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Shimizu M, Makiguchi M, Yokota Y, Shimamura E, Matsuta M, Nakamura Y, Harano M, Yamazaki H. Simple confirmation methods for rare but impaired variants of human flavin-containing monooxygenase 3 (FMO3) found in an updated genome resource databank. Drug Metab Pharmacokinet 2023; 53:100528. [PMID: 37856929 DOI: 10.1016/j.dmpk.2023.100528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 10/21/2023]
Abstract
Forty-seven new nonsense or missense human flavin-containing monooxygenase 3 (FMO3) variants were recently identified in an updated Japanese population reference panel. Of these, 20 rare single-nucleotide substitutions resulted in moderately or severely impaired FMO3 activity. To easily identify these 20 FMO3 variants (2 stop codon mutations, 2 frameshifts, and 16 amino-acid substitutions) in the clinical setting, simple confirmation methods for impaired FMO3 variants are proposed using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) or allele-specific PCR methods. Using PCR-RFLP, FMO3 variants p.Arg51Gly, p.Met66Lys, p.Asn80Lys, p.Val151Glu, p.Val187fsTer25, p.Gly193Arg, p.Val283Ala, p.Asp286His, p.Val382Ala, and p.Phe451Leu were digested by the designated restriction enzymes and confirmed using reference cDNAs. In contrast, the FMO3 variants p.Gly39Val, p.Arg238Ter, p.Arg387Cys, p.Arg387His, p.Leu457Trp, and p.Met497Arg were not digested, whereas the wild type was digested. FMO3 variants p.Gly11Asp, p.Lys416fsTer72, p.Gln427Ter, and p.Thr453Pro were confirmed using allele-specific PCR systems. The previously identified FMO3 p.Arg500Ter variant has a relatively high frequency and was differentiated from p.Arg500Gln in two steps, i.e., enzyme restriction followed by allele-specific PCR, similar to the method for p.Arg387Cys and p.Arg387His. These systems should facilitate easy detection in the clinical setting of FMO3 variants in Japanese subjects susceptible to low drug clearance possibly caused by impaired FMO3 function.
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Affiliation(s)
- Makiko Shimizu
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Miaki Makiguchi
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Yuka Yokota
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Erika Shimamura
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Moegi Matsuta
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Yuria Nakamura
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Mizuki Harano
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan.
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Raschia MA, Caffaro ME, Rossi ÚA, Poli MA. Modification of a previously patented method to unequivocally score A2-like and A1-like bovine β-casein variants. MethodsX 2023; 10:102183. [PMID: 37424753 PMCID: PMC10326427 DOI: 10.1016/j.mex.2023.102183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/13/2023] [Indexed: 07/11/2023] Open
Abstract
A growing interest in the production and commercialization of A2 cow's milk has been observed in many countries in the last few years due to the beneficial properties for human health attributed to A2 β-casein variant. Methods of varying complexity and different equipment requirements have been proposed for the determination of the β-casein genotype of individual cows. We proposed herein a modification of a previously patented method based on an amplification-created restriction site PCR followed by restriction fragment length polymorphism analysis. This method allows to identify and differentiate A2-like from A1-like β-casein variants, after differential endonuclease cleavage flanking the nucleotide that determines the amino acid at position 67 of β-casein. The advantages of this method are that it: • enables to unequivocally score A2-like as well as A1-like β-casein variants, • can be performed at low cost in simply equipped molecular biology laboratories, and • can be scaled up to analyze hundreds of samples per day. For these reasons, and based on the results obtained from the analysis carried out in this work, it showed to be a reliable method for the screening of herds to selective breeding of homozygous cows and bulls for A2 or A2-like alleles.
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Affiliation(s)
- María Agustina Raschia
- Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIA, Instituto de Genética “Ewald A. Favret”. Nicolás Repetto y de Los Reseros s/n, Hurlingham B1686, Buenos Aires, Argentina
| | - María Eugenia Caffaro
- Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIA, Instituto de Genética “Ewald A. Favret”. Nicolás Repetto y de Los Reseros s/n, Hurlingham B1686, Buenos Aires, Argentina
| | - Úrsula Amaranta Rossi
- Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIA, Instituto de Patobiología-IPVET (UEDD INTA-CONICET), Nicolás Repetto y de Los Reseros s/n, Hurlingham B1686, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Mario Andrés Poli
- Instituto Nacional de Tecnología Agropecuaria, CICVyA-CNIA, Instituto de Genética “Ewald A. Favret”. Nicolás Repetto y de Los Reseros s/n, Hurlingham B1686, Buenos Aires, Argentina
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Kaushik H, Mahajan R, Dabas G, Shrivastava N, Ashraf R, De D, Pal A, Kumar R, Handa S. A cross-sectional study to find association of VDR gene polymorphism with non-syndromic congenital ichthyosis and with vitamin D deficiency. Arch Dermatol Res 2023; 315:551-557. [PMID: 36192561 DOI: 10.1007/s00403-022-02399-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 08/22/2022] [Accepted: 09/12/2022] [Indexed: 11/27/2022]
Abstract
Though development of vitamin D deficiency and rickets in patients with congenital ichthyosis (CI) have recently been observed, yet exact cause of such association is not properly understood. To evaluate association between Vitamin D Receptor (VDR) polymorphism and CI, and to identify risk factors responsible for development of vitamin D deficiency in ichthyosis. In this cross-sectional study, detailed history of patients and controls was noted and certain biochemical investigations were made. Immunohistochemical staining of skin tissue was done for VDR expression in epidermal and dermal region of ichthyosis patients. VDR polymorphism was assessed in all participants. Ninety-six subjects, were recruited. Mean serum vitamin D was significantly lower among ichthyosis patients. Cdx-2 polymorphism was found to be significantly associated with ichthyosis (p = 0.009). Within the diseased group, Fok-1 (p = 0.035), age (p = 0.020) and alkaline phosphatase (ALP) (p = 0.007) emerged as factors which might be associated with vitamin D deficiency. Cdx2 polymorphism was significantly associated with CI patients. Also, association of Fok-1 polymorphism along with age and raised serum ALP levels emerged as potential factors for determining CI-related vitamin D deficiency.
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Affiliation(s)
- Hitaishi Kaushik
- Department of Dermatology, Venereology and Leprology, PGIMER, Chandigarh, 160012, India
| | - Rahul Mahajan
- Department of Dermatology, Venereology and Leprology, PGIMER, Chandigarh, 160012, India.
| | - Garima Dabas
- Department of Dermatology, Venereology and Leprology, PGIMER, Chandigarh, 160012, India
| | - Niharika Shrivastava
- Department of Dermatology, Venereology and Leprology, PGIMER, Chandigarh, 160012, India
| | - Raihan Ashraf
- Department of Dermatology, Venereology and Leprology, PGIMER, Chandigarh, 160012, India
| | - Dipankar De
- Department of Dermatology, Venereology and Leprology, PGIMER, Chandigarh, 160012, India
| | - Arnab Pal
- Department of Biochemistry, PGIMER, Chandigarh, 160012, India
| | - Rakesh Kumar
- Endocrinology Division, Department of Pediatrics, PGIMER, Chandigarh, 160012, India
| | - Sanjeev Handa
- Department of Dermatology, Venereology and Leprology, PGIMER, Chandigarh, 160012, India
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El-Ghamrawy M, El-Gharbawi N, Shahin G, Abdelhady A, Sayed R, Diaa N, Bishai I. Combined tumor necrosis factor-α (-308 G/A) and tumor necrosis factor-β (+ 252 A/G) nucleotide polymorphisms and chronicity in Egyptian children with immune thrombocytopenia. Int J Hematol 2023; 117:856-862. [PMID: 36802017 DOI: 10.1007/s12185-023-03551-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 02/21/2023]
Abstract
BACKGROUND Primary immune thrombocytopenia (ITP) is a common autoimmune disorder. Secretion of TNF-α, TNF-β and IFN-γ plays a major role in the pathogenesis of ITP. OBJECTIVE This cross-sectional study aimed to detect TNF-α (-308 G/A) and TNF-β (+ 252 A/G) gene polymorphism in a cohort of Egyptian children with chronic ITP (cITP) to clarify their possible association with progression to chronic disease. METHODS The study included 80 Egyptian cITP patients and 100 unrelated age- and sex-matched controls. Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). RESULTS Patients with TNF-α homozygous (A/A) genotype had significantly higher mean age, longer disease duration and lower platelet counts (p values 0.005, 0.024 and 0.008, respectively). TNF-α wild (G/G) genotype was significantly more frequent among responders (p = 0.049). Complete response was more frequent among wild (A/A) TNF-β genotype patients (p = 0.011), and platelet count was significantly lower among homozygous (G/G) genotype (p = 0.018) patients. Combined polymorphisms were strongly associated with susceptibility to chronic ITP. CONCLUSION Homozygosity in either gene might contribute to a worse course of disease, increased severity and poor response to therapy. Patients expressing combined polymorphisms are more prone to progression to chronic disease, severe thrombocytopenia and longer disease duration.
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Affiliation(s)
- Mona El-Ghamrawy
- Pediatric Hematology & BMT Unit, Pediatrics Department, Faculty of Medicine, Cairo University, Cairo, Egypt.
| | - Nesrine El-Gharbawi
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Gehan Shahin
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Alaa Abdelhady
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Rasha Sayed
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Nehal Diaa
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Irene Bishai
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
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Shimizu M, Yamamoto A, Makiguchi M, Shimamura E, Yokota Y, Harano M, Yamazaki H. A family study of compound variants of flavin-containing monooxygenase 3 (FMO3) in Japanese subjects found by urinary phenotyping for trimethylaminuria. Drug Metab Pharmacokinet 2023; 50:100490. [PMID: 36889044 DOI: 10.1016/j.dmpk.2023.100490] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/12/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Phenotype-gene analyses and the increasing availability of mega-databases have revealed the impaired human flavin-containing monooxygenase 3 (FMO3) variants associated with the metabolic disorder trimethylaminuria. In this study, a novel compound variant of FMO3, p.[(Val58Ile; Tyr229His)], was identified in a 1-year-old Japanese girl who had impaired FMO3 metabolic capacity (70%) in terms of urinary trimethylamine N-oxide excretion levels divided by total levels of trimethylamine and its N-oxide. One cousin in the family had the same p.[(Val58Ile); (Tyr229His)]; [(Glu158Lys; Glu308Gly)] FMO3 haplotype and had a similar FMO3 metabolic capacity (69%). In a family study, the novel p.[(Val58Ile); (Tyr229His)] compound FMO3 variant was also detected in the proband 1's mother and aunt. Another novel compound FMO3 variant p.[(Glu158Lys; Met260Lys; Glu308Gly; Ile426Thr)] was identified in a 7-year-old girl, proband 2. This novel compound FMO3 variant was inherited from her mother. Recombinant FMO3 Val58Ile; Tyr229His variant and Glu158Lys; Met260Lys; Glu308Gly; Ile426Thr variant showed moderately decreased capacities for trimethylamine N-oxygenation compared to wild-type FMO3. Analysis of trimethylaminuria phenotypes in family studies has revealed compound missense FMO3 variants that impair FMO3-mediated N-oxygenation in Japanese subjects; moreover, these variants could result in modified drug clearances.
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Affiliation(s)
- Makiko Shimizu
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Akane Yamamoto
- Kobe City Medical Center General Hospital, Kobe, Hyogo, 650-0047, Japan
| | - Miaki Makiguchi
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Erika Shimamura
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Yuka Yokota
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Mizuki Harano
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan
| | - Hiroshi Yamazaki
- Laboratory of Drug Metabolism and Pharmacokinetics, Showa Pharmaceutical University, Machida, Tokyo, 194-8543, Japan.
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Oryan A, Yazdi HS, Alidadi S, Doostmohammadi S. Use of a gyrB PCR-RFLP method to diagnose tuberculosis and identify the causative Mycobacterium sp. in cattle and humans. Comp Immunol Microbiol Infect Dis 2022; 82:101767. [PMID: 35180476 DOI: 10.1016/j.cimid.2022.101767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 10/19/2022]
Abstract
GyrB PCR-restriction fragment length polymorphism (RFLP) could be applied to diagnose bovine and human tuberculosis and detect the causative agent. The lymph nodes and lungs from 50 cattle positive in tuberculin skin test were examined by histopathology and PCR-RFLP of a 1020-bp fragment of the gyrB gene. Swab smear samples from the nasal cavity, pleural, and abdominal cavities were also evaluated by cytological methods. Furthermore, the cultures of 50 sputum samples from the patients were assessed by PCR-RFLP using RsaI, TaqI, SacII enzymes. In histopathology, 39 cattle were positive and the acid-fast bacilli were seen in the Ziehl-Neelsen stained sections. Using gyrB PCR-RFLP, M. bovis was found as the etiological agent in 41 cattle. In terms of the human samples, the causative agent in 41 samples was M. tuberculosis, and M. bovis was isolated from two samples. It seems that gyrB PCR-RFLP could be applied as an accurate and reliable method for identifying the M. tuberculosis complex (MBTC) MBTC species. The isolation of M. bovis from the human specimens should be considered in the control strategies for tuberculosis.
