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Franci J, Lam KW, Chuah TS, Cha TS. Genetic diversity and in silico evidence of target-site mutation in the EPSPS gene in endowing glyphosate resistance in Eleusine indica (L.) from Malaysia. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 165:104556. [PMID: 32359543 DOI: 10.1016/j.pestbp.2020.104556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 06/11/2023]
Abstract
Glyphosate-resistant populations of Eleusine indica are widespread in several states of Malaysia. A whole-plant bioassay confirmed that eight out of the 17 populations tested were resistant to glyphosate at double the recommended rate of 2.44 kg ha-1. Screening with allele-specific PCR (AS-PCR) revealed that resistant plants contained an EPSPS gene with either the homozygous S/S-106 or the heterozygous P/S-106 alleles. All susceptible plants contained only the homozygous P/P-106 allele. In addition, DNA sequences of the full-length EPSPS gene from one susceptible (SB) and four resistant (R2, R6, R8 and R11) populations revealed an amino acid substitution of T102I in all the resistant plants, while another substitution of P381L was only found in resistant populations R6 and R11. The significance of the P381L mutation was examined by Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) and residue interaction network (RIN) analyses, which suggests the P381L mutation may contribute to resistance. Mutations at 102 and 106 occur widely in the EPSPS gene of glyphosate-resistant E. indica populations from Malaysia with the TIPS mutation. In addition, the P381L mutation could also contribute to resistance.
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Affiliation(s)
- Julop Franci
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
| | - Kok Wai Lam
- Drugs and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300 Kuala Lumpur, Malaysia.
| | - Tse Seng Chuah
- Faculty of Plantation and Agotechnology, Universiti Teknologi Mara, 02600 Arau, Perlis, Malaysia.
| | - Thye San Cha
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia.
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Abrosimova LA, Migur AY, Kubareva EA, Zatsepin TS, Gavshina AV, Yunusova AK, Perevyazova TA, Pingoud A, Oretskaya TS. A study on endonuclease BspD6I and its stimulus-responsive switching by modified oligonucleotides. PLoS One 2018; 13:e0207302. [PMID: 30475809 PMCID: PMC6261011 DOI: 10.1371/journal.pone.0207302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/28/2018] [Indexed: 11/18/2022] Open
Abstract
Nicking endonucleases (NEases) selectively cleave single DNA strands in double-stranded DNAs at a specific site. They are widely used in bioanalytical applications and in genome editing; however, the peculiarities of DNA-protein interactions for most of them are still poorly studied. Previously, it has been shown that the large subunit of heterodimeric restriction endonuclease BspD6I (Nt.BstD6I) acts as a NEase. Here we present a study of interaction of restriction endonuclease BspD6I with modified DNA containing single non-nucleotide insertion with an azobenzene moiety in the enzyme cleavage sites or in positions of sugar-phosphate backbone nearby. According to these data, we designed a number of effective stimulus-responsive oligonucleotide inhibitors bearing azobenzene or triethylene glycol residues. These modified oligonucleotides modulated the functional activity of Nt.BspD6I after cooling or heating. We were able to block the cleavage of T7 phage DNA by this enzyme in the presence of such inhibitors at 20-25°C, whereas the Nt.BspD6I ability to hydrolyze DNA was completely restored after heating to 45°C. The observed effects can serve as a basis for the development of a platform for regulation of NEase activity in vitro or in vivo by external signals.
