Search results for: spatial genotype

Authors: Yasir Ali, Farhatullah

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The present study was conducted to estimate the genetic variability, heritability and genetic advance in six parental lines and their 56 genotypes derived from five introgressed brassica populations on the basis of morphological and biochemical traits. The experiment was laid out in a randomized complete block design with two replications at The University of Agriculture Peshawar-Pakistan during growing season of 2015-2016. The ANOVA of all traits of F5:6 populations showed highly significant differences (P ≤ 0.01) for all morphological and biochemical traits. Among F5:6 populations, the genotype 2(526) was earlier in flowering (108.65 days), and genotype 14(485) was earlier in maturity (170 days). Tallest plants (182.5 cm), largest main raceme (91.5 cm) and maximum number of pods (80.5) on main raceme were recorded for genotype 17(34). Maximum primary branches plant-1(6.2) and longest pods (10.26 cm) were recorded for genotype 15, while genotype 16(171) had more seeds pod⁻¹ (22) and gave maximum yield plant-1 (30.22 g). The maximum 100-seed weight (0.60 g) was observed for genotype 10(506) while high protein content (22.61%) was recorded for genotype 4(99). Maximum oil content (54.08 %) and low linoleic acid (7.07 %) were produced by genotype (12(138) and low glucosinolate (59.01 µMg⁻¹) was recorded for genotype 21(113). The genotype 27(303) having high oleic acid content (51.73 %) and genotype 1(209) gave low erucic acid (35.97 %). Among the F5:6 populations moderate to high heritability observed for all morphological and biochemical traits coupled with high genetic advance. Cluster analysis grouped the 56 F5:6 populations along their parental lines into seven different groups. Each group was different from the other group on the basis of morphological and biochemical traits. Moreover all the F5:6 populations showed sufficient variability. Genotypes 10(506) and 16(171) were superior for high seed yield⁻¹, 100-seeds weight, and seed pod⁻¹ and are recommended for future breeding program.

Keywords: Brassicaceae, biochemical characterization, introgression, morphological characterization

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Authors: Nahida Sultana

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Globally, an estimated 58 million people have chronic hepatitis C virus infection, with about 1.5 million new infections occurring per year. The hepatitis C virus is a blood-borne virus, and most infections occur through exposure to blood from unsafe injection practices, unsafe health care, unscreened blood transfusion, injection drug use, and sexual practices that lead to exposure to blood. Hepatitis C virus (HCV) causes chronic infections that mainly affect the liver leading to liver diseases. This study aimed to determine whether there is any significant association between HCV transmission risk factors in relation to genotypes in HCV-infected Bangladeshi patients. After quantification of HCV viral load, 36 samples were randomly selected for HCV genotyping and risk factor measurement. A greater proportion of genotype 1 (p > 0.05) patients (40%) underwent blood transfusion compared to patients (22.6%) with genotype 3 infections. More genotype 1 patient underwent surgery and invasive procedures (20%), and rather than those with genotype 3 patients (16.1%). The history of IDUs (25.8%) and sexual exposure (3.2%) are only prevalent in genotype 3 patients and absent in patients with genotype 1 (p >0.05). There was no significant statistical difference found in HCV transmission risk factors (blood transfusion, IDUs, Surgery& interventions, sexual transmission) between patients infected with genotypes 1 and 3. In HCV infection, genotype may have no relation to transmission risk factors among Bangladeshi patients.

Keywords: HCV genotype, alanine aminotransferase (ALT), HCV viral load, IDUs

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Authors: S. Petrovska, D. Jonkus, D. Smiltiņa

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κ-casein is one of milk proteins which are very important for milk processing. Genotypes of κ-casein affect milk yield, fat, and protein content. The main factors which affect local Latvian dairy breed milk yield and composition are analyzed in research. Data were collected from 88 Latvian brown and 82 Latvian blue cows in 2015. AA genotype was 0.557 in Latvian brown and 0.232 in Latvian blue breed. BB genotype was 0.034 in Latvian brown and 0.207 in Latvian blue breed. Highest milk yield was observed in Latvian brown (5131.2 ± 172.01 kg), significantly high fat content and fat yield also was in Latvian brown (p < 0.05). Significant differences between κ-casein genotypes were not found in Latvian brown, but highest milk yield (5057 ± 130.23 kg), protein content (3.42 ± 0.03%), and protein yield (171.9 ± 4.34 kg) were with AB genotype. Significantly high fat content was observed in Latvian blue breed with BB genotype (4.29 ± 0.17%) compared with AA genotypes (3.42 ± 0.19). Similar tendency was found in protein content – 3.27 ± 0.16% with BB genotype and 2.59 ± 0.16% with AA genotype (p < 0.05). Milk yield increases by increasing parity. We did not obtain major tendency of changes of milk fat and protein content according parity.

Keywords: dairy cows, κ-casein, milk productivity, polymorphism

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Authors: Maryam Vaezjalali, Koroush Rahimian, Maryam Asli, Tahmineh Kandelouei, Foad Davoodbeglou, Amir H. Kashi

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Objectives: The present study was conducted to assess the HBV molecular profiles including genotypes, subgenotypes, subtypes & mutations in hepatitis B genes. Materials/Patients and Methods: This study was conducted on 229 intravenous drug users who referred to three Drop- in-Centers and a hospital in Tehran. HBV DNA was extracted from HBsAg positive serum samples and amplified by Nested PCR. HBV genotype, subgenotypes, subtype and genes mutation were determined by direct sequencing. Phylogenetic tree was constructed using neighbor- joining (NJ) method. Statistical analyses were carried out by SPSS 20. Results: HBV DNA was found in 3 HBsAg positive cases. Phylogenetic tree of derived HBV DNAs showed the existence of genotype D (subgenotype D1, subtype ayw2). Also immune escape mutations were determined in S gene. Conclusion: There were a few variations and genotypes and subtypes among infected intravenous drug users. This study showed the predominance of genotype D among intravenous drug users. Our study concurs with other reports from Iran, that all showing currently only genotype D is the only detectable genotype in Iran.