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Affiliation(s)
- Ahmad Oryan
- Department of Pathology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran.
| | - Hassan Sharifi Yazdi
- Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Soodeh Alidadi
- Department of Pathology, School of Veterinary Medicine, Ferdowsi University, Mashhad, Iran
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Yamaguchi N, Zhang XH, Morad M. CRISPR/Cas9 Gene Editing of RYR2 in Human iPSC-Derived Cardiomyocytes to Probe Ca 2+ Signaling Aberrancies of CPVT Arrhythmogenesis. Methods Mol Biol 2022; 2573:41-52. [PMID: 36040585 DOI: 10.1007/978-1-0716-2707-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Human-induced pluripotent stem cells (hiPSCs) provide a powerful platform to study biophysical and molecular mechanisms underlying the pathophysiology of genetic mutations associated with cardiac arrhythmia. Human iPSCs can be generated by reprograming of dermal fibroblasts of normal or diseased individuals and be differentiated into cardiac myocytes. Obtaining biopsies from patients afflicted with point mutations causing arrhythmia is often a cumbersome process even when patients are available. Recent development of CRISPR/Cas9 gene editing system makes it, however, possible to introduce arrhythmia-associated point mutations at the desired loci of the wild-type hiPSCs in relatively short times. This platform was used by us to compare the Ca2+ signaling phenotypes of cardiomyocytes harboring point mutations in cardiac Ca2+ release channel, type-2 ryanodine receptor (RyR2), since over 200 missense mutations in RYR2 gene appear to be associated with catecholaminergic polymorphic ventricular tachycardia (CPVT1). We have created cardiac myocytes harboring mutations in different domains of RyR2, to study not only their Ca2+ signaling consequences but also their drug and domain specificity as related to CPVT1 pathology. In this chapter, we describe our procedures to establish CRISPR/Cas9 gene-edited hiPSC-derived cardiomyocytes.
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Affiliation(s)
- Naohiro Yamaguchi
- Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina, and Clemson University, Charleston, SC, USA.
- Department of Cell Biology and Anatomy, University of South Carolina, Charleston, SC, USA.
| | - Xiao-Hua Zhang
- Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina, and Clemson University, Charleston, SC, USA
- Department of Cell Biology and Anatomy, University of South Carolina, Charleston, SC, USA
| | - Martin Morad
- Cardiac Signaling Center of University of South Carolina, Medical University of South Carolina, and Clemson University, Charleston, SC, USA.
- Department of Cell Biology and Anatomy, University of South Carolina, Charleston, SC, USA.
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Sano H, Wakui A, Kawachi M, Washio J, Abiko Y, Mayanagi G, Yamaki K, Tanaka K, Takahashi N, Sato T. Profiling system of oral microbiota utilizing polymerase chain reaction- restriction fragment length polymorphism analysis. J Oral Biosci 2021; 63:292-297. [PMID: 34111508 DOI: 10.1016/j.job.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES Profiling of oral microbiota has traditionally been performed using conventional methods. These methods are relatively time-consuming and labor-intensive. Metagenomic analysis of oral microbiota using high-speed next-generation sequencing is a highly promising technology. However, it is expensive. This study sought to develop a simple and cost-effective profiling method for oral microbiota using 16S rRNA gene polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of PCR-amplified 16S ribosomal RNA genes. METHODS Oral isolates of 59 bacterial species from human saliva, including Streptococcus, Actinomyces, and Veillonella, were cultured anaerobically on CDC Anaerobe 5% sheep blood agar plates. Genomic DNA was extracted from single colonies and 16S rRNA genes were PCR-amplified using the 27F and 1492R universal primers. The PCR products were purified and characterized by single digestion with HpaII restriction endonuclease. 16S rRNA gene sequences were obtained from the GenBank database, and the expected restriction profiles were compared with the RFLP patterns obtained from agarose gel electrophoresis. RESULTS Sixty-five RFLP patterns were obtained from 27 genera and 59 species. The expected fragment sizes of these species were calculated based on GenBank 16S rRNA gene sequences. Fifty-nine patterns were obtained from the analysis of GenBank sequences. The RFLP patterns produced with HpaII distinguished many oral bacterial species. RFLP patterns enabling identification of oral bacteria were generated. The 16S rRNA gene PCR-RFLP analysis did not require expensive equipment and reagents and was cost-effective. CONCLUSION PCR-RFLP analysis based on 16S rRNA genes could be an alternative method for oral microbiota analysis in smaller laboratories.
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Affiliation(s)
- Hiroto Sano
- Division of Clinical Chemistry, Niigata University Graduate School of Health Sciences, Niigata 951-8518, Japan
| | - Anna Wakui
- Division of Clinical Chemistry, Niigata University Graduate School of Health Sciences, Niigata 951-8518, Japan
| | - Miho Kawachi
- Division of Clinical Chemistry, Niigata University Graduate School of Health Sciences, Niigata 951-8518, Japan
| | - Jumpei Washio
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai 980-0872, Japan
| | - Yuki Abiko
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai 980-0872, Japan
| | - Gen Mayanagi
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai 980-0872, Japan
| | - Keiko Yamaki
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai 980-0872, Japan
| | - Kaori Tanaka
- Division of Anaerobic Research, Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Nobuhiro Takahashi
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai 980-0872, Japan
| | - Takuichi Sato
- Division of Clinical Chemistry, Niigata University Graduate School of Health Sciences, Niigata 951-8518, Japan.
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Hodge JM, Yurchenko AA, Karagodin DA, Masri RA, Smith RC, Gordeev MI, Sharakhova MV. The new Internal Transcribed Spacer 2 diagnostic tool clarifies the taxonomic position and geographic distribution of the North American malaria vector Anopheles punctipennis. Malar J 2021; 20:141. [PMID: 33691700 PMCID: PMC7944907 DOI: 10.1186/s12936-021-03676-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Background The malaria mosquito Anopheles punctipennis, a widely distributed species in North America, is capable of transmitting human malaria and is actively involved in the transmission of the ungulate malaria parasite Plasmodium odocoilei. However, molecular diagnostic tools based on Internal Transcribed Spacer 2 (ITS2) of ribosomal DNA are lacking for this species. Anopheles punctipennis is a former member of the Anopheles maculipennis complex but its systematic position remains unclear. Methods In this study, ITS2 sequences were obtained from 276 An. punctipennis specimens collected in the eastern and midwestern United States and a simple and robust Restriction Fragment Length Polymorphism approach for species identification was developed. The maximum-likelihood phylogenetic tree was constructed based on ITS2 sequences available through this study and from GenBank for 20 species of Anopheles. Results The analysis demonstrated a consistent ITS2 sequence length and showed no indications of intragenomic variation among the samples based on ITS2, suggesting that An. punctipennis represents a single species in the studied geographic locations. In this study, An. punctipennis was found in urban, rural, and forest settings, suggesting its potential broad role in pathogen transmission. Phylogeny based on ITS2 sequence comparison demonstrated the close relationship of this species with other members of the Maculipennis group. Conclusions This study developed molecular tools based on ITS2 sequences for the malaria vector An. punctipennis and clarified the phylogenetic position of the species within the Maculipennis group.
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Affiliation(s)
- James M Hodge
- Department of Entomology and the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Andrey A Yurchenko
- Department of Entomology and the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.,Laboratory of Evolutionary Genomics of Insects, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Kurchatov Genomics Center, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | - Dmitriy A Karagodin
- Laboratory of Evolutionary Genomics of Insects, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Reem A Masri
- Department of Entomology and the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Ryan C Smith
- Department of Entomology, Iowa State University, Ames, IA, USA
| | - Mikhail I Gordeev
- Department of General Biology and Ecology, Moscow Region State University, Moscow, Russia
| | - Maria V Sharakhova
- Department of Entomology and the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA. .,Laboratory of Evolutionary Genomics of Insects, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
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Tarki SE, Far IS, Aminimoghaddam S, Fooladi B, Sarhangi N, Farahani MS, Klashami ZN, Hamidi AK, Amoli MM. Investigating the association of matrix metalloproteinase-2 gene variants with endometriosis in an Iranian population. Eur J Obstet Gynecol Reprod Biol 2021; 258:353-357. [PMID: 33535146 DOI: 10.1016/j.ejogrb.2020.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 11/16/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
OBJECTIVES matrix metalloproteinases including matrix metalloproteinase-2 play a key role in endometrial extra cellular matrix breakdown in endometriosis. Aberrant expression of matrix metalloproteinase-2 has been reported in eutopic and ectopic endometrial tissue of endometriosis patients so altered expression of matrix metalloproteinase-2 due to polymorphisms may lead to establishment and progression of endometriosis. In this study the association between -735 C/T (rs2285053) and -1575 G/A (rs243866) variants of matrix metalloproteinase-2 gene with presence of endometriosis in an Iranian population were investigated for the first time. STUDY DESIGN A case-control association study was conducted to investigate the role of MMP-2-735 C/T and _1575 G/A variants in development of endometriosis. Polymerase chain reaction-restriction fragment length polymorphism method was used to determine genotype frequencies of these variants in 100 endometriosis patients and 200 normal samples. Total genomic DNA was extracted from blood samples and single-nucleotide polymorphism flanking regions were amplified using designed specific primers. Enzymatic digestion was performed using Pag I and Hinf I restriction enzymes for rs2285053 and rs243866 variants, respectively. Statistical analysis was ascertained using statistical package for social science version 16 and "SHEsis" software. RESULTS There were no significant differences in genotype frequencies of rs2285035 (-735C/T) variant between case and control groups (CC + CT vs. TT p = 0.40; OR = 0.50, 95 % CI 0.100-2.551). There were also no significant differences for C allele frequencies in both case and control groups (p = 0.9). For variant rs243866 (-1575 G/A) the differences in genotype frequencies between case and controls group were determined to be significant (GG + GA vs. AA p = 0.041; OR = 6.46, 95 % CI 0.82-50.43). The frequency of G allele was significantly different in case and control groups (p = 0.037). CONCLUSION In conclusion, existence of rs243866 variant in promoter region of matrix metalloproteinase-2 gene can increase the risk of endometriosis in Iranian women.
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Affiliation(s)
- Saeedeh Ebrahimi Tarki
- Department of Genetics, School of Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Iman Salahshouri Far
- Department of Biology, School of Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Soheila Aminimoghaddam
- Department of Obstetrics and Gynecology, Iran University of Medical Sciences, Tehran, Iran.
| | - Bahareh Fooladi
- Department of Obstetrics and Gynecology, Iran University of Medical Sciences, Tehran, Iran.
| | - Negar Sarhangi
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Maryam Shahrabi Farahani
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Zeynab Nickhah Klashami
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Armita Kakavand Hamidi
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mahsa Mohammad Amoli
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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11
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Ghareeb D, Abdelazem AS, Hussein EM, Al-Karamany AS. Association of TNF-α-308 G>A (rs1800629) polymorphism with susceptibility of metabolic syndrome. J Diabetes Metab Disord 2021; 20:209-215. [PMID: 34178832 DOI: 10.1007/s40200-021-00732-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/04/2021] [Indexed: 01/17/2023]
Abstract
Background Metabolic Syndrome (MetS) mainly comprises hyperglycemia, hypertension and dyslipidemia, and has been proven to increase the risk for type 2 diabetes mellitus (T2DM) and cardiovascular disease. Studies have suggested that many factors may be involved in the pathogenesis of MetS, but tumor necrosis factor alpha (TNF- α) may play a strong role as its gene polymorphism was associated with insulin resistance and obesity. The aim of this study was to evaluate the possible association of TNF-α-308 G > A (rs1800629) polymorphism with susceptibility of metabolic syndrome. Methods a case-control study was conducted upon 128 participants recruited from Suez Canal University Hospital (Ismailia, Egypt), divided into the MetS group (n = 64) and the control group (n = 64). Genotyping of the TNF-α-308 G > A (rs1800629) polymorphism was performed by restriction fragment length polymorphism (PCR-RFLP). Results The A allele was significantly higher among MetS patients (40%) than controls (11%) (p < 0.0001). A significant association was observed between the healthy and MetS groups under the influence of co-dominant, dominant and over-dominant genetic models (p < 0.05). Also, there were positive correlations between TNF-α-308 (G/A) polymorphism and risk factors of metabolic syndrome like body mass index (BMI); fasting blood sugar; cholesterol and low density lipoprotein (LDL) (p < 0.05). Regression analysis was done for predictors of MetS and the A allele was found to be a strong predictor (OR 2.752; 95% CI = 1.106 to 6.847; p = 0.03), as well as, BMI; triglyceride (TG); high density lipoprotein (HDL); LDL and cholesterol (p < 0.05). Conclusions TNF-α-308 G > A (rs1800629) polymorphism may be play an important role in the development of metabolic syndrome and A allele is a strong predictor in Egyptians.
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Affiliation(s)
- Dalia Ghareeb
- Department of Clinical Pathology, Faculty of Medicine, Suez University, Suez, Egypt
| | - Abdallah S Abdelazem
- Department of Medical Biochemistry, Faculty of Medicine, Suez University, Suez, Egypt
| | - Ekhlas M Hussein
- Department of Cardiology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Amira S Al-Karamany
- Department of Medical Biochemistry, Faculty of Medicine, Zagazig University, Zagazig, Egypt
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12
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Hashemi SA, Khoshi A, Ghasemzadeh-Moghaddam H, Ghafouri M, Taghavi M, Namdar-Ahmadabad H, Azimian A. Development of a PCR-RFLP method for detection of D614G mutation in SARS-CoV-2. Infect Genet Evol 2020; 86:104625. [PMID: 33166683 PMCID: PMC7648195 DOI: 10.1016/j.meegid.2020.104625] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/31/2020] [Accepted: 11/04/2020] [Indexed: 12/05/2022]
Abstract
In late 2019, an outbreak of respiratory disease named COVID-19 started in the world. To date, thousands of cases of infection are reported worldwide. Most researchers focused on epidemiology and clinical features of COVID-19, and a small part of studies was performed to evaluate the genetic characteristics of this virus. Regarding the high price and low availability of sequencing techniques in developing countries, here we describe a rapid and inexpensive method for the detection of D614G mutation in SARS-CoV-2. Using bioinformatics databases and software, we designed the PCR-RFLP method for D614G mutation detection. We evaluated 144 SARS-CoV-2 positive samples isolated in six months in Northeastern Iran. Our results showed that the prevalent type is S-D in our isolates, and a small number of isolated belongs to the S-G type. Of 144 samples, 127 (88.2%) samples have belonged to type S-D, and 13 (9%) samples typed S-G. The first S-G type was detected on 2020 June 10. We have little information about the prevalence of D614G mutation, and it seems that the reason is the lack of cheap and fast methods. We hope that this method will provide more information on the prevalence and epidemiology of D614G mutations worldwide. SARS-CoV-2 is the major viral pathogen today. SARS-CoV-2 has mutations that lead to change in pathogenesis. The D614G mutation lead to the change of infectivity. We lack the rapid and inexpensive method for detection of this mutation. We designed the rapid and inexpensive method for detection of this mutation.
