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Lafuente-Ibáñez-de-Mendoza I, Marichalar-Mendia X, Setién-Olarra A, García-de-la-Fuente AM, Martínez-Conde-Llamosas R, Aguirre-Urizar JM. Genetic polymorphisms of inflammatory and bone metabolism related proteins in a population with dental implants of the Basque Country. A case-control study. BMC Oral Health 2024; 24:659. [PMID: 38840172 PMCID: PMC11155173 DOI: 10.1186/s12903-024-04319-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Peri-implantitis (PI) is a frequent inflammatory disorder characterised by progressive loss of the supporting bone. Not all patients with recognised risk factors develop PI. The aim of this study is to evaluate the presence of single nucleotide polymorphisms (SNP) of inflammatory and bone metabolism related proteins in a population treated with dental implants from the Basque Country (Spain). METHODS We included 80 patients with diagnosis of PI and 81 patients without PI, 91 women and 70 men, with a mean age of 60.90 years. SNPs of BMP-4, BRINP3, CD14, FGF-3, FGF-10, GBP-1, IL-1α, IL-1β, IL-10, LTF, OPG and RANKL proteins were selected. We performed a univariate and bivariate analysis using IBM SPSS® v.28 statistical software. RESULTS Presence of SNPs GBP1 rs7911 (p = 0.041) and BRINP3 rs1935881 (p = 0.012) was significantly more common in patients with PI. Patients with PI who smoked (> 10 cig/day) showed a higher presence of OPG rs2073617 SNP (p = 0.034). Also, BMP-4 rs17563 (p = 0.018) and FGF-3 rs1893047 (p = 0.014) SNPs were more frequent in patients with PI and Type II diabetes mellitus. CONCLUSIONS Our findings suggest that PI could be favoured by an alteration in the osseointegration of dental implants, based on an abnormal immunological response to peri-implant infection in patients from the Basque Country (Spain).
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Affiliation(s)
- Irene Lafuente-Ibáñez-de-Mendoza
- Research Group: GIU21/042, University of the Basque Country (UPV/EHU), Leioa, Spain
- Department of Stomatology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Xabier Marichalar-Mendia
- Research Group: GIU21/042, University of the Basque Country (UPV/EHU), Leioa, Spain.
- Department of Nursery I, Barrio Sarriena s/n, Leioa, 48940, Bizkaia, Spain.
- Biobizkaia Health Research Institute, Barakaldo, Spain.
| | - Amaia Setién-Olarra
- Research Group: GIU21/042, University of the Basque Country (UPV/EHU), Leioa, Spain
- Department of Nursery I, Barrio Sarriena s/n, Leioa, 48940, Bizkaia, Spain
| | - Ana María García-de-la-Fuente
- Research Group: GIU21/042, University of the Basque Country (UPV/EHU), Leioa, Spain
- Department of Stomatology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | | | - José Manuel Aguirre-Urizar
- Research Group: GIU21/042, University of the Basque Country (UPV/EHU), Leioa, Spain
- Department of Stomatology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
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Gao Y, Li S, Yuan G, Fang J, Shen G, Tian Z. Comparison of Biological and Genetic Characteristics between Two Most Common Broad-Leaved Weeds in Paddy Fields: Ammannia arenaria and A. multiflora (Lythraceae). BIOLOGY 2023; 12:936. [PMID: 37508367 PMCID: PMC10375975 DOI: 10.3390/biology12070936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/16/2023] [Accepted: 06/25/2023] [Indexed: 07/30/2023]
Abstract
Ammannia arenaria and A. multifloras, morphologically similar at the seedling stage, are the most common broad-leaved weeds in paddy fields. Our study showed that A. arenaria occupied more space than A. multifloras when competing with rice. However, A. multifloras germination has lower temperature adaptability. No difference in sensitivity to common herbicides between two Ammannia species was observed. Chloroplast (cp) genomes could be conducive to clarify their genetic relationship. The complete cp genome sequences of A. arenaria (158,401 bp) and A. multiflora (157,900 bp) were assembled for the first time. In A. arenaria, there were 91 simple sequence repeats, 115 long repeats, and 86 protein-encoding genes, one, sixteen, and thirty more than those in A. multiflora. Inverted repeats regions expansion and contraction and the phylogenetic tree based on cp genomes demonstrated the closely relationship between the two species. However, in A. arenaria, 20 single nucleotide polymorphisms in the CDS region were detected compared to A. multiflora, which can be used to distinguish the two species. Moreover, there was one unique gene, infA, only in A. arenaria. This study provides reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure, and biodiversity of Ammannia species.
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Affiliation(s)
- Yuan Gao
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Shenghui Li
- College of Agriculture, Anshun University, Anshun 561000, China
| | - Guohui Yuan
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jiapeng Fang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Guohui Shen
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Zhihui Tian
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
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3
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Gao Y, Shen G, Yuan G, Tian Z. Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields. Int J Mol Sci 2022; 23:ijms232213864. [PMID: 36430336 PMCID: PMC9698722 DOI: 10.3390/ijms232213864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/30/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022] Open
Abstract
Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, we assembled the complete cp genome sequences of Echinochloa crus-galli var. crus-galli (139,856 bp), E. crus-galli var. zelayensis (139,874 bp), and E. glabrescens (139,874 bp), which exhibited a typical circular tetramerous structure, large and small single-copy regions, and a pair of inverted repeats. In Echinochloa crus-galli var. crus-galli, there were 136 simple sequence (SSRs) and 62 long (LRs) repeats, and in the other two species, 139 SSRs and 68 LRs. Each cp genome contains 92 protein-encoding genes. In Echinochloa crus-galli var. crus-galli and E. glabrescens, 321 and 1 single-nucleotide polymorphisms were detected compared to Echinochloa crus-galli var. zelayensis. IR expansion and contraction revealed small differences between the three species. The phylogenetic tree based on cp genomes demonstrated the phylogenetic relationship between ten barnyard grass species and other common Gramineae plants, showing new genetic relationships of the genus Echinochloa. This study provides valuable information on cp genomes, useful for identifying and classifying the genus Echinochloa and studying its phylogenetic relationships and evolution.
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Choi W, Park E, Bae S, Choi KH, Han S, Son KH, Lee DY, Cho IJ, Seong H, Hwang KS, Nam JM, Choi J, Lee H, Choi N. Multiplex SNP Genotyping Using SWITCH: Sequence-Specific Nanoparticle with Interpretative Toehold-Mediated Sequence Decoding in Hydrogel. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105538. [PMID: 34923738 DOI: 10.1002/smll.202105538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Single nucleotide polymorphisms (SNPs) that can alter phenotypes of individuals play a pivotal role in disease development and, more importantly, responses to therapy. However, SNP genotyping has been challenging due to the similarity of SNP alleles and their low concentration in biological samples. Sequence-specific nanoparticle with interpretative toehold-mediated sequence decoding in hydrogel (SWITCH) for multiplex SNP genotyping is presented. The encoding with gold nanoparticle probes transduces each SNP target to ≈1000 invaders with prominently different sequences between wild and mutant types, featuring polymerase chain reaction (PCR)-free amplification. Subsequently, the toehold-mediated DNA replacement in hydrogel microparticles decodes the invaders via SNP-specific fluorescence signals. The 4-plex detection of the warfarin-associated SNP targets spiked in commercially validated human serum (S1-100ML, Merck) is successfully demonstrated with excellent specificity. This work is the first technology development presenting PCR-free, multiplex SNP genotyping with a single reporting fluorophore, to the best of knowledge.
