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Zeng R, Du Z, Ma H, Meng X, Li E, Li J. The 60 nm gold nanoparticles improve qPCR amplification efficiency through specific palindromic sequences (GGATCC or ACCGGT) in primers. Biochim Biophys Acta Gen Subj 2024; 1868:130560. [PMID: 38211821 DOI: 10.1016/j.bbagen.2024.130560] [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: 09/18/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND Polymerase chain reaction (PCR) technology and quantitative real-time PCR (qPCR) technology are widely used in clinical diagnosis and research, but amplification efficiency and sensitivity are still key problems for researchers. An increasing number of reports show that gold nanoparticles (AuNPs) can be used to improve the sensitivity and amplification efficiency of PCR. Here, we found that 60 nm gold nanoparticles with a positive charge (60 nm- Au+) can enhance the amplification efficiency of qPCR. METHODS Mouse DNA was extracted by the alkaline lysis method. Primer 5.0 software was used to design primers and mutation primers, and the DNA fragments were obtained by the method of synthesizing plasmids. The qPCR was applied to amplify target gene fragments. RESULTS The amplification efficiency of qPCR was improved by about 1.828 times in the experimental group with 60 nm- Au+ compared with the control group without 60 nm- Au+. The primer pair contains a specific palindromic sequence (GGATCC or ACCGGT). And 60 nm Au+ did not enhance the amplification efficiency of qPCR when the above primer was mutated. CONCLUSIONS The primers contain special palindrome sequences (GGATCC or ACCGGT) with 60 nm- Au+ can enhance the amplification efficiency of qPCR. Therefore, it suggests a more in-depth understanding of the mechanism and function of gold nanoparticles and primer sequences. This study has presented some implications for gold nanoparticles application in the development of qPCR technology.
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Affiliation(s)
- Ruyu Zeng
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Zhiqun Du
- The Department of Pathology, Dongyang People's Hospital, Zhejiang, China
| | - Hongliang Ma
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiuqiong Meng
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Erhua Li
- Guangzhou BDS Biological Technology Co., Ltd. Guangzhou, China
| | - Jiangchao Li
- The Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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McKean EL, Grill E, Choi YJ, Mitreva M, O'Halloran DM, Hawdon JM. Altered larval activation response associated with multidrug resistance in the canine hookworm Ancylostoma caninum. Parasitology 2024; 151:271-281. [PMID: 38163962 PMCID: PMC11007283 DOI: 10.1017/s0031182023001385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/03/2024]
Abstract
Parasitic gastrointestinal nematodes pose significant health risks to humans, livestock, and companion animals, and their control relies heavily on the use of anthelmintic drugs. Overuse of these drugs has led to the emergence of resistant nematode populations. Herein, a naturally occurring isolate (referred to as BCR) of the dog hookworm, Ancylostoma caninum, that is resistant to 3 major classes of anthelmintics is characterized. Various drug assays were used to determine the resistance of BCR to thiabendazole, ivermectin, moxidectin and pyrantel pamoate. When compared to a drug-susceptible isolate of A. caninum, BCR was shown to be significantly resistant to all 4 of the drugs tested. Multiple single nucleotide polymorphisms have been shown to impart benzimidazole resistance, including the F167Y mutation in the β-tubulin isotype 1 gene, which was confirmed to be present in BCR through molecular analysis. The frequency of the resistant allele in BCR was 76.3% following its first passage in the lab, which represented an increase from approximately 50% in the founding hookworm population. A second, recently described mutation in codon 134 (Q134H) was also detected at lower frequency in the BCR population. Additionally, BCR exhibits an altered larval activation phenotype compared to the susceptible isolate, suggesting differences in the signalling pathways involved in the activation process which may be associated with resistance. Further characterization of this isolate will provide insights into the mechanisms of resistance to macrocyclic lactones and tetrahydropyrimidine anthelmintics.