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Affiliation(s)
- Seyed Ahmad Hashemi
- Department of Infectious Diseases, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Amirhosein Khoshi
- Department of Pathobiology and Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Hamed Ghasemzadeh-Moghaddam
- Department of Pathobiology and Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Majid Ghafouri
- Department of Infectious Diseases, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mohammadreza Taghavi
- Department of Infectious Diseases, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Hasan Namdar-Ahmadabad
- Department of Pathobiology and Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Amir Azimian
- Department of Pathobiology and Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran.
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13
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Sankari SL, Mahalakshmi K, Kumar VN. A comparative study of Candida species diversity among patients with oral squamous cell carcinoma and oral potentially malignant disorders. BMC Res Notes 2020; 13:488. [PMID: 33081839 PMCID: PMC7576765 DOI: 10.1186/s13104-020-05336-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/14/2020] [Indexed: 01/04/2023] Open
Abstract
Objectives To determine the prevalence of Candida species by PCR–RFLP method in the saliva of patients with oral squamous cell carcinoma (OSCC), oral potentially malignant disorders (OPMD) and healthy cohorts. Unstimulated saliva was collected from patients with OSCC (n = 97), OPMD (n = 200), and healthy controls (n = 200). Candida species were isolated using the standard protocol. The isolates were identified using phenotypic and genotypic methods. The odds/risk ratio was calculated using Pearson’s Chi-square test. The significance of Candidal carriage was calculated by independent T-test. Results Oral Candidal carriage was 72.2%, 58% and 20.5% among patients with OSCC, OPMD, and healthy controls respectively. The oral Candidal carriage in OSCC and OPMD was highly significant (p = 0.0001). Non albicans Candida predominated over Candida albicans. Candida species were diverse among the study groups with a predominance of Candida krusei, Candida tropicalis, and Pichia anomala formerly Candida pelliculosa. P. anomala occurrence outnumbered in health. The odds/risk ratio for OSCC and OPMD were 4.25/11.87 and 3.52/6.99 respectively. A high prevalence of non albicans Candida was observed both in all the three groups (OSCC, OPMD and healthy controls). High odds and risk ratio associates Candida species to OSCC and OPMD. Candida famata may be associated with OSCC and OPMD.
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Affiliation(s)
- Sankar Leena Sankari
- Department of Oral Pathology and Microbiology, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, 600100, India
| | - Krishnan Mahalakshmi
- Department of Microbiology, Research Lab for Oral-systemic Health, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, 600100, Tamil Nadu, India.
| | - Venkatesan Naveen Kumar
- Research Lab for Oral-systemic Health, Sree Balaji Dental College and Hospital/ImmuGenix Biosciences Pvt Ltd, No 16/2 Nattal Garden 1st Street, Perambur, Chennai, Tamil Nadu, 600011, India
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14
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Golestanpour H, Javadi G, Sheikhha MH. Association of GRIA1 polymorphisms with ovarian response to human menopausal gonadotropin in Iranian women. Clin Exp Reprod Med 2020; 47:207-212. [PMID: 32829568 PMCID: PMC7482950 DOI: 10.5653/cerm.2020.03370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/10/2020] [Indexed: 11/28/2022] Open
Abstract
Objective Glutamate ionotropic receptor AMPA type subunit 1 (GRIA1) is a subunit of a ligand-gated ion channel that regulates the secretion of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) by controlling the release of gonadotropin-releasing hormone. Few studies have investigated the association between the GRIA1 gene and human infertility. This study evaluated the association of the GRIA1 rs548294 C > T and rs2195450 G > A polymorphisms with the ovarian response to human menopausal gonadotropin (HMG) in Iranian women. Methods One hundred women with histories of at least 1 year of infertility were included. On the second day of menstruation, patients were injected with HMG; on the third day, blood samples were collected. After hormonal analysis, the GRIA1 rs548294 C > T and rs2195450 G > A genotypes of samples were identified via the restriction fragment length polymorphism method, and on day 9, the number of follicles was assessed via ultrasound. Results For the GRIA1 rs548294 C > T and rs2195450 G > A single nucleotide polymorphisms, the subjects with CT and GG genotypes, respectively, displayed the highest mean FSH level, LH level, and number of follicles on day 9 of the menstrual cycle (p < 0.05). Significant positive correlations were observed between LH and FSH (p < 0.01), LH and follicle count (p < 0.01), FSH and age (p < 0.05), follicle count and age (p = 0.048), and FSH and follicle count (p < 0.01). Conclusion This study showed a significant relationship between GRIA1 polymorphisms and ovarian response to the induction of ovulation. Therefore, determining patients’ GRIA1 genotype may be useful for improving treatment and prescribing suitable doses of ovulation-stimulating drugs.
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Affiliation(s)
- Hossein Golestanpour
- Yazd Cardiovascular Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Gholamreza Javadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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15
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Kumar R, Gupta N, Singh V, Kumar V, Haq A, Mirza AA, Sharma A. Unveiling molecular associations of polymorphic variants of VDR gene (FokI, BsmI and ApaI) in multiple myeloma patients of Indian population. J Steroid Biochem Mol Biol 2020; 199:105588. [PMID: 32004705 DOI: 10.1016/j.jsbmb.2020.105588] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/20/2022]
Abstract
Multiple myeloma (MM) is a plasma cell malignancy frequently accompanied with skeletal co-morbidity. Vitamin D (1,25(OH)2D) is an important mediator of skeletal homeostasis that mediates its effect by binding to vitamin D receptor (VDR), a steroid family receptor and modulates various downstream pathways. Multiple polymorphisms have been determined in VDR gene that witnessed significant association with cancer development and progression. Therefore, in this maiden study, we recruited 75 newly diagnosed MM patients and 75 control subjects. 25-hydroxy vitamin D (25(OH)D) levels were measured in all recruited study subjects. Further, PCR-RFLP was performed in DNA samples of recruited study subjects. Results demonstrated significantly decreased 25(OH)D levels in MM patients compared to controls. Additionally, decreased 25(OH)D levels in MM patients inversely associated with disease severity. Further, single nucleotide polymorphism (SNP) analysis of VDR gene showed significantly higher risk of MM disease development in Ff + ff, Aa + aa, and Bb + bb genotypes. Additionally, FokI f, ApaI a and BsmI b alleles were significantly associated with MM occurrence. In conclusion, this study provided initial evidences of association between 25(OH)D insufficiency, VDR gene polymorphism and MM development. Thus, we suggest that a study involving assessment of 25(OH)D levels and VDR gene polymorphism in large patients' cohort might substantiate their role in MM development which would further provide impetus to give 25(OH)D supplementation along with conventional chemotherapeutic agents for myeloma treatment in future.
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Affiliation(s)
- Raman Kumar
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), New Delhi, India; Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rishikesh, India
| | - Nidhi Gupta
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Vishwajeet Singh
- Department of Biostatistics, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Vimal Kumar
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Afrozul Haq
- Department of Food Technology, Jamia Hamdard, New Delhi, India.
| | - Anissa Atif Mirza
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rishikesh, India
| | - Alpana Sharma
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), New Delhi, India.
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Slathia P, Narang D, Chandra M, Sharma A, Narang A. Detection of non-tuberculous mycobacterial species using PCR-RFLP analysis in trans-tracheal washes in cattle and buffaloes with respiratory distress. Iran J Vet Res 2020; 21:136-140. [PMID: 32849894 PMCID: PMC7430363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/11/2020] [Accepted: 01/13/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Bovine tuberculosis (bTB) is a chronic disease of cattle with high economic importance in livestock farming caused by Mycobacterium bovis and bears a zoonotic potential. There are some non-tuberculous mycobacteria (NTM) which cause disease similar to bTB and interfere with diagnosis of bTB. Non-tuberculous mycobacteria are saprophytic in nature but some of them may cause pulmonary infections, mastitis, lesions in respiratory tract and lymph nodes of cattle, due to which they are being recognized worldwide and interfere with the diagnosis of bTB. AIMS The aim of the study was to detect NTM species from cattle and buffaloes with respiratory distress using biochemical test and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis (PRA). METHODS A total of 50 trans-tracheal washes were collected from cattle (n=41) and buffaloes (n=9) with respiratory distress. The samples were inoculated on Middlebrook 7H10 media after proper decontamination with 4% NaOH. The isolate obtained was identified by biochemical testing. Extracted DNA from samples and isolate was subjected to PRA which involved hsp65 gene amplification (439 bp) and RFLP analysis of amplified product. RESULTS Out of 50 trans-tracheal washes only one isolate of Mycobacterium kansasii (n=1) (2%) was obtained which was confirmed by biochemical testing and PRA. Mycobacterium kansasii (n=4) (8%), Mycobacterium intracellulare (n=1) (2%), and Mycobacterium vaccae (n=1) (2%) were identified by PRA. CONCLUSION The study emphasizes the importance of NTM in animals. Polymerase chain reaction-restriction fragment length polymorphism analysis is a more reliable and rapid method for identification of NTM than conventional methods.
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Affiliation(s)
- P. Slathia
- Ph.D. Student in Veterinary Microbiology, Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141004, Punjab, India
| | - D. Narang
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141004, Punjab, India
| | - M. Chandra
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141004, Punjab, India
| | - A. Sharma
- Department of Veterinary Medicine, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141004, Punjab, India
| | - A. Narang
- Department of Veterinary Medicine, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141004, Punjab, India
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17
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Shehjar F, Dil-Afroze, Misgar RA, Malik SA, Laway BA. A significant association of the CTLA4 gene variants with the risk of autoimmune Graves' disease in ethnic Kashmiri population. Cell Immunol 2020; 347:103995. [PMID: 31708111 DOI: 10.1016/j.cellimm.2019.103995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/08/2019] [Accepted: 10/19/2019] [Indexed: 01/03/2023]
Abstract
Graves' disease (GD) is the commonest cause of hyperthyroidism in populations with adequate iodine intake. It results from an abnormality in the immune system, which produces unique antibodies causing over production of thyroid hormones and glandular hyperplasia in individuals with genetic susceptibility. The Cytotoxic Lymphocyte Associated Antigen-4 (CTLA4) gene product serves the important function of immunomodulation, thereby helping in maintenance of peripheral self-tolerance. Studies on the association of the CTLA4 SNPs with GD have shown variations in the results from different populations. Since no such study has been carried out in ethnic Kashmiri population, we aimed to study a possible association of the CTLA4 SNPs (+49 A/G, -318C/T, CT 60 A/G and -1661 A/G) with GD. A total of 285 individuals (135 patients with GD and 150 healthy individuals) were genotyped using PCR-RFLP method and the results showed statistically significant differences in genotypic and allelic frequencies of cases and controls for + 49 A/G SNP (p=<0.001; OR = 5.14; CI = 2.17-12.19) and CT 60 A/G SNP (p = < 0.001; OR = 6.9; CI = 2.8-16.6), while -318C/T and -1661 A/G SNPs showed no significant association. We also studied the mRNA expression of the CTLA4 in patients with GD and healthy individuals by Real-Time PCR and found a decreased expression of the CTLA4 mRNA in PBMCs of patients with GD as compared to healthy controls with a -3.71-fold change. We conclude that the CTLA4 + 49 A/G and CT 60 A/G SNPs have a significant association with the risk of GD development in Kashmiri population and CTLA4 mRNA expression is significantly decreased in GD.
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Stejskalova K, Janova E, Horecky C, Horecka E, Vaclavek P, Hubalek Z, Relling K, Cvanova M, D'Amico G, Mihalca AD, Modry D, Knoll A, Horin P. Associations between the presence of specific antibodies to the West Nile Virus infection and candidate genes in Romanian horses from the Danube delta. Mol Biol Rep 2019; 46:4453-4461. [PMID: 31175514 DOI: 10.1007/s11033-019-04900-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/29/2019] [Indexed: 01/09/2023]
Abstract
The West Nile virus (WNV) is a mosquito-borne flavivirus causing meningoencephalitis in humans and animals. Due to their particular susceptibility to WNV infection, horses serve as a sentinel species. In a population of Romanian semi-feral horses living in the Danube delta region, we have analyzed the distribution of candidate polymorphic genetic markers between anti WNV-IgG seropositive and seronegative horses. Thirty-six SNPs located in 28 immunity-related genes and 26 microsatellites located in the MHC and LY49 complex genomic regions were genotyped in 57 seropositive and 32 seronegative horses. The most significant association (pcorr < 0.0002) was found for genotypes composed of markers of the SLC11A1 and TLR4 genes. Markers of five other candidate genes (ADAM17, CXCR3, IL12A, MAVS, TNFA), along with 5 MHC class I and LY49-linked microsatellites were also associated with the WNV antibody status in this model horse population. The OAS1 gene, previously associated with WNV-induced clinical disease, was not associated with the presence of anti-WNV antibodies.