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Affiliation(s)
- Woongsun Choi
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Korea
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Eunhye Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Seojin Bae
- OPTOLANE Technologies, Inc., Seongnam, 13494, Korea
| | | | - Sangeun Han
- OPTOLANE Technologies, Inc., Seongnam, 13494, Korea
| | - Kuk-Hui Son
- Department of Thoracic and Cardiovascular Surgery, Gachon University Gil Medical Center, Incheon, 21936, Korea
| | - Do Young Lee
- OPTOLANE Technologies, Inc., Seongnam, 13494, Korea
| | - Il-Joo Cho
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
- Yonsei-KIST Convergence Research Institute, Yonsei University, Seoul, 03722, Korea
- School of Electrical and Electronics Engineering, Yonsei University, Seoul, 03722, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Korea
| | - Hyejeong Seong
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Kyo Seon Hwang
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Jungkyu Choi
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Korea
| | - Hyojin Lee
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Korea
| | - Nakwon Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Korea
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Chu PY, Li JX, Hsu TH, Gong HY, Lin CY, Wang JH, Huang CW. Identification of Genes Related to Cold Tolerance and Novel Genetic Markers for Molecular Breeding in Taiwan Tilapia ( Oreochromis spp.) via Transcriptome Analysis. Animals (Basel) 2021; 11:ani11123538. [PMID: 34944312 PMCID: PMC8697892 DOI: 10.3390/ani11123538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Taiwan tilapia is one of the primary species used in aquaculture practices in Taiwan. However, as a tropical fish, it is sensitive to cold temperatures that can lead to high mortality rates during winter months. Genetic and broodstock management strategies using marker-assisted selection and breeding are the best tools currently available to improve seed varieties for tilapia species. The purpose of this study was to develop molecular markers for cold stress-related genes using digital gene expression analysis of next-generation transcriptome sequencing in Taiwan tilapia (Oreochromis spp.). We constructed and sequenced cDNA libraries from the brain, gill, liver, and muscle tissues of cold-tolerance (CT) and cold-sensitivity (CS) strains. Approximately 35,214,833,100 nucleotides of raw sequencing reads were generated, and these were assembled into 128,147 unigenes possessing a total length of 185,382,926 bp and an average length of 1446 bp. A total of 25,844 unigenes were annotated using five protein databases and Venny analysis, and 38,377 simple sequence repeats (SSRs) and 65,527 single nucleotide polymorphisms (SNPs) were identified. Furthermore, from the 38-cold tolerance-related genes that were identified using differential gene expression analysis in the four tissues, 13 microsatellites and 37 single nucleotide polymorphism markers were identified. The results of the genotype analysis revealed that the selected markers could be used for population genetics. In addition to the diversity assessment, one of the SNP markers was determined to be significantly related to cold-tolerance traits and could be used as a molecular marker to assist in the selection and verification of cold-tolerant populations. The specific genetic markers explored in this study can be used for the identification of genetic polymorphisms and cold tolerance traits in Taiwan tilapia, and they can also be used to further explore the physiological and biochemical molecular regulation pathways of fish that are involved in their tolerance to environmental temperature stress.
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Affiliation(s)
- Pei-Yun Chu
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-Y.C.); (J.-X.L.); (T.-H.H.); (H.-Y.G.)
| | - Jia-Xian Li
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-Y.C.); (J.-X.L.); (T.-H.H.); (H.-Y.G.)
| | - Te-Hua Hsu
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-Y.C.); (J.-X.L.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung City 20224, Taiwan
| | - Hong-Yi Gong
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-Y.C.); (J.-X.L.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung City 20224, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan;
| | - Jung-Hua Wang
- Department of Electrical Engineering, National Taiwan Ocean University, Keelung City 20224, Taiwan;
- AI Research Center, National Taiwan Ocean University, Keelung City 20224, Taiwan
| | - Chang-Wen Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung City 20224, Taiwan; (P.-Y.C.); (J.-X.L.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung City 20224, Taiwan
- Correspondence: ; Tel.: +886-2-2462-2192 (ext. 5238)
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Ferrante JA, Smith CH, Thompson LM, Hunter ME. Genome-wide SNP analysis of three moose subspecies at the southern range limit in the contiguous United States. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01402-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractGenome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose (Alces alces) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated > 20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.
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The Impact of SNCA Variations and Its Product Alpha-Synuclein on Non-Motor Features of Parkinson's Disease. Life (Basel) 2021; 11:life11080804. [PMID: 34440548 PMCID: PMC8401994 DOI: 10.3390/life11080804] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022] Open
Abstract
Parkinson’s disease (PD) is a common and progressive neurodegenerative disease, caused by the loss of dopaminergic neurons in the substantia nigra pars compacta in the midbrain, which is clinically characterized by a constellation of motor and non-motor manifestations. The latter include hyposmia, constipation, depression, pain and, in later stages, cognitive decline and dysautonomia. The main pathological features of PD are neuronal loss and consequent accumulation of Lewy bodies (LB) in the surviving neurons. Alpha-synuclein (α-syn) is the main component of LB, and α-syn aggregation and accumulation perpetuate neuronal degeneration. Mutations in the α-syn gene (SNCA) were the first genetic cause of PD to be identified. Generally, patients carrying SNCA mutations present early-onset parkinsonism with severe and early non-motor symptoms, including cognitive decline. Several SNCA polymorphisms were also identified, and some of them showed association with non-motor manifestations. The functional role of these polymorphisms is only partially understood. In this review we explore the contribution of SNCA and its product, α-syn, in predisposing to the non-motor manifestations of PD.
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SNPRBb: economically important trait specific SNP resources of buffalo (Bubalus bubalis). CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01210-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Ajadi MB, Soremekun OS, Adewumi AT, Kumalo HM, Soliman MES. Functional Analysis of Single Nucleotide Polymorphism in ZUFSP Protein and Implication in Pathogenesis. Protein J 2021; 40:28-40. [PMID: 33512633 DOI: 10.1007/s10930-021-09962-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2021] [Indexed: 11/25/2022]
Abstract
Researches have revealed that functional non-synonymous Single Nucleotide Polymorphism (nsSNPs) present in the Zinc-finger with UFM1-Specific Peptidase domain protein (ZUFSP) may be involved in genetic instability and carcinogenesis. For the first time, we employed in-silico approach using predictive tools to identify and validate potential nsSNPs that could be pathogenic. Our result revealed that 8 nsSNPs (rs 112738382, rs 140094037, rs 201652589, rs 201847265, rs 202076827, rs 373634906, rs 375114528, rs 772591104) are pathogenic after being subjected to rigorous filtering process. The structural impact of the nsSNPs on ZUFSP structure indicated that the nsSNPs affect the stability of the protein by lowering ZUFSP protein stability. Furthermore, conservation analysis showed that rs 201652589, rs 140094037, rs 201847265, and rs 772591104 were highly conserved. Interestingly, the protein-protein affinity between ZUFSP and Ubiquitin was altered rs 201652589, rs 140094037, rs 201847265, and rs 772591104 had a binding affinity of - 0.46, - 0.83, - 1.62, and - 1.12 kcal/mol respectively. Our study has been able to identify potential nsSNPs that could be used as genetic biomarkers for some diseases arising as a result of aberration in the ZUFSP structure, however, being a predictive study, the identified nsSNPs need to be experimentally investigated.
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Affiliation(s)
- Mary B Ajadi
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Howard Campus, Durban, 4000, South Africa
- Chemical Pathology Department, Faculty of Basic Medical Sciences, College of Health Sciences, Ladoke Akintola University of Technology, PMB 4400, Osogbo, Nigeria
| | - Opeyemi S Soremekun
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Adeniyi T Adewumi
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Hezekiel M Kumalo
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Howard Campus, Durban, 4000, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
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Aziz MA, Akter T, Hussain MS, Millat MS, Uddin MS, Sajal M, Jafrin S, Aka TD, Akter T, Das C, Islam MS. Association of rs363598 and rs360932 polymorphisms with autism spectrum disorder in the Bangladeshi children. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Zimmerman SJ, Aldridge CL, Oyler-McCance SJ. An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern. BMC Genomics 2020; 21:382. [PMID: 32487020 PMCID: PMC7268520 DOI: 10.1186/s12864-020-06783-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/14/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the promise of increased precision in population genetic parameter estimates and identification of demographically and evolutionarily independent groups, as well as questions about the future usefulness of the more traditional genetic tools. At present, few empirical comparisons of population genetic parameters and clustering analyses performed with microsatellites and SNPs have been conducted. RESULTS Here we used microsatellite and SNP data generated from Gunnison sage-grouse (Centrocercus minimus) samples to evaluate concordance of the results obtained from each dataset for common metrics of genetic diversity (HO, HE, FIS, AR) and differentiation (FST, GST, DJost). Additionally, we evaluated clustering of individuals using putatively neutral (SNPs and microsatellites), putatively adaptive, and a combined dataset of putatively neutral and adaptive loci. We took particular interest in the conservation implications of any differences. Generally, we found high concordance between microsatellites and SNPs for HE, FIS, AR, and all differentiation estimates. Although there was strong correlation between metrics from SNPs and microsatellites, the magnitude of the diversity and differentiation metrics were quite different in some cases. Clustering analyses also showed similar patterns, though SNP data was able to cluster individuals into more distinct groups. Importantly, clustering analyses with SNP data suggest strong demographic independence among the six distinct populations of Gunnison sage-grouse with some indication of evolutionary independence in two or three populations; a finding that was not revealed by microsatellite data. CONCLUSION We demonstrate that SNPs have three main advantages over microsatellites: more precise estimates of population-level diversity, higher power to identify groups in clustering methods, and the ability to consider local adaptation. This study adds to a growing body of work comparing the use of SNPs and microsatellites to evaluate genetic diversity and differentiation for a species of conservation concern with relatively high population structure and using the most common method of obtaining SNP genotypes for non-model organisms.