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Affiliation(s)
- Elise L. McKean
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC, USA
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Emilia Grill
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Young-Jun Choi
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Makedonka Mitreva
- Infectious Diseases Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Damien M. O'Halloran
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - John M. Hawdon
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC, USA
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3
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Cosseboom SD, Agarwal C, Hu M. CRISPR-enabled investigation of fitness costs associated with the E198A mutation in β-tubulin of Colletotrichum siamense. FRONTIERS IN PLANT SCIENCE 2023; 14:1278133. [PMID: 38023927 PMCID: PMC10654983 DOI: 10.3389/fpls.2023.1278133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
Introduction Understanding fitness costs associated with fungicide resistance is critical to improve resistance management strategies. E198A in b-tubulin confers resistance to the fungicide thiophanate-methyl and has been widely reported in several plant pathogens including Colletotrichum siamense. Method To better understand potential fitness costs associated with the resistance, a ribonucleoprotein (RNP) complex mediated CRISPR/Cas9 system was used to create a point mutation (E198A) through homology directed repair (HDR) in each of the sensitive (E198) C. siamense isolates collected from strawberries, raspberries, and peaches. The RNP complex was delivered into fungal protoplasts using polyethylene glycol-mediated (PEG) transfection. Results The transformation efficiency, the proportion of transformants of sensitive parental isolates containing the E198A mutation, averaged 72%. No off-target mutations were observed when sequences similar to the b-tubulin target region with a maximum of four mismatch sites were analyzed, suggesting that the CRISPR/Cas9 system used in this study was highly specific for genome editing in C. siamense. Of the 41 comparisons of fitness between mutant and wild type isolates through in vitro and detached fruit assays, mutant isolates appeared to be as fit (24 of 41 comparisons), if not more fit than wild-type isolates (10 of 41 comparisons). Discussion The use of CRISPR/Cas9 to evaluate fitness costs associated with point mutations in this study represents a novel and useful method, since wild-type and mutant isolates were genetically identical except for the target mutation.
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Affiliation(s)
| | | | - Mengjun Hu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
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Strauss J, Deng L, Gao S, Toseland A, Bachy C, Zhang C, Kirkham A, Hopes A, Utting R, Joest EF, Tagliabue A, Löw C, Worden AZ, Nagel G, Mock T. Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans. Nat Microbiol 2023; 8:2050-2066. [PMID: 37845316 PMCID: PMC10627834 DOI: 10.1038/s41564-023-01498-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Microbial rhodopsins are photoreceptor proteins that convert light into biological signals or energy. Proteins of the xanthorhodopsin family are common in eukaryotic photosynthetic plankton including diatoms. However, their biological role in these organisms remains elusive. Here we report on a xanthorhodopsin variant (FcR1) isolated from the polar diatom Fragilariopsis cylindrus. Applying a combination of biophysical, biochemical and reverse genetics approaches, we demonstrate that FcR1 is a plastid-localized proton pump which binds the chromophore retinal and is activated by green light. Enhanced growth of a Thalassiora pseudonana gain-of-function mutant expressing FcR1 under iron limitation shows that the xanthorhodopsin proton pump supports growth when chlorophyll-based photosynthesis is iron-limited. The abundance of xanthorhodopsin transcripts in natural diatom communities of the surface oceans is anticorrelated with the availability of dissolved iron. Thus, we propose that these proton pumps convey a fitness advantage in regions where phytoplankton growth is limited by the availability of dissolved iron.
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Affiliation(s)
- Jan Strauss
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany.
- German Maritime Centre, Hamburg, Germany.
| | - Longji Deng
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Shiqiang Gao
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Charles Bachy
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Sorbonne Université, CNRS, FR2424, Station biologique de Roscoff, Roscoff, France
| | - Chong Zhang
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Amy Kirkham
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert Utting
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Eike F Joest
- Department of Biology, Biocenter, University of Würzburg, Wuerzburg, Germany
| | | | - Christian Löw
- European Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Marine Biological Laboratory, Woods Hole, MA, USA
| | - Georg Nagel
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, Wuerzburg, Germany
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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5
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Madden DE, McCarthy KL, Bell SC, Olagoke O, Baird T, Neill J, Ramsay KA, Kidd TJ, Stewart AG, Subedi S, Choong K, Fraser TA, Sarovich DS, Price EP. Rapid fluoroquinolone resistance detection in Pseudomonas aeruginosa using mismatch amplification mutation assay-based real-time PCR. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background. Antimicrobial resistance (AMR) is an ever-increasing global health concern. One crucial facet in tackling the AMR epidemic is earlier and more accurate AMR diagnosis, particularly in the dangerous and highly multi-drug-resistant ESKAPE pathogen,
Pseudomonas aeruginosa
.
