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Oliveira PV, de Almeida FAN, Lugon MD, Britto KB, Oliveira-Costa J, Santos AR, Paneto GG. Using high-resolution melting to identify Calliphoridae (blowflies) species from Brazil. PeerJ 2020; 8:e9680. [PMID: 33335803 PMCID: PMC7713596 DOI: 10.7717/peerj.9680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/17/2020] [Indexed: 01/22/2023] Open
Abstract
Forensic entomology is the study of insects and other arthropods used in the solution of crimes. Most of entomological evidences strongly depend on accurate species identification. Therefore, new methods are being developed due to difficulties in morphological identification, including molecular methods such as High-Resolution Melting. In this study, we reported a new HRM primer set to identify forensically important Calliphoridae (blowflies) from Brazil. For such purpose, Calliphoridae species of forensic importance in Brazil were listed and confirmed by specialists. Mitochondrial COI sequences of those species were downloaded from databases and aligned, and polymorphic variations were selected for distinction between species. Based on it, HRM primers were designed. Forty-three fly samples representing six species were tested in the HRM assay. All samples had the COI gene sequenced to validate the result. Identifying and differentiating the six species proposed using a combination of two amplicons was possible. The protocol was effective even for old insect specimens, collected and preserved dried for more than ten years, unlike the DNA sequencing technique that failed for those samples. The HRM technique proved to be an alternative tool to DNA sequencing, with advantage of amplifying degraded samples and being fast and cheaper than the sequencing technique.
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Affiliation(s)
- Pablo Viana Oliveira
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | | | - Magda Delorence Lugon
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Karolinni Bianchi Britto
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Janyra Oliveira-Costa
- Polícia Civil do Estado do Rio de Janeiro, Instituto Médico Legal Afrânio Peixoto, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Rosa Santos
- Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
| | - Greiciane Gaburro Paneto
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
- Centro de Ciências Exatas, Naturais e da Saúde, Universidade Federal do Espírito Santo, Alegre, Espírito Santo, Brazil
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Galuszynski NC, Potts AJ. Application of High Resolution Melt analysis (HRM) for screening haplotype variation in a non-model plant genus: Cyclopia (Honeybush). PeerJ 2020; 8:e9187. [PMID: 32461839 PMCID: PMC7233275 DOI: 10.7717/peerj.9187] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
Aim This study has three broad aims: to (a) develop genus-specific primers for High Resolution Melt analysis (HRM) of members of Cyclopia Vent., (b) test the haplotype discrimination of HRM compared to Sanger sequencing, and (c) provide an example of using HRM to detect novel haplotype variation in wild C. subternata Vogel. populations. Location The Cape Floristic Region (CFR), located along the southern Cape of South Africa. Methods Polymorphic loci were detected through a screening process of sequencing 12 non-coding chloroplast DNA segments across 14 Cyclopia species. Twelve genus-specific primer combinations were designed around variable cpDNA loci, four of which failed to amplify under PCR; the eight remaining were applied to test the specificity, sensitivity and accuracy of HRM. The three top performing HRM Primer combinations were then applied to detect novel haplotypes in wild C. subternata populations, and phylogeographic patterns of C. subternata were explored. Results We present a framework for applying HRM to non-model systems. HRM accuracy varied across the PCR products screened using the genus-specific primers developed, ranging between 56 and 100%. The nucleotide variation failing to produce distinct melt curves is discussed. The top three performing regions, having 100% specificity (i.e. different haplotypes were never grouped into the same cluster, no false negatives), were able to detect novel haplotypes in wild C. subternata populations with high accuracy (96%). Sensitivity below 100% (i.e. a single haplotype being clustered into multiple unique groups during HRM curve analysis, false positives) was resolved through sequence confirmation of each cluster resulting in a final accuracy of 100%. Phylogeographic analyses revealed that wild C. subternata populations tend to exhibit phylogeographic structuring across mountain ranges (accounting for 73.8% of genetic variation base on an AMOVA), and genetic differentiation between populations increases with distance (p < 0.05 for IBD analyses). Conclusions After screening for regions with high HRM clustering specificity-akin to the screening process associated with most PCR based markers-the technology was found to be a high throughput tool for detecting genetic variation in non-model plants.