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Affiliation(s)
- Shawna J Zimmerman
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Bldg. C, Fort Collins, CO, 80526, USA.
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80526, USA.
| | - Cameron L Aldridge
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Bldg. C, Fort Collins, CO, 80526, USA
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80526, USA
| | - Sara J Oyler-McCance
- U.S. Geological Survey, Fort Collins Science Center, 2150 Centre Avenue, Bldg. C, Fort Collins, CO, 80526, USA
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Takahashi T, Fukagawa M, Sakurai T, Hoshino H. Non-hybridization single nucleotide polymorphism detection and genotyping assay through direct discrimination of single base mutation by capillary electrophoretic separation of single-stranded DNA. J Sep Sci 2019; 43:657-662. [PMID: 31707747 DOI: 10.1002/jssc.201900897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022]
Abstract
The significant demands for single nucleotide polymorphism detection and genotyping assays have grown. Most common assays are based on the recognition of the target sequence by the hybridization with its specific probe having the complementary sequence of the target. Herein, a simple, label-free, and economical non-hybridization assay was developed for single nucleotide polymorphism detection and genotyping, based on the direct discrimination of single base mutation by simple capillary electrophoresis separation for single-stranded DNA in an acidic electrophoretic buffer solution containing urea. Capillary electrophoresis separation of single-base sequential isomers of DNA was achieved due to charge differences resulting from the different protonation properties of the DNA bases. Single nucleotide polymorphism detection and genotyping were achieved by discriminating the electropherogram pattern change, that is, peak number in the electropherogram, obtained by the proposed method. The successful practical application of the proposed method was demonstrated through single nucleotide polymorphism detection and genotyping on a known gene region of 84-mer, in which guanine to adenine single-base mutation is commonly observed, using a human hair sample in combination with genomic DNA extraction, polymerase chain reaction amplification, DNA purification from polymerase chain reaction products, and capillary electrophoresis separation.
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Affiliation(s)
- Toru Takahashi
- Department of applied chemistry and biotechnology, Graduate school of engineering, University of Fukui, Fukui, Japan
| | - Mayu Fukagawa
- Department of applied chemistry and biotechnology, Faculty of engineering, University of Fukui, Fukui, Japan
| | - Takao Sakurai
- Department of Environmental Benign Systems, Graduate school of environmental studies, Tohoku University, Sendai, Japan
| | - Hitoshi Hoshino
- Department of Environmental Benign Systems, Graduate school of environmental studies, Tohoku University, Sendai, Japan
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Norezzine A, Duksi F, Tsvetkova AD, Ulybina EA, Gins MS, Yacer RN, Klenovitsky AA, Nikishov AA, Amirshoev F, Digha J, Gladyr EA. Genetic characterization of White Fulani cattle in Nigeria: A comparative study. J Adv Vet Anim Res 2019; 6:474-480. [PMID: 31819874 PMCID: PMC6882711 DOI: 10.5455/javar.2019.f370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 08/25/2019] [Accepted: 08/25/2019] [Indexed: 11/03/2022] Open
Abstract
Objective The objective of the present study was to evaluate heterozygosis in cattle population, and to characterize White Fulani breed by identifying DNA markers considering microsatellites. Materials and Methods A total of 41 cattle were randomly selected and used for sample (wool) collection for the characterization and identification of phenotypic traits of cattle in Nigeria. The DNA samples from the samples were prepared. Twelve microsatellite primers were used for the microsatellite analysis in the genomic DNA of cattle. The reinforced products were analyzed to determine polymorphic alleles and their frequencies. Results White Fulani is characterized by a high degree of genetic diversity. The microsatellites have multiple alleles and may show heterozygosity frequencies of at least 70%. White Fulani cows and their F1 descendants form a common cluster, to which the bulls of the Kuru and Red Boro breeds are adjacent. There is a clear differentiation of purebred populations of Tajik zebu-like cattle (Q = 98.7%) and a significant proportion of white Fulani (Q = 81.8%) from Nigeria. The microsatellite analysis of zebu of Nigeria allowed identifying a total of 80 alleles. In the KURU and PAX-KR-BOR rocks, 17 and 19 alleles were identified, respectively. In F1, 51 alleles were detected. Conclusion White Fulani cattle are characterized by a high degree of genetic diversities. This makes it a highly informative source in genetic analysis. The results can be applied in dealing with the conservation and sustainable applications of genetic resources in the Nigerian cattle population.
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Affiliation(s)
| | - Fatima Duksi
- People's Friendship University of Russia, Moskva, Russia
| | | | | | - Murat S Gins
- People's Friendship University of Russia, Moskva, Russia
| | | | - Aleksandr A Klenovitsky
- People's Friendship University of Russia, Moskva, Russia.,All-Russian Research Institute for Animal Husbandry (VIZh) named after Academy Member L. K. Ernst, Russia
| | | | - Firuz Amirshoev
- Institute of Animal Science, Tajik Academy of Agricultural Sciences, Dushanbe, Tajikistan
| | - Jim Digha
- People's Friendship University of Russia, Moskva, Russia
| | - Elena A Gladyr
- All-Russian Research Institute for Animal Husbandry (VIZh) named after Academy Member L. K. Ernst, Russia
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Confronting two biomolecular techniques to detect NRF2 gene polymorphism biomarkers. Future Sci OA 2019; 5:FSO361. [PMID: 30820344 PMCID: PMC6391633 DOI: 10.4155/fsoa-2018-0075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/29/2018] [Indexed: 11/17/2022] Open
Abstract
Aim: Gene polymorphism biomarkers identify individual susceptibility to environmental and occupational hazards. The conventional approach considers polymerase chain reaction (PCR) followed by restriction fragment length polymorphism analysis (RFLP), a reliable but expensive and time-consuming two-step procedure. Therefore we evaluated the simpler method confronting two-pair primers (CTPP)–PCR for its robustness and applicability to epidemiologic studies. Materials & methods: We compared CTPP–PCR and PCR–RFLP techniques to detect two NRF2 polymorphisms in a set of biological samples. Results: CTPP–PCR produced contradictory results and required the orthogonal technique for confirming the data. Conclusion: In contrast to PCR-RFLP, CTPP–PCR of NRF2 polymorphisms resulted in ambiguous genotyping which strongly jeopardized heterozygosis classification. The necessity of long optimization and control procedures nullified the potential advantages of CTPP–PCR in terms of costs and time. Confronting two-pair primers-polymerase chain reaction (CTPP–PCR) is potentially a fast, simple and cost-efficient method for the detection of gene polymorphism biomarkers. This technique was used to genotype two SNPs of NRF2 gene in a set of biological samples but resulted in ambiguous results. Therefore, it was necessary to validate the CTPP–PCR genotyping data with the orthogonal technique PCR-RFLP. Since reproducibility is a critical issue in both biomedical research and diagnostics, we advise pairing CTPP–PCR with control methods and evaluating whether the overall package is still convenient for massive genetic screening.