Objectives. We aimed to develop two SYBR Green-based mismatch amplification mutation assays (SYBR-MAMAs) targeting GyrA T83I (gyrA248) and GyrA D87N, D87Y and D87H (gyrA259). Together, these variants cause the majority of fluoroquinolone (FQ) AMR in
P. aeruginosa
.
Methods. Following assay validation, the gyrA248 and gyrA259 SYBR-MAMAs were tested on 84 Australian clinical
P. aeruginosa
isolates, 46 of which demonstrated intermediate/full ciprofloxacin resistance according to antimicrobial susceptibility testing.
Results. Our two SYBR-MAMAs correctly predicted an AMR phenotype in the majority (83%) of isolates with intermediate/full FQ resistance. All FQ-sensitive strains were predicted to have a sensitive phenotype. Whole-genome sequencing confirmed 100 % concordance with SYBR-MAMA genotypes.
Conclusions. Our GyrA SYBR-MAMAs provide a rapid and cost-effective method for same-day identification of FQ AMR in
P. aeruginosa
. An additional SYBR-MAMA targeting the GyrB S466Y/S466F variants would increase FQ AMR prediction to 91 %. Clinical implementation of our assays will permit more timely treatment alterations in cases where decreased FQ susceptibility is identified, leading to improved patient outcomes and antimicrobial stewardship.
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Affiliation(s)
- Danielle E. Madden
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Kate L. McCarthy
- University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
- Infectious Diseases Unit, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | - Scott C. Bell
- Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia
- Child Health Research Centre, The University of Queensland, South Brisbane, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Olusola Olagoke
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
| | - Timothy Baird
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Respiratory Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Jane Neill
- Respiratory Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Kay A. Ramsay
- Child Health Research Centre, The University of Queensland, South Brisbane, Queensland, Australia
| | - Timothy J. Kidd
- Central Microbiology, Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Adam G. Stewart
- Infectious Diseases Unit, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
- University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Shradha Subedi
- Infectious Diseases Unit, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
| | - Keat Choong
- Infectious Diseases Unit, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
| | - Tamieka A. Fraser
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Derek S. Sarovich
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Erin P. Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Infection Research Network Sunshine Coast, Birtinya, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
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Manukyan H, Wahid R, Ansari A, Tritama E, Macadam A, Konz J, Chumakov K, Laassri M. Quantitative RT-PCR Assays for Quantification of Undesirable Mutants in the Novel Type 2 Oral Poliovirus Vaccine. Vaccines (Basel) 2022; 10:vaccines10091394. [PMID: 36146473 PMCID: PMC9502871 DOI: 10.3390/vaccines10091394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 01/09/2023] Open
Abstract
Emergence of mutations is an inherent property of RNA viruses with several implications for their replication, pathogenesis, and evolutionary adaptation. Oral poliovirus vaccine (OPV), developed by Albert Sabin, is composed of live attenuated polioviruses of three serotypes that can revert to neurovirulence during replication in cell culture and in vaccine recipients. Recently, a new modified variant of Sabin 2 virus was developed by introducing changes in its genome, making it more genetically stable to prevent the reversion. The new strain was used to manufacture novel OPV2 (nOPV2), which was approved by the World Health Organization for emergency use to stop outbreaks caused by circulating vaccine-derived poliovirus (cVDPV2). Manufacture of this improved vaccine requires close attention to the genetic heterogenicity to ensure that the levels of the undesirable mutations are limited. Preliminary studies using whole-genome Illumina sequencing (NGS) identified several genomic sites where mutations tend to occur with regularity. They include VP1-I143T amino acid change at the secondary attenuation site; VP1-N171D, a substitution that modestly increases neurovirulence in mice; and VP1-E295K, which may reduce the immunogenicity of the nOPV2. Therefore, to ensure the molecular consistency of vaccine batches, the content of these mutants must be quantified and kept within specifications. To do this, we have developed quantitative, multiplex, one-step reverse-transcriptase polymerase chain reactions (qmosRT-PCRs) as simple methods for quantification of these mutations. Each method uses specific short TaqMan probes with different dyes for the analysis of both mutants and non-mutants in the same sample. The quantification is done using calibration curves developed using validated reference materials. To evaluate the sensitivity and the linearity of the qmosRT-PCR method, the mutant viruses were spiked in non-mutant viruses, and nOPV2 batches were used to validate the method. The spiked samples and the nOPV2 batches were analyzed by qmosRT-PCR and NGS assays. The results showed that qmosRT-PCR is sensitive enough to detect around 1% of mutants. The percentages of mutants determined by qmosRT-PCR correlate well with the results of the NGS. Further, the analysis of the nOPV2 batches showed that the results of qmosRT-PCR correlated well with the results of NGS. In conclusion, the qmosRT-PCR is a specific, sensitive, and linear method. It could be used for quality control of the nOPV2 batches.
