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Valenzuela-Moreno LF, Méndez-Cruz ST, Rico-Torres CP, Cedillo-Peláez C, Correa D, Caballero-Ortega H. SAG3 Toxoplasma gondii cloning reveals unexpected fivefold infection in the blood of feral cats in the Mexican Caribbean. BMC Vet Res 2022; 18:33. [PMID: 35031031 PMCID: PMC8759159 DOI: 10.1186/s12917-021-03129-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/23/2021] [Indexed: 12/02/2022] Open
Abstract
Background Currently, more than 300 genotypes of Toxoplasma gondii (T. gondii) have been described throughout the world, demonstrating its wide genetic diversity. The SAG3 locus is one of the genes included in the genotyping panel of this parasite. It is associated with its virulence since it participates during the invasion process of the host cells. Therefore, cloning, sequencing, and bioinformatic analysis were used to deepen the understanding of the SAG3 locus genetic diversity of T. gondii in blood samples from feral cats. Results Six different SAG3 sequences were detected, five of which were detected in one feline. Three sequences were first reported here; one of them was an intragenic recombinant. In the cladogram, four out of ten SAG3 sequences did not share nodes with others reported worldwide. Conclusions Cloning and sequencing of samples with more than one restriction pattern by PCR-RFLP were very helpful tools to demonstrate the presence of more than three genotypes of T. gondii in the blood of feral cats from southeastern Mexico. This suggests a potential mixed infection of multiple T. gondii strains and high genetic diversity of the parasites in felines in this tropical region of Mexico. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-021-03129-9.
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Affiliation(s)
- Luis Fernando Valenzuela-Moreno
- Laboratorio de Inmunología Experimental, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C, Colonia Insurgentes-Cuicuilco, Delegación Coyoacán, Insurgentes Sur 3700C, Col. Insurgentes Cuicuilco, C.P. 04530, Ciudad de México, México
| | - Sara Teresa Méndez-Cruz
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C, Colonia Insurgentes-Cuicuilco, Delegación Coyoacán, C.P. 04530, Ciudad de México, México
| | - Claudia Patricia Rico-Torres
- Laboratorio de Inmunología Experimental, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C, Colonia Insurgentes-Cuicuilco, Delegación Coyoacán, Insurgentes Sur 3700C, Col. Insurgentes Cuicuilco, C.P. 04530, Ciudad de México, México
| | - Carlos Cedillo-Peláez
- Laboratorio de Inmunología Experimental, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C, Colonia Insurgentes-Cuicuilco, Delegación Coyoacán, Insurgentes Sur 3700C, Col. Insurgentes Cuicuilco, C.P. 04530, Ciudad de México, México
| | - Dolores Correa
- Laboratorio de Inmunología Experimental, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C, Colonia Insurgentes-Cuicuilco, Delegación Coyoacán, Insurgentes Sur 3700C, Col. Insurgentes Cuicuilco, C.P. 04530, Ciudad de México, México
| | - Heriberto Caballero-Ortega
- Laboratorio de Inmunología Experimental, Instituto Nacional de Pediatría, Insurgentes Sur 3700-C, Colonia Insurgentes-Cuicuilco, Delegación Coyoacán, Insurgentes Sur 3700C, Col. Insurgentes Cuicuilco, C.P. 04530, Ciudad de México, México.
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Pineda S, Sigdel TK, Liberto JM, Vincenti F, Sirota M, Sarwal MM. Characterizing pre-transplant and post-transplant kidney rejection risk by B cell immune repertoire sequencing. Nat Commun 2019; 10:1906. [PMID: 31015506 PMCID: PMC6479061 DOI: 10.1038/s41467-019-09930-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 04/02/2019] [Indexed: 01/25/2023] Open
Abstract
Studying immune repertoire in the context of organ transplant provides important information on how adaptive immunity may contribute and modulate graft rejection. Here we characterize the peripheral blood immune repertoire of individuals before and after kidney transplant using B cell receptor sequencing in a longitudinal clinical study. Individuals who develop rejection after transplantation have a more diverse immune repertoire before transplant, suggesting a predisposition for post-transplant rejection risk. Additionally, over 2 years of follow-up, patients who develop rejection demonstrate a specific set of expanded clones that persist after the rejection. While there is an overall reduction of peripheral B cell diversity, likely due to increased general immunosuppression exposure in this cohort, the detection of specific IGHV gene usage across all rejecting patients supports that a common pool of immunogenic antigens may drive post-transplant rejection. Our findings may have clinical implications for the prediction and clinical management of kidney transplant rejection.