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Mishra A, Sundaravadivel P, Tripathi SK, Jha RK, Badrukhiya J, Basak N, Anerao I, Sharma A, Idowu AE, Mishra A, Pandey S, Kumar U, Singh S, Nizamuddin S, Tupperwar NC, Jha AN, Thangaraj K. Variations in macrophage migration inhibitory factor gene are not associated with visceral leishmaniasis in India. J Infect Public Health 2019; 12:380-387. [PMID: 30611734 DOI: 10.1016/j.jiph.2018.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 11/24/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The host genetic factors play important role in determining the outcome of visceral leishmaniasis (VL). Macrophage migration inhibitory factor (MIF) is an important host cytokine, which is a key regulator of innate immune system. Genetic variants in MIF gene have been found to be associated with several inflammatory and infectious diseases. Role of MIF is well documented in leishmaniasis diseases, including Indian visceral leishmaniasis, where elevated level of serum MIF has been associated with VL phenotypes. However, there was no genetic study to correlate MIF variants in VL, therefore, we aimed to study the possible association of three reported MIF gene variants -794 CATT, -173G > C and non-coding RNA gene LOC284889 in Indian VL phenotype. METHODS Study subjects comprised of 214 VL patients along with ethnically and demographically matched 220 controls from VL endemic regions of Bihar state in India. RESULTS We found no significant difference between cases and controls in allelic, genotypic and haplotype frequency of the markers analysed [-794 CATT repeats (χ2=0.86; p=0.35; OR=0.85; 95% CI=0.61-1.19); -173 G>C polymorphism (χ2=1.11; p=0.29; OR=0.83; 95% CI=0.59-1.16); and LOC284889 (χ2=0.78; p=0.37; OR=0.86; 95% CI=0.61-1.20)]. CONCLUSION Since we did not find any significant differences between case and control groups, we conclude that sequencing of complete MIF gene and extensive study on innate and adaptive immunity genes may help in identifying genetic variations that are associated with VL susceptibility/resistance among Indians.
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Affiliation(s)
- Anshuman Mishra
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Vinoba Bhave Research Institute, Allahabad, India; Institute of Advanced Materials, Linkoping, Sweden
| | | | | | - Rajan Kumar Jha
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Nipa Basak
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Academy of Scientific and Innovative Research, India
| | - Isha Anerao
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Akshay Sharma
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ajayi Ebenezer Idowu
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Osun State University, Oshogbo, Nigeria
| | | | | | - Umesh Kumar
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sakshi Singh
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Aditya Nath Jha
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India; Sickle Cell Institute Chhattisgarh, Raipur, India
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Vijay A, Garg I, Ashraf MZ. Perspective: DNA Copy Number Variations in Cardiovascular Diseases. Epigenet Insights 2018; 11:2516865718818839. [PMID: 30560231 PMCID: PMC6291864 DOI: 10.1177/2516865718818839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022] Open
Abstract
Human genome contains many variations, often called mutations, which are difficult to detect and have remained a challenge for years. A substantial part of the genome encompasses repeats and when such repeats are in the coding region they may lead to change in the gene expression profile followed by pathological conditions. Structural variants are alterations which change one or more sequence feature in the chromosome such as change in the copy number, rearrangements, and translocations of a sequence and can be balanced or unbalanced. Copy number variants (CNVs) may increase or decrease the copies of a given region and have a pivotal role in the onset of many diseases including cardiovascular disorders. Cardiovascular disorders have a magnitude of well-established risk factors and etiology, but their correlation with CNVs is still being studied. In this article, we have discussed history of CNVs and a summary on the diseases associated with CNVs. To detect such variations, we shed light on the number of techniques introduced so far and their limitations. The lack of studies on cardiovascular diseases to determine the frequency of such variants needs clinical studies with larger cohorts. This review is a compilation of articles suggesting the importance of CNVs in multitude of cardiovascular anomalies. Finally, future perspectives for better understanding of CNVs and cardiovascular disorders have also been discussed.
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Affiliation(s)
- Aatira Vijay
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Iti Garg
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Mohammad Zahid Ashraf
- Genomics Division, Defence Institute of Physiology and Allied Sciences, DRDO, Delhi, India
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Shen T, You Y, Joseph C, Mirzaei M, Klistorner A, Graham SL, Gupta V. BDNF Polymorphism: A Review of Its Diagnostic and Clinical Relevance in Neurodegenerative Disorders. Aging Dis 2018; 9:523-536. [PMID: 29896439 PMCID: PMC5988606 DOI: 10.14336/ad.2017.0717] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/17/2017] [Indexed: 12/17/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) has a unique role in the neuronal development, differentiation, and survival in the developing and adult nervous system. A common single-nucleotide polymorphism in the pro-region of the human BDNF gene, resulting in a valine to methionine substitution (Val66Met), has been associated with the susceptibility, incidence, and clinical features of several neurodegenerative disorders. Much research has been dedicated to evaluating the effects of polymorphism in the past decade, and functional effects of this genetic variation. A better understanding of how this naturally occurring polymorphism associates with or influences physiology, anatomy, and cognition in both healthy and diseased adults in neurodegenerative conditions will help understand neurochemical mechanisms and definable clinical outcomes in humans. Here we review the role and relevance of the BDNF Val66Met polymorphism in neurodegenerative diseases, with particular emphasis on glaucoma, multiple sclerosis (MS), Alzheimer’s disease (AD) and Parkinson’s disease (PD). Several controversies and unresolved issues, including small effect sizes, possible ethnicity, gender, and age effects of the BDNF Val66Met are also discussed with respect to future research.
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Affiliation(s)
- Ting Shen
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia
| | - Yuyi You
- 2Save Sight Institute, Sydney University, Sydney, Australia
| | - Chitra Joseph
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia
| | - Mehdi Mirzaei
- 3Faculty of Science and Engineering, Macquarie University, Australia
| | - Alexander Klistorner
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia.,2Save Sight Institute, Sydney University, Sydney, Australia
| | - Stuart L Graham
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia.,2Save Sight Institute, Sydney University, Sydney, Australia
| | - Vivek Gupta
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia
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Mauger F, How-Kit A, Tost J. COLD-PCR Technologies in the Area of Personalized Medicine: Methodology and Applications. Mol Diagn Ther 2018; 21:269-283. [PMID: 28101802 DOI: 10.1007/s40291-016-0254-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation. CO-amplification at Lower Denaturation temperature Polymerase Chain Reaction (COLD-PCR) methods such as full-, fast-, ice- (improved and complete enrichment), enhanced-ice, and temperature-tolerant COLD-PCR make use of a critical temperature in the polymerase chain reaction to selectively denature wild-type-mutant heteroduplexes, allowing the enrichment of rare mutations. Mutations can subsequently be identified using a variety of laboratory technologies such as high-resolution melting, digital polymerase chain reaction, pyrosequencing, Sanger sequencing, or next-generation sequencing. COLD-PCR methods are sensitive, specific, and accurate if appropriately optimized and have a short time to results. A large variety of clinical samples (tumor DNA, circulating cell-free DNA, circulating cell-free fetal DNA, and circulating tumor cells) have been studied using COLD-PCR in many different applications including the detection of genetic changes in cancer and infectious diseases, non-invasive prenatal diagnosis, detection of microorganisms, or DNA methylation analysis. In this review, we describe in detail the different COLD-PCR approaches, highlighting their specificities, advantages, and inconveniences and demonstrating their use in different fields of biological and biomedical research.
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Affiliation(s)
- Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Fondation Jean Dausset-CEPH, 75010, Paris, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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19
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Vaghefi N, Kikkert JR, Bolton MD, Hanson LE, Secor GA, Nelson SC, Pethybridge SJ. Global genotype flow in Cercospora beticola populations confirmed through genotyping-by-sequencing. PLoS One 2017; 12:e0186488. [PMID: 29065114 PMCID: PMC5655429 DOI: 10.1371/journal.pone.0186488] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/01/2017] [Indexed: 11/18/2022] Open
Abstract
Genotyping-by-sequencing (GBS) was conducted on 333 Cercospora isolates collected from Beta vulgaris (sugar beet, table beet and swiss chard) in the USA and Europe. Cercospora beticola was confirmed as the species predominantly isolated from leaves with Cercospora leaf spot (CLS) symptoms. However, C. cf. flagellaris also was detected at a frequency of 3% in two table beet fields in New York. Resolution of the spatial structure and identification of clonal lineages in C. beticola populations using genome-wide single nucleotide polymorphisms (SNPs) obtained from GBS was compared to genotyping using microsatellites. Varying distance thresholds (bitwise distance = 0, 1.854599 × 10-4, and 1.298 × 10-3) were used for delineation of clonal lineages in C. beticola populations. Results supported previous reports of long distance dispersal of C. beticola through genotype flow. The GBS-SNP data set provided higher resolution in discriminating clonal lineages; however, genotype identification was impacted by filtering parameters and the distance threshold at which the multi-locus genotypes (MLGs) were contracted to multi-locus lineages. The type of marker or different filtering strategies did not impact estimates of population differentiation and structure. Results emphasize the importance of robust filtering strategies and designation of distance thresholds for delineating clonal lineages in population genomics analyses that depend on individual assignment and identification of clonal lineages. Detection of recurrent clonal lineages shared between the USA and Europe, even in the relaxed-filtered SNP data set and with a conservative distance threshold for contraction of MLGs, provided strong evidence for global genotype flow in C. beticola populations. The implications of intercontinental migration in C. beticola populations for CLS management are discussed.