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Affiliation(s)
- Liudmila A. Abrosimova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Anzhela Yu. Migur
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Elena A. Kubareva
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Timofei S. Zatsepin
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, Russia
| | - Aleksandra V. Gavshina
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alfiya K. Yunusova
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Tatiana A. Perevyazova
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig University, Giessen, Germany
| | - Tatiana S. Oretskaya
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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Arterial Calcification Due to Deficiency of CD73 (ACDC) As One of Rheumatic Diseases Associated With Periarticular Calcification. J Clin Rheumatol 2016; 21:216-20. [PMID: 26010187 DOI: 10.1097/rhu.0000000000000245] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In 2011, St Hilaire et al (N Engl J Med. 2011;364:432-442) identified mutations in the ecto-5'-nucleotidase (NT5E) gene, which encodes CD73, in members of 3 families with symptomatic arterial and joint calcifications. The deficiency of CD73 involves the extracellular adenosine metabolism that influences inorganic pyrophosphate and phosphate metabolism and leads to tissue calcification. Herein, we report an additional case with arterial calcification due to deficiency of CD73. Genetic analyses revealed that the patient was a compound heterozygote of mutations in the NT5E gene. The present case had intermittent monoarthritis of the finger joints and early-onset osteoarthritis in the hands. Occlusion of calcified peripheral arteries is the most important outcome of the disease. However, the rheumatic manifestations may be important clues to the diagnosis. Rheumatologists should recognize deficiency of CD73 as a rheumatic disease.
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Erythrocyte selenium concentration predicts intensive care unit and hospital mortality in patients with septic shock: a prospective observational study. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2014; 18:R92. [PMID: 24887198 PMCID: PMC4057214 DOI: 10.1186/cc13860] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 04/25/2014] [Indexed: 12/22/2022]
Abstract
Introduction Selenoenzymes can modulate the extent of oxidative stress, which is recognized as a key feature of septic shock. The pathophysiologic role of erythrocyte selenium concentration in patients with septic shock remains unknown. Therefore, the objective of this study was to evaluate the association of erythrocyte selenium concentration with glutathione peroxidase (GPx1) activity, GPx1 polymorphisms and with ICU and hospital mortality in septic shock patients. Methods This prospective study included all patients older than 18 years with septic shock on admission or during their ICU stay, admitted to one of the three ICUs of our institution, from January to August 2012. At the time of the patients’ enrollment, demographic information was recorded. Blood samples were taken within the first 72 hours of the patients’ admission or within 72 hours of the septic shock diagnosis for determination of selenium status, protein carbonyl concentration, GPx1 activity and GPx1 Pro198Leu polymorphism (rs 1050450) genotyping. Results A total of 110 consecutive patients were evaluated. The mean age was 57.6 ± 15.9 years, 63.6% were male. Regarding selenium status, only erythrocyte selenium concentration was lower in patients who died in the ICU. The frequencies for GPx1 Pro198Leu polymorphism were 55%, 38% and 7% for Pro/Pro, Pro/Leu and Leu/Leu, respectively. In the logistic regression models, erythrocyte selenium concentration was associated with ICU and hospital mortality in patients with septic shock even after adjustment for protein carbonyl concentration and acute physiology and chronic health evaluation II score (APACHE II) or sequential organ failure assessment (SOFA). Conclusions Erythrocyte selenium concentration was a predictor of ICU and hospital mortality in patients with septic shock. However, this effect was not due to GPx1 activity or Pro198Leu polymorphism.
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Cha TS, Najihah MG, Sahid IB, Chuah TS. Molecular basis for resistance to ACCase-inhibiting fluazifop in Eleusine indica from Malaysia. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2014; 111:7-13. [PMID: 24861927 DOI: 10.1016/j.pestbp.2014.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/24/2014] [Accepted: 04/24/2014] [Indexed: 06/03/2023]
Abstract
Eleusine indica (goosegrass) populations resistant to fluazifop, an acetyl-CoA carboxylase (ACCase: EC6.4.1.2)-inhibiting herbicide, were found in several states in Malaysia. Dose-response assay indicated a resistance factor of 87.5, 62.5 and 150 for biotypes P2, P3 and P4, respectively. DNA sequencing and allele-specific PCR revealed that both biotypes P2 and P3 exhibit a single non-synonymous point mutation from TGG to TGC that leads to a well known Trp-2027-Cys mutation. Interestingly, the highly resistant biotype, P4, did not contain any of the known mutation except the newly discovered target point Asn-2097-Asp, which resulted from a nucleotide change in the codon AAT to GAT. ACCase gene expression was found differentially regulated in the susceptible biotype (P1) and highly resistant biotype P4 from 24 to 72h after treatment (HAT) when being treated with the recommended field rate (198gha(-1)) of fluazifop. However, the small and erratic differences of ACCase gene expression between biotype P1 and P4 does not support the 150-fold resistance in biotype P4. Therefore, the involvement of the target point Asn-2097-Asp and other non-target-site-based resistance mechanisms in the biotype P4 could not be ruled out.