Keywords: drug users, genotype, HBV, phylogenetic tree

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Authors: Upasana Bhumbla

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Background: Hepatitis C virus is a major cause of chronic hepatitis, which can further lead to cirrhosis of the liver and hepatocellular carcinoma. Worldwide the burden of Hepatitis C infection has become a serious threat to the human race. Hepatitis C virus (HCV) has population-specific genotypes and provides valuable epidemiological and therapeutic information. Genotyping and assessment of viral load in HCV patients are important for planning the therapeutic strategies. The aim of the study is to study the changing trends of prevalence and genotypic distribution of hepatitis C virus in a tertiary care hospital in Western India. Methods: It is a retrospective study; blood samples were collected and tested for anti HCV antibodies by ELISA in Dept. of Microbiology. In seropositive Hepatitis C patients, quantification of HCV-RNA was done by real-time PCR and in HCV-RNA positive samples, genotyping was conducted. Results: A total of 114 patients who were seropositive for Anti HCV were recruited in the study, out of which 79 (69.29%) were HCV-RNA positive. Out of these positive samples, 54 were further subjected to genotype determination using real-time PCR. Genotype was not detected in 24 samples due to low viral load; 30 samples were positive for genotype. Conclusion: Knowledge of genotype is crucial for the management of HCV infection and prediction of prognosis. Patients infected with HCV genotype 1 and 4 will have to receive Interferon and Ribavirin for 48 weeks. Patients with these genotypes show a poor sustained viral response when tested 24 weeks after completion of therapy. On the contrary, patients infected with HCV genotype 2 and 3 are reported to have a better response to therapy.

Keywords: hepatocellular, genotype, ribavarin, seropositive

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Authors: Man Guo, Wenyong Tan

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By combining spatial syntax with data obtained from field visits, this paper interprets the internal relationship between spatial morphology and spatial cognition in Lidukou Village. By comparing the obtained data, it is recognized that the spatial integration degree of Lidukou Village is positively correlated with the spatial cognitive intention of local villagers. The part with a higher spatial cognitive degree within the village is distributed along the axis mainly composed of Shuxiang Road. And the accessibility of historical relics is weak, and there is no systematic relationship between them. Aiming at the morphological problem of Lidukou Village, optimization strategies have been proposed from multiple perspectives, such as optimizing spatial mechanisms and shaping spatial nodes.

Keywords: traditional villages, spatial syntax, spatial integration degree, morphological problem

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Authors: Aleksandr Nagay, Gulnoz Khamidullayeva

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It is known that an unbalanced intake of salt (NaCI), lifestyle and genetic predisposition to pathology is a key component of the risk and the development of essential hypertension (EH). Purpose: To study the relationship between salt-sensitivity and blood pressure (BP) on systolic (SBP) and diastolic (DBP) blood pressure, depending on the C825T polymorphism of GNB3 in individuals of Uzbek nationality with EH. Method: studied 148 healthy and 148 patients with EH with I-II degree (WHO/ISH, 2003) with disease duration 6,5±1,3 years. Investigation of the gene GNB3 was produced by PCR-RFLP method. Determination of salt-sensitivity was performed by the method of R. Henkin. Results: For a comparative analysis of BP, the groups with carriage of CТ and TT genotypes were combined. The analysis showed that carriers of CC genotype and low salt-sensitivity were determined by higher levels of SBP compared with carriers of CT and TT genotypes, and low salt-sensitivity of SBP: 166,2±4,3 against 158,2±9,1 mm Hg (p=0,000). A similar analysis on the values of DBP also showed significantly higher values of blood pressure in carriers of CC genotype DBP: 105,8±10,6 vs. 100,5±7,2 mm Hg, respectively (p=0,001). The average values of SBP and DBP in groups with carriers of CC genotype at medium or high salt-sensitivity in comparison with carriers of CT or TT genotype did not differ statistically SBP: 165,0±0,1 vs. 160,0±8,6 mm Hg (p=0,275) and DBP: 100,1±0,1 vs. 101,6±7,6 mm Hg (p=0,687), respectively. Conclusion: It is revealed that in patients with EH CC genotype of the gene GNB3 given salt-sensitivity has a negative effect on blood pressure profile. Since patients with EH with the CC genotype of GNB3 gene with low-salt taste sensitivity is determined by a higher level of blood pressure, both on SBP and DBP.

Keywords: salt sensitivity, essential hypertension EH, blood pressure BP, genetic predisposition

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Authors: Christakis Chatzichristou, Elias Kranos

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Architectural awards, especially if they are given by the state, recognize excellence in the field and, at the same time, strongly contribute to the making of the architectural culture of a place. The present research looks at the houses that have been awarded through such a system in Cyprus in order to discuss the values promoted, directly or not, by such a setup which is quite similar to other prestigious award systems such as the Mies van de Rohe Prize in Europe. In fact, many of the projects signed out through the state award system end up being selected to represent the country for the European awards. The residential architecture encouraged by such systems is quite interesting in that the most public of institutions influence how the most private unit of society is architecturally accommodated. The methodology uses both qualitative as well as quantitative research tools in order to analyze: the official state call for entries to the competition; the final report of the evaluation committee; the spatial characteristics of the houses through the Space Syntax methodology; the statements of the architects regarding their intentions and the final outcome; the feelings of the owners and users of the houses regarding the design process as well as the degree of satisfaction regarding the final product. The above-mentioned analyses allow for a more thorough discussion regarding not only the values promoted explicitly by the system through the brief that describes what the evaluation committee is looking for but also the values that are actually being promoted indirectly through the results of the actual evaluation itself. The findings suggest that: the strong emphasis in brief on bioclimatic design and issues of sustainability weakens significantly, if at all present, in the actual selection process; continuous improvement seems to be fuzzily used as a concept; most of the houses tend to have a similar spatial genotype; most of the houses have similar aesthetic qualities; discrepancies between the proposed lifestyle through the design and the actual use of the spaces do not seem to be acknowledged in the evaluation as an issue; the temporal factor seems to be ignored as the projects are required to be ‘finished projects’ as though the users and their needs do not change through time. The research suggests that, rather than preserving a critical attitude regarding the role of the architect in society, the state award system tends, like any other non-reflective social organism, to simply promote its own unexamined values as well as prejudices. This is perhaps more evident in the shared aesthetic character of the awarded houses and less so in the hidden spatial genotype to which they belong. If the design of houses is indeed a great opportunity for architecture to contribute in a more deliberate manner to the evolution of society, then what the present study shows is that this opportunity seems to be largely missed. The findings may serve better less as a verdict and more as a chance for introspection and discussion.