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Affiliation(s)
- K Stejskalova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, 61242, Brno, Czech Republic
| | - E Janova
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, 61242, Brno, Czech Republic.,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, 61242, Brno, Czech Republic
| | - C Horecky
- Department of Animal Morphology, Physiology and Genetics, Faculty of Agronomy, Mendel University in Brno, Zemědělská 1/1665, 613 00, Brno, Czech Republic.,CEITEC-MENDELU, Mendel University in Brno, Zemědělská 1/1665, 613 00, Brno, Czech Republic
| | - E Horecka
- Department of Animal Morphology, Physiology and Genetics, Faculty of Agronomy, Mendel University in Brno, Zemědělská 1/1665, 613 00, Brno, Czech Republic.,CEITEC-MENDELU, Mendel University in Brno, Zemědělská 1/1665, 613 00, Brno, Czech Republic
| | - P Vaclavek
- SVU Jihlava, Rantirovska 93/20, Horni Kosov, 58601, Jihlava, Czech Republic
| | - Z Hubalek
- Institute of Vertebrate Biology of the Academy of Sciences, Květná 8, 60365, Brno, Czech Republic
| | - K Relling
- Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Palackeho tr. 1, 612 42, Brno, Czech Republic
| | - M Cvanova
- Faculty of Medicine, Institute of Biostatistics and Analyses, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - G D'Amico
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Mănăştur 3-5, 400362, Cluj-Napoca, Romania
| | - A D Mihalca
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Mănăştur 3-5, 400362, Cluj-Napoca, Romania
| | - D Modry
- CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, 61242, Brno, Czech Republic.,Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Palackeho tr. 1, 612 42, Brno, Czech Republic.,Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, 370 05, Czech Republic
| | - A Knoll
- Department of Animal Morphology, Physiology and Genetics, Faculty of Agronomy, Mendel University in Brno, Zemědělská 1/1665, 613 00, Brno, Czech Republic.,CEITEC-MENDELU, Mendel University in Brno, Zemědělská 1/1665, 613 00, Brno, Czech Republic
| | - P Horin
- Department of Animal Genetics, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, 61242, Brno, Czech Republic. .,CEITEC-VFU, University of Veterinary and Pharmaceutical Sciences, Palackeho 1, 61242, Brno, Czech Republic.
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Teixeira FH, Fernandes CE, do Souto RP, de Oliveira E. Polymorphism rs1800255 from COL3A1 gene and the risk for pelvic organ prolapse. Int Urogynecol J 2020; 31:73-8. [PMID: 31041498 DOI: 10.1007/s00192-019-03965-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/18/2019] [Indexed: 12/17/2022]
Abstract
INTRODUCTION AND HYPOTHESIS Genetic variations of type III collagen may compromise the supportive structures of the female pelvic floor and consequently favor pelvic organ prolapse. The single nucleotide polymorphism G/A rs1800255 located in the coding region for type III collagen (COL3A1) was evaluated as a risk factor for pelvic organ prolapse. METHODS A single-center prospective cohort study including women with clinical diagnosis of stage III and IV prolapse (POP group) and prolapse stage 0 or I (control group). Sociodemographic, clinical data and obstetric history were retrieved by physician interview. DNA including the rs1800255 polymorphism was amplified by polymerase chain reaction from blood genomic cells and digested with AluI restriction enzyme for distinction of G and A variants. Qualitative variables were compared using the chi-square and Fisher's exact tests and unpaired t-test for quantitative variables. After stratification of the groups, risk factors for POP were estimated using odds ratios (ORs) from the binary logistic regression model. RESULTS A total of 292 women were included, 112 in the POP group and 180 in the control group. There was no significant difference between groups regarding rs1800255. Age and home birth were the only significant risk factors for pelvic organ prolapse. CONCLUSION Polymorphism rs1800255 from COL3A1 gene was not a risk factor for pelvic organ prolapse.
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Tolba FM, Diab SM, Abdelrahman AMN, Behairy OG, Almonaem ERA, Mogahed MM, Mohamed SA. Assessment of IL-17F rs763780 gene polymorphism in immune thrombocytopenia. Blood Cells Mol Dis 2019; 75:20-5. [PMID: 30594845 DOI: 10.1016/j.bcmd.2018.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/08/2018] [Accepted: 12/12/2018] [Indexed: 12/18/2022]
Abstract
Interleukin-17F rs763780 (7488A/G) gene polymorphism obviously affecting the expression and activity of IL17F and may affect primary immune thrombocytopenia (PIT) susceptibility and its clinical features in Egyptian children and adults. 105 ITP patients divided into (63 pediatric and 42 adult patient) and 112 age and sex matched healthy controls were enrolled in this case control study. All patients were subjected to history taking; clinical examination, CBC, bone marrow aspiration and genotyping of IL17F rs763780 polymorphism by (PCR-RFLP) technique. Our results revealed significant decrease in the mutant heterozygous genotype AG and also in IL-17F mutant allele G frequency in ITP patient group and associated with increased risk for ITP compared with the control group (P = 0.04 and P = 0.005 respectively). Furthermore, the mutant allele G frequency was significantly decreased in childhood onset than adult onset ITP (OR = 0.31, P = 0.02) and also was significantly lower in chronic ITP when compared with newly diagnosed and persistent ITP (P = 0.005). Patients with the AA genotype showed severe thrombocytopenic state at diagnosis than those with the AG genotype (P = 0.04). We concluded from our results that interleukin-17F rs763780 (7488A/G) polymorphism is strongly correlated with susceptibility and severity of ITP.
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Amandito R, Putradista R, Jikesya C, Utaminingsih D, Rusin J, Rohsiswatmo R, Malik A. UGT1A1 gene and neonatal hyperbilirubinemia: a preliminary study from Bengkulu, Indonesia. BMC Res Notes 2018. [PMID: 29534743 PMCID: PMC5851072 DOI: 10.1186/s13104-018-3284-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Objective The genetic involvement in unconjugated neonatal hyperbilirubinemia has been extensively studied. Despite the high incidence of hyperbilirubinemia in Indonesia, studies are lacking. The objective of this study is to elucidate the role of polymorphism in the UGT1A1 in Neonatal Hyperbilirubinemia in Bengkulu, Indonesia. Results There were 41 neonates enrolled in the study; 30 had a total serum bilirubin level ≥ 15 mg/dL (hyperbilirubinemia neonates) while 11 has < 15 mg/dL (control neonates). Genetic mutations in Exon 1, UGT1A1*6 (c211g > a) and one in promoter region, UGT1A1*60 (c3279t > g) were determined by polymerase chain reaction–restriction fragment length polymorphism. We found 18 (60%) mutation in exon 1 in hyperbilirubinemia group and 7 (64%) in the control group with an identical allele frequency of 0.3 in both groups. We found heterozygous UGT1A1*60 4 times (13.3%) and homozygous 26 times (86.7%) in the hyperbilirubinemia group, with an identical allele frequency of 0.935 in hyperbilirubinemia and 1 in control group. This study supports the involvement of genetic factors in the development of unconjugated hyperbilirubinemia in Bengkulu population.
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Affiliation(s)
- Radhian Amandito
- M Yunus General Hospital, Jl Bhayangkara, Bengkulu City, Bengkulu, Indonesia.,Neonatal Intensive Care Unit, Pondok Indah General Hospital, Jl Metro Duta Kav. UE, Pondok Indah, Jakarta, Indonesia
| | - Raihandhana Putradista
- Division of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmacy, Universitas Indonesia, UI Depok Campus, Depok, West Java, 16424, Indonesia
| | - Clara Jikesya
- Division of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmacy, Universitas Indonesia, UI Depok Campus, Depok, West Java, 16424, Indonesia
| | - Dwi Utaminingsih
- Division of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmacy, Universitas Indonesia, UI Depok Campus, Depok, West Java, 16424, Indonesia
| | - Jumnalis Rusin
- Department of Pediatrics, M Yunus General Hospital, Jl Bhayangkara, Bengkulu City, Bengkulu, Indonesia
| | - Rinawati Rohsiswatmo
- Neonatal Intensive Care Unit, Pondok Indah General Hospital, Jl Metro Duta Kav. UE, Pondok Indah, Jakarta, Indonesia.,Division of Perinatology, Department of Pediatrics, Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Jl Pangeran Diponegoro No. 71, Central Jakarta, Jakarta, Indonesia
| | - Amarila Malik
- Division of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmacy, Universitas Indonesia, UI Depok Campus, Depok, West Java, 16424, Indonesia.
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Shehjar F, Afroze D, Misgar RA, Malik SA, Laway BA. Association of polymorphic variants of IL-1β and IL-1RN genes in the development of Graves' disease in Kashmiri population (North India). Hum Immunol 2018; 79:228-232. [PMID: 29454070 DOI: 10.1016/j.humimm.2018.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 11/30/2022]
Abstract
PURPOSE Graves' disease (GD) is a multigenic, organ specific autoimmune disorder with a strong genetic predisposition and IL-1β has been shown to be involved in its pathogenesis. The present study was aimed to determine the genetic associations between polymorphisms of IL-1β gene promoter region (-511 T>C) (rs16944), exon 5 (+3954 C>T) (rs1143634) and IL-1RN gene VNTR (rs2234663) polymorphism in patients with GD in ethnic Kashmiri population. METHODS A total of 135 Graves' disease patients and 150 healthy individuals were included in the study. PCR and PCR-based restriction analysis methods were done for IL-1RNVNTR and IL-1β gene polymorphisms respectively. RESULTS We found statistically significant increased frequencies of the C/C + CT genotype (P = 0.001; odds ratio (OR) = 5.04, 95% confidence interval (CI) = 3.02-8.42) and the C allele (P = 0.001; OR = 3.10, 95% CI = 2.14-4.50) in IL-1β gene promoter polymorphism (rs16944) with GD patients compared to normal controls. Also in the exon 5 (rs1143634), a significant increase in frequency of the C/C homozygous genotype (P = 0.001; OR = 0.18, 95% CI = 0.11-0.30) and C allele (P = 0.001; OR = 0.31, 95% CI = 0.20-0.48) was observed in GD cases as against controls. For IL-1RNVNTR (rs2234663), we didn't observe any significant difference in the allelic and genotypic frequencies between cases and controls. CONCLUSION Our findings suggest that both promoter and exon polymorphisms of IL-1β gene have a significant role in the risk of developing GD, whereas IL-1RNVNTR has no association with GD.
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Affiliation(s)
- Faheem Shehjar
- Department of Endocrinology, Sher-i-Kashmir Institute of Medical Sciences, Srinagar, Jammu & Kashmir, India
| | - Dil Afroze
- Immunology and Molecular Medicine, Sher-i-Kashmir Institute of Medical Sciences, Srinagar, Jammu & Kashmir, India
| | - Raiz A Misgar
- Department of Endocrinology, Sher-i-Kashmir Institute of Medical Sciences, Srinagar, Jammu & Kashmir, India
| | - Sajad A Malik
- Department of Endocrinology, Sher-i-Kashmir Institute of Medical Sciences, Srinagar, Jammu & Kashmir, India
| | - Bashir A Laway
- Department of Endocrinology, Sher-i-Kashmir Institute of Medical Sciences, Srinagar, Jammu & Kashmir, India.
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Zawada JW, Dahan-Moss YL, Muleba M, Dabire RK, Maïga H, Venter N, Davies C, Hunt RH, Coetzee M, Koekemoer LL. Molecular and physiological analysis of Anopheles funestus swarms in Nchelenge, Zambia. Malar J 2018; 17:49. [PMID: 29370805 PMCID: PMC5785822 DOI: 10.1186/s12936-018-2196-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 01/19/2018] [Indexed: 11/10/2022] Open
Abstract
Background Anopheles funestus has been recognized as a major malaria vector in Africa for over 100 years, but knowledge on many aspects of the biology of this species is still lacking. Anopheles funestus, as with most other anophelines, mate through swarming. A key event that is crucial for the An. funestus male to mate is genitalia rotation. This involves the 135° to 180° rotation of claspers, which are tipped with claws. This physical change then enables the male to grasp the female during copulation. The aim of this investigation was to molecularly characterize wild An. funestus swarms from Zambia and examine the degree of genitalia rotation within the swarm. Methods Anopheles funestus swarms were collected from Nchelenge, northern Zambia, during dusk periods in May 2016. All the adults from the swarm were analysed morphologically and identified to species level using a multiplex PCR assay. Anopheles funestus s.s. specimens were molecularly characterized by restriction fragment length polymorphism type and Clade type assays. The different stages of genitalia rotation were examined in the adult males. Results A total of six swarms were observed during the study period and between 6 and 26 mosquitoes were caught from each swarm. Species analysis revealed that 90% of the males from the swarms were An. funestus s.s. MW-type, with 84% belonging to clade I compared to 14% clade II and 2% failed to amplify. Very few specimens (3.4%) were identified as Anopheles gambiae s.s. Eighty percent of the males from the swarm had complete genitalia rotation. Conclusions This is the first time that An. funestus swarms have been molecularly identified to species level. Anopheles funestus swarms appear to be species-specific with no evidence of clade-type differentiation within these swarms. The An. funestus swarms consist mainly of males with fully rotated genitalia, which strongly suggests that swarming behaviour is triggered primarily when males have matured.
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Affiliation(s)
- Jacek W Zawada
- Wits Research Institute for Malaria; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Center for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Yael L Dahan-Moss
- Wits Research Institute for Malaria; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Center for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa
| | | | - Roch K Dabire
- Institut de Recherche en Sciences de la Santé/Centre Muraz, BP 545, Bobo-Dioulasso, Burkina Faso
| | - Hamid Maïga
- Institut de Recherche en Sciences de la Santé/Centre Muraz, BP 545, Bobo-Dioulasso, Burkina Faso
| | - Nelius Venter
- Wits Research Institute for Malaria; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Center for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Craig Davies
- Wits Research Institute for Malaria; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Center for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Richard H Hunt
- Wits Research Institute for Malaria; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Center for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Maureen Coetzee
- Wits Research Institute for Malaria; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Center for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Lizette L Koekemoer
- Wits Research Institute for Malaria; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Center for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa.