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Affiliation(s)
- Niloofar Vaghefi
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, New York, United States of America
| | - Julie R. Kikkert
- Cornell Cooperative Extension, Canandaigua, New York, United States of America
| | - Melvin D. Bolton
- United States Department of Agriculture–Agricultural Research Service (USDA-ARS), Red River Valley Agricultural Research Center, Fargo, North Dakota, United States of America
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Linda E. Hanson
- USDA-ARS, Sugar Beet and Bean Research Unit, Michigan State University, Michigan, United States of America
| | - Gary A. Secor
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Scot C. Nelson
- College of Tropical Agriculture and Human Resources, Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Sarah J. Pethybridge
- School of Integrative Plant Science, Plant Pathology & Plant-Microbe Biology Section, Cornell University, Geneva, New York, United States of America
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20
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SNP discovery in spotted halibut (Verasper variegatus) using restriction site-associated DNA sequencing(RAD-seq). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0837-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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21
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Sakurai T, Hoshino H, Takahashi T. Separation of single-base sequential isomers of single-stranded DNA by capillary electrophoresis and its application in the discrimination of single-base DNA mutations. J Sep Sci 2017; 40:3153-3160. [DOI: 10.1002/jssc.201700443] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/30/2017] [Accepted: 05/30/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Takao Sakurai
- Department of Environmental Benign Systems; Graduate School of Environmental studies; Tohoku University; Sendai Japan
| | - Hitoshi Hoshino
- Department of Environmental Benign Systems; Graduate School of Environmental studies; Tohoku University; Sendai Japan
| | - Toru Takahashi
- Department of Applied Chemistry and Biotechnology; Graduate School of Engineering; University of Fukui; Fukui Japan
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Abstract
Whole-genome sequencing of wild-derived rat species can provide novel genomic resources, which may help decipher the genetics underlying complex phenotypes. As a notorious pest, reservoir of human pathogens, and colonizer, the Asian house rat, Rattus tanezumi, is successfully adapted to its habitat. However, little is known regarding genetic variation in this species. In this study, we identified over 41,000,000 single-nucleotide polymorphisms, plus insertions and deletions, through whole-genome sequencing and bioinformatics analyses. Moreover, we identified over 12,000 structural variants, including 143 chromosomal inversions. Further functional analyses revealed several fixed nonsense mutations associated with infection and immunity-related adaptations, and a number of fixed missense mutations that may be related to anticoagulant resistance. A genome-wide scan for loci under selection identified various genes related to neural activity. Our whole-genome sequencing data provide a genomic resource for future genetic studies of the Asian house rat species and have the potential to facilitate understanding of the molecular adaptations of rats to their ecological niches.
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Yang DU, Kim MK, Mohanan P, Mathiyalagan R, Seo KH, Kwon WS, Yang DC. Development of a single-nucleotide-polymorphism marker for specific authentication of Korean ginseng ( Panax ginseng Meyer) new cultivar "G-1". J Ginseng Res 2015; 41:31-35. [PMID: 28123319 PMCID: PMC5223065 DOI: 10.1016/j.jgr.2015.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 11/25/2022] Open
Abstract
Background Korean ginseng (Panax ginseng) is a well-known medicinal plant of Oriental medicine that is still in practice today. Until now, a total of 11 Korean ginseng cultivars with unique features to Korean ginseng have been developed based on the pure-line-selection method. Among them, a new cultivar namely G-1 with different agricultural traits related to yield and content of ginsenosides, was developed in 2012. Methods The aim of this study was to distinguish the new ginseng cultivar G-1 by identifying the unique single-nucleotide polymorphism (SNP) at its 45S ribosomal DNA and Panax quinquefolius region than other Korean ginseng cultivars using multiplex amplification-refractory mutation system–polymerase chain reaction (ARMS-PCR). Results A SNP at position of 45S ribosomal DNA region between G-1, P. quinquefolius, and the other Korean ginseng cultivars was identified. By designing modified allele-specific primers based on this site, we could specifically identified G-1 and P. quinquefolius via multiplex PCR. The unique primer for the SNP yielded an amplicon of size 449 bp in G-1 cultivar and P. quinquefolius. This study presents an effective method for the genetic identification of the G-1 cultivar and P. quinquefolius. Conclusion The results from our study shows that this SNP-based approach to identify the G-1 cultivar will be a good way to distinguish accurately the G-1 cultivar and P. quinquefolius from other Korean ginseng cultivars using a SNP at 45S ribosomal DNA region.
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Affiliation(s)
- Dong-Uk Yang
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Suwon, Korea
| | - Min-Kyeoung Kim
- KM Fundamental Research Division, Korea Institute of Oriental Medicine, Daejeon, Korea
| | - Padmanaban Mohanan
- Graduate School of Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Yongin, Korea
| | - Ramya Mathiyalagan
- Graduate School of Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Yongin, Korea
| | - Kwang-Hoon Seo
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Suwon, Korea
| | - Woo-Saeng Kwon
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Suwon, Korea
| | - Deok-Chun Yang
- Department of Oriental Medicinal Biotechnology, College of Life Science, Kyung Hee University, Suwon, Korea; Graduate School of Biotechnology and Ginseng Bank, College of Life Sciences, Kyung Hee University, Yongin, Korea
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Schrell AM, Roper MG. Frequency-encoded laser-induced fluorescence for multiplexed detection in infrared-mediated quantitative PCR. Analyst 2015; 139:2695-701. [PMID: 24448431 DOI: 10.1039/c3an02334f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A frequency-modulated fluorescence encoding method was used as a means to increase the number of fluorophores monitored during infrared-mediated polymerase chain reaction. Laser lines at 488 nm and 561 nm were modulated at 73 and 137 Hz, respectively, exciting fluorescence from the dsDNA intercalating dye, EvaGreen, and the temperature insensitive dye, ROX. Emission was collected in a color-blind manner using a single photomultiplier tube for detection and demodulated by frequency analysis. The resulting frequency domain signal resolved the contribution from the two fluorophores as well as the background from the IR lamp. The detection method was successfully used to measure amplification of DNA samples containing 10(4)-10(7) starting copies of template producing an amplification efficiency of 96%. The utility of this methodology was further demonstrated by simultaneous amplification of two genes from human genomic DNA using different color TaqMan probes. This method of multiplexing fluorescence detection with IR-qPCR is ideally suited as it allows isolation of the signals of interest from the background in the frequency domain and is expected to further reduce the complexity of multiplexed microfluidic IR-qPCR instrumentation.
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Affiliation(s)
- Adrian M Schrell
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Dittmer Building, Tallahassee, FL 32306, USA.
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Jang EK, Yang M, Pack SP. Highly-efficient T4 DNA ligase-based SNP analysis using a ligation fragment containing a modified nucleobase at the end. Chem Commun (Camb) 2015; 51:13090-3. [DOI: 10.1039/c5cc03761a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A highly accurate ligase-based SNP analysis was developed by using modified base-end downstream ligation fragments as detection probes, which can clearly distinguish C/T SNP types without any “false-positive” results.