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Affiliation(s)
- Nicholas C Galuszynski
- Department of Botany, Nelson Mandela University, Port Elizabeth, Eastern Cape, South Africa
| | - Alastair J Potts
- Department of Botany, Nelson Mandela University, Port Elizabeth, Eastern Cape, South Africa
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Teng S, Lin X, Fang J, Chai X, Xiao G. Characterization of 108 novel expressed sequence tag-derived single-nucleotide polymorphism markers in the blood clam Tegillarca granosa using a transcriptome database. J Genet 2018. [DOI: 10.1007/s12041-018-0884-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Das S, Sarker S, Ghorashi SA, Forwood JK, Raidal SR. A comparison of PCR assays for beak and feather disease virus and high resolution melt (HRM) curve analysis of replicase associated protein and capsid genes. J Virol Methods 2016; 237:47-57. [PMID: 27565820 DOI: 10.1016/j.jviromet.2016.08.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/20/2016] [Accepted: 08/22/2016] [Indexed: 12/22/2022]
Abstract
Beak and feather disease virus (BFDV) threatens a wide range of endangered psittacine birds worldwide. In this study, we assessed a novel PCR assay and genetic screening method using high-resolution melt (HRM) curve analysis for BFDV targeting the capsid (Cap) gene (HRM-Cap) alongside conventional PCR detection as well as a PCR method that targets a much smaller fragment of the virus genome in the replicase initiator protein (Rep) gene (HRM-Rep). Limits of detection, sensitivity, specificity and discriminatory power for differentiating BFDV sequences were compared. HRM-Cap had a high positive predictive value and could readily differentiate between a reference genotype and 17 other diverse BFDV genomes with more discriminatory power (genotype confidence percentage) than HRM-Rep. Melt curve profiles generated by HRM-Cap correlated with unique DNA sequence profiles for each individual test genome. The limit of detection of HRM-Cap was lower (2×10-5ng/reaction or 48 viral copies) than that for both HRM-Rep and conventional BFDV PCR which had similar sensitivity (2×10-6ng or 13 viral copies/reaction). However, when used in a diagnostic setting with 348 clinical samples there was strong agreement between HRM-Cap and conventional PCR (kappa=0.87, P<0.01, 98% specificity) and HRM-Cap demonstrated higher specificity (99.9%) than HRM-Rep (80.3%).
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Affiliation(s)
- Shubhagata Das
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, NSW 2678, Australia.
| | - Subir Sarker
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, NSW 2678, Australia.
| | - Seyed Ali Ghorashi
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, NSW 2678, Australia.
| | - Jade K Forwood
- School of Biomedical Sciences, Faculty of Science, Charles Sturt University, Wagga Wagga, NSW 2650, Australia.
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Faculty of Science, Charles Sturt University, NSW 2678, Australia.