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MESH Headings
- Adolescent
- Adult
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Child
- Child, Preschool
- Clone Cells
- Female
- Gene Expression
- Graft Rejection/genetics
- Graft Rejection/immunology
- Graft Rejection/pathology
- Graft Survival/genetics
- Humans
- Immunocompromised Host
- Infant
- Kidney/immunology
- Kidney/pathology
- Kidney/surgery
- Kidney Transplantation
- Longitudinal Studies
- Male
- Middle Aged
- Polymorphism, Genetic/immunology
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Renal Insufficiency, Chronic/genetics
- Renal Insufficiency, Chronic/immunology
- Renal Insufficiency, Chronic/pathology
- Renal Insufficiency, Chronic/surgery
- Sequence Analysis, DNA
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Affiliation(s)
- Silvia Pineda
- Bakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), 550 16th Street, San Francisco, CA, 94158, USA.
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA.
| | - Tara K Sigdel
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Juliane M Liberto
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Flavio Vincenti
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), 550 16th Street, San Francisco, CA, 94158, USA.
- Department of Pediatrics, University of California, San Francisco (UCSF), 550 16th Street, San Francisco, CA, 94158, USA.
| | - Minnie M Sarwal
- Division of Transplant Surgery, Department of Surgery, University of California, San Francisco (UCSF), 505 Parnassus Ave, San Francisco, CA, 94143, USA.
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3
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Huang CW, Lin YT, Ding ST, Lo LL, Wang PH, Lin EC, Liu FW, Lu YW. Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection. ACTA ACUST UNITED AC 2015; 4:570-95. [PMID: 27600241 PMCID: PMC4996412 DOI: 10.3390/microarrays4040570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/16/2015] [Accepted: 10/28/2015] [Indexed: 11/16/2022]
Abstract
The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on the genetic sequences of interest, it thereby reduces the evaluation time and cost. Compared to traditional approaches, SNP genotyping techniques incorporate informative genetic background, improve the breeding prediction accuracy and acquiesce breeding quality on the farm. This article therefore reviews the typical procedures of animal breeding using SNPs and the current status of related techniques. The associated SNP information and genotyping techniques, including microarray and Lab-on-a-Chip based platforms, along with their potential are highlighted. Examples in pig and poultry with different SNP loci linked to high economic trait values are given. The recommendations for utilizing SNP genotyping in nimal breeding are summarized.
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Affiliation(s)
- Chao-Wei Huang
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Yu-Tsung Lin
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Shih-Torng Ding
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Ling-Ling Lo
- Department of Animal Science, Chinese Culture University, Taipei 11114, Taiwan.