Keywords: award systems, houses, spatial genotype, aesthetic qualities

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Authors: Chidiebere C. Agoha, Armstong C. Awuzie, Chukwuebuka N. Onwubuariri, Joy O. Njoku

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Spatial analysis is a field of study that utilizes geographic or spatial information to understand and analyze patterns, relationships, and trends in data. It is characterized by the use of geographic or spatial information, which allows for the analysis of data in the context of its location and surroundings. It is different from non-spatial or aspatial techniques, which do not consider the geographic context and may not provide as complete of an understanding of the data. Spatial analysis is applied in a variety of fields, which includes urban planning, environmental science, geosciences, epidemiology, marketing, to gain insights and make decisions about complex spatial problems. This review paper explores definitions of spatial analysis from various sources, including examples of its application and different analysis techniques such as Buffer analysis, interpolation, and Kernel density analysis (multi-distance spatial cluster analysis). It also contrasts spatial analysis with non-spatial analysis.

Keywords: aspatial technique, buffer analysis, epidemiology, interpolation

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Authors: G. Shiha, S. Seif, W. Samir, K. Zalata

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Prospective Validation of the FibroTest Score in assessing Liver Fibrosis in Hepatitis C Infection with Genotype 4 FibroTest (FT) is non-invasive score of liver fibrosis that combines the quantitative results of 5 serum biochemical markers (alpha-2-macroglobulin, haptoglobin, apolipoprotein A1, gamma glutamyl transpeptidase (GGT) and bilirubin) and adjusted with the patient's age and sex in a patented algorithm to generate a measure of fibrosis. FT has been validated in patients with chronic hepatitis C (CHC) (Halfon et al., Gastroenterol. Clin Biol.( 2008), 32 6suppl 1, 22-39). The validation of fibro test ( FT) in genotype IV is not well studied. Our aim was to evaluate the performance of FibroTest in an independent prospective cohort of hepatitis C patients with genotype 4. Subject was 122 patients with CHC. All liver biopsies were scored using METAVIR system. Our fibrosis score(FT) were measured, and the performance of the cut-off score were done using ROC curve. Among patients with advanced fibrosis, the FT was identically matched with the liver biopsy in 18.6%, overestimated the stage of fibrosis in 44.2% and underestimated the stage of fibrosis in 37.7% of cases. Also in patients with no/mild fibrosis, identical matching was detected in 39.2% of cases with overestimation in 48.1% and underestimation in 12.7%. So, the overall results of the test were identical matching, overestimation and underestimation in 32%, 46.7% and 21.3% respectively. Using ROC curve it was found that (FT) at the cut-off point of 0.555 could discriminate early from advanced stages of fibrosis with an area under ROC curve (AUC) of 0.72, sensitivity of 65%, specificity of 69%, PPV of 68%, NPV of 66% and accuracy of 67%. As FibroTest Score overestimates the stage of advanced fibrosis, it should not be considered as a reliable surrogate for liver biopsy in hepatitis C infection with genotype 4.

Keywords: fibrotest, chronic Hepatitis C, genotype 4, liver biopsy

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Authors: Man Guo

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This paper delves into the intricate interplay between spatial morphology and spatial cognition in Lidukou Village, utilizing a combined approach of spatial syntax and field data. Through a comparative analysis of the gathered data, it emerges that the spatial integration level of Lidukou Village exhibits a direct positive correlation with the spatial cognitive preferences of its inhabitants. Specifically, the areas within the village that exhibit a higher degree of spatial cognition are predominantly distributed along the axis primarily defined by Shuxiang Road. However, the accessibility to historical relics remains limited, lacking a coherent systemic relationship. To address the morphological challenges faced by Lidukou Village, this study proposes optimization strategies that encompass diverse perspectives, including the refinement of spatial mechanisms and the shaping of strategic spatial nodes.

Keywords: traditional villages, spatial syntax, spatial integration degree, morphological problem

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Authors: Paula Simões, Isabel Natário

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This paper reviews a number of theoretical aspects for implementing an explicit spatial perspective in econometrics for modelling non-continuous data, in general, and count data, in particular. It provides an overview of the several spatial econometric approaches that are available to model data that are collected with reference to location in space, from the classical spatial econometrics approaches to the recent developments on spatial econometrics to model count data, in a Bayesian hierarchical setting. Considerable attention is paid to the inferential framework, necessary for structural consistent spatial econometric count models, incorporating spatial lag autocorrelation, to the corresponding estimation and testing procedures for different assumptions, to the constrains and implications embedded in the various specifications in the literature. This review combines insights from the classical spatial econometrics literature as well as from hierarchical modeling and analysis of spatial data, in order to look for new possible directions on the processing of count data, in a spatial hierarchical Bayesian econometric context.

