug metabolism. We report here on a prospective clinical pharmacogenomics/pharmacokinetic study of Bantu-speaking children, importantly, over a period of 24 months post-initiation of EFV-based treatment in South Africa. We characterized the HIV-1-infected children (n = 60) for the CYP2B6 c.516G>T, c.785A>G, c.983T>C, and c.1459C>T single nucleotide polymorphisms (SNPs). These SNPs were determined using polymerase chain reaction/restricted fragment length polymorphism and SNaPshot genotyping. Longitudinal mid-dose EFV plasma concentrations were determined by LC-MS/MS and association analyses with genotypes and haplotypes at 1, 3, and 24 months were performed. The CYP2B6 c.516T/T genotype showed significantly higher EFV plasma concentrations (p < 0.001) compared to non 516T-allele carriers at all three time points. The minor allele frequencies (MAF) for CYP2B6 c.516T, c.785G, c.983C, and c.1459T were 0.410, 0.408, 0.110, and 0.000 respectively. Haplotypes were constructed using CYP2B6 c.516G>T,-c.785A>G and c.983T>C. The haplotype T-G-T presented with significantly increased EFV plasma concentrations compared to the reference G-A-T haplotype at 1, 3, and 24 months (p = 0.009; p = 0.003; p = 0.001), suggesting that the T-G-T haplotype predisposes a risk of EFV plasma concentrations >4 μg/mL. The clinical implications of these pharmacogenomics observations for EFV toxicity and treatment resistance warrant further future research.

Relationship between RAGE gene polymorphisms and cardiovascular disease prognosis in the Chinese Han population.

Cardiovascular disease (CVD) is the leading cause of death in China. This study aimed to investigate whether RAGE gene polymorphisms are associated with the prognosis of various cardiovascular diseases in the Chinese Han population. This study was conducted from July 2004 to December 2005 and a total of 425 subjects from Guangdong province were enrolled. Genotyping of the three polymorphisms (-429T/C, 1704G/T, and G82S) in the RAGE gene was performed with polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP). Patients were followed for 6.5years to watch for the development of cardiovascular events and mortality. Subjects with the S mutation of the G82S polymorphism had a significantly higher risk of all-cause mortality and acute myocardial infarction (AMI) than did those with wild-type homozygosity. Logistic regression analysis and Kaplan-Meier analysis all revealed that the G82S polymorphism of the RAGE gene was associated with a significantly increased risk of all-cause mortality and AMI. However, the -429T/C and 1704G/T polymorphisms were not shown to have any effect on prognosis. In conclusion, the G82S variant of the RAGE gene was significantly associated with an increased risk of all-cause mortality and AMI in the Chinese Han population.

A Strong Relationship Between Oral Squamous Cell Carcinoma and DNA Repair Genes.

Single nucleotide polymorphisms of DNA repair genes alter protein function and modulate DNA repair efficiency in various cancers. The X-ray repair cross-complementing group (XRCC) is responsible for the repair of DNA base damage and single-strand breaks. The aim of our study was to investigate the association of XRCC1 Arg399Gln and XRCC3 Thr241Met polymorphisms with the susceptibility to develop oral squamous cell carcinoma (OSCC) in Turkish subjects. One hundred eleven patients with OSCC and 148 healthy controls were recruited for the study. Genetic analysis was performed using polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP). We found that the XRCC1 Arg399Gln Gln/Gln genotype and Gln allele were risk factors for OSCC. Also, Arg/Arg genotype and Arg allele had protective effects against OSCC. Relative to XRCC3 Thr241Met polymorphism, carrying homozygote variants (Thr/Thr and Met/Met) was related with elevated OSCC risk. However, the heterozygote genotype and Thr allele variants were shown to be protective against OSCC. We suggest that XRCC1 Arg399Gln Gln/Gln genotype, Gln allele, and homozygote variants of XRCC3 Thr241Met polymorphism may be a risk factor for predisposition of OSCC in Turkish. In addition, XRCC3 Thr241Met genotype could be associated with tumor size and level of daily smoking.