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Darwish H, El-Shorbagy H, Abou-Eisha A, El-Din A, Farag I. New polymorphism in the 5' flanking region of IGF-1 gene and its association with wool traits in Egyptian Barki sheep. J Genet Eng Biotechnol 2017; 15:437-441. [PMID: 30647684 PMCID: PMC6296639 DOI: 10.1016/j.jgeb.2017.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 05/06/2017] [Accepted: 08/01/2017] [Indexed: 11/17/2022]
Abstract
Insulin-like growth factor-1 gene (IGF-1) is considered as a major candidate gene for the economic traits of animal production. Polymorphism of 5′ flanking region of IGF-1 gene in Barki sheep (n = 91) and its association with wool traits were studied using the polymerase chain reaction coupled with single-strand conformation polymorphism technique (PCR-SSCP), PCR-restriction fragment length polymorphism (PCR-RFLP), sequence analysis and different measurements of wool traits (clean fleece weight and fiber diameter). PCR-SSCP analysis revealed three different banding patterns corresponding with three genotypes frequencies GG (0.25), GA (0.58), AA (0.17). PCR-RFLP and corresponding sequence analysis revealed nucleotide transversion from Guanine (G) to Cytosine (C) at nucleotide position 85 and transition from (G) to Adenine (A) at position 87. This is the first study that recorded two SNPs within the 5′ flanking region of IGF-1 gene in Egyptian Barki sheep, which were submitted to DNA Data Bank OF Japan (DDBJ) with Accession No. LC151463.1. The genotype GG showed positive significant association (P < 0.001) with clean fleece weight (CFW) trait (Odd Ratio = 2.83). By contrast, genotype AA had negative significant association (P < 0.05) with such trait (Odd Ratio = 0.15). On the other hand, fiber diameter (FD) measurements showed no significant association (P > 0.05) with different IGF-1 genotypes. This study adds evidence of the association between IGF-1 gene polymorphism and CFW of wool in Egyptian Barki sheep. Therefore; it is important to consider IGF-1 gene as a candidate gene marker for wool weight traits and it should be identified before using successful breeding program.
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Affiliation(s)
- H.R. Darwish
- Cell Biology Department, National Research Centre, Dokki, Giza, P.O. Box 12622, Egypt
| | - H.M. El-Shorbagy
- Zoology Department, Faculty of Science, Cairo University, Giza, P.O. Box 12613, Egypt
- Corresponding author.
| | - A.M. Abou-Eisha
- Cell Biology Department, National Research Centre, Dokki, Giza, P.O. Box 12622, Egypt
| | - A.E. El-Din
- Cell Biology Department, National Research Centre, Dokki, Giza, P.O. Box 12622, Egypt
| | - I.M. Farag
- Cell Biology Department, National Research Centre, Dokki, Giza, P.O. Box 12622, Egypt
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Youssef DM, El-Shal AS, Hussein S, Salah K, Ahmed AERE. Tumor necrosis factor alpha gene polymorphisms and haplotypes in Egyptian children with nephrotic syndrome. Cytokine 2017; 102:76-82. [PMID: 28803697 DOI: 10.1016/j.cyto.2017.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 05/31/2017] [Accepted: 06/27/2017] [Indexed: 11/25/2022]
Abstract
BACKGROUND Nephrotic syndrome (NS) characterized by complex pathogenesis and clinical course with relapses; and needs novel breakthroughs for decades. Polymorphisms of cytokines genes including tumor necrosis factor alpha (TNF-α)may influence susceptibility to NS as well as different patients' steroid responses. In the current study, we demonstrated the potential roles of TNF-α promoter gene polymorphisms [-238, -308, -863] and haplotypes in susceptibility to childhood NS. Also, elucidating their possible influence on patients' steroid response and serum TNF-α level. METHODS This case-control study included 150 children suffering from NS and 150 healthy children. Polymerase chain reaction- restriction-fragment length polymorphism (PCR-RFLP) was performed to evaluate different TNF-α gene polymorphism. TNF-α serum levels were assessed by ELISA. RESULTS Serum TNF-α levels were significantly higher in NS patients than in controls and in steroid resistant NS (SRNS) than in steroid sensitive NS (SSNS) (P<0.001 for each). The risk of NS in patients carrying TNF-α-238GA genotype, and TNF-α-308GA or AA genotypes and allele A was significantly increased compared to healthy children. While no significant association was detected between TNF-α-863 and NS. The risk of resistance to steroid therapy was significantly high in NS carrying TNF-α-238GA genotype and A allele, TNF-α-308, AA genotypes and A allele, and TNF-α-863CA, AA genotypes and A allele. The TNF-α GCG (-308/-863/-238) haplotype has protective roles against NS and steroid resistance. However, the risk of NS was significantly high in TNF-α AAG and AAA haplotype's carriers compared to healthy children. Additionally the risk of steroid resistance was significantly high in TNF-α AAA haplotype's NS carrier (OR (95%CI): 2.2 (1.19-4.36), P=0.01). Moreover, we found significant higher serum TNF-α levels NS patients including SSNS and SRNS carrying mutant allele TNF-α-238GA genotype, -308GA and AA and -863CA and AA wild genotype's carriers than in those GG, GG and CC respectively. Interstingely, TNF-α levels were significantly higher in healthy children carrying TNF-α(-308/-863/-238) [AAG and AAA haplotypes], NS cases carrying [ACA, AAG, AAA haplotypes], and in SSNS carrying [ACA and AAA haplotypes] than in those carrying GCG, haplotype of wild alleles. CONCLUSION This study reported, for the first time, that TNF-α promoter gene polymorphisms and/or haplotypes are risk factors of NS and resistance to steroid among Egyptian children.
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Affiliation(s)
- Doaa M Youssef
- Pediatrics Department, Faculty of Medicine, Zagazig University, Egypt
| | - Amal S El-Shal
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Zagazig University, Egypt.
| | - Samia Hussein
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Zagazig University, Egypt
| | - Khaled Salah
- Pediatrics Department, Faculty of Medicine, Zagazig University, Egypt
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Kambale PR, Haldar D, Kabi BC, Kambale KP. Study of Vitamin D Receptor Gene Polymorphism (FokI, TaqI and ApaI) Among Prostate Cancer Patients in North India. J Clin Diagn Res 2017; 11:BC05-BC08. [PMID: 28764147 DOI: 10.7860/jcdr/2017/24290.9976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/09/2017] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Incidence of prostate cancer is rising worldwide. Multiple factors have been suggested for the aetiology of prostate cancer including ethnic, genetic and diet. Vitamin D (calcitriol) has been shown to have role in cell growth and differentiation and its deficiency is implicated as one of the aetiological factors in prostate cancer. Prostatic epithelial cells express Vitamin D Receptor (VDR) as well as 1α- hydroxylase enzyme that are required for the synthesis of calcitriol and its action. Polymorphism in VDR gene has been associated with prostate cancer in some epidemiological studies; but, there is paucity of information in the Indian context. AIM The present study was aimed to explore the association of VDR gene polymorphism with the development of prostate cancer. MATERIALS AND METHODS Three Single Nucleotide Polymorphisms (SNP) sites viz., FokI, TaqI and ApaI were analysed in 120 cases of prostate cancer which were compared with their 120 healthy first degree relatives and 120 non-related controls in the Department of Biochemistry in collaboration with the Department of Urology. RESULTS Analysis showed significantly decreased incidence of Tt and Aa genotype in prostate cancer patients as compared to healthy non-relative controls (p=0.016 and 0.043 respectively). As compared to first degree relatives, incidence of Tt genotype is significantly lower in cases (p=0.005). No significant association was found with FokI polymorphism. CONCLUSION This study suggests the protective role of heterozygous genotypes of TaqI and ApaI polymorphism against the development of prostate cancer.
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Affiliation(s)
- Pankaj Ramrao Kambale
- Assistant Professor, Department of Biochemistry, S.M.B.T. Institute of Medical Sciences and Research Centre, Nashik, Maharashtra, India
| | - Deepa Haldar
- Senior Resident, Department of Biochemistry, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - B C Kabi
- Professor Director, Department of Biochemistry, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Kalpana Pankaj Kambale
- Senior Lecturer, Department of Periodontology, S.M.B.T. Institute of Dental Sciences and Research, Nasik, Maharashtra, India
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Alizadeh K, Mosavari N, Nazari R. Restriction fragment length polymorphism pattern of Mycobacterium isolates from rodents in infected cattle farms. Int J Mycobacteriol 2017; 5 Suppl 1:S191-S192. [PMID: 28043547 DOI: 10.1016/j.ijmyco.2016.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 10/01/2016] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE/BACKGROUND Mycobacterium tuberculosis, the etiologic agent of tuberculosis, causes large-scale morbidity and mortality, particularly in developing countries. In recent years, there has been a significant increase in the drug-resistant ability of M. tuberculosis, triggering a major public health crisis. A detailed analysis of the evolution of the mycobacterial genome helps to better understand the genotype-phenotype relationship in this bacterium. Different strain typing methods have already revealed the worldwide diversity of mycobacterial isolates. Therefore, DNA-fingerprinting tools have been developed to improve tuberculosis case detection and control. Molecular typing techniques allow to detect and follow the spread of individual strains of the M. tuberculosis complex (MTC), complementing conventional epidemiological methods. Among these techniques, restriction fragment length polymorphism (RFLP) has been considered the standard method for genotyping of MTC. The aim of this work was to isolate M. tuberculosis from rodents in cattle farms contaminated with MTC located in the city of Booin-Zahra, Iran. METHODS A total of 100 samples were collected from the rodents in the contaminated farms and analyzed for the presence of Mycobacterium by growing the samples on Lowenstein-Jensen medium. All isolates were further identified by RFLP and DNA hybridization studies. RESULTS As much as five samples showed the presence of Mycobacterium and these were subjected to PCR-16SrRNA, PCR-IS6110, and RD Typing (RD1, RD4, RD9, and RD12) methods. Further differentiation was performed with PvuII digestion (RFLP) and DNA hybridization using the polymorphic guanine/cytosine-rich repetitive sequences (PGRS) probe. The PGRS probe results classified two of the isolates as belonging to one cluster, whereas the remaining isolates were classified as belonging to different clusters. An analysis of the obtained genetic pattern and a comparison of these patterns with the genetic pattern of other infected farms allowed us to record the similarities and difference. The results indicated the transmission of Mycobacterium from infected rodents to the cows located in the same farm. CONCLUSION These results highlight the possible danger of transmission of Mycobacterium among animals.
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Affiliation(s)
- Khatereh Alizadeh
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | - Nader Mosavari
- Bovine Tuberculosis Reference Laboratory, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran.
| | - Razieh Nazari
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
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Mahdavipour M, Zarei S, Fatemi R, Edalatkhah H, Heidari-Vala H, Jeddi-Tehrani M, Idali F. Polymorphisms in the Estrogen Receptor Beta Gene and the Risk of Unexplained Recurrent Spontaneous Abortion. Avicenna J Med Biotechnol 2017; 9:150-154. [PMID: 28706612 PMCID: PMC5501144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Recurrent Spontaneous Abortion (RSA) is caused by multiple genetic and non-genetic factors. Around 50% of the RSA cases have no known etiology and are considered as Unexplained RSA (URSA). Estrogens, via binding to their receptors, play an important role in female reproduction. This study aimed to investigate whether single nucleotide polymorphisms (SNPs; +1082G/A, +1730G/A and rs1256030 C/T) in the estrogen receptor beta (ESR2) gene are associated with susceptibility to URSA in a population of Iranian women. METHODS In this case-control study, the study groups consisted of 240 subjects with a history of URSA and 102 fertile women as controls. Serum levels of follicle stimulating hormone (FSH), luteinizing hormone (LH), and estradiol (E2) were measured on day 2-3 of menstrual cycle. Two functional SNPs, +1082G/A (a silent mutation in exon 5) and +1730G/A (3' untranslated region of the exon 8), and one intron, rs1256030C/T, in the ESR2 gene were genotyped, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. RESULTS Serum levels of LH were significantly increased in URSA women. No significant differences in distribution of +1082G/A, +1730G/A and rs1256030C/T between URSA and control groups were observed. CONCLUSION Our findings suggest that the studied SNPs on ESR2 gene may not be associated with URSA.
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Affiliation(s)
- Marzieh Mahdavipour
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Saeed Zarei
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Ramina Fatemi
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Haleh Edalatkhah
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Hamed Heidari-Vala
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mahmood Jeddi-Tehrani
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Farah Idali
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran,Corresponding author: Farah Idali, Ph.D., Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran P.O.Box: 19615-1177, Postal code: 1936773493, Tel: +98 21 22432020, Fax: +98 21 22432021, E-mail:
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Hong G, Park HD, Choi R, Jin DK, Kim JH, Ki CS, Lee SY, Song J, Kim JW. CYP21A2 mutation analysis in Korean patients with congenital adrenal hyperplasia using complementary methods: sequencing after long-range PCR and restriction fragment length polymorphism analysis with multiple ligation-dependent probe amplification assay. Ann Lab Med 2016. [PMID: 26206692 PMCID: PMC4510508 DOI: 10.3343/alm.2015.35.5.535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
CYP21A2 mutation analysis of congenital adrenal hyperplasia (CAH) is challenging because of the genomic presence of a homologous CYP21A2 pseudogene and the significant incidence of pseudogene conversion and large deletions. The objective of this study was to accurately analyze the CYP21A2 genotype in Korean CAH patients using a combination of complementary methods. Long-range PCR and restriction fragment length polymorphism analyses were performed to confirm valid amplification of CYP21A2 and to detect large gene conversions and deletions before direct sequencing. Multiple ligation-dependent probe amplification (MLPA) analysis was conducted concurrently in 14 CAH-suspected patients and six family members of three patients. We identified 27 CYP21A2 mutant alleles in 14 CAH-suspected patients. The c.293-13A>G (or c.293-13C>G) was the most common mutation, and p.Ile173Asn was the second, identified in 25% and 17.9% of alleles, respectively. A novel frame-shift mutation of c.492delA (p.Glu 164Aspfs*24) was detected. Large deletions were detected by MLPA in 10.7% of the alleles. Mutation studies of the six familial members for three of the patients aided in the identification of haplotypes. In summary, we successfully identified CYP21A2 mutations using both long-range PCR and sequencing and dosage analyses. Our data correspond relatively well with the previously reported mutation spectrum analysis.