Keywords: spatial data analysis, spatial econometrics, Bayesian hierarchical models, count data

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Authors: Saad Khalid Niaz, Arif Mahmood Siddiqui, Afzal Haqi

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Background: Estimated prevalence of Hepatitis C in Pakistan is 5% of which 78 % are Genotype 3, in which Response to conventional interferon is reported to be 70%. Objective: To determine the efficacy of pegylated interferon 20 kDa (Unipeg) plus ribavirin (Ribazole) in HCV genotype 3 patients who relapsed to conventional interferon. Methods: This is an ongoing study of 20 enrolled patients. Pegylated interferon alfa-2a 20 kDa 180 mcg weekly with ribavirin, were administered for a period of 24 weeks. Virological Responses were measured by Qualitative HCV RNA at weeks 4, 12, 24 and 48 to determine Rapid Virological Response (RVR), Early Virological Response (EVR), End of Treatment (ETR) and Sustained Virological Response (SVR), respectively. EVR was done for those who didn’t achieve RVR. Results: Males were 12 (60%) and mean age was 38.5 ±7.62 years. Out of 20 recruited patients, all completed 4 weeks therapy; RVR was achieved in 8 (40%) patients. One patient was lost to follow up and one yet to visit at 12 weeks. From 10 patients, 8 (80%) patients achieved EVR. Out of intent-to-treat patients, 15 completed 24 weeks therapy, ETR was achieved in 14 (93%) patients and 9 patients completed post therapy follow-up, of which, 8 (89%) patients achieved SVR. Conclusion: Our interim data demonstrates that Pegylated Interferon alfa-2a 20 kDa 180 mcg (Unipeg) in combination with Ribavirin (Ribazole) has shown promising results in treating HCV Genotype 3 patients who relapsed to conventional interferon. We recommend use of Pegylated Interferon in Relapsers with Genotype 3 when financial constraints limit the use of oral antivirals.

Keywords: pegylated interferon (unipeg), hepatitis c, relapsers, Pakistan

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Authors: Amitha Puranik, V. S. Binu, Seena Biju

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Missing data is a common problem in spatial analysis especially at the aggregate level. Missing can either occur in covariate or in response variable or in both in a given location. Many missing data techniques are available to estimate the missing data values but not all of these methods can be applied on spatial data since the data are autocorrelated. Hence there is a need to develop a method that estimates the missing values in both response variable and covariates in spatial data by taking account of the spatial autocorrelation. The present study aims to develop a model to estimate the missing data points at the aggregate level in spatial data by accounting for (a) Spatial autocorrelation of the response variable (b) Spatial autocorrelation of covariates and (c) Correlation between covariates and the response variable. Estimating the missing values of spatial data requires a model that explicitly account for the spatial autocorrelation. The proposed model not only accounts for spatial autocorrelation but also utilizes the correlation that exists between covariates, within covariates and between a response variable and covariates. The precise estimation of the missing data points in spatial data will result in an increased precision of the estimated effects of independent variables on the response variable in spatial regression analysis.

Keywords: spatial regression, missing data estimation, spatial autocorrelation, simulation analysis

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Authors: Supaporn Yamuangmorn, Chanakan Prom-U-Thai

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Wetland and upland purple rice are the two major types classified by its original ecotypes in Northern Thailand. Wetland rice is grown under flooded condition from transplanting until the mutuality, while upland rice is naturally grown under well-drained soil known as aerobic cultivations. Both ecotypes can be grown and adapted to the reverse systems but little is known on its responses of grain yield and qualities between the 2 ecotypes. This study evaluated responses of grain yield as well as anthocyanin and antioxidant capacity between the wetland and upland purple rice genotypes grown in the submerged and aerobic conditions. A factorial arrangement in a randomized complete block design (RCBD) with two factors of rice genotype and water condition were carried out in three replications. The two wetland genotypes (Kum Doi Saket: KDK and Kum Phayao: KPY) and two upland genotypes (Kum Hom CMU: KHCMU and Pieisu1: PES1) were used in this study by growing under submerged and aerobic conditions. Grain yield was affected by the interaction between water condition and rice genotype. The wetland genotypes, KDK and KPY grown in the submerged condition produced about 2.7 and 0.8 times higher yield than in the aerobic condition, respectively. The 0.4 times higher grain yield of upland genotype (PES1) was found in the submerged condition than in the aerobic condition, but no significant differences in KHCMU. In the submerged condition, all genotypes produced higher yield components of tiller number, panicle number and percent filled grain than in the aerobic condition by 24% and 32% and 11%, respectively. The thousand grain weight and spikelet number were affected by water condition differently among genotypes. The wetland genotypes, KDK and KPY, and upland genotype, PES1, grown in the submerged condition produced about 19-22% higher grain weight than in the aerobic condition. The similar effect was found in spikelet number which the submerged condition of wetland genotypes, KDK and KPY, and the upland genotype, KHCMU, had about 28-30% higher than the aerobic condition. In contrast, the anthocyanin concentration and antioxidant capacity were affected by both the water condition and genotype. Rice grain grown in the aerobic condition had about 0.9 and 2.6 times higher anthocyanin concentration than in the submerged condition was found in the wetland rice, KDK and upland rice, KHCMU, respectively. Similarly, the antioxidant capacity of wetland rice, KDK and upland rice, KHCMU were 0.5 and 0.6 times higher in aerobic condition than in the submerged condition. There was a negative correlation between grain yield and anthocyanin concentration in wetland genotype KDK and upland genotype KHCMU, but it was not found in the other genotypes. This study indicating that some rice genotype can be adapted in the reverse ecosystem in both grain yield and quality, especially in the wetland genotype KPY and upland genotype PES1. To maximize grain yield and quality of purple rice, proper water management condition is require with a key consideration on difference responses among genotypes. Increasing number of rice genotypes in both ecotypes is needed to confirm their responses on water management.