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Affiliation(s)
- Eui Kyoung Jang
- Department of Biotechnology and Bioinformatics
- Korea University
- Jochiwon
- Korea
| | - Munhee Yang
- Department of Psychology
- University of Texas
- Austin
- USA
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics
- Korea University
- Jochiwon
- Korea
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Mesak F, Tatarenkov A, Earley RL, Avise JC. Hundreds of SNPs vs. dozens of SSRs: which dataset better characterizes natural clonal lineages in a self-fertilizing fish? Front Ecol Evol 2014. [DOI: 10.3389/fevo.2014.00074] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Rajatileka S, Luyt K, Williams M, Harding D, Odd D, Molnár E, Váradi A. Detection of three closely located single nucleotide polymorphisms in the EAAT2 promoter: comparison of single-strand conformational polymorphism (SSCP), pyrosequencing and Sanger sequencing. BMC Genet 2014; 15:80. [PMID: 24996834 PMCID: PMC4112986 DOI: 10.1186/1471-2156-15-80] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 07/02/2014] [Indexed: 11/15/2022] Open
Abstract
Background Single-strand conformational polymorphism (SSCP) is still a frequently used genotyping method across different fields for the detection of single nucleotide polymorphisms (SNPs) due to its simplicity, requirement for basic equipment accessible in most laboratories and low cost. This technique was previously used to detect rs4354668:A > C (g.-181A > C) SNP in the promoter of astroglial glutamate transporter (EAAT2) and the same approach was initially used here to investigate this promoter region in a cohort of newborns. Results Unexpectedly, four distinct DNA migration patterns were identified by SSCP. Sanger sequencing revealed two additional SNPs: g.-200C > A and g.-168C > T giving a rise to a total of ten EAAT2 promoter variants. SSCP failed to distinguish these variants reliably and thus pyrosequencing assays were developed. g.-168C > T was found in heterozygous form in one infant only with minor allele frequency (MAF) of 0.0023. In contrast, g.-200C > A and -181A > C were more common (with MAF of 0.46 and 0.49, respectively) and showed string evidence of linkage disequilibrium (LD). In a systematic comparison, 16% of samples were miss-classified by SSCP with 25-31% errors in the identification of the wild-type and homozygote mutant genotypes compared to pyrosequencing or Sanger sequencing. In contrast, SSCP and pyrosequencing of an unrelated single SNP (rs1835740:C > T), showed 94% concordance. Conclusion Our data suggest that SSCP cannot always detect reliably several closely located SNPs. Furthermore, caution is needed in the interpretation of the association studies linking only one of the co-inherited SNPs in the EAAT2 promoter to human diseases.
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Affiliation(s)
| | | | | | | | | | | | - Anikó Váradi
- Centre for Research in Biosciences, Department of Biological, Biomedical and Analytical Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol BS16 1QY, UK.
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Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics. Int J Mol Sci 2014; 15:9670-717. [PMID: 24886813 PMCID: PMC4100115 DOI: 10.3390/ijms15069670] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 12/25/2022] Open
Abstract
DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and expressed proteins. The ability to predict whether a given mutation is disease-causing or harmless is of great importance for the early detection of patients with a high risk of developing a particular disease and would pave the way for personalized medicine and diagnostics. Here we review existing methods and techniques to study and predict the effects of DNA mutations from three different perspectives: in silico, in vitro and in vivo. It is emphasized that the problem is complicated and successful detection of a pathogenic mutation frequently requires a combination of several methods and a knowledge of the biological phenomena associated with the corresponding macromolecules.
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Yao J, Yang M, Duan Y. Chemistry, Biology, and Medicine of Fluorescent Nanomaterials and Related Systems: New Insights into Biosensing, Bioimaging, Genomics, Diagnostics, and Therapy. Chem Rev 2014; 114:6130-78. [DOI: 10.1021/cr200359p] [Citation(s) in RCA: 592] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jun Yao
- Research
Center of Analytical Instrumentation, Analytical and Testing Center,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Mei Yang
- Research
Center of Analytical Instrumentation, Analytical and Testing Center,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yixiang Duan
- Research
Center of Analytical Instrumentation, Analytical and Testing Center,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
- Research
Center of Analytical Instrumentation, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, China
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Ferreira KAM, Fajardo EF, Baptista RP, Macedo AM, Lages-Silva E, Ramírez LE, Pedrosa AL. Species-specific markers for the differential diagnosis of Trypanosoma cruzi and Trypanosoma rangeli and polymorphisms detection in Trypanosoma rangeli. Parasitol Res 2014; 113:2199-207. [PMID: 24728520 DOI: 10.1007/s00436-014-3872-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
Trypanosoma cruzi and Trypanosoma rangeli are kinetoplastid parasites which are able to infect humans in Central and South America. Misdiagnosis between these trypanosomes can be avoided by targeting barcoding sequences or genes of each organism. This work aims to analyze the feasibility of using species-specific markers for identification of intraspecific polymorphisms and as target for diagnostic methods by PCR. Accordingly, primers which are able to specifically detect T. cruzi or T. rangeli genomic DNA were characterized. The use of intergenic regions, generally divergent in the trypanosomatids, and the serine carboxypeptidase gene were successful. Using T. rangeli genomic sequences for the identification of group-specific polymorphisms and a polymorphic AT(n) dinucleotide repeat permitted the classification of the strains into two groups, which are entirely coincident with T. rangeli main lineages, KP1 (+) and KP1 (-), previously determined by kinetoplast DNA (kDNA) characterization. The sequences analyzed totalize 622 bp (382 bp represent a hypothetical protein sequence, and 240 bp represent an anonymous sequence), and of these, 581 (93.3%) are conserved sites and 41 bp (6.7%) are polymorphic, with 9 transitions (21.9%), 2 transversions (4.9%), and 30 (73.2%) insertion/deletion events. Taken together, the species-specific markers analyzed may be useful for the development of new strategies for the accurate diagnosis of infections. Furthermore, the identification of T. rangeli polymorphisms has a direct impact in the understanding of the population structure of this parasite.
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Affiliation(s)
- Keila Adriana Magalhães Ferreira
- Instituto de Ciências Biológicas e Naturais, Universidade Federal do Triângulo Mineiro, Avenida Frei Paulino, 30, Bairro Abadia, Uberaba, Minas Gerais, 38025-180, Brazil
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31
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Khrustaleva AM, Gritsenko OF, Klovach NV. Single-nucleotide polymorphism in populations of sockeye salmon Oncorhynchus nerka from Kamchatka Peninsula. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413110094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Lightfoot DA, Iqbal MJ. Molecular mapping and breeding with microsatellite markers. Methods Mol Biol 2013; 1006:297-317. [PMID: 23546799 DOI: 10.1007/978-1-62703-389-3_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In genetics databases for crop plant species across the world, there are thousands of mapped loci that underlie quantitative traits, oligogenic traits, and simple traits recognized by association mapping in populations. The number of loci will increase as new phenotypes are measured in more diverse genotypes and genetic maps based on saturating numbers of markers are developed. A period of locus reevaluation will decrease the number of important loci as those underlying mega-environmental effects are recognized. A second wave of reevaluation of loci will follow from developmental series analysis, especially for harvest traits like seed yield and composition. Breeding methods to properly use the accurate maps of QTL are being developed. New methods to map, fine map, and isolate the genes underlying the loci will be critical to future advances in crop biotechnology. Microsatellite markers are the most useful tool for breeders. They are codominant, abundant in all genomes, highly polymorphic so useful in many populations, and both economical and technically easy to use. The selective genotyping approaches, including genotype ranking (indexing) based on partial phenotype data combined with favorable allele data and bulked segregation event (segregant) analysis (BSA), will be increasingly important uses for microsatellites. Examples of the methods for developing and using microsatellites derived from genomic sequences are presented for monogenic, oligogenic, and polygenic traits. Examples of successful mapping, fine mapping, and gene isolation are given. When combined with high-throughput methods for genotyping and a genome sequence, the use of association mapping with microsatellite markers will provide critical advances in the analysis of crop traits.
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Affiliation(s)
- David A Lightfoot
- Department of Plant, Soil and General Agriculture, Center of Excellence in Soybean Research, Teaching and Outreach, Southern Illinois University at Carbondale, Carbondale, IL, USA
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Chen X, Zang W, Xue F, Shen Z, Zhang Q. Bioinformatics analysis reveals potential candidate drugs for different subtypes of glioma. Neurol Sci 2012; 34:1139-43. [PMID: 23053832 DOI: 10.1007/s10072-012-1198-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 09/07/2012] [Indexed: 10/27/2022]
Abstract
Gliomas are the most common primary brain tumors of the central nervous system. However, current approaches for treating glioma have limited success, with a low 5-year survival rate. Besides, gliomas can be classified based on various criteria and the exact method of grading changes over time, it is hard for the surgeons to choose the suitable treatment strategies for glioma patients. In present study, we sought to explore the commonalities between different subtypes of glioma, and then identify biologically active small molecules capable of targeting all subtypes of glioma using a computational bioinformatics analysis of gene expression. Results showed that there were common differentially expressed genes between different subtypes of glioma. Pathways related to tumorigenesis and signaling transduction were dysfunctional in the progression of glioma. Further, we identified a group of small molecules. Candidate agents identified by our approach may provide the groundwork for a combination therapy approach for glioma. However, further evaluation for their potential use in the treatment of glioma is still needed.