| | - Pei-Hwa Wang
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - En-Chung Lin
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Fang-Wei Liu
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Yen-Wen Lu
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
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Feuillie C, Merheb MM, Gillet B, Montagnac G, Daniel I, Hänni C. Detection of DNA sequences refractory to PCR amplification using a biophysical SERRS assay (Surface Enhanced Resonant Raman Spectroscopy). PLoS One 2014; 9:e114148. [PMID: 25502338 PMCID: PMC4264738 DOI: 10.1371/journal.pone.0114148] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 11/04/2014] [Indexed: 11/18/2022] Open
Abstract
The analysis of ancient or processed DNA samples is often a great challenge, because traditional Polymerase Chain Reaction – based amplification is impeded by DNA damage. Blocking lesions such as abasic sites are known to block the bypass of DNA polymerases, thus stopping primer elongation. In the present work, we applied the SERRS-hybridization assay, a fully non-enzymatic method, to the detection of DNA refractory to PCR amplification. This method combines specific hybridization with detection by Surface Enhanced Resonant Raman Scattering (SERRS). It allows the detection of a series of double-stranded DNA molecules containing a varying number of abasic sites on both strands, when PCR failed to detect the most degraded sequences. Our SERRS approach can quickly detect DNA molecules without any need for DNA repair. This assay could be applied as a pre-requisite analysis prior to enzymatic reparation or amplification. A whole new set of samples, both forensic and archaeological, could then deliver information that was not yet available due to a high degree of DNA damage.
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Affiliation(s)
- Cécile Feuillie
- Laboratoire de Géologie de Lyon – Terre, Planètes, Environnement, UMR 5276, ENS de Lyon, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d′Italie, 69364 Lyon Cedex 07, France
- * E-mail:
| | - Maxime M. Merheb
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d′Italie, 69364 Lyon Cedex 07, France
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d′Italie, 69364 Lyon Cedex 07, France
- Plateforme nationale de Paléogénétique PALGENE, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d′Italie, 69364 Lyon Cedex 07, France
| | - Gilles Montagnac
- Laboratoire de Géologie de Lyon – Terre, Planètes, Environnement, UMR 5276, ENS de Lyon, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d′Italie, 69364 Lyon Cedex 07, France
| | - Isabelle Daniel
- Laboratoire de Géologie de Lyon – Terre, Planètes, Environnement, UMR 5276, ENS de Lyon, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d′Italie, 69364 Lyon Cedex 07, France
| | - Catherine Hänni
- Institut de Génomique Fonctionnelle de Lyon, UMR 5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d′Italie, 69364 Lyon Cedex 07, France
- Plateforme nationale de Paléogénétique PALGENE, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d′Italie, 69364 Lyon Cedex 07, France
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Affiliation(s)
- Yuji Wakimoto
- Department of Genetics, Harvard Medical School Boston Massachusetts
| | - Jianming Jiang
- Department of Genetics, Harvard Medical School Boston Massachusetts
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School Boston Massachusetts
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Leiske DL, Chow A, Dettloff R, Farinas J. Single-molecule enzymology based on the principle of the Millikan oil drop experiment. Anal Biochem 2013; 448:30-7. [PMID: 24291542 DOI: 10.1016/j.ab.2013.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/09/2013] [Accepted: 11/15/2013] [Indexed: 10/26/2022]
Abstract
The ability to monitor the progress of single-molecule enzyme reactions is often limited by the need to use fluorogenic substrates. A method based on the principle of the Millikan oil drop experiment was developed to monitor the change in charge of substrates bound to a nanoparticle and offers a means of detecting single-enzyme reactions without fluorescence detection. As a proof of principle of the ability to monitor reactions that result in a change in substrate charge, polymerization on a single DNA template was detected. A custom oligonucleotide was synthesized that allowed for the attachment of single DNA templates to gold nanoparticles with a single polymer tether. The nanoparticles were then tethered to the surface of a microfluidic channel where the positions of the nanoparticles, subjected to an oscillating electric field, were monitored using dark field microscopy. With short averaging times, the signal-to-noise level was low enough to discriminate changes in charge of less than 1.2%. Polymerization of a long DNA template demonstrated the ability to use the system to monitor single-molecule enzymatic activity. Finally, nanoparticle surfaces were modified with thiolated moieties to reduce and/or shield the number of unproductive charges and allow for improved sensitivity.
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Affiliation(s)
| | - Andrea Chow
- Promega BioSystems, Sunnyvale, CA 94085, USA
| | - Roger Dettloff
- Caerus Molecular Diagnostics, Mountain View, CA 94043, USA
| | - Javier Farinas
- Caerus Molecular Diagnostics, Mountain View, CA 94043, USA.