Keywords: purple rice, water condition, anthocyanin, grain yield

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Authors: Tety Hartatik, Dian Kurniawati, Adiarto

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The aim of the research was to determine the associations between polymorphism of the bovine growth hormone (GH) gene (Leu/Val, L/V) and milk production of Friesian Holstein Cattle. A total of 62 cows which consist of two Friesian Holstein groups (cattle from New Zealand are 19 heads and cattle from Australia are 43 heads). We perform the PCR and RFLP method for analyzing the genotype of the target gene GH 211 bp in the part of intron 4 and exon 5 of GH gene. The frequencies of genotypes LL were higher than genotype LV. The number of genotype LL in New Zealand and Australia groups are 84% and 79%, respectively. The number of genotype LV in New Zealand and Australia groups are 16% and 21%, respectively. The association between Leu/Val polymorphism on milk production, fat and protein content in both groups does not show the significant effect. However base on the groups (cows from New Zealand compare with those from Australia) show the significant effect on fat and protein content.

Keywords: Friesian Holstein, fat content, growth hormone gene, milk production, PCR-RLFP, protein content

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Authors: Jae Woong Sull

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Lipid levels are related to the risk of cardiovascular diseases. Cholesterol ester transfer protein (CETP) gene is one of the candidate genes of cardiovascular diseases. A total of 2,304 persons were chosen from a Hospital (N=4,294) in South Korea. Female subjects with the CG/GG genotype had a 2.03 -fold (p=0.0001) higher risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. Male subjects with the CG/GG genotype had a 1.34 -fold (p=0.0019) higher risk than subjects with the CC genotype. When analyzed by body mass index, the association with CETP was much stronger in male subjects with BMI>=25.69 (OR=1.55, 95% CI: 1.15-2.07, P=0.0037) than in male lean subjects. When analyzed by family history of diabetes, the association with CETP was much stronger in male subjects with positive family history of low physical activity (OR=4.82, 95% CI: 1.86-12.5, P=0.0012) than in male subjects with negative family history of diabetes. This study clearly demonstrates that genetic variants in CETP influence HDL cholesterol levels in Korean adults.

Keywords: CETP, diabetes, obesity, polymorphisms

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Authors: Nazira B. Bekenova, Lydia A. Mukovozova, Andrej M. Grjibovski, Alma Z. Tokayeva, Yerbol M. Smail, Nurlan E. Aukenov

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Erysipelas is an infectious disease with socio-economic significance and prone to prolonged recurrent course (30%). Contribution of genetic factors, in particular the gene polymorphism of cytokines, can be essential in disease etiology and pathogenesis. Interleukin – 17 A are produced by T helpers of 17 type and plays a key role in development of local inflammation process. Local inflammatory process is a dominant in the clinic of erysipelas. Established that the skin and mucosas are primary areas of migration (homing) Th17-cell and their cytokines are stimulate the barrier function of the epithelium. We studied associations between gene polymorphism of IL-17A (C737T) rs 8193036 and IL-17A level in patients with erysipelas Kazakh population. Altogether, 90 cases with erysipelas and 90 healthy controls from an ethnic Kazakh population comprised the sample. Cases were identified at Clinical Infectious Diseases Hospital of Semey (Kazakhstan). The IL-17A (rs8193036) polymorphism was analyzed by a real time polymerase chain reaction. Plasma levels of IL-17 A were assessed by immuneenzyme analysis method using ‘Vector-Best’ test-system (Russia). Differences in levels of IL-17 A between CC, TT, CT groups were studied using Kruskal — Wallis test. Pairwise comparisons were performed using Mann-Whitney tests with Bonferroni correction (New significance level was set to 0.025). We found, that in patients with erysipelas with CC genotype the level of IL-17 A was higher (p= 0, 010) compared to the carriers of CT genotype. When compared the level of IL – 17 A between the patients with TT genotype and patients with CC genotype, also between the patients with CT genotype and patients with TT genotype statistically significant differences are not revealed (p = 0.374 and p = 0.043, respectively). Comparisons of IL-17 A plasma levels between the CC and CT genotypes, between the CC and TT genotypes, and between the TT and CT in healthy patients did not reveal significant differences (p = 0, 291). Therefore, we are determined the associations of gene polymorphism of IL-17 A (C737T) with its level in patients erysipelas carriers CC genotype.

Keywords: erysipelas, interleukin – 17 A, Kazakh, polymorphism

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Authors: Wang Xingjuan, Qian Dongming

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As a common thinking ability, spatial thinking ability plays an increasingly important role in the information age. The key to cultivating students' spatial thinking ability is to cultivate students' ability to process and transform graphics. The 3D printing course enables students to constantly touch the rotation and movement of objects during the modeling process and to understand spatial graphics from different views. To this end, this article combines the classic PSVT: R test to explore the impact of 3D printing courses on the spatial thinking ability of middle school students. The results of the study found that: (1) Through the study of the 3D printing course, the students' spatial ability test scores have been significantly improved, which indirectly reflects the improvement of the spatial thinking ability level. (2) The student's spatial thinking ability test results are influenced by the parent's occupation.

Keywords: 3D printing, middle school students, spatial thinking ability, influence

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Authors: Lale Efe, Zeynep Gokce

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In this study carried out in 2013-14 growing season in East Mediterranean Region of Turkey, it was aimed to investigate the effects of different sowing times on the seed yield and quality of fenugreek (Trigonella foenum graceum L.). Three fenugreek genotypes (Gürarslan, Candidate Line-1 and Genotype-1) were sown on 13.11.2013 and 07.03.2014 according to factorial randomized block design with 3 replications. Plant height (cm), branch number per plant, first pod height (cm), pod length (mm), seed number per pod (g), seed yield per plant (g), seed yield per decar (kg), thousand seed weight (g), mucilage rate (%), seed protein ratio (%), seed oil ratio (%), oleic acid (%), linoleic acid (%), palmitic acid (%) and stearic acid (%) were investigated. Among genotypes, while the highest seed yield per plant was obtained from Genotype-1 (5 g/plant), the lowest seed yield per plant was obtained from cv. Gürarslan (3.4 g/plant). According to genotype x sowing date interactions, it can be said that the highest seed yield per plant was taken in autumn sowing from Genotype-1 (6.6 g/plant) and the lowest seed yield per plant was taken in spring sowing from cv. Gürarslan (2.9 g/plant). Genotype-1 had the highest linoleic acid ratio (41.6 %). Cv. Gürarslan and Candidate Line-1 had the highest oleic acid ratio (respectively 17.8 % and 17.6%).