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Affiliation(s)
- Geehay Hong
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyung Doo Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Rihwa Choi
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Dong Kyu Jin
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Hyeon Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chang Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soo Youn Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Junghan Song
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Jong Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Sałagacka-Kubiak A, Zebrowska M, Jeleń A, Mirowski M, Balcerczak E. Assessment of TNFA polymorphisms at positions -857 and -863 in Polish peptic ulcer patients. Adv Med Sci 2016; 61:164-8. [PMID: 26774268 DOI: 10.1016/j.advms.2015.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/28/2015] [Accepted: 12/01/2015] [Indexed: 11/28/2022]
Abstract
PURPOSE Peptic ulceration connected with chronic inflammation in gastrointestinal mucosa could be induced by Helicobacter pylori infection. Tumor necrosis factor alpha (TNF-α) encoded by TNFA gene is a key mediator in the inflammation process. There are several polymorphisms in the promoter of TNFA influencing its transcriptional activity. -857C>T (rs1799724) and -863C>A (rs1800630) substitutions may be responsible for increased TNFA transcription and TNF-α production. The association of these two polymorphisms with peptic ulceration and the development of H. pylori infection in peptic ulcer patients in Poles were evaluated. MATERIAL AND METHODS Polymorphisms were assessed by PCR-RFLP in 203 peptic ulcer patients. H. pylori infection was confirmed by rapid urease test. The results of genotyping were compared with those obtained for 248 healthy Polish individuals. RESULTS There were no significant differences in genotype and allele frequencies for both investigated polymorphisms between peptic ulcer patients and healthy individuals. No associations between frequencies of particular genotypes and alleles for both SNPs and the presence of H. pylori infection in peptic ulcer patients and in subgroups of peptic ulcer women and men were confirmed. CONCLUSIONS The investigated SNPs are not risk factors for peptic ulcer development. They are not risk factors for H. pylori infection in ulcer patients.
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Affiliation(s)
- Aleksandra Sałagacka-Kubiak
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Łódź, Poland
| | - Marta Zebrowska
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Łódź, Poland
| | - Agnieszka Jeleń
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Łódź, Poland
| | - Marek Mirowski
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Łódź, Poland
| | - Ewa Balcerczak
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Łódź, Poland.
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Parchwani DN, Patel DD, Rawtani J, Dikshit N. Association of Mbo I-RFLP at the Renin Locus (rs2368564) with Essential Hypertension. Indian J Clin Biochem 2016; 31:431-8. [PMID: 27605740 DOI: 10.1007/s12291-015-0546-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/28/2015] [Indexed: 12/28/2022]
Abstract
Several lines of experimental and clinical evidence have alluded a pivotal role of renin in blood pressure homeostasis and therefore a relevance of molecular variants of the renin gene and essential hypertension have been speculated. This study was designed to evaluate the pattern, alliance and risk of renin Mbo I (10631A>G; rs2368564) polymorphism at the locus intron 9 for a possible role in modulating essential hypertension in adult population from Gujarat (India). A total of 257 consecutively enrolled essential hypertensive patients and 270 controls were genotyped using polymerase chain reaction-restriction fragment length polymorphism method for the selected marker. Suitable descriptive statistics was used for different variables. Genotypic (x(2) 10.43, p 0.0054) and allelic (x(2) 11.46, p 0.0007) distribution of this SNP displayed significant differences between cases and controls with an increased frequency of the A allele (x(2) 6.275; p 0.0122) and A/A geno-type (x(2) 8.247; p 0.0041) in hypertensive individuals. However, it showed no deviation from Hardy-Weinberg equilibrium in either affected or control group. A significant association was found in the A/A variant of rs2368564 with essential hypertension (p 0.0032), along with a statistically significant increase in odds of hypertension (OR 1.69; CI 1.46-2.28; p 0.02), even after confounding factors were adjusted in multiple logistic regression analysis and is substantiated by inter-genotypic variations in the mean systolic and diastolic blood pressure in patients. In conclusion, renin 10631A>G gene mutation at the ninth intron play critical roles in BP (dys)regulation and can be implicated in an individual's susceptibility for hypertension.
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Affiliation(s)
| | - Digisha D Patel
- Gujarat Adani Institute of Medical Sciences, Bhuj, Gujarat India
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Shahsavari S, Noormohammadi Z, Zare Karizi S. Association of kinase insert domain-containing receptor (KDR) gene polymorphism/ haplotypes with recurrent spontaneous abortion and genetic structure. Int J Reprod Biomed 2015; 13:755-64. [PMID: 27141535 PMCID: PMC4827512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Recurrent spontaneous abortion is one of the diseases that can lead to physical, psychological, and, economical problems for both individuals and society. Recently a few numbers of genetic polymorphisms in kinase insert domain-containing receptor (KDR) gene are examined that can endanger the life of the fetus in pregnant women. OBJECTIVE The risk of KDR gene polymorphisms was investigated in Iranian women with idiopathic recurrent spontaneous abortion (RSA). MATERIALS AND METHODS A case controlled study was performed. One hundred idiopathic recurrent spontaneous abortion patients with at least two consecutive pregnancy losses before 20 weeks of gestational age with normal karyotypes were included in the study. Also, 100 healthy women with at least one natural pregnancy were studied as control group. Two functional SNPs located in KDR gene; rs1870377 (Q472H), and rs2305948 (V297I) as well as one tag SNP in the intron region (rs6838752) were genotyped by using PCR based restriction fragment length polymorphism (PCR-RFLP) technique. Haplotype frequency was determined for these three SNPs' genotypes. Analysis of genetic STRUCTURE and K means clustering were performed to study genetic variation. RESULTS Functional SNP (rs1870377) was highly linked to tag SNP (rs6838752) (D´ value=0. 214; χ(2) = 16.44, p<0. 001). K means clustering showed that k = 8 as the best fit for the optimal number of genetic subgroups in our studied materials. This result was in agreement with Neighbor Joining cluster analysis. CONCLUSION In our study, the allele and genotype frequencies were not associated with RSA between patient and control individuals. Inconsistent results in different populations with different allele frequencies among RSA patients and controls may be due to ethnic variation and used sample size.
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Rathod SB, Tripathy AS. TGF-β1 gene - 509C > T promoter polymorphism modulates TGF-β1 levels in hepatitis E patients. Meta Gene 2015; 6:53-8. [PMID: 26504745 PMCID: PMC4576361 DOI: 10.1016/j.mgene.2015.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 08/28/2015] [Accepted: 08/31/2015] [Indexed: 02/07/2023] Open
Abstract
Elevated levels of transforming growth factor-β1 (TGF-β1) and its positive correlation with Foxp3 expression in hepatitis E patients have indicated involvement of TGF-β1 in hepatitis E pathogenesis. The current study determined polymorphisms in TGF-β1 gene, plasma TGF-β1 levels and T effector (Teff) cell proliferation and explored their association in a case control study. Polymorphisms in three selected sites (- 509C > T, + 869T > C and + 915G > C) of TGF-β1 gene by PCR & restriction fragment length polymorphism methods, plasma TGF-β1 quantitation by ELISA and Teff (CD4 + CD25 -) cell proliferation by CFSE method were carried out in 277 hepatitis E patients (HE) with self-limiting infection and 233 ethnically matched healthy controls (HCs) from western India. Frequency of CT genotype of - 509C > T site was significantly higher in hepatitis E patients compared to healthy controls (p = 0.017; OR 1.53, 95% CI 1.07-2.17). Plasma TGF-β1 levels were significantly higher in HE compared to HCs. TGF-β1 level of patient group having CT genotype of - 509C > T site was significantly higher compared to those having CC or TT genotypes. Teff cell proliferation was negatively correlated with plasma TGF-β1 levels in HE patients (r = - 0.568; p = 0.014). Influence of TGF-β1 promoter (- 509C > T) polymorphism on plasma TGF-β1 levels and inverse correlation of Teff cell proliferation with plasma TGF-β1 levels in self-limiting hepatitis E patients suggest key role of TGF-β1 in augmentation of reported T regulatory cell mediated pathogenesis in hepatitis E.
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Key Words
- ALT, alanine transaminase
- CI, confidence interval
- HBV, hepatitis B virus
- HCV, hepatitis C virus
- HCs, healthy controls
- HE, hepatitis E patients
- HEV, hepatitis E virus
- Hepatitis E
- OR, odds ratio
- PBMCs, peripheral blood mononuclear cells
- RFLP, restriction fragment length polymorphism
- Restriction fragment length polymorphism
- Single nucleotide polymorphism
- T effector cell proliferation
- TGF-β1, transforming growth factor beta 1
- Teff, T effector cells
- Transforming growth factor beta 1
- Treg, T regulatory cells
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Affiliation(s)
- Sanjay B Rathod
- Hepatitis Group, National Institute of Virology, Pune, India
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Fallah S, Korani M, Hajimirza M, Seifi M. Association Between Genetic Variants of Akt1 and Endometrial Cancer. Biochem Genet 2015; 53:281-90. [PMID: 26296520 DOI: 10.1007/s10528-015-9690-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 08/16/2015] [Indexed: 12/29/2022]
Abstract
Akt isoforms have critical roles in the cause and regulation of cancer cells invasive, migration, and metastatic dissemination. In the present study, the association between Akt1 polymorphisms and endometrial cancer was investigated in patients with endometrial cancer and controls. Thirty premenopaused patients diagnosed with endometrial cancer and 30 premenopaused women with no clinically documented abnormalities of the endometrium undergoing hysterectomy were included in this study. Genotypes were determined by polymerase chain reaction and restriction fragment length polymorphism. There was no significant difference between Akt1 gene polymorphisms of patients (SNP1, SNP2 and SNP3) with endometrial cancer and controls (p > 0.05). Difference between alleles frequency of SNP1, SNP2, SNP3 of patients with endometrial cancer and controls was not significant (p > 0.05). SNPs (rs72715985), (rs2494750), and (rs74090038) of Akt1 gene are not associated with endometrial cancer in Iranian subjects.
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Affiliation(s)
- Soudabeh Fallah
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, 14155-5983, Tehran, Iran. .,Research Center of Pediatric Infectious Disease, Rasool Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.
| | - Mohsen Korani
- Department of Biochemistry, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Milad Hajimirza
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, 14155-5983, Tehran, Iran
| | - Morteza Seifi
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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Liu K, Lu Y, Ai L, Jiao B, Yu J, Zhang B, Liu Q. Association between FOXE1 and non-syndromic orofacial clefts in a northeastern Chinese population. Br J Oral Maxillofac Surg 2015; 53:705-10. [PMID: 26100861 DOI: 10.1016/j.bjoms.2015.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 05/22/2015] [Indexed: 01/07/2023]
Abstract
Non-syndromic orofacial clefts are among the most common congenital defects, and several reports have shown that the FOXE1 gene has strong associations with them. To find out if the gene was a risk factor we used a case-control and family-based analysis, and recruited 230 patients with non-syndromic oral clefts including 179 with non-syndromic cleft lip with or without cleft palate, and 51 with non-syndromic cleft palate alone, their parents (166 mothers and 161 fathers, including 135 complete trios), and 180 healthy controls. Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) were used to genotype the 2 most strongly associated markers (rs4460498 and rs3758249) in FOXE1, and case-control and family-based associations were analysed. In the case-control analyses we found a significant association with non-syndromic cleft lip and palate in rs4460498 (p=0.009) and rs3758249 (p=0.014), but no association in patients with cleft palate alone. For rs4460498 in FOXE1, the odds ratio (OR) for cases with CC homozygotes compared with TC+CC genotypes was 1.813 (95% CI 1.176 to 2.796), and for rs3758249 in FOXE1, the OR for cases with GG homozygotes compared with those with AG+AA genotypes was 0.561 (95%CI 0.371 to 0.848). The results of transmission-disequilibrium tests for rs4460698 and rs3758249 for non-syndromic orofacial clefts were p=0.003, OR=2.781 (95% CI 1.414 to 5.469) and p=0.001, OR=2.552 (95%CI 1.574 to 4.138), respectively. This suggests that FOXE1 (rs4460498 and rs3758249) is strongly associated with non-syndromic cleft lip and palate in populations in northeast China, and further study between FOXE1 and non-syndromic orofacial clefts is necessary.