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Affiliation(s)
- Hasmik Manukyan
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Rahnuma Wahid
- Center for Vaccine Innovation and Access, PATH, Seattle, WA 98121, USA
| | - Azeem Ansari
- Center for Vaccine Innovation and Access, PATH, Seattle, WA 98121, USA
| | - Erman Tritama
- Research and Development Division, PT. Bio Farma, Bandung, West Java 40161, Indonesia
| | - Andrew Macadam
- National Institute for Biological Standards and Control (NIBSC), Hertfordshire EN6 3QG, UK
| | - John Konz
- Center for Vaccine Innovation and Access, PATH, Seattle, WA 98121, USA
| | - Konstantin Chumakov
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Majid Laassri
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
- Correspondence: ; Tel.: +1-(240)-402-9656; Fax: +1-3015951440
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Claus A, Simões K, De Mio LLM. SdhC-I86F Mutation in Phakopsora pachyrhizi Is Stable and Can Be Related to Fitness Penalties. PHYTOPATHOLOGY 2022; 112:1413-1421. [PMID: 35080435 DOI: 10.1094/phyto-10-21-0419-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Succinate dehydrogenase inhibitors (SDHIs) fungicides are used to control Asian soybean rust (Phakopsora pachyrhizi), and the SdhC-I86F mutation is related to pathogen resistance. The objective of this study was to determine whether fitness penalties are associated with SDHI resistance (SdhC-I86F mutation) in P. pachyrhizi populations. Moreover, the study investigated whether the SdhC-I86F mutation remained stable after the fungus propagation both in the absence and presence of fungicide. The populations used in this study presented mutations for all genes analyzed (Cyp51, Cytb, and SdhC), except for a wild-type population (WTSdhC) found with no SdhC-I86F mutation. The frequencies of the SdhC-I86F mutant populations were stable after 36 generations in the absence of fungicide. However, in the case of the WTSdhC population, the SdhC-I86F mutation was further detected after one generation of the fungus in the presence of the SDHI fungicide, according to the results of a detached leaf assay. Three tests were performed to evaluate fitness components and sensitivity to fungicides (half maximal effective concentration). SdhC-I86F mutant populations were more sensitive to osmotic and oxidative stress than the WTSdhC population; however, the sensitivity to ultraviolet radiation was similar for both populations. All mutated populations were less sensitive than the WTSdhC when using SDHI (azoxystrobin + benzovindiflupyr), but more sensitive to mancozeb. The presence of fitness penalties, the mutation stability, and the sensitivity to mancozeb presented by the SdhC-I86F mutant populations can be relevant to the management of the disease in the field.
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Affiliation(s)
- Alexandre Claus
- Instituto Federal Catarinense, 89703-720 Concórdia, SC, Brazil
- Universidade Federal do Paraná, Curitiba 80035-050, Brazil
| | - Kelly Simões
- BASF S.A., Santo Antônio de Posse, 13833-612 São Paulo/SP, Brazil
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Le CT, Price EP, Sarovich DS, Nguyen TTA, Powell D, Vu-Khac H, Kurtböke Dİ, Knibb W, Chen SC, Katouli M. Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam. Microb Genom 2022; 8. [PMID: 35786440 PMCID: PMC9455698 DOI: 10.1099/mgen.0.000845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South Central Coast region of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. PFGE identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and SNP genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0–5 SNPs). There was no association between geographical origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. The Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 220 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55 to 7.96 Mbp in size, have an average G+C content of 68.2 % and encode 7 602–7958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into the epidemiology and pathogenicity of N. seriolae and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.