Keywords: fenugreek, seed yield and quality, sowing times, Trigonella foenum graecum L.

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Authors: Khabat Barkhordari

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Hepatitis delta virus (HDV) is a RNA virus that needs the function of hepatitis B virus (HBV) for its propagation and assembly. Infection by HDV can occur spontaneously with HBV infection and cause acute hepatitis or develop as secondary infection in HBV suffering patients. Based on genome sequence analysis, HDV has several genotypes which show broad geographic and diverse clinical features. The aim of current study is determine the molecular epidemiology of hepatitis delta virus genotype in patients with positive HBsAg among different ethnic groups of Iran. This systematic review study reviews the results of different studies which examined 2000 Iranian patients with HBV infection from 2010 to 2015. Among 2000 patients in this study, 16.75 % were containing anti-HDV antibody and HDV RNA was found in just 1.75% cases. All of positive cases also have genotype I.

Keywords: HDV, genotype, epidemiology, distribution

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Authors: Olusegun D. Badewa, E. K. Tsado, A. S. Gana, K. D. Tolorunse, R. U. Okechukwu, P. Iluebbey, S. Ibrahim

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Farmers are faced with varying production challenges ranging from unstable weather due to climate change, low yield, malnutrition, cattle invasion, and bush fires that have always affected their livelihood. Research effort must therefore be centered on improving farmers’ livelihood, nutrition, and health by providing early bulking biofortified cassava varieties that could be harvested earlier with reasonable root yield and thereby preventing long stay of the crop on their farmland. This study evaluated cassava genotypes at different harvesting months of 3, 6, 9, and 12 months after planting in order to evaluate their bulking rate at different agroecology of Mokwa and Ubiaja. Data were collected on fresh storage root yield, Harvest index, and Dry matter content. It was shown from the study that traits FSRY, HI, and DM were significant for genotype and months after planting and variable among the genotype while location had no effect on the yield traits. Early bulking genotypes were not high yielding and showed discontinuity at some point across the months. The retrogression in yield performance across months had no effect on the highest yielding. Also, for all the genotypes and across evaluated months, FSRY reduces at 9 MAP due to a reduction in dry matter content during the same month, and the best performing genotype was the genotype IBA90581, followed by IBA120036, IBA130896, and IBA980581 while the least performing was genotype IBA130818.

Keywords: early bulking, dry mater, harvest index, high yielding, root yield

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Authors: E. Chakwizira, D. J. Moot, M. Andrews, E. Teixeira

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Partitioning of macro-nutrients in wheat (Triticum aestivum L.) plant organs have not been extensively studied, particularly for modern genotypes grown under contrasting N supply. Nutrient accumulation and partitioning of phosphorus, potassium, calcium, magnesium and sulphur (P, K, Ca, Mg and S) were determined for six wheat genotypes [12S2-2021, 12S3-3019, 13S3-2026, Discovery, Duchess and Reliance] grown with (200 kg/ha) or without (0 kg/ha) nitrogen (N), in a fully irrigated field experiment in 2017-18 season at Lincoln, New Zealand. Data were collected at three growth stages (GS): tillering (GS21), anthesis (GS60) and grain maturity (GS92). Grain yield varied with both N and genotype; from 6-7.5 t/ha for the 0 kg N/ha crops and 8.1-9.3 t/ha for the 200 kg N/ha treatments. Plant nutrient uptake at maturity responded to both N supply and genotype for all nutrients, except S which did not differ among the genotypes. For example, total P uptake averaged 13.5 (12.4-14.3) kg/ha for the 0 kg N/ha treatments and 17.8 (15.1-19.7) kg/ha when 200 kg N/ha was applied. Similarly, K uptake increased from an average of 23 (21.6-25.3) for the 0 kg N/ha treatments to 34.3 (32.4-40.8) kg/ha when 200 kg N/ha was applied. Similar trends were observed for Ca and Mg. The S content only responded to N supply but not to genotype, increasing from 7.9 kg/ha for the 0 kg N treatments to 12.8 kg/ha when 200 kg N was applied. Relative nutrient content at anthesis compared with those at maturity were 30% for P, 100% for both K and Ca and 34% of Mg. Sulphur content at anthesis decreased 29% with N supply and was highest for genotypes 12S2-2021 compared with the other five genotype. At grain maturity, the ratio of nutrients in grain to total plant nutrient, defined as the nutrient harvest index (NHI) varied with both N supply and genotype. Averaged across treatments, the NHI was 0.96 for P, 0.53 for K, 0.58 for Ca, 0.90 for Mg and 0.85 for S. These results suggest that Ca and K should be provided earlier in the season as there is limited or no uptake after anthesis. These results also show that Ca and K are important for structural functions, while P, Mg and S are remobilised to the grains and become important for quality.

Keywords: anthesis, genotype, nutrient harvests index, NHI, Triticum aestivum L.

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Authors: Shahram Nanekarania, Majid Goodarzia

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Calpastatin and callipyge have been known as one of the candidate genes in meat quality and quantity. Calpastatin gene has been located to chromosome 5 of sheep and callipyge gene has been localized in the telomeric region on ovine chromosome 18. The objective of this study was identification of calpastatin and callipyge genes polymorphism and analysis of genotype structure in population of Lori sheep kept in Iran. Blood samples were taken from 120 Lori sheep breed and genomic DNA was extracted by salting out method. Polymorphism was identified using the PCR-RFLP technique. The PCR products were digested with MspI and FaqI restriction enzymes for calpastatin gene and callipyge gene, respectively. In this population, three patterns were observed and AA, AB, BB genotype have been identified with the 0.32, 0.63, 0.05 frequencies for calpastatin gene. The results obtained for the callipyge gene revealed that only the wild-type allele A was observed, indicating that only genotype AA was present in the population under consideration.