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Affiliation(s)
- Kun Liu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Yongping Lu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, Liaoning 110002, PR China.
| | - Lisi Ai
- Department of Periodontics,School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Boqiang Jiao
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Jiantao Yu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Bin Zhang
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Qiang Liu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
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Sałagacka A, Żebrowska M, Jeleń A, Mirowski M, Balcerczak E. Investigation of -308G>A and -1031T>C polymorphisms in the TNFA promoter region in Polish peptic ulcer patients. Gut Liver 2014; 8:632-6. [PMID: 25368751 PMCID: PMC4215449 DOI: 10.5009/gnl13224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/27/2013] [Accepted: 10/21/2013] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND/AIMS Tumor necrosis factor α (TNF-α) encoded by TNFA is a key mediator in inflammation, a precursor condition for peptic ulceration. Promoter polymorphisms of TNFA that influence its transcriptional activity and TNF-α production are known. TNFA-308G>A (rs1800629) and TNFA-1031T>C (rs1799964), which are responsible for increased TNFA transcription, could influence the risk of peptic ulceration. This study aimed to investigate these polymorphisms and to evaluate their association with peptic ulcer disease and Helicobacter pylori infection in the Polish population. METHODS Gastric mucosa specimens obtained from 177 Polish peptic ulcer patients were used to conduct rapid urease tests and to assess the investigated polymorphisms by polymerase chain reaction-restriction fragment length polymorphism. Genotyping data were compared with the results obtained from healthy individuals of Polish origin. RESULTS There were no significant differences in genotype and allele frequency of the investigated polymorphisms between peptic ulcer patients and healthy individuals. No associations between the frequencies of particular genotypes and alleles for both single-nucleotide polymorphisms (SNPs) and the presence of H. pylori infection in peptic ulcer patients and in subgroups of men and women with peptic ulcer disease were found. CONCLUSIONS The investigated SNPs are not risk factors for either peptic ulcer or H. pylori infection development in the Polish population. The results require verification in a larger cohort.
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Affiliation(s)
- Aleksandra Sałagacka
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Marta Żebrowska
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Agnieszka Jeleń
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Marek Mirowski
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Ewa Balcerczak
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry, Medical University of Lodz, Lodz, Poland
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Mohammadzadeh G, Ghaffari MA, Bafandeh A, Hosseini SM. Effect of leptin receptor Q223R polymorphism on breast cancer risk. Iran J Basic Med Sci 2014; 17:588-94. [PMID: 25422752 PMCID: PMC4240793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 02/08/2014] [Indexed: 11/23/2022]
Abstract
OBJECTIVES Leptin receptor (LEPR) is a member of the class I cytokine receptor super-family that is known implicated in the initiation and progression of breast cancer. We have investigated the effect of Q223R polymorphism on the breast cancer susceptibly in a sample of Iranian subjects. MATERIALS AND METHODS We utilized a polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) method to investigate the association of LEPR Q223R polymorphism with breast cancer risk in a case control study consisting of 100 breast cancer cases and 100 controls without breast cancer. Serum levels of leptin and soluble leptin receptor (sOB-R) were measured by ELISA method. RESULTS The genotype (QQ, QR, and RR) distributions were 25, 56, and 19 % in breast cancer cases and 54, 40, and 6% in controls, respectively. The frequency of 223 RR genotype was significantly elevated in breast cancer cases as compared to controls (χ(2)= 20.072, P<0.001). Similar significance differences were also found in allele frequencies for Q and R between two groups (χ(2)= 19.027, P< 0.001). Additionally, there were significant association between Q223R genotypes and breast cancer risk; homozygotes for RR genotype (OR= 6.840; 95% confidence interval [CI] = 2.434-19.218), heterozygotes for QR (OR=3.024; 95% CI = 1.620-5.644, P = 0.001), and QR+RR genotype (OR= 3.522; 95% CI = 1.934-6.414, P < 0.001), respectively. CONCLUSION Our results showed that the LEPR Q223R polymorphism is associated with increased breast cancer risk as well as tumor grade in a sample of Iranian subjects.
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Affiliation(s)
- Ghorban Mohammadzadeh
- Hyperlipidemia Research Center, Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
,Corresponding author: Ghorban Mohammadzadeh. Hyperlipidemia Research Center, Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. Fax: + 98-611-3332063;
| | - Mohammad-Ali Ghaffari
- Cellular and Molecular Research Center, Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ahmmad Bafandeh
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sayed-Mohammad Hosseini
- Department of Radiation and Oncology of Golestan University Hospital, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Jung HJ, Kim SY, Jung JW, Park HJ, Lee YW, Choe YB, Ahn KJ. Identification of dermatophytes by polymerase chain reaction- restriction fragment length polymorphism analysis of metalloproteinase-1. Ann Dermatol 2014; 26:338-42. [PMID: 24966633 PMCID: PMC4069644 DOI: 10.5021/ad.2014.26.3.338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 06/13/2013] [Accepted: 07/09/2013] [Indexed: 11/16/2022] Open
Abstract
Background Transgenic research on metalloproteinase-1 is an emerging field in the area of plant molecular biology. The new method reported here can similarly be applied in fungal molecular biology to identify different dermatophytes. Our method is more accurate than traditional methods such as molecular analyses. Objective To identify Trichophyton rubrum, T. mentagrophytes var. mentagrophytes, T. tonsurans, T. mentagrophytes var. interdigitale, Microsporum canis and M. gypseum, by using the restriction fragment length polymorphism (RFLP) analysis and polymerase chain reaction (PCR) to detect polymorphisms in the metalloproteinase-1 gene (MEP1). Methods From each fungal strain, we isolated genomic DNA and performed PCR to amplify the region coding for metalloproteinase-1. Primers for the metalloproteinase-1 gene were designed based on the sequence in NCBI GenBank. Subsequently, we purified the amplified PCR product and performed RFLP analysis. After restriction enzyme digestion, BsrDI (NEB, England), the samples were subjected to electrophoresis. Four different patterns of DNA fragments were observed among 6 fungal species. Results The DNA fragments for T. mentagrophytes var. mentagrophytes, T. mentagrophytes var. interdigitale and T. tonsurans showed similar patterns on electrophoresis and were not distinguishable, whereas T. rubrum, M. canis, and M. gypseum showed different patterns. Conclusion To our knowledge, it is the first study to introduce the analysis of the nucleotide sequence of metalloproteinase-1 enzyme to study differentiation in dermatophytes. Based on our results, more accurate differentiation and subtyping of T. rubrum and T. mentagrophytes var. interdigitale might be possible. This might contribute to better understanding of the epidemiology and pathogenesis of dermatophyte.
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Affiliation(s)
- Ho Jung Jung
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea
| | - Soo Young Kim
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea
| | - Jae Wook Jung
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea
| | - Hyun Jung Park
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea
| | - Yang Won Lee
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea. ; Research Institute of Medical Science, Konkuk University, Seoul, Korea
| | - Yong Beom Choe
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea. ; Research Institute of Medical Science, Konkuk University, Seoul, Korea
| | - Kyu Joong Ahn
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Korea. ; Research Institute of Medical Science, Konkuk University, Seoul, Korea
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Hoteit M, Arabi A, Habib R, Mahfouz R, Baddoura R, Halaby G, El-Hajj Fuleihan G. Estrogen receptor α is not a candidate gene for metabolic syndrome in Caucasian elderly subjects. Metabolism 2014; 63:50-60. [PMID: 24140101 DOI: 10.1016/j.metabol.2013.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/22/2013] [Accepted: 08/09/2013] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Variants of estrogen receptor α (ERα) have been associated with obesity, dyslipidemia, diabetes and blood pressure. The Middle East registers some of the highest rate of metabolic syndrome worldwide. The aim of this study is to investigate the relationship between metabolic syndrome, a clustered combination of these metabolic factors, and polymorphisms PvuII and XbaI of ERα in Lebanese Caucasian elderly overweight subjects. MATERIAL/METHODS 250 Caucasian Lebanese unrelated elderly men and women, median age 71 years, were studied. ERα intronic polymorphisms variants, PvuII and XbaI diplotypes and genotypes, were examined. Associations with metabolic syndrome, defined by the American Heart Association/National Heart, Lung, and Blood Institute (AHA/NHLBI), and its components, namely high density lipoprotein (HDL), fasting glucose levels, blood pressure, and waist circumference were evaluated in regression models. RESULTS ER α diplotypes and genotypes distributions were similar between participants with and without metabolic syndrome, in the overall group of subjects, and by gender. No consistent associations between the diplotypes and genotypes tested and metabolic syndrome, or its components, could be detected. CONCLUSIONS Genetic variants in ERα were not associated with metabolic syndrome or its components, in a group of 250 Lebanese Caucasian elderly participants, a group with a high prevalence of metabolic syndrome.
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Affiliation(s)
- Maha Hoteit
- Calcium Metabolism and Osteoporosis Program, WHO Collaborating Center for Metabolic Bone Disorders, American University of Beirut Medical Center, Beirut, Lebanon
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Kalkan G, Yigit S, Karakuş N, Ateş O, Bozkurt N, Ozdemir A, Pancar GŞ. Methylenetetrahydrofolate reductase C677T mutation in patients with alopecia areata in Turkish population. Gene 2013; 530:109-12. [PMID: 23954881 DOI: 10.1016/j.gene.2013.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 08/01/2013] [Accepted: 08/03/2013] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Methylene-tetrahydrofolate reductase (MTHFR) is a key enzyme regulating folate metabolism and it is thought to influence DNA methylation and nucleic acid synthesis. Mutations in the MTHFR gene have been associated with several autoimmune disorders in previous studies. Alopecia areata (AA) is considered to be a tissue-specific autoimmune disease as the hair follicle has been targeted and antibodies to their own hair follicle structures have been developed. Since there is a common shared pathway between AA and other autoimmune disorders, we aimed to investigate a possible association between the MTHFR gene C677T mutation and AA susceptibility in the Turkish population. METHODS The study included 136 patients affected by AA and 130 healthy controls. Genomic DNA was isolated and genotyped using a polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) assay for the MTHFR gene C677T mutation. RESULTS The distributions of genotype and allele frequencies of MTHFR gene C677T mutation were statistically different between AA patients and the control group (p=0.036 and p=0.011, respectively). High differences were also observed when the patients and controls were compared according to CC versus CT+TT (p=0.012). CT+TT genotypes and T allele of MTHFR gene C677T mutation were found to be a susceptibility factor for AA in the Turkish population. CONCLUSION The results suggest that MTHFR gene C677T mutation may have an effect on the risk of alopecia areata in the Turkish population. This is the first study reporting the association between the MTHFR (C677T) genotype and AA.
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Affiliation(s)
- Göknur Kalkan
- Gaziosmanpasa University, School of Medicine, Department of Dermatology, Tokat, Turkey.
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Chen X, Liao B, Song J, Pang X, Han J, Chen S. A fast SNP identification and analysis of intraspecific variation in the medicinal Panax species based on DNA barcoding. Gene 2013; 530:39-43. [PMID: 23933277 DOI: 10.1016/j.gene.2013.07.097] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/22/2013] [Accepted: 07/29/2013] [Indexed: 11/18/2022]
Abstract
Medicinal plants of the Panax genus belonging to Araliaceae family are well-known, rare plants used as tonics in traditional Chinese medicine and have been described in the Chinese Pharmacopoeia. Because of the high price and the huge human demand, these commercial products often contain adulterants. In this study, 377 sequences from four species were analyzed. Single nucleotide polymorphisms (SNPs) were detected and patterns of intragenomic variation in internal transcribed spacer 2 (ITS2) from the four Panax species were studied. Intraspecific variations were analyzed based on three typical DNA barcodings (ITS2, matK and psbA-trnH). Results from this study revealed that intraspecific genetic distances in Panax ginseng and Panax quinquefolius were quite low (0-0.002) and the multi-copy ITS2 could be considered a single locus in the genomes of these two species. Five stable SNPs were detected in ITS2 region to identify the Panax medicinal species. Considering the mixed powder of P. ginseng and P. quinquefolius, double peaks could be clearly examined at SNP positions and the height of the peaks could indicate the mixed ratio roughly. Our findings indicate that SNP-based molecular barcodes could be developed as a routine method for the identification of the Panax genus with closely related species and the mixed powder P. ginseng and P. quinquefolius.
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Affiliation(s)
- Xiaochen Chen
- Center for Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, PR China
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Maher BH, Taylor M, Stuart S, Okolicsanyi RK, Roy B, Sutherland HG, Haupt LM, Griffiths LR. Analysis of 3 common polymorphisms in the KCNK18 gene in an Australian Migraine case-control cohort. Gene 2013; 528:343-6. [PMID: 23911303 DOI: 10.1016/j.gene.2013.07.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/14/2013] [Accepted: 07/07/2013] [Indexed: 10/26/2022]
Abstract
Migraine is a common neurological disorder characterised by temporary disabling attacks of severe head pain and associated disturbances. There is significant evidence to suggest a genetic aetiology to the disease however few causal mutations have been conclusively linked to the migraine subtypes Migraine with (MA) or without Aura (MO). The Potassium Channel, Subfamily K, member 18 (KCNK18) gene, coding the potassium channel TRESK, is the first gene in which a rare mutation resulting in a non-functional truncated protein has been identified and causally linked to MA in a multigenerational family. In this study, three common polymorphisms in the KCNK18 gene were analysed for genetic variation in an Australian case-control migraine population consisting of 340 migraine cases and 345 controls. No association was observed for the polymorphisms examined with the migraine phenotype or with any haplotypes across the gene. Therefore even though the KCNK18 gene is the only gene to be causally linked to MA our studies indicate that common genetic variation in the gene is not a contributor to MA.
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Affiliation(s)
- B H Maher
- Genomics Research Centre, Griffith Health Institute, School of Medical Science, Griffith University Gold Coast, Parklands Drive, Southport, Queensland 4215, Australia
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Motawi TK, Shaker OG, Ismail MF, Sayed NH. Genetic variants associated with the progression of hepatocellular carcinoma in hepatitis C Egyptian patients. Gene 2013; 527:516-20. [PMID: 23845776 DOI: 10.1016/j.gene.2013.06.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 05/10/2013] [Accepted: 06/16/2013] [Indexed: 12/20/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) associated to infection with hepatitis C virus (HCV) has become the fastest-rising cause of cancer-related deaths. Genetic variations may play an important role in the development of HCC in HCV patients. Ghrelin exerts anti-inflammatory, antifibrotic and hepatoprotective effects on chronically injured hepatic tissues. Ghrelin gene shows several single nucleotide polymorphisms (SNPs) including -604G/A, Arg51Gln, and Leu72Met. Hemochromatosis gene (HFE) mutations namely C282Y and H63D may cause hepatic iron overload, thus increasing the risk of HCC in HCV patients. AIM To investigate the association of progression of HCC with ghrelin and HFE gene polymorphisms in HCV Egyptian patients. METHODS Seventy-nine chronic HCV patients (thirty-nine developed HCC and forty did not), and forty healthy control subjects were included in the study. The polymorphisms were evaluated by PCR/RFLP analysis, and related protein levels were measured by either ELISA or colorimetric assays. RESULTS The three tested SNPs on ghrelin gene were detected in the studied groups, only one SNP (Arg51Gln) showed significantly higher GA, AA genotypes and A allele frequencies in hepatitis C patients who developed HCC than in hepatitis C patients without HCC and controls. Of the two mutations studied on HFE gene only H63D heterozygous allele was detected, and its frequency did not statistically differ among studied groups. CONCLUSION Our results suggest that A allele at position 346 of the ghrelin gene is associated with susceptibility to HCC in hepatitis C patients.