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Affiliation(s)
- Thye San Cha
- School of Fundamental Science, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia; Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia.
| | - Mohamed Ghazani Najihah
- School of Fundamental Science, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
| | - Ismail Bin Sahid
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Tse Seng Chuah
- School of Food Science and Technology, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia.
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Birdsell DN, Pearson T, Price EP, Hornstra HM, Nera RD, Stone N, Gruendike J, Kaufman EL, Pettus AH, Hurbon AN, Buchhagen JL, Harms NJ, Chanturia G, Gyuranecz M, Wagner DM, Keim PS. Melt analysis of mismatch amplification mutation assays (Melt-MAMA): a functional study of a cost-effective SNP genotyping assay in bacterial models. PLoS One 2012; 7:e32866. [PMID: 22438886 PMCID: PMC3306377 DOI: 10.1371/journal.pone.0032866] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 02/01/2012] [Indexed: 11/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are abundant in genomes of all species and biologically informative markers extensively used across broad scientific disciplines. Newly identified SNP markers are publicly available at an ever-increasing rate due to advancements in sequencing technologies. Efficient, cost-effective SNP genotyping methods to screen sample populations are in great demand in well-equipped laboratories, but also in developing world situations. Dual Probe TaqMan assays are robust but can be cost-prohibitive and require specialized equipment. The Mismatch Amplification Mutation Assay, coupled with melt analysis (Melt-MAMA), is flexible, efficient and cost-effective. However, Melt-MAMA traditionally suffers from high rates of assay design failures and knowledge gaps on assay robustness and sensitivity. In this study, we identified strategies that improved the success of Melt-MAMA. We examined the performance of 185 Melt-MAMAs across eight different pathogens using various optimization parameters. We evaluated the effects of genome size and %GC content on assay development. When used collectively, specific strategies markedly improved the rate of successful assays at the first design attempt from ∼50% to ∼80%. We observed that Melt-MAMA accurately genotypes across a broad DNA range (∼100 ng to ∼0.1 pg). Genomic size and %GC content influence the rate of successful assay design in an independent manner. Finally, we demonstrated the versatility of these assays by the creation of a duplex Melt-MAMA real-time PCR (two SNPs) and conversion to a size-based genotyping system, which uses agarose gel electrophoresis. Melt-MAMA is comparable to Dual Probe TaqMan assays in terms of design success rate and accuracy. Although sensitivity is less robust than Dual Probe TaqMan assays, Melt-MAMA is superior in terms of cost-effectiveness, speed of development and versatility. We detail the parameters most important for the successful application of Melt-MAMA, which should prove useful to the wider scientific community.
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Affiliation(s)
- Dawn N. Birdsell
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Talima Pearson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erin P. Price
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heidie M. Hornstra
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Roxanne D. Nera
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nathan Stone
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey Gruendike
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Emily L. Kaufman
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Amanda H. Pettus
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Audriana N. Hurbon
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jordan L. Buchhagen
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - N. Jane Harms
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Gvantsa Chanturia
- National Center for Disease Control and Public Health and Ilia State University, Tbilisi, Georgia, United States of America
| | - Miklos Gyuranecz
- Veterinary Medical Research Institute, Hungarian Academy of Sciences, Budapest, Hungary
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul S. Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * E-mail:
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Guga P, Koziołkiewicz M. Phosphorothioate nucleotides and oligonucleotides - recent progress in synthesis and application. Chem Biodivers 2012; 8:1642-81. [PMID: 21922655 DOI: 10.1002/cbdv.201100130] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, PL-90-363 Łódź.