Keywords: polymorphism, calpastatin, callipyge, PCR-RFLP, Lori sheep

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Authors: Mohammed A. Alazawi, Shiguo Jiang, Steven F. Messner

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Research has long focused on two main spatial aspects of crime: spatial patterns and spatial processes. When analyzing these patterns and processes, a key issue has been to determine the proper spatial scale. In addition, it is important to consider the possibility that these patterns and processes might differ appreciably for different temporal scales and might vary across geographic units of analysis. We examine the spatial-temporal dependence of residential burglary. This dependence is tested at varying geographical scales and temporal aggregations. The analyses are based on recorded incidents of crime in Columbus, Ohio during the 1994-2002 period. We implement point pattern analysis on the crime points using Ripley’s K function. The results indicate that spatial point patterns of residential burglary reveal spatial scales of clustering relatively larger than the average size of census tracts of the study area. Also, spatial scale is independent of temporal scale. The results of our analyses concerning the geographic scale of spatial patterns and processes can inform the development of effective policies for crime control.

Keywords: inhomogeneous K function, residential burglary, spatial point pattern, spatial scale, temporal scale

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Authors: Maha Ali Al-Mohaya, Lubna Majed Al-Otaibi, Ebtissam Nassir Al-Bakr, Abdulrahman Al-Asmari

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Objectives: Oral lichen planus (OLP) is a chronic inflammatory oral mucosal disease. Cytokines play an important role in the pathogenesis and disease progression of OLP. The purpose of this study was to investigate the association of tumor necrosis factor (TNF)-α, TNF-β and interleukin (IL)-10 gene polymorphisms with the OLP risk. Material and Methods: Forty-two unrelated patients with OLP and 211 healthy volunteers were genotyped for TNF-α (-308 G/A), TNF-β (+252A/G), IL-10 (-1082G/A), IL-10 (-819C/T), and IL-10 (-592C/A) polymorphisms. Results: The frequencies of allele A and genotype GA of TNF-α (-308G/A) were significantly higher while allele G and GG genotypes were lower in OLP patients as compared to the controls (P < 0.001). The frequency of GA genotype of TNF-β (+252A/G) was significantly higher in patients than in controls while the AA genotype was completely absent in OLP patients. These results indicated that allele A and genotype GA of TNF-α (-308G/A) as well as the GA genotype of TNF-β (+252A/G) polymorphisms are associated with OLP risk. The frequencies of alleles and genotypes of -1082G/A, -819C/T and -592C/A polymorphisms in IL-10 gene did not differ significantly between OLP patients and controls (P > 0.05). However, haplotype ATA extracted from 1082G/A, -819C/T, -592C/A polymorphisms of IL-10 were more prevalent in OLP patients when compared to controls indicating its possible association with OLP susceptibility. Conclusion: It is concluded that TNF-α (-308G/A), TNF-β (+252A/G) and IL-10 (-1082G/A, -819C/T and -592C/A) polymorphisms are associated with the susceptibility of OLP, thus giving additional support for the genetic basis of this disease. Further studies are required using a larger sample size to confirm this association and determine the prognostic values of these findings.

Keywords: oral lichen planus, cytokines, polymorphism, genetic

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Authors: Ghaleb Bin Huraib

Abstract:

Atopic dermatitis (AD), also known as atopic eczema, is a chronic inflammatory skin disease characterized by severe itching and recurrent, relapsing eczema-like skin lesions, affecting up to 20% of children and 10% of adults in industrialized countries. AD is a complex multifactorial disease, and its exact etiology and pathogenesis have not been fully elucidated. The aim of this study was to investigate the impact of gene polymorphisms of T helper cell subtype Th1 and Th2 cytokines, interferon-gamma (IFN-γ), interleukin-6 (IL-6) and transforming growth factor (TGF)-β1on AD susceptibility in a Saudi cohort. One hundred four unrelated patients with AD and 195 healthy controls were genotyped for IFN-γ (874A/T), IL-6 (174G/C) and TGF-β1 (509C/T) polymorphisms using ARMS-PCR and PCR-RFLP technique. The frequency of genotypes AA and AT of IFN-γ (874A/T) differed significantly among patients and controls (P 0.001). The genotype AT was increased while genotype AA was decreased in AD patients as compared to controls. AD patients also had a higher frequency of T-containing genotypes (AT+TT) than controls (P = 0.001). The frequencies of alleles T and A were statistically different in patients and controls (P = 0.04). The frequencies of genotype GG and allele G of IL-6 (174G/C) were significantly higher, while genotype GC and allele C were lower in AD patients than in controls. There was no significant difference in the frequencies of alleles and genotypes of TGF-β1 (509C/T) polymorphism between the patient and control groups. These results showed that susceptibility to AD is influenced by the presence or absence of genotypes of IFN-γ (874A/T) and IL-6 (174G/C) polymorphisms. It is concluded T-allele and T-containing genotypes (AT+TT) of IFN-γ (874A/T) and G-allele and GG genotype ofIL-6 (174G/C) polymorphisms are susceptible to AD in Saudis. On the other hand, the TGF-β1 (509C/T) polymorphism may not be associated with AD risk in our population; however, further studies with large sample sizes are required to confirm these results.