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment

Soil moisture and nitrogen (N) are two important factors influencing N2O emissions and the growth of microorganisms. Here, we carried out a microcosm experiment to evaluate effects of soil moisture level and N fertilizer type on N2O emissions and abundances and composition of associated microbial communities in the two typical arable soils. The abundances and community composition of functional microbes involved in nitrification and denitrification were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP), respectively. Results showed that N2O production was higher at 90% water-filled pore (WFPS) than at 50% WFPS. The N2O emissions in the two soils amended with ammonium were higher than those amended with nitrate, especially at relatively high moisture level. In both soils, increased soil moisture stimulated the growth of ammonia-oxidizing bacteria (AOB) and nitrite reducer (nirK). Ammonium fertilizer treatment increased the population size of AOB and nirK genes in the alluvial soil, while reduced the abundances of ammonia-oxidizing archaea (AOA) and denitrifiers (nirK and nosZ) in the red soil. Nitrate addition had a negative effect on AOA abundance in the red soil. Total N2O emissions were positively correlated to AOB abundance, but not to other functional genes in the two soils. Changed soil moisture significantly affected AOA rather than AOB community composition in both soils. The way and extent of N fertilizers impacted on nitrifier and denitrifier community composition varied with N form and soil type. These results indicate that N2O emissions and the succession of nitrifying and denitrifying communities are selectively affected by soil moisture and N fertilizer form in the two contrasting types of soil.

Polymorphism in LRP5 (rs556442) is associated with higher TG levels in Iranian children

Background: Wnt signalling/LRP5 is involved in adipogenesis by down-regulating adipogenic transcription factors. Therefore polymorphisms in components of this pathway may lead to metabolic disorders.Aim: This study tested the impact of LRP5 polymorphism on lipid profile in Iranian children.Methods: The study population was comprised of 9–18 year old children (125 boys, 137 girls). Total cholesterol (TC), High Density Lipoprotein (HDL), Low-Density Lipoprotein (LDL), Non-HDL cholesterol and Triglyceride (TG) levels were checked. Body composition was measured by the Hologic system DXA. PCR/restriction fragment length polymorphism (RFLP) was done for LRP5 (rs556442) genotyping. Multiple association analyses for TG level and genotype frequencies were assessed using logistic regression analysis, with adjustment for age, sex, BMI and puberty.Results: The results revealed that LRP5 (rs556442) had a significant influence on TG levels in unadjusted analysis and when adjusted for interacting factors. Higher TG levels were observed in AA/AG genotype of rs566442 in comparison to GG genotype (OR = 2.028, 95% CI = 0.997–4.127, p = 0.049).Conclusion: It is concluded that allele A has an important impact on increasing TG level in LRP5 in the studied population.

Investigation of paraoxonase 1 activity of the workers at the plant, who have long-term contact with organophosphorus compounds

Background. Liver enzyme paraoxonase 1 (PON1) plays an important role in protection the organism from toxic effects of organophosphorus compounds (OPs) via their hydrolysis whose rate and efficiency depend on PON1 serum level activity. PON1 activity is largely determined by the polymorphic variants of the PON1 gene. Effect of long-term work with exposure to the toxic OPs on the PON1 activity is almost unknown. The aim of the present work was to study the effect of long-term work with exposure to the toxic OPs on PON1 serum enzymatic activity depending on polymorphisms Q191R, L54M, C(-108)T PON1 gene. Materials and methods. PON1 serum enzymatic activity and PON1 polymorphisms were determined in men, who were categorized in 2 groups: workers of companies providing storage and disposal of the OPs (68) and control group (37). The PON1 191, PON1 55 and PON1 108 polymorphisms were studied by polymerase chain reaction/restriction fragment length polymorphism. PON1 serum enzymatic activity was measured by a spectrophotometric method using paraoxon. Results. PON1 activity in workers with exposure to the toxic OPs relative was increased compared to the control group (p = 0,027). Differences in serum PON1 activity was shown for the carriers of certain genotypes of the PON1 gene: PON1 serum activity was higher in workers compared to controls only for LL genotype (L54M polymorphism) and C allele (C(-108)T polymorphism) carriers (p 0,001 and p = 0,002, correspondently). Conclusion. We suggest that the increase in serum PON1 activity in workers providing storage and disposal of OPs could be modulated with the polymorphic variants of the PON1 gene.