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7
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Svobodová M, Pinto A, Nadal P, O' Sullivan CK. Comparison of different methods for generation of single-stranded DNA for SELEX processes. Anal Bioanal Chem 2012; 404:835-42. [PMID: 22733247 DOI: 10.1007/s00216-012-6183-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 06/04/2012] [Indexed: 12/24/2022]
Abstract
Single-stranded DNA (ssDNA) generation is a crucial step in several molecular biology applications, such as sequencing or DNA chip and microarray technology. Molecules of ssDNA also play a key role in the selection of ssDNA aptamers through Systematic Evolution of Ligands by EXponential enrichment (SELEX). With particular interest for this application, herein we present a comparative study of the most used methods for generation of ssDNA used in SELEX, such as asymmetric PCR, enzyme digestion and magnetic separation with streptavidin beads. In addition, we evaluate a new technique that combines asymmetric PCR and enzyme digestion with the aim to achieve the maximum efficiency in ssDNA generation. The methods studied were compared in terms of quality of ssDNA using electrophoretic analysis and generated ssDNA yields were quantitatively measured using an Enzyme-Linked OligoNucleotide Assay (ELONA).
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Affiliation(s)
- M Svobodová
- Nanobiotechnology and Bioanalysis group, Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain
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8
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Daguer JP, Ciobanu M, Alvarez S, Barluenga S, Winssinger N. DNA-templated combinatorial assembly of small molecule fragments amenable to selection/amplification cycles. Chem Sci 2011. [DOI: 10.1039/c0sc00574f] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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9
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dcDegenerate oligonucleotide primed-PCR for multilocus, genome-wide analysis from limited quantities of DNA. ACTA ACUST UNITED AC 2009; 18:165-75. [PMID: 19704262 DOI: 10.1097/pdm.0b013e31818d34d1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This study modified the degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR)-based whole genome amplification method for improvement of downstream genome-wide analysis of low copy number DNA samples (<or= 0.100 ng). Experiments involved altering the degeneracy of the DOP primer, nonspecific cycle number, and adding proofreading polymerases. Increasing the degeneracy of the primer and the number of cycles that use a low annealing temperature should improve the nonspecific amplification of the DOP-PCR reaction. The addition of proofreading enzymes should allow for longer amplification products, increasing the genome coverage of the reaction. Low-input DNA quantities were examined for the primer and the cycle number studies using standard DOP-PCR parameters. The optimized DOP-PCR technique was then implemented for the polymerase study. All DOP-PCR products were amplified by using a multiplex microsatellite amplification kit to evaluate products from multiple chromosomes, followed by separation and detection by capillary electrophoresis. The 10 N primer, 12 nonspecific cycles, and the addition of the DeepVent proofreading enzyme all significantly increased the number of short tandem repeat alleles successfully amplified. All modifications also lowered the rate of allele drop-in, or sporadic additional allele occurrence, when compared with DOP-PCR results published earlier. Further, an average of > 0.50 intralocus heterozygote peak ratios were observed for most DNA input quantities examined. These results show that modifications of the traditional DOP-PCR reaction (dcDOP-PCR) to include the use of a more degenerate primer (10 N), 12 nonspecific cycles, and a proofreading enzyme allows for a more complete, balanced chromosome amplification from limited and/or compromised clinical and biological samples.