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Zhang N, Zhang L, Tao Y, Guo L, Sun J, Li X, Zhao N, Peng J, Li X, Zeng L, Chen J, Yang G. Construction of a high density SNP linkage map of kelp (Saccharina japonica) by sequencing Taq I site associated DNA and mapping of a sex determining locus. BMC Genomics 2015; 16:189. [PMID: 25887315 PMCID: PMC4369078 DOI: 10.1186/s12864-015-1371-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kelp (Saccharina japonica) has been intensively cultured in China for almost a century. Its genetic improvement is comparable with that of rice. However, the development of its molecular tools is extremely limited, thus its genes, genetics and genomics. Kelp performs an alternative life cycle during which sporophyte generation alternates with gametophyte generation. The gametophytes of kelp can be cloned and crossed. Due to these characteristics, kelp may serve as a reference for the biological and genetic studies of Volvox, mosses and ferns. RESULTS We constructed a high density single nucleotide polymorphism (SNP) linkage map for kelp by restriction site associated DNA (RAD) sequencing. In total, 4,994 SNP-containing physical (tag-defined) RAD loci were mapped on 31 linkage groups. The map expanded a total genetic distance of 1,782.75 cM, covering 98.66% of the expected (1,806.94 cM). The length of RAD tags (85 bp) was extended to 400-500 bp with Miseq method, offering us an easiness of developing SNP chips and shifting SNP genotyping to a high throughput track. The number of linkage groups was in accordance with the documented with cytological methods. In addition, we identified a set of microsatellites (99 in total) from the extended RAD tags. A gametophyte sex determining locus was mapped on linkage group 2 in a window about 9.0 cM in width, which was 2.66 cM up to marker_40567 and 6.42 cM down to marker_23595. CONCLUSIONS A high density SNP linkage map was constructed for kelp, an intensively cultured brown alga in China. The RAD tags were also extended so that a SNP chip could be developed. In addition, a set of microsatellites were identified among mapped loci, and a gametophyte sex determining locus was mapped. This map will facilitate the genetic studies of kelp including for example the evaluation of germplasm and the decipherment of the genetic bases of economic traits.
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Affiliation(s)
- Ning Zhang
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Linan Zhang
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Ye Tao
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Li Guo
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Juan Sun
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Xia Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Nan Zhao
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Jie Peng
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Xiaojie Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Liang Zeng
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Jinsa Chen
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Guanpin Yang
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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Rapid genotyping of beak and feather disease virus using high-resolution DNA melt curve analysis. J Virol Methods 2014; 208:47-55. [DOI: 10.1016/j.jviromet.2014.07.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/21/2014] [Accepted: 07/25/2014] [Indexed: 11/21/2022]
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Meistertzheim AL, Calvès I, Roussel V, Van Wormhoudt A, Laroche J, Huchette S, Paillard C. New genetic markers to identify European resistant abalone to vibriosis revealed by high-resolution melting analysis, a sensitive and fast approach. MARINE BIOLOGY 2014. [DOI: 10.1007/s00227-014-2470-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Wang J, Qi H, Li L, Que H, Wang D, Zhang G. Discovery and validation of genic single nucleotide polymorphisms in the Pacific oyster Crassostrea gigas. Mol Ecol Resour 2014; 15:123-35. [PMID: 24823694 DOI: 10.1111/1755-0998.12278] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 12/01/2022]
Abstract
The economic and ecological importance of the oyster necessitates further research on the molecular mechanisms, which both regulate the commercially important traits of the oyster and help it to survive in the variable marine environment. Single nucleotide polymorphisms (SNPs) have been widely used to assess genetic variation and identify genes underlying target traits. In addition, high-resolution melting (HRM) analysis is a potentially powerful method for validating candidate SNPs. In this study, we adopted a rapid and efficient pipeline for the screening and validation of SNPs in the genic region of Crassostrea gigas based on transcriptome sequencing and HRM analysis. Transcriptomes of three wild oyster populations were sequenced using Illumina sequencing technology. In total, 50-60 million short reads, corresponding to 4.5-5.4 Gbp, from each population were aligned to the oyster genome, and 5.8 × 10(5) SNPs were putatively identified, resulting in a predicted SNP every 47 nucleotides on average. The putative SNPs were unevenly distributed in the genome and high-density (≥2%), nonsynonymous coding SNPs were enriched in genes related to apoptosis and responses to biotic stimuli. Subsequently, 1,671 loci were detected by HRM analysis, accounting for 64.7% of the total selected candidate primers, and finally, 1,301 polymorphic SNP markers were developed based on HRM analysis. All of the validated SNPs were distributed into 897 genes and located in 672 scaffolds, and 275 of these genes were stress inducible under unfavourable salinity, temperature, and exposure to air and heavy metals. The validated SNPs in this study provide valuable molecular markers for genetic mapping and characterization of important traits in oysters.