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Affiliation(s)
- Cuong T. Le
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Institute for Aquaculture, Nha Trang University, Nha Trang, Vietnam
| | - Erin P. Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Derek S. Sarovich
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Thu T. A. Nguyen
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
| | - Daniel Powell
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Hung Vu-Khac
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - D. İpek Kurtböke
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Wayne Knibb
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan, ROC
| | - Mohammad Katouli
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- *Correspondence: Mohammad Katouli,
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9
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Bergallo M, Montanari P, Loiacono E, Galliano I. A novel TaqMAMA assay for allelic discrimination of immunoproteasome subunit PSMB8 in pediatric patients. Minerva Pediatr (Torino) 2022; 74:301-307. [DOI: 10.23736/s2724-5276.16.04675-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Sudo M, Osakabe M. freqpcr: Estimation of population allele frequency using qPCR ΔΔCq measures from bulk samples. Mol Ecol Resour 2022; 22:1380-1393. [PMID: 34882971 PMCID: PMC9300209 DOI: 10.1111/1755-0998.13554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022]
Abstract
PCR techniques, both quantitative (qPCR) and nonquantitative, have been used to estimate the frequency of a specific allele in a population. However, the labour required to sample numerous individuals and subsequently handle each sample renders the quantification of rare mutations (e.g., pesticide resistance gene mutations at the early stages of resistance development) challenging. Meanwhile, pooling DNA from multiple individuals as a "bulk sample" combined with qPCR may reduce handling costs. The qPCR output for a bulk sample, however, contains uncertainty owing to variations in DNA yields from each individual, in addition to measurement errors. In this study, we have developed a statistical model to estimate the frequency of the specific allele and its confidence interval when the sample allele frequencies are obtained in the form of ΔΔCq in the qPCR analyses on multiple bulk samples collected from a population. We assumed a gamma distribution as the individual DNA yield and developed an R package for parameter estimation, which was verified using real DNA samples from acaricide-resistant spider mites, as well as a numerical simulation. Our model resulted in unbiased point estimates of the allele frequency compared with simple averaging of the ΔΔCq values. The confidence intervals suggest that dividing the bulk samples into more parts will improve precision if the total number of individuals is equal; however, if the cost of PCR analysis is higher than that of sampling, increasing the total number and pooling them into a few bulk samples may also yield comparable precision.
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Affiliation(s)
- Masaaki Sudo
- Division of Fruit Tree and Tea Pest Control ResearchInstitute for Plant ProtectionNARO: Kanaya Tea Research StationShimadaJapan
| | - Masahiro Osakabe
- Laboratory of Ecological InformationGraduate School of AgricultureKyoto UniversityKyotoJapan
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11
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Araújo-Filho JVD, Ribeiro WLC, André WPP, Cavalcante GS, Santos JMLD, Monteiro JP, Macedo ITF, Oliveira LMBD, Bevilaqua CML. Phenotypic and genotypic approaches for detection of anthelmintic resistant sheep gastrointestinal nematodes from Brazilian northeast. ACTA ACUST UNITED AC 2021; 30:e005021. [PMID: 34133616 DOI: 10.1590/s1984-29612021048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/13/2021] [Indexed: 11/22/2022]
Abstract
The aim of this study was to characterize the anthelmintic resistance (AR) of a sheep gastrointestinal nematode population, named Caucaia, from northeastern Brazil. Phenotypic tests performed were: egg hatch (EHT), larval development (LDT) and fecal egg count reduction (FECRT). Benzimidazoles (BZs) genotypic evaluation was by frequency of single nucleotide polymorphisms (SNPs) F200Y, F167Y and E198A, and for levamisole (LEV), by frequency of resistance alleles of Hco-acr-8 gene. The primers were designed specifically for Haemonchus contortus. Effective concentrations 50% (EC50) for BZs (EHT), and for macrocyclic lactones (MLs) and LEV (LDT) were 1.02 µg/mL, 1.81 ng/mL and 0.04 µg/mL, respectively. Resistance ratios for MLs and LEV were 0.91 and 3.07, respectively. FECRT efficacies of BZs, MLs, monepantel (MPTL) and LEV were 52.4; 87.0; 94.5 and 99.6%, respectively. qPCR for BZs demonstrated resistance allele frequencies of 0%, 26.24% and 69.08% for SNPs E198A, F200Y and F167Y, respectively. For LEV, 54.37% of resistance alleles were found. There was agreement between EHT, FECRT and qPCR for BZs, and agreement between LDT and qPCR for LEV. Thus, based on higher sensitivity of qPCR, and phenotypic evaluation, the Caucaia population was considered resistant to BZs, MLs, LEV and suspect for MPTL.