Keywords: atopic dermatitis, Polymorphism, Interferon, IL-6

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Authors: Recep Kesli, Huseyin Bilgin, Yasar Unlu, Gokhan Gungor

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Aim: The aim of this study was to compare diagnostic values of two different molecular-based tests (GenoType® HelicoDR ve Seeplex® H. pylori-ClaR- ACE Detection) in detection presence of the H. pylori from gastric biopsy specimens. In addition to this also was aimed to determine resistance ratios of H. pylori strains against to clarytromycine and quinolone isolated from gastric biopsy material cultures by using both the genotypic (GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection) and phenotypic (gradient strip, E-test) methods. Material and methods: A total of 266 patients who admitted to Konya Education and Research Hospital Department of Gastroenterology with dyspeptic complaints, between January 2011-June 2013, were included in the study. Microbiological and histopathological examinations of biopsy specimens taken from antrum and corpus regions were performed. The presence of H. pylori in all the biopsy samples was investigated by five differnt dignostic methods together: culture (C) (Portagerm pylori-PORT PYL, Pylori agar-PYL, GENbox microaer, bioMerieux, France), histology (H) (Giemsa, Hematoxylin and Eosin staining), rapid urease test (RUT) (CLOtest, Cimberly-Clark, USA), and two different molecular tests; GenoType® HelicoDR, Hain, Germany, based on DNA strip assay, and Seeplex ® H. pylori -ClaR- ACE Detection, Seegene, South Korea, based on multiplex PCR. Antimicrobial resistance of H. pylori isolates against clarithromycin and levofloxacin was determined by GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection, and gradient strip (E-test, bioMerieux, France) methods. Culture positivity alone or positivities of both histology and RUT together was accepted as the gold standard for H. pylori positivity. Sensitivity and specificity rates of two molecular methods used in the study were calculated by taking the two gold standards previously mentioned. Results: A total of 266 patients between 16-83 years old who 144 (54.1 %) were female, 122 (45.9 %) were male were included in the study. 144 patients were found as culture positive, and 157 were H and RUT were positive together. 179 patients were found as positive with GenoType® HelicoDR and Seeplex ® H. pylori -ClaR- ACE Detection together. Sensitivity and specificity rates of studied five different methods were found as follows: C were 80.9 % and 84.4 %, H + RUT were 88.2 % and 75.4 %, GenoType® HelicoDR were 100 % and 71.3 %, and Seeplex ® H. pylori -ClaR- ACE Detection were, 100 % and 71.3 %. A strong correlation was found between C and H+RUT, C and GenoType® HelicoDR, and C and Seeplex ® H. pylori -ClaR- ACE Detection (r:0.644 and p:0.000, r:0.757 and p:0.000, r:0.757 and p:0.000, respectively). Of all the isolated 144 H. pylori strains 24 (16.6 %) were detected as resistant to claritromycine, and 18 (12.5 %) were levofloxacin. Genotypic claritromycine resistance was detected only in 15 cases with GenoType® HelicoDR, and 6 cases with Seeplex ® H. pylori -ClaR- ACE Detection. Conclusion: In our study, it was concluded that; GenoType® HelicoDR and Seeplex ® H. pylori -ClaR- ACE Detection was found as the most sensitive diagnostic methods when comparing all the investigated other ones (C, H, and RUT).

Keywords: Helicobacter pylori, GenoType® HelicoDR, Seeplex ® H. pylori -ClaR- ACE Detection, antimicrobial resistance

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Authors: J. Bernasovska, I. Boronova, J. Poracova, M. Mydlarova Blascakova, V. Szabadosova, P. Ruzbarsky, E. Petrejcikova, I. Bernasovsky

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The paper presents the results of the molecular genetics analysis in sports research, with special emphasis to use genetic information in diagnosing of motoric predispositions in Roma boys from East Slovakia. The ability and move are the basic characteristics of all living organisms. The phenotypes are influenced by a combination of genetic and environmental factors. Genetic tests differ in principle from the traditional motoric tests, because the DNA of an individual does not change during life. The aim of the presented study was to examine motion abilities and to determine the frequency of ACTN3 (R577X) gene in Roma children. Genotype data were obtained from 138 Roma and 155 Slovak boys from 7 to 15 years old. Children were investigated on physical performance level in association with their genotype. Biological material for genetic analyses comprised samples of buccal swabs. Genotypes were determined using Real Time High resolution melting PCR method (Rotor-Gene 6000 Corbett and Light Cycler 480 Roche). The software allows creating reports of any analysis, where information of the specific analysis, normalized and differential graphs and many information of the samples are shown. Roma children of analyzed group legged to non-Romany children at the same age in all the compared tests. The % distribution of R and X alleles in Roma children was different from controls. The frequency of XX genotype was 9.26%, RX 46.33% and RR was 44.41%. The frequency of XX genotype was 9.26% which is comparable to a frequency of an Indian population. Data were analyzed with the ANOVA test.

Keywords: ACTN3 gene, R577X polymorphism, Roma children, sport performance, Slovakia

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Authors: Mulata Haile Nega, Derebew Fikadu Berhe, Vera Ribeiro Marques

Abstract:

There is no epidemiologic data on this gene polymorphism in several countries. Therefore, this study aimed to assess the genotype and allele frequencies of the gene variant in three countries. This study involved healthy individuals from Colombia, Mozambique, and Portugal. Genomic DNA was isolated from blood samples using the Qiamp DNA Extraction Kit (Qiagen). The isolated DNA was genotyped using Polymerase Chain Reaction (PCR) - Restriction Fragment Length Polymorphism. Microstat and GraphPad quick cal software were used for the Chi-square test and evaluation of Hardy-Weinberg equilibrium, respectively. A total of 181 individuals’ blood sample was analyzed. Overall, TT (74.0%) genotype was the highest, and CC (7.8%) was the lowest. Country wise genotypic frequencies were Colombia 47(70.2%) TT, 12(17.9%) TC and 8(11.9%) CC; Mozambique 47(88.7%) TT, 5(9.4%) TC, and 1(1.9%) CC; and Portugal 40(65.6%) TT, 16(26.2%) TC, and 5(8.2%) CC. The reference (T) allele was highest among Mozambicans (93.4%) compared to Colombians (79.1%) and Portuguese (78.7%). Mozambicans showed statistically significant genotypic and allelic frequency differences compared to Colombians (p<0.01) and Portuguese (p <0.01). Overall and country-wise, the CC genotype was less frequent and relatively high for Colombians and Portuguese populations. This finding may imply statins risk-benefit variability associated with CC genotype among these populations that needs further understanding.

Keywords: c.521T>C, polymorphism, SLCO1B1, SNP, statins

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