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Affiliation(s)
- Jiafeng Wang
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Affiliated Hospital of Guangdong Medical College, Guangdong, 524001, China
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Huang J, Zhang Y, Li J, Yu Z. Development of SNP markers in Crassostrea hongkongensis based on the next-generation sequencing and high resolution melting analysis. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0218-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Kuroyanagi M, Katayama T, Imai T, Yamamoto Y, Chisada SI, Yoshiura Y, Ushijima T, Matsushita T, Fujita M, Nozawa A, Suzuki Y, Kikuchi K, Okamoto H. New approach for fish breeding by chemical mutagenesis: establishment of TILLING method in fugu (Takifugu rubripes) with ENU mutagenesis. BMC Genomics 2013; 14:786. [PMID: 24225309 PMCID: PMC3830513 DOI: 10.1186/1471-2164-14-786] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 11/04/2013] [Indexed: 11/26/2022] Open
Abstract
Background In fish breeding, it is essential to discover and generate fish exhibiting an effective phenotype for the aquaculture industry, but screening for natural mutants by only depending on natural spontaneous mutations is limited. Presently, reverse genetics has become an important tool to generate mutants, which exhibit the phenotype caused by inactivation of a gene. TILLING (Targeting Induced Local Lesions INGenomes) is a reverse genetics strategy that combines random chemical mutagenesis with high-throughput discovery technologies for screening the induced mutations in target genes. Although the chemical mutagenesis has been used widely in a variety of model species and also genetic breeding of microorganisms and crops, the application of the mutagenesis in fish breeding has been only rarely reported. Results In this study, we developed the TILLING method in fugu with ENU mutagenesis and high-resolution melting (HRM) analysis to detect base pair changes in target sequences. Fugu males were treated 3 times at weekly intervals with various ENU concentrations, and then the collected sperm after the treatment was used to fertilize normal female for generating the mutagenized population (F1). The fertilization and the hatching ratios were similar to those of the control and did not reveal a dose dependency of ENU. Genomic DNA from the harvested F1 offspring was used for the HRM analysis. To obtain a fish exhibiting a useful phenotype (e.g. high meat production and rapid growth), fugu myostatin (Mstn) gene was examined as a target gene, because it has been clarified that the mstn deficient medaka exhibited double-muscle phenotype in common with MSTN knockout mice and bovine MSTN mutant. As a result, ten types of ENU-induced mutations were identified including a nonsense mutation in the investigated region with HRM analysis. In addition, the average mutation frequency in fugu Mstn gene was 1 mutant per 297 kb, which is similar to values calculated for zebrafish and medaka TILLING libraries. Conclusions These results demonstrate that the TILLING method in fugu was established. We anticipate that this TILLING approach can be used to generate a wide range of mutant alleles, and be applicable to many farmed fish that can be chemically mutagenized.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Kiyoshi Kikuchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 2971-4 Bentenjima, Maisaka, Hamamatsu, Shizuoka 431-0214, Japan.