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Affiliation(s)
- Tarek Kamal Motawi
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Radtanakatikanon A, Keawcharoen J, Charoenvisal NT, Poovorawan Y, Prompetchara E, Yamaguchi R, Techangamsuwan S. Genotypic lineages and restriction fragment length polymorphism of canine distemper virus isolates in Thailand. Vet Microbiol 2013; 166:76-83. [PMID: 23830775 DOI: 10.1016/j.vetmic.2013.05.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 05/17/2013] [Accepted: 05/22/2013] [Indexed: 11/26/2022]
Abstract
Canine distemper virus (CDV) is known to cause multisystemic disease in all families of terrestrial carnivores. Attenuated live vaccines have been used to control CDV in a variety of species for many decades, yet a number of CDV infections in vaccinated dogs are still observed. The aims of this study were to investigate the genetic diversity of CDV lineages based on phosphoprotein (P), hemagglutinin (H) and fusion protein (F) genes and to develop the restriction fragment length polymorphism (RFLP) technique for effective differentiation among individual wild-type and vaccine lineages in Thailand. Four commercial vaccine products, thirteen conjunctival swabs and various tissues from 9 necropsied dogs suspected of having CDV infections were included. Virus isolation was performed using Vero cell expressing canine signaling lymphocyte activation molecules (Vero-DST cells). Reverse-transcription polymerase chain reaction (RT-PCR) on 3 gene regions from the dog derived specimens and the vaccines were carried out, then RFLP analysis upon F-gene amplified fragments was developed. Nucleotide sequence and phylogenetic analysis were compared with other CDV lineages in Genbank. Phylogenetic relationships revealed that CDV field isolates were separated from the vaccine lineage and could be divided into two clusters; one of which belonged to the Asia-1 lineage and another, not related to any previous recognized lineages was proposed as 'Asia-4'. RFLP patterns demonstrating concordance with phylogenetic trees of the distemper virus allowed for differentiation between the Asia-1, Asia-4 and vaccine lineages. Thus, RFLP technique is able to effectively distinguish individual wild-type canine distemper virus from vaccine lineages in Thailand.
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Affiliation(s)
- Araya Radtanakatikanon
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
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Liu RD, Chen RX, Li WR, Huang YL, Li WH, Cai GR, Zhang H. The Glu727 Allele of Thyroid Stimulating Hormone Receptor Gene is Associated with Osteoporosis. N Am J Med Sci 2012; 4:300-4. [PMID: 22866266 PMCID: PMC3409653 DOI: 10.4103/1947-2714.98588] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background: Published data indicate that thyroid stimulating hormone receptor (TSHR) activities are associated with osteoporosis in some patients. Aim: This study aimed to elucidate whether a given polymorphism of the TSHR gene is associated with osteoporosis. Materials and Methods: One hundred and fifty subjects with osteoporosis were recruited in this study. The diagnosis of osteoporosis was performed with quantitative ultrasound system. The TSHR gene polymorphism was examined by polymerase chain reaction–restriction fragment length polymorphism. Results: The results showed a nucleotide substitution in the first position of codon 36 of the TSHR gene. The nucleotide substitution was from G to C, leading to a 36D → 36H change (D36H) in the predicted amino acid sequence of the receptor. The change did not show significance between healthy subjects and patients with osteoporosis (P > 0.05). On the other hand, we identified another single nucleotide polymorphism that is a C-to-G substitution at codon 727 (GAC to GAG); its frequency was significantly higher in patients with osteoporosis than that in healthy subjects. Using logistic regression analysis, significant correlation was revealed between the genotype D727E and the serum levels of TSH, or the quantitative ultrasound value of the calcaneal bone. Conclusions: The present study suggests that the genotype D727E of the TSHR, but not the genotype D36H, may be a genetic risk factor for osteoporosis.
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Affiliation(s)
- Ren-De Liu
- Department of Orthopedics, Shaoguan First People's Hospital, Guangdong Medical University, Shaoguan, China
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Kalghatgi AT, Praharaj AK, Sahni AK, Pradhan D, Kumaravelu S, Prasad PL, Nagendra A. Detection of Bacterial Pathogens in Cerebrospinal Fluid using Restriction Fragment Length Polymorphism. Med J Armed Forces India 2011; 64:29-32. [PMID: 27408075 DOI: 10.1016/s0377-1237(08)80141-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 10/10/2006] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Polymerase chain reaction (PCR) is useful for rapid microbial detection in body fluids with low microbial load. It is easier to use universal or broad range primers for the amplification of conserved stretches of DNA common to all bacteria like 16S rRNA gene, followed by restriction fragment length polymorphism (RFLP) of PCR products. METHODS Forty samples of cerebrospinal fluid were collected. After DNA extraction, universal or broad range PCR was performed using two universal primers U1-5'-CCAGCAGCCGCGGTAATACG-3', corresponding to nucleotides 518 to 537 of the Escherichia coli 16S rRNA gene, and U2 - 5'-ATCGG(C/T)TACCTTGTTACGACTTC-3', corresponding to nucleotides 1513 to 1491 of the same gene. The PCR product was subjected to digestion by endonucleases- HaeIII, Mn11, BstB1 and Alu1. Restriction pattern obtained was compared with that of standard organisms to identify the pathogen. The results were compared with conventional methods. RESULT Universal PCR could detect pathogens in 20% samples within 13-18 hours as compared to 16% by conventional methods. The analytical sensitivity was 10 Gram negative and 250 Gram positive organisms per 200 μl sample. Overall sensitivity was 83.3% and specificity was 91.2%. CONCLUSION Universal PCR followed by RFLP of PCR product is a good alternative to conventional diagnosis of bacterial pathogens.
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Affiliation(s)
- A T Kalghatgi
- Senior Advisor (Pathology), Command Hospital (Central Command), Lucknow
| | | | - A K Sahni
- Senior Advisor (Pathology), AH(R&R), Delhi Cantt
| | - D Pradhan
- Post Graduate Trainee (Department of Microbiology), AFMC Pune-40
| | | | - P L Prasad
- Senior Advisor (Paediatrics), Command Hospital (Central Command), Lucknow
| | - A Nagendra
- Ex- Dy Comdt, Command Hospital (Western Command), Chandigarh
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Tee SF, Tang PY, Loh HC. Genetic Association Analysis of Dopamine DRD3 Ser9Gly Polymorphism and Schizophrenia in Malay Population. Iran J Public Health 2011; 40:6-10. [PMID: 23113067 PMCID: PMC3481775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 05/03/2011] [Indexed: 11/14/2022]
Abstract
BACKGROUND Molecular components of the dopamine receptor (DRD3) play an important role in the pathophysiology of schizophrenia (SCZ). Previous studies have demonstrated an association between the DRD3 Ser9Gly polymorphism and SCZ but the results have been inconclusive. METHOD In this study, we investigated this controversial association between the Ser9Gly (A/G) polymorphism and SCZ using Malay cases-control (261 cases/157 controls) samples. PCR-RFLP was performed to genotype the distribution of the DRD3 Ser9Gly polymorphism. RESULTS Both healthy control and SCHZ patient groups were in of Hardy-Weinberg equilibrium for the analyzed genetic variability. There was a significant association between the genotype distribution DRD3 polymorphisms and SCZ (χ(2)= 9.359; df = 2; P = 0.009). CONCLUSION We believe that further studies are required to examine the association between others dopamine-related genes and the behavioral phenotypes of SCZ.
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Affiliation(s)
| | | | - HC Loh
- Corresponding author: Tel: +60341079802, Fax: +60341079803, E-mail:
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Deng YN, Wang LL, Tang Q, Chen XQ, Chen P, Shan QW, Lian SJ, Yun X. Association between BSEP V444A polymorphism and risk of idiopathic neonatal hepatitis/cholestasis. Shijie Huaren Xiaohua Zazhi 2011; 19:38-43. [DOI: 10.11569/wcjd.v19.i1.38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To explore the association between the V444A polymorphism in the bile salt export pump (BSEP) gene and the risk of idiopathic neonatal hepatitis/cholestasis.
METHODS: Eighty-one infants with idiopathic hepatitis/cholestasis (case group) and 48 healthy infants without intrahepatic cholestasis (control group) were included in this study. The V444A polymorphism was genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).
RESULTS: There are three V444A genotypes: AA homozygote, GA heterozygote, and GG homozygote. The frequencies of AA and AG and GG genotypes were 0.6%, 4.9% and 44.4% in the case group and 14.6%, 62.5% and 22.9% in the control group, respectively, with a significant difference between the two groups (P = 0.019). The distribution of GG genotype was significantly different between the two groups (P < 0.05, OR = 2.691, 95%CI: 1.205-6.008). The risk of suffering from idiopathic intrahepatic cholestasis in G allele carriers was 1.951 times higher than that in A allele carriers (OR = 1.951, 95%CI: 1.56-3.291).
CONCLUSION: The G allele of the BSEP V444A G polymorphism may be a risk factor for idiopathic intrahepatic cholestasis in infants.
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Jafarian M, Aghali-Merza M, Farnia P, Ahmadi M, Masjedi MR, Velayati AA. Synchronous Comparison of Mycobacterium tuberculosis Epidemiology Strains by "MIRU-VNTR" and "MIRU-VNTR and Spoligotyping" Technique. Avicenna J Med Biotechnol 2010; 2:145-52. [PMID: 23408229 PMCID: PMC3558156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2010] [Accepted: 09/25/2010] [Indexed: 11/07/2022] Open
Abstract
Molecular epidemiology analyses are frequently used in determining epidemiology of tuberculosis. Recently, Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) and Spoligotyping has become an important method, as it allows high-through put, discriminatory and reproducible analysis of clinical isolate. The purpose of this study is to compare techniques of "MIRU-VNTR" versus "MIRU-VNTR and Spoligotyping" together for study of genetic pattern of Mycobacterium tuberculosis (M. tuberculosis) strains. Sixty M. tuberculosis (MTB) isolates were selected (30 susceptible, 30 multi-drug resistant) for this study. Thereafter, the "MIRU-VNTR and Spoligotyping" were performed to identify their genetic patterns. The frequency of unknown genetic pattern of MTB was compared using technique of "MIRU-VNTR" alone versus "MIRU-VNTR and Spoligotyping" together. The MIRU-VNTR allelic diversity at each of the loci was calculated by Hunter - Gaston Discriminatory Index (HGDI). Based on differentiation index of all strains 10, 16, 26, 31 and 40 loci were identified as the most distinctive (HGI ≥0.6) and 2, 4, 20 and 24 as the weakest distinctive locus (HGI ≤0.3). By using MIRU-VNTR technique 38% (n = 23) of isolates could not be typed, whereas by applying "MIRU-VNTR and Spoligotyping" together only 15% (n = 9) of isolates remained unknown (p = 0.004). For sensitive strains, the difference was significant (67% vs. 90%, p = 0.028), but only marginally significant for drug resistant strains (57% vs. 80%, p = 0.052). The discrimination power of 12-locus MIRU-VNTR and Spoligotyping was equal to that of MIRU-VNTR analysis. If appropriate loci are added to the standard MIRU analysis, MIRU-VNTR genotyping could be a valuable tool for strain typing and epidemiological research of M. tuberculosis. With this approach a more clear understanding about genetic pattern of MTB can be achieved.
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Affiliation(s)
- Mehdi Jafarian
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran,Corresponding author: Mehdi Jafarian, M.Sc., Mycobacteriology Research Center (MRC), National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran. Tel: +98 21 20109505. E-mail:
| | - Muayed Aghali-Merza
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parissa Farnia
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojtaba Ahmadi
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Masjedi
- National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Akbar Velayati
- National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Zhang ZQ, Wang Q, Wang BJ. Relationship between TRPV1 gene polymorphism and irritable bowel syndrome. Shijie Huaren Xiaohua Zazhi 2009; 17:3514-3518. [DOI: 10.11569/wcjd.v17.i34.3514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the relationship between transient receptor potential vanilloid 1 (TRPV1) gene polymorphism and irritable bowel syndrome (IBS).
METHODS: Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct sequence analysis were used to comparatively analyze the polymorphism of the TRPV1 gene in patients with IBS (n = 73) fulfilling the Rome III criteria and healthy controls (n = 65).
RESULTS: A total of three genotypes were detected in IBS patients and healthy controls: CC, CT and TT. The frequencies of CC genotype and C allele in IBS patients were significantly higher than those in healthy controls (genotype: χ2 = 6.858, P = 0.032; allele: χ2 = 4.174, P = 0.041). A significant difference was found in TRPV1 gene polymorphism between IBS and healthy controls (P < 0.05).
CONCLUSION: The TRPV1 gene polymorphism is associated with the development of IBS. The presence of CC genotype and C allele probably increases the susceptibility of individuals to IBS. TRPV1 may be a novel therapeutic target for IBS.
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