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Cominetti C, de Bortoli MC, Purgatto E, Ong TP, Moreno FS, Garrido AB, Cozzolino SMF. Associations between glutathione peroxidase-1 Pro198Leu polymorphism, selenium status, and DNA damage levels in obese women after consumption of Brazil nuts. Nutrition 2011; 27:891-6. [DOI: 10.1016/j.nut.2010.09.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 07/27/2010] [Accepted: 09/18/2010] [Indexed: 10/18/2022]
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D'Agata R, Corradini R, Grasso G, Marchelli R, Spoto G. Ultrasensitive detection of DNA by PNA and nanoparticle-enhanced surface plasmon resonance imaging. Chembiochem 2009; 9:2067-70. [PMID: 18680134 DOI: 10.1002/cbic.200800310] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Roberta D'Agata
- Dipartimento di Scienze Chimiche, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
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Design of allele-specific primers and detection of the human ABO genotyping to avoid the pseudopositive problem. Electrophoresis 2009; 29:4130-40. [PMID: 18991264 DOI: 10.1002/elps.200800097] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PCR experiments using DNA primers forming mismatch pairing with template lambda DNA at the 3' end were carried out in order to develop allele-specific primers capable of detecting SNP in genomes without generating pseudopositive amplification products, and thus avoiding the so-called pseudopositive problem. Detectable amounts of PCR products were obtained when primers forming a single or two mismatch pairings at the 3' end were used. In particular, 3' terminal A/C or T/C (primer/template) mismatches tended to allow PCR amplification to proceed, resulting in pseudopositive results in many cases. While less PCR product was observed for primers forming three terminal mismatch pairings, target DNA sequences were efficiently amplified by primers forming two mismatch pairings next to the terminal G/C base pairing. These results indicate that selecting a primer having a 3' terminal nucleotide that recognizes the SNP nucleotide and the next two nucleotides that form mismatch pairings with the template sequence can be used as an allele-specific primer that eliminates the pseudopositive problem. Trials with the human ABO genes demonstrated that this primer design is also useful for detecting a single base pair difference in gene sequences with a signal-to-noise ratio of at least 45.
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Cheng Y, Li Z, Zhang X, Du B, Fan Y. Homogeneous and label-free fluorescence detection of single-nucleotide polymorphism using target-primed branched rolling circle amplification. Anal Biochem 2008; 378:123-6. [PMID: 18420020 DOI: 10.1016/j.ab.2008.03.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Revised: 03/19/2008] [Accepted: 03/24/2008] [Indexed: 10/22/2022]
Abstract
We present a simple, sensitive, and cost-effective fluorescent assay of single-nucleotide polymorphism (SNP) with target-primed branched rolling circle amplification (TPBRCA). Designed padlock probe is circularized after perfect hybridization to mutant DNA. Then rolling circle amplification (RCA) reaction can be initiated from the mutant DNA that acts as primer and generates a long tandem single-stranded DNA (ssDNA) product. At the same time, the introduction of a reverse primer complementary to the target-primed RCA products leads to the branched RCA and eventually generates the various lengths of ssDNA and double-stranded DNA products, which are sensitively detected using SYBR Green I (SG) fluorescence dye. In contrast, the wild DNA contains a single mismatched base with the padlock probe and primes only a limited extension with the unligated padlock probe, generating weak background fluorescence with the addition of SG. Due to the excellent specificity and powerful amplification of TPBRCA reaction, the mutant DNA was distinctively differentiated from the wild DNA in a homogeneous and label-free manner. The assay is sensitive and specific enough to detect 5-amol (8.6-fM) mutant DNA strands. It was possible to accurately determine the mutant allele frequency as low as 1.0%.
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Affiliation(s)
- Yongqiang Cheng
- College of Chemistry and Environment Science, Hebei University, Baoding, Hebei Province 071002, People's Republic of China
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