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Affiliation(s)
- Xianzhen Chen
- Department of Neurosurgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
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Ben-Selma W, Harizi H, Letaief M, Boukadida J. Age- and gender-specific effects on NRAMP1 gene polymorphisms and risk of the development of active tuberculosis in Tunisian populations. Int J Infect Dis 2012; 16:e543-50. [PMID: 22609013 DOI: 10.1016/j.ijid.2011.11.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 09/28/2011] [Accepted: 11/16/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Studies that have assessed NRAMP1 polymorphisms and their association with susceptibility to tuberculosis (TB) in humans have yielded conflicting results. In this study, we evaluated the association between NRAMP1 gene polymorphisms and the risk of the development of active TB in Tunisian populations. METHODS The distribution of 3'-UTR and D543N polymorphisms in 223 TB patients (168 patients with pulmonary TB (PTB) and 55 patients with extrapulmonary TB (EPTB)) and 150 healthy donors was determined by PCR-restriction fragment length polymorphism (RFLP) method. RESULTS We found that AA and AG genotypes appeared to be associated with susceptibility to PTB (odds ratio (OR) 10.8, 95% confidence interval (CI) 1.37-230.8; p corrected for the number of genotypes (pc)=0.018) and EPTB (OR 4.37, 95% CI 1.64-11.82; pc=0.0024), respectively, in patients aged less than 30 years. However, wild-type GG genotype appeared to be associated with resistance against PTB in females (OR 0.1, 95% CI 0.01-0.74; pc=0.03). The 3'-UTR del/del genotype appeared to be associated with susceptibility to PTB in patients aged less than 30 years (OR 3.75, 95% CI 1.5-9.52; pc=0.003). In contrast, TGTG+/del might be associated with resistance against the development of active PTB (OR 0.23, 95% CI 0.08-0.65; pc=0.003). A-del haplotype appeared to be associated with susceptibility to PTB (OR 1.79, 95% CI 1.11-2.9; pc=0.04). CONCLUSIONS Collectively, our results suggest an association of NRAMP1 3'-UTR and D543N polymorphisms with susceptibility to mycobacterial infection in Tunisian populations in relation to age and sex.
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Affiliation(s)
- Walid Ben-Selma
- Laboratory of Microbiology and Immunology, UR02SP13, Farhat Hached University Hospital, Av. Ibn el Jazzar, 4000 Sousse, Tunisia.
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Rajendran A, Endo M, Sugiyama H. Single-molecule analysis using DNA origami. Angew Chem Int Ed Engl 2011; 51:874-90. [PMID: 22121063 DOI: 10.1002/anie.201102113] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Indexed: 11/11/2022]
Abstract
During the last two decades, scientists have developed various methods that allow the detection and manipulation of single molecules, which have also been called "in singulo" approaches. Fundamental understanding of biochemical reactions, folding of biomolecules, and the screening of drugs were achieved by using these methods. Single-molecule analysis was also performed in the field of DNA nanotechnology, mainly by using atomic force microscopy. However, until recently, the approaches used commonly in nanotechnology adopted structures with a dimension of 10-20 nm, which is not suitable for many applications. The recent development of scaffolded DNA origami by Rothemund made it possible for the construction of larger defined assemblies. One of the most salient features of the origami method is the precise addressability of the structures formed: Each staple can serve as an attachment point for different kinds of nanoobjects. Thus, the method is suitable for the precise positioning of various functionalities and for the single-molecule analysis of many chemical and biochemical processes. Here we summarize recent progress in the area of single-molecule analysis using DNA origami and discuss the future directions of this research.
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Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Rajendran A, Endo M, Sugiyama H. Einzelmolekülanalysen mithilfe von DNA-Origami. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102113] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Detection of single-base mutation in RNA using T4 RNA ligase-based nick-joining or DNAzyme-based nick-generation. Anal Biochem 2011; 414:303-5. [DOI: 10.1016/j.ab.2011.03.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 03/23/2011] [Accepted: 03/24/2011] [Indexed: 11/21/2022]
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Giestas L, Lima JC, Baptista PV. Coupling single base extension to a spectral codification tool for increased throughput screening. J Biotechnol 2011; 154:199-204. [DOI: 10.1016/j.jbiotec.2011.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 05/09/2011] [Accepted: 05/25/2011] [Indexed: 10/18/2022]
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Ben-Selma W, Harizi H, Bougmiza I, Ben Kahla I, Letaief M, Boukadida J. Polymorphisms in the RANTES gene increase susceptibility to active tuberculosis in Tunisia. DNA Cell Biol 2011; 30:789-800. [PMID: 21510799 DOI: 10.1089/dna.2010.1200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
RANTES plays a pivotal role in attracting and activating various leukocyte populations that control Mycobacterium tuberculosis infection. The present study investigated the relationship between the RANTES polymorphisms (-28C/G; rs2280788, and -403G/A; rs2107538) and susceptibility to active tuberculosis (TB) in Tunisian populations. A total of 168 patients with pulmonary TB (pTB), 55 with extrapulmonary TB (epTB), and 150 control subjects were studied. Genotype analyses were carried out using polymerase chain reaction-restriction fragment length polymorphism method. We found that the -28 GG genotype was significantly associated with susceptibility to pTB (odds ratio [OR]=11.19; 95% confidence intervals [CI], 5.14-25; P corrected for the number of genotypes [Pc]=10(-8)) and epTB (OR=11.67; 95% CI, 4.74-29.33; Pc=10(-8)). However, the -28 CC genotype was found to be significantly associated with resistance to pTB (OR=0.08; 95% CI, 0.04-0.16; Pc=10(-8)) and epTB development (OR=0.11; 95% CI, 0.05-0.27; Pc=10(-8)). -403A allele was associated with increased risk development of epTB (OR=2.21; 95% CI, 1.18-4.14; p=0.007). G-G and A-C haplotypes and the AG/GC diplotype were associated with increase susceptibility to pTB (OR=7.88, 95% CI, 5.38-11.55; Pc=3.10(-8); OR=2.32, 95% CI, 1.32-4.11; Pc=3.10(-3); OR=13.26, 95% CI, 6.06-29.89; Pc=3.10(-8); respectively) and epTB (OR=6.64, 95% CI, 4-11.05; Pc=3.10(-8); OR=2.6, 95% CI, 1.26-5.35; Pc=12.10(-3); OR=11.26, 95% CI, 4.44-29.28; Pc=3.10(-8); respectively). Collectively, our findings suggested an association of the RANTES -28C/G and -403G/A functional polymorphisms with susceptibility to Mycobacterium tuberculosis infection in Tunisian populations.
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Affiliation(s)
- Walid Ben-Selma
- Laboratory of Microbiology and Immunology, Farhat Hached University Hospital, Department of Community Medicine, Sousse, Tunisia.
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40
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Bichenkova EV, Lang Z, Yu X, Rogert C, Douglas KT. DNA-mounted self-assembly: New approaches for genomic analysis and SNP detection. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:1-23. [PMID: 21111076 DOI: 10.1016/j.bbagrm.2010.11.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/07/2010] [Accepted: 11/12/2010] [Indexed: 11/25/2022]
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Knapp EW, Irausquin SJ, Friedman R, Hughes AL. PolyAna: analyzing synonymous and nonsynonymous polymorphic sites. CONSERV GENET RESOUR 2010; 3:429-431. [PMID: 21731595 DOI: 10.1007/s12686-010-9372-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
PolyAna (available at http://www.biol.sc.edu/~austin/) aids in the analysis of natural selection on protein-coding sequences by estimating sample gene diversity at individual polymorphic nucleotide sites, which are classified as synonymous, non-synonymous, or ambiguous.