Nutrient Intake, Apolipoprotein A5 -1131T>C Polymorphism and Its Relationship with Obesity

Obesity is associated with the development of some of the most prevalent diseases of modern society. The World Health Organization estimates that at least 2.8 million adult die each year as result of being obesity. Nutrient intake is a key environmental factor that may interact with genotype to affect risk of obesity. The aim of study was assess the relation between nutrient intake and apolipoprotein A5 -1131T>C polimorphism with obesity. A cross sectional study has been carried out on 139 subjects. Nutrient intake data was collected by using a 24 hour dietary recall and analyzed by nutrisurvey software. Anthropometric variables were measured and body mass index (BMI). Apolipoprotein A5 -1131T>C polymorphism was visualized with 5% agarose gel after restriction length fragment polymorphism (RFLP) digested with MseI. Results : Subjects in this study were 55 male and 84 female, with average age 19.20 ± 1.08, 75 had obese and 64 non obese. Based on the chi square test is found a relationship between total energy intake and protein intake in obese group compared to the non-obese group (p = 0.029, p = 0.006) and no relationship was found in Apolipoprotein A5 -1131T> C polymorphism with obesity. These findings indicate that nutrient intake no depending with apolipoprotein A5 gene variant to modulate obesity

NRAMPI (SLC11A1) Gene-1703 G/A Polymorphisms as Prognostic and Diagnostic Marker of Rheumatoid Arthritis in Egyptian Population

Rheumatoid arthritis (RA) is an autoimmune disease with difficulty to diagnose. The association of natural resistance-associated macrophage protein-1 (NRAMP-1) gene polymorphisms with rheumatoid arthritis (RA) is the aim of this study. Methods: Two hundred individuals who were divided into two groups: RA patients group (100 Patients with RA) and control group: (100 apparently healthy subjects). NRAMP1 polymorphisms were determined by the polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) method, including D543N. Results: Rheumatoid arthritis patients demonstrated significant increase in C-reactive protein (CRP), Rheumatoid Factor Ab, Human cartilage oligomeric matrix protein (COMP) and Anti-Cyclic Citrullinated Peptide (anti-CCP) in comparison to normal. Clinical disease activity index (CDAI) and the radiological erosion score of joints in RA patients were 29.8 ± 5.3 and 60.03 ± 38.71 respectively. The G/G, G/A and A/A genotypes were 64, 33, and 3% respectively in RA patients and were 60, 25, and 15% respectively in controls with a significant difference between RA patients and controls. The CDAI and radiological erosion score of joints had the least values in NN followed by DN while DD patients had the highest levels. The patients with phenotype DD had a grade III of disease in 40 patients and grade IV in 21 patients while grade II found in three patients. However, in patients with phenotype DN, the grading of disease II, III and IV were found to be 10, 20 and 3 respectively. All patients with NN phenotype showed a grade II of disease. There was a significant difference in percentage between RA patients and controls as regard to G or A alleles distribution. The nodule associated with G/G genotype in 58.8% while bone erosion associated with G/G genotype in 65% of RA patients. Conclusion: The present study showed that NRAMP1 1703G (543D) is a risk factor for the development of RA. The estimated NRAMP1 1703G haplotype is associated with susceptibility to RA. In RA patients with 1703A, development of rheumatoid nodule is absent.