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Joseph N, Duppatla V, Rao DN. Prokaryotic DNA Mismatch Repair. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2006; 81:1-49. [PMID: 16891168 DOI: 10.1016/s0079-6603(06)81001-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nimesh Joseph
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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11
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Buhariwalla HK, B J, Eshwar K, Crouch JH. Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus. BMC PLANT BIOLOGY 2005; 5:16. [PMID: 16107212 PMCID: PMC1215491 DOI: 10.1186/1471-2229-5-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Accepted: 08/17/2005] [Indexed: 05/04/2023]
Abstract
BACKGROUND Chickpea is a major crop in many drier regions of the world where it is an important protein-rich food and an increasingly valuable traded commodity. The wild annual Cicer species are known to possess unique sources of resistance to pests and diseases, and tolerance to environmental stresses. However, there has been limited utilization of these wild species by chickpea breeding programs due to interspecific crossing barriers and deleterious linkage drag. Molecular genetic diversity analysis may help predict which accessions are most likely to produce fertile progeny when crossed with chickpea cultivars. While, trait-markers may provide an effective tool for breaking linkage drag. Although SSR markers are the assay of choice for marker-assisted selection of specific traits in conventional breeding populations, they may not provide reliable estimates of interspecific diversity, and may lose selective power in backcross programs based on interspecific introgressions. Thus, we have pursued the development of gene-based markers to resolve these problems and to provide candidate gene markers for QTL mapping of important agronomic traits. RESULTS An EST library was constructed after subtractive suppressive hybridization (SSH) of root tissue from two very closely related chickpea genotypes (Cicer arietinum). A total of 106 EST-based markers were designed from 477 sequences with functional annotations and these were tested on C. arietinum. Forty-four EST markers were polymorphic when screened across nine Cicer species (including the cultigen). Parsimony and PCoA analysis of the resultant EST-marker dataset indicated that most accessions cluster in accordance with the previously defined classification of primary (C. arietinum, C. echinospermum and C. reticulatum), secondary (C. pinnatifidum, C. bijugum and C. judaicum), and tertiary (C. yamashitae, C. chrossanicum and C. cuneatum) gene-pools. A large proportion of EST alleles (45%) were only present in one or two of the accessions tested whilst the others were represented in up to twelve of the accessions tested. CONCLUSION Gene-based markers have proven to be effective tools for diversity analysis in Cicer and EST diversity analysis may be useful in identifying promising candidates for interspecific hybridization programs. The EST markers generated in this study have detected high levels of polymorphism amongst both common and rare alleles. This suggests that they would be useful for allele-mining of germplasm collections for identification of candidate accessions in the search for new sources of resistance to pests / diseases, and tolerance to abiotic stresses.
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Affiliation(s)
- Hutokshi K Buhariwalla
- c/o JH. Crouch, Centro International de Mejoramiento de Maiz Y trigo (CIMMYT), Apdo. postal 6-641, 06600 Mexico, D.F., Mexico
| | - Jayashree B
- International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502 324, India
| | - K Eshwar
- International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Andhra Pradesh 502 324, India
| | - Jonathan H Crouch
- Centro International de Mejoramiento de Maiz Y trigo (CIMMYT), Apdo. postal 6-641, 06600 Mexico, D.F., Mexico
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Bi LJ, Zhou YF, Zhang XE, Deng JY, Wen JK, Zhang ZP. Construction and characterization of different MutS fusion proteins as recognition elements of DNA chip for detection of DNA mutations. Biosens Bioelectron 2005; 21:135-44. [PMID: 15967361 DOI: 10.1016/j.bios.2004.08.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 08/17/2004] [Accepted: 08/20/2004] [Indexed: 11/18/2022]
Abstract
Three MutS fusion systems were designed as the mutation recognition and signal elements of DNA chips for detection of DNA mutations. The expression vectors containing the encoding sequences of three recombinant proteins, Trx-His6-GFP-(Ser-Gly)6-MutS (THGLM), Trx-His6-(Ser-Gly)6-Strep tagII-(Ser-Gly)6-MutS (THLSLM) and Trx-His6-(Ser-Gly)6-MutS (THLM), were constructed by gene slicing in vitro. THGLM, THLSLM and THLM were then expressed in Escherichia coli AD494(DE3), respectively. SDS-PAGE analysis revealed that each of the expected proteins was approximately 30% of the total bacterial proteins. The recombinant proteins were purified to the purity over 90% by immobilized metal (Co2+) chelation affinity chromatography. Bioactivity assay indicated that three fusion proteins retained the mismatch-binding activity and the functions of other fusion partners. DNA chips arrayed both mismatched and unpaired DNA oligonucleotides as well as rpoB gene from Mycobacterium tuberculosis were prepared. THGLM, THLSLM and THLM that was labeled with Fluorolinktrade mark Cy3 reactive dye, were then used as both mutation recognition and labeling elements of DNA chips. The resulting DNA chips were used to detect the mismatched and unpaired mutations in the synthesized oligonucleotides and single base mutation in rpoB gene of M. tuberculosis that is resistant to rifamycin.