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New approach for fish breeding by chemical mutagenesis: establishment of TILLING method in fugu (Takifugu rubripes) with ENU mutagenesis. BMC Genomics 2013. [PMID: 24225309 DOI: 10.1186/1471-2164-14-786.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In fish breeding, it is essential to discover and generate fish exhibiting an effective phenotype for the aquaculture industry, but screening for natural mutants by only depending on natural spontaneous mutations is limited. Presently, reverse genetics has become an important tool to generate mutants, which exhibit the phenotype caused by inactivation of a gene. TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse genetics strategy that combines random chemical mutagenesis with high-throughput discovery technologies for screening the induced mutations in target genes. Although the chemical mutagenesis has been used widely in a variety of model species and also genetic breeding of microorganisms and crops, the application of the mutagenesis in fish breeding has been only rarely reported. RESULTS In this study, we developed the TILLING method in fugu with ENU mutagenesis and high-resolution melting (HRM) analysis to detect base pair changes in target sequences. Fugu males were treated 3 times at weekly intervals with various ENU concentrations, and then the collected sperm after the treatment was used to fertilize normal female for generating the mutagenized population (F1). The fertilization and the hatching ratios were similar to those of the control and did not reveal a dose dependency of ENU. Genomic DNA from the harvested F1 offspring was used for the HRM analysis. To obtain a fish exhibiting a useful phenotype (e.g. high meat production and rapid growth), fugu myostatin (Mstn) gene was examined as a target gene, because it has been clarified that the mstn deficient medaka exhibited double-muscle phenotype in common with MSTN knockout mice and bovine MSTN mutant. As a result, ten types of ENU-induced mutations were identified including a nonsense mutation in the investigated region with HRM analysis. In addition, the average mutation frequency in fugu Mstn gene was 1 mutant per 297 kb, which is similar to values calculated for zebrafish and medaka TILLING libraries. CONCLUSIONS These results demonstrate that the TILLING method in fugu was established. We anticipate that this TILLING approach can be used to generate a wide range of mutant alleles, and be applicable to many farmed fish that can be chemically mutagenized.
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Johnson IM, Prakash H, Prathiba J, Raghunathan R, Malathi R. Spectral analysis of naturally occurring methylxanthines (theophylline, theobromine and caffeine) binding with DNA. PLoS One 2012; 7:e50019. [PMID: 23236361 PMCID: PMC3517612 DOI: 10.1371/journal.pone.0050019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 10/17/2012] [Indexed: 12/13/2022] Open
Abstract
Nucleic acids exist in a dynamic equilibrium with a number of molecules that constantly interact with them and regulate the cellular activities. The inherent nature of the structure and conformational integrity of these macromolecules can lead to altered biological activity through proper targeting of nucleic acids binding ligands or drug molecules. We studied the interaction of naturally occurring methylxanthines such as theophylline, theobromine and caffeine with DNA, using UV absorption and Fourier transform infrared (FTIR) spectroscopic methods, and especially monitored their binding affinity in the presence of Mg(2+) and during helix-coil transitions of DNA by temperature (T(m)) or pH melting profiles. The study indicates that all these molecules effectively bind to DNA in a dose dependent manner. The overall binding constants of DNA-theophylline = 3.5×10(3) M(-1), DNA-theobromine = 1.1×10(3) M(-1), and DNA-Caffeine = 3.8×10(3) M(-1). On the other hand T(m)/pH melting profiles showed 24-35% of enhanced binding activity of methylxanthines during helix-coil transitions of DNA rather than to its native double helical structure. The FTIR analysis divulged that theophylline, theobromine and caffeine interact with all the base pairs of DNA (A-T; G-C) and phosphate group through hydrogen bond (H-bond) interaction. In the presence of Mg(2+), methylxanthines altered the structure of DNA from B to A-family. However, the B-family structure of DNA remained unaltered in DNA-methylxanthines complexes or in the absence of Mg(2+). The spectral analyses indicated the order of binding affinity as "caffeine≥theophylline>theobromine" to the native double helical DNA, and "theophylline≥theobromine>caffeine to the denatured form of DNA and in the presence of divalent metal ions.
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Affiliation(s)
- Irudayam Maria Johnson
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- Department of Genetics, Taramani Campus, University of Madras, Chennai, India
- * E-mail: (IMJ); (RM)
| | - Halan Prakash
- National Centre for Ultrafast Processes, Taramani Campus, University of Madras, Chennai, India
| | - Jeyaguru Prathiba
- Department of Genetics, Taramani Campus, University of Madras, Chennai, India
| | | | - Raghunathan Malathi
- Department of Genetics, Taramani Campus, University of Madras, Chennai, India
- * E-mail: (IMJ); (RM)
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