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From genome to gene: A review of genes and genetic variations associated with type 2 diabetes
Mahdi Safarpour , Ahmad Ebrahimi , Maryam Sadat Daneshpour ,
Volume 73, Issue 9 (12-2015)
Abstract

Despite the valuable results achieved in identification of genes and genetic changes associated with type 2 diabetes (T2D), lack of consistency and reproducibility of these results in different populations is one of the challenges lie ahead in introduction of T2D candidate genes. Therefore, the present review article aimed to provide an overview of the most important genes and genetic variations associated with development of T2D based on a systematic search in well-known genetic databases. For this purpose, the National Center for Biotechnology Information, Database of Genotypes and Phenotypes (NCBI dbGaP) and Human Genome Epidemiology Network (HuGENet) database were searched to find the most important genes associated with T2D. In addition, a gray literature search was conducted to collect any available information released by laboratories offering genetic tests such as deCODE genetics and 23andMe. Candidate genes were selected among the results of all databases based on the highest level of similarity. Subsequently, without any time restriction, PubMed, Scopus and Google scholar databases were searched using relevant Medical Subject Headings (MeSH) terms to access related articles. The relevant articles were screened to make a conclusion about the genes and genetic variations associated with T2D. The results revealed that four selected candidate genes, in order of importance, were TCF7L2, CDKAL1, KCNJ11, and FTO. The most significant single nucleotide polymorphism (SNP) associated with T2D in the TCF7L2 gene was rs7903146 however, the results showed a wide range of variation from slight association in the Amish (P= 5.0×10-2) to strong association in European descent populations (P= 2.0×10-51). Then, rs10440833 mapping to the intronic region of the CDKAL1 gene showed significant association with T2D (P= 2.0×10-22). In the KCNJ11 gene, a missense variation (rs5215) in exon one was found to have the highest association with T2D compared with other SNPs discovered in this gene (P= 5.0×10-11). Finally, rs8050136 located in the first intron of the FTO gene had the strongest association with T2D (P= 2.0×10-17). On the basis of these results, it can be concluded that the current study can be introduced as a model for achieving well-documented results among spectrum of information available in genetic databases based on a systematic search strategy. The candidate genes and genetic variations presented in this review article might be applied for early diagnosis, prevention, and treatment of T2D.


Study of genetics, phenotypic and behavioral properties of eubacteria and archaebacteria
Hamid Kazemian , Zahra Pakbaz , Seyed Mostafa Hosseini , Mohammad Reza Pourmand ,
Volume 74, Issue 3 (6-2016)
Abstract

Background: The genome of the bacteria has considerable diversity in terms of sequence of nucleotide bases and change over the time. With the advancement of bioinformatics science possibility of the vast comparison to living organisms has risen. During the last two decades many information about genome sequencing of pathogenic and non-pathogenic bacteria have been published. Using this information and to find connections between them and many phenotypic characteristics and behavior of bacteria could be used in many studies. In this study we compared some of the genetic, phenotypic and behavioral properties of archaebacteria and eubacteria.

Methods: In this analytical study, genomic Information of 286 species of archaebacteria and 122 species of eubacteria were collected from the NCBI (National Center for Biotechnology Information) site which was conducted in April to June 2015. Mean of gene size, gene number, protein number and C+G content compared in the two groups of archaebacteria and eubacteria. Association of genomic characterization of bacteria with several other characteristics were analyzed using SPSS statistical software version 19 (Chicago, IL, USA). For this purpose, the Pearson correlation coefficient (Pearson), Student’s t-test and ANOVA test (One-way analysis of variance) was used. The P values less than 0.05 was considered as significant level.

Results: There was significant association between means discrepancy in two group (P= 0.01). The genome size of eubacteria and archaebacteria have significant association with some of the characteristics of bacteria, such as the C+G content, the number of proteins, genes and habitats of the bacteria (P= 0.01). As well as there was significant association between genome size and features such as number of pseudogene, mobility and type of breathing in eubacteria (P= 0.01) but not in archaebacterial (P˃ 0.05).

Conclusion: Many characteristics of eubacteria and archaebacteria are significantly associated with genomic properties. Comparison genomics of bacteria will help in identification of evolutionary origins as well as differences between different categories of bacterial.


Associations of common polymorphisms in GCKR with metabolic syndrome
Asiyeh Sadat Zahedi , Bahareh Sedaghati-Khayat , Sara Behnami , Fereidoun Azizi , Maryam Sadat Daneshpour ,
Volume 76, Issue 7 (10-2018)
Abstract
Background: Metabolic syndrome (MetS) is characterized by a combination of cardio-metabolic risk factors. Given that genetic factors have been shown to contribute to individual susceptibility to MetS, the identification of genetic markers for disease risk is essential. Recent studies revealed that rs780094 and rs1260326 of glucokinase regulatory gene (GCKR) are associated with serum triglycerides, plasma glucose levels and metabolic syndrome. The aim of this study was to investigate associations of GCKR gene variants with metabolic syndrome and its components.
Methods: This case-control study was conducted from April to August 2017. In this study, 8710 adults (3522 males and 5188 females), over 19 years, were randomly selected from the Tehran Lipid and Glucose Study (TLGS) population. Based on joint interim statement (JIS) criteria, the subjects were divided into two groups: case and control. Genotyping was performed by HumanOmniExpress-24 v1.0 BeadChips (Illumina, San Diego, CA, USA).
Results: Allele frequencies were in conformity with Hardy-Weinberg equilibrium. Comparisons of allele frequencies by the Chi-square test revealed that frequencies of TT genotype of both polymorphisms were significantly higher among patient group than healthy group. Logistic regression analysis with adjustment for age, gender and CRP revealed that the GCKR polymorphisms (rs1260326: odds ratio 2.7, 95% CI 1.6-4.6, rs780094: odds ratio 2.5, 95% CI 1.5-4.2) were significantly associated with MetS. Frequency of TT genotype was more in persons who had C-reactive protein (CRP) levels above 3 mg/l. The minor T allele of both polymorphisms was significantly associated with increases in the blood serum concentration triglyceride and to a decrease in fasting plasma glucose levels.
Conclusion: The results of our study indicated that, rs780094 and rs1260326 common polymorphisms of the GCKR gene were associated with serum triglycerides levels, fasting plasma glucose levels, and metabolic syndrome in a sample of the Tehranian population (TLGS), as it was already confirmed the inverse effect of this polymorphisms on triglycerides and glucose levels in previous studies.

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