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Affiliation(s)
- Li-Jun Bi
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, People's Republic of China
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13
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Baum L, Ng A, Leung WK. Developing the use of mismatch binding proteins for discovering rare somatic mutations. Mol Cell Probes 2005; 19:163-8. [PMID: 15797815 DOI: 10.1016/j.mcp.2004.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2004] [Revised: 10/21/2004] [Accepted: 11/10/2004] [Indexed: 11/17/2022]
Abstract
A method for detecting rare, unknown, somatic mutations could allow presymptomatic cancer screening from human fluids. Immobilized mismatch binding protein can bind DNA heteroduplexes while allowing homoduplexes to be washed away, thus enriching for rare mutations. We examined the potential use, for mutation enrichment, of a fusion protein of maltose binding protein and the mismatch binding protein TaqMutS (MBP-MutS). Unlabeled and fluorescent-labeled oligonucleotides, either perfectly complementary or with single nucleotide mismatches or deletions, were combined to form homo- or heteroduplexes that were then mixed at low ratios of hetero- to homoduplexes and enriched for heteroduplexes. Enrichment was observed using a capillary DNA sequencer. A single base deletion oligonucleotide was enriched by a factor of 29, and a mismatch oligonucleotide was enriched by a factor of 2. N-1 oligonucleotide synthesis fragments were enriched more than were mismatches, suggesting that these deletion fragments may compete for MutS and impede enrichment of mismatches. Purification of oligonucleotides by high pressure liquid chromatography or polyacrylamide gel electrophoresis failed to remove n-1 fragments, thus overcoming this obstacle to enrichment of mismatch mutations may require alternative strategies, such as developing new purification methods or avoiding the use of synthetic oligonucleotides before enrichment.
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Affiliation(s)
- Larry Baum
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Shatin, Hong Kong, China.
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14
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Pincas H, Pingle MR, Huang J, Lao K, Paty PB, Friedman AM, Barany F. High sensitivity EndoV mutation scanning through real-time ligase proofreading. Nucleic Acids Res 2004; 32:e148. [PMID: 15514109 PMCID: PMC528826 DOI: 10.1093/nar/gnh150] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The ability to associate mutations in cancer genes with the disease and its subtypes is critical for understanding oncogenesis and identifying biomarkers for clinical diagnosis. A two-step mutation scanning method that sequentially used endonuclease V (EndoV) to nick at mismatches and DNA ligase to reseal incorrectly or nonspecifically nicked sites was previously developed in our laboratory. Herein we report an optimized single-step assay that enables ligase to proofread EndoV cleavage in real-time under a compromise between buffer conditions. Real-time proofreading results in a dramatic reduction of background cleavage. A universal PCR strategy that employs both unlabeled gene-specific primers and labeled universal primers, allows for multiplexed gene amplification and precludes amplification of primer dimers. Internally labeled PCR primers eliminate EndoV cleavage at the 5' terminus, enabling high-throughput capillary electrophoresis readout. Furthermore, signal intensity is increased and artifacts are reduced by generating heteroduplexes containing only one of the two possible mismatches (e.g. either A/C or G/T). The single-step assay improves sensitivity to 1:50 and 1:100 (mutant:wild type) for unknown mutations in the p53 and K-ras genes, respectively, opening prospects as an early detection tool.
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Affiliation(s)
- Hanna Pincas
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
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