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Affiliation(s)
- Ethan W Knapp
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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42
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Wegrzyn JL, Eckert AJ, Choi M, Lee JM, Stanton BJ, Sykes R, Davis MF, Tsai CJ, Neale DB. Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem. THE NEW PHYTOLOGIST 2010; 188:515-32. [PMID: 20831625 DOI: 10.1111/j.1469-8137.2010.03415.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
• An association genetics approach was used to examine individual genes and alleles at the loci responsible for complex traits controlling lignocellulosic biosynthesis in black cottonwood (Populus trichocarpa). Recent interest in poplars as a source of renewable energy, combined with the vast genomic resources available, has enabled further examination of their genetic diversity. • Forty candidate genes were resequenced in a panel of 15 unrelated individuals to identify single nucleotide polymorphisms (SNPs). Eight hundred and seventy-six SNPs were successfully genotyped in a clonally replicated population (448 clones). The association population (average of 2.4 ramets per clone) was phenotyped using pyrolysis molecular beam mass spectrometry. Both single-marker and haplotype-based association tests were implemented to identify associations for composite traits representing lignin content, syringyl : guaiacyl ratio and C6 sugars. • Twenty-seven highly significant, unique, single-marker associations (false discovery rate Q < 0.10) were identified across 40 candidate genes in three composite traits. Twenty-three significant haplotypes within 11 genes were discovered in two composite traits. • Given the rapid decay of within-gene linkage disequilibrium and the high coverage of amplicons across each gene, it is likely that the numerous polymorphisms identified are in close proximity to the causative SNPs and the haplotype associations reflect information present in the associations between markers.
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Affiliation(s)
- Jill L Wegrzyn
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
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Wan Y, Lao R, Liu G, Song S, Wang L, Li D, Fan C. Multiplexed Electrochemical DNA Sensor for Single-Nucleotide Polymorphism Typing by Using Oligonucleotide-Incorporated Nonfouling Surfaces. J Phys Chem B 2010; 114:6703-6. [DOI: 10.1021/jp100871u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ying Wan
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Ruojun Lao
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Gang Liu
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Shiping Song
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Lihua Wang
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Di Li
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Chunhai Fan
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
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Development of gene-targeted SNP markers for genomic mapping in Pacific abalone Haliotis discus hannai Ino. Mol Biol Rep 2010; 37:3779-84. [PMID: 20217241 DOI: 10.1007/s11033-010-0032-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 02/24/2010] [Indexed: 10/19/2022]
Abstract
Useful and novel DNA markers are needed for aquaculture genetics and breeding. In this study, we report the discovery and development of gene-targeted single nucleotide polymorphisms (SNPs) for genomic mapping in the Pacific abalone Haliotis discus hannai Ino. Single EST or EST-contigs from 66 genes that had positive BLASTx matches (E-value ≤ 1e-8) were used for polymerase chain reaction (PCR) amplification. PCR products from the two parents of one mapping family were directly sequenced, and 83 SNP loci were found from 17 genes. Allele-specific PCR (AS-PCR) was developed and optimized for genotyping of 11 SNP loci in 120 progeny of the mapping family. Nine of the loci conformed to the expected Mendelian ratio of 1:1 based on the χ(2) test (P > 0.05) and could potentially be used for linkage map construction. Our data also indicate that the sequencing of two parents may be a practical strategy for the discovery of informative SNPs for linkage mapping in a particular mapping population.
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Wong AK, Marushchak DO, Gradinaru CC, Krull UJ. A mixed film composed of oligonucleotides and poly(2-hydroxyethyl methacrylate) brushes to enhance selectivity for detection of single nucleotide polymorphisms. Anal Chim Acta 2010; 661:103-10. [DOI: 10.1016/j.aca.2009.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 11/29/2009] [Accepted: 12/01/2009] [Indexed: 10/20/2022]
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Davies MA, Conley Y, Roth BL. Functional SNPs in Genes Encoding the 5-HT2A Receptor Modify the Affinity and Potency of Several Atypical Antipsychotic Drugs. Biol Res Nurs 2010; 13:55-60. [DOI: 10.1177/1099800409358760] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Atypical antipsychotic drugs (AADs) are the standard treatment for both the acute and long-term management of schizophrenia and an augmentation to mood stabilizers for bipolar disorder (BD). Yet many individuals who take AADs do not fully respond to them, while others experience side effects that include weight gain and metabolic disorder. This in vitro pharmacogenetic study examined whether allelic variants in the 5-hydroxytryptamine (HT)2A receptor alter the in vitro pharmacology of six AADs (clozapine, olanzapine, risperidone, quetiapine, ziprasidone, and aripiprazole). We selected 4 functional single-nucleotide polymorphisms (SNPs) for investigation (Thr25Asn, Ile197Val, Ala447Val, and His452Tyr), conducted site-directed mutagenesis studies to induce variants into human HEK-293 cell lines, and screened allelic variants for their effects on 5-HT 2A receptors in the cell lines. We conducted numerous binding assays and fluorescence-based assay system (FLEX station) experiments using the six AADs. Our results indicated that three polymorphic 5-HT2A receptors (Ile197Val, Ala447Val, and His452Tyr) exhibited statistically significant, though modest, changes in atypical antipsychotic affinity. In addition, three polymorphic receptors (Thr25Asn, Ile197Val, and His452Try) altered AAD potency. Our findings support in vivo evidence that functional SNPs in genes encoding neuroreceptor drug targets could explain interindividual differences in AAD drug response and tolerability. We suggest that more in vivo pharmacogenetic studies of well-characterized patients who are prescribed AADs be indicated. Future pharmacogenetic studies of well-characterized patients will likely involve tagging SNPs and the use of haplotypes related to other genes encoding neuroreceptor drug targets.
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Affiliation(s)
- Marilyn A. Davies
- Department of Community and Health Systems, School of Nursing, University of Pittsburgh, PA, USA,
| | - Yvette Conley
- Department of Health Promotion and Development, School of Nursing, University of Pittsburgh, PA, USA, Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA
| | - Bryan L. Roth
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, USA
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Fan A, Lau C, Lu J. Hydroxylamine-amplified gold nanoparticles for the naked eye and chemiluminescent detection of sequence-specific DNA with notable potential for single-nucleotide polymorphism discrimination. Analyst 2009; 134:497-503. [DOI: 10.1039/b817047a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Corrie S, Sova P, Lawrie G, Battersby B, Kiviat N, Trau M. Development of a multiplexed bead-based assay for detection of DNA methylation in cancer-related genes. MOLECULAR BIOSYSTEMS 2008; 5:262-8. [PMID: 19225617 DOI: 10.1039/b813077a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we report a method for the detection of methylated CpG dinucleotides located within CpG islands in genomic DNA using multiplexed bead-based assays and standard flow cytometry instrumentation. Four CpG "clusters" were identified in the TFPI2 and SPARC CpG islands whose methylation status was highly correlated with the incidence of invasive cervical cancer in our previous studies. Eight probes in total were designed for both the methylated and unmethylated forms of each cluster and attached to different fluorescently-encoded organosilica bead sets. Probe design was investigated by changing either the length of probes whilst keeping the melting temperature constant, or changing the melting temperature and keeping the probe length constant. Asymmetric polymerase chain reaction (PCR) methods designed without methylation-specific primers were used to prepare fluorescently-labelled targets based on bisulfite-converted genomic DNA. After investigating the specificity of the probes in a model system using fluorescently-labelled synthetic oligonucleotides, cancer cell-line DNA was analysed and the constant length probe design facilitated the correct genotyping of all clusters with respect to negative controls.
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Affiliation(s)
- Simon Corrie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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Abstract
The 5'-nuclease allelic discrimination assay, or TaqMan assay, is a PCR-based assay for genotyping single nucleotide polymorphisms (SNPs). The region flanking the SNP is amplified in the presence of two allele-specific fluorescent probes. The probes do not fluoresce in solution because of a quencher at the 3' end. The presence of two probes allows the detection of both alleles in a single tube. Moreover, because probes are included in the PCR, genotypes are determined without any post-PCR processing, a feature that is unavailable with most other genotyping methods. This unit describes probe and primer design and PCR conditions.
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Affiliation(s)
- Lester Hui
- Bristol-Myers Squibb, Princeton, New Jersey, USA
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