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Affiliation(s)
- José Vilemar de Araújo-Filho
- Laboratório de Doenças Parasitárias, Programa de Pós-graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Estadual do Ceará - UECE, Fortaleza, CE, Brasil
| | | | - Weibson Paz Pinheiro André
- Laboratório de Doenças Parasitárias, Programa de Pós-graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Estadual do Ceará - UECE, Fortaleza, CE, Brasil
| | - Géssica Soares Cavalcante
- Laboratório de Doenças Parasitárias, Programa de Pós-graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Estadual do Ceará - UECE, Fortaleza, CE, Brasil
| | | | - Jomar Patrício Monteiro
- Centro Universitário INTA - UNINTA, Sobral, CE, Brasil.,Embrapa Caprinos e Ovinos, Sobral, CE, Brasil
| | - Iara Tersia Freitas Macedo
- Laboratório de Doenças Parasitárias, Programa de Pós-graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Estadual do Ceará - UECE, Fortaleza, CE, Brasil
| | - Lorena Mayana Beserra de Oliveira
- Laboratório de Doenças Parasitárias, Programa de Pós-graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Estadual do Ceará - UECE, Fortaleza, CE, Brasil
| | - Claudia Maria Leal Bevilaqua
- Laboratório de Doenças Parasitárias, Programa de Pós-graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Estadual do Ceará - UECE, Fortaleza, CE, Brasil
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12
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Song J, Kim S, Kim HY, Hur KH, Kim Y, Park HG. A novel method to detect mutation in DNA by utilizing exponential amplification reaction triggered by the CRISPR-Cas9 system. NANOSCALE 2021; 13:7193-7201. [PMID: 33720266 DOI: 10.1039/d1nr00438g] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We, herein, describe a novel method to detect mutation in DNA by utilizing exponential amplification reaction (EXPAR) triggered by clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9, called CRISPR-EXPAR. The CRISPR system consisting of two Cas9/sgRNA complexes was designed to cut out a specific mutation region within the target DNA, which would consequently promote EXPAR by continuously repeated extension and nicking reactions. As a consequence, a large number of final EXPAR products, which can be monitored through duplex-specific fluorescent staining, are produced. Based on this design principle, we successfully identified a model target mutation within the human epidermal growth factor receptor 2 (HER2) gene down to 437 aM with excellent specificity. The practical capability of this method was verified by reliably identifying the target mutation directly from the genomic DNA (gDNA) extracted from the lung cancer cell line, NCI-H1781 (H1781), and its universal applicability was further confirmed by identifying another EFGF L858R mutation. This technique could serve as a new isothermal platform to identify various mutations by rationally redesigning single guide RNA (sgRNA) according to the target mutation site.
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Affiliation(s)
- Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon 34141, Republic of Korea.
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13
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Hou M, Xu G, Ran M, Luo W, Wang H. APOE-ε4 Carrier Status and Gut Microbiota Dysbiosis in Patients With Alzheimer Disease. Front Neurosci 2021; 15:619051. [PMID: 33732104 PMCID: PMC7959830 DOI: 10.3389/fnins.2021.619051] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/14/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Alternations in gut microbiota and a number of genes have been implicated as risk factors for the development of Alzheimer disease (AD). However, the interactions between the altered bacteria and risk genetic variants remain unclear. OBJECTIVE We aimed to explore associations of the risk genetic variants with altered gut bacteria in the onset of AD. METHODS We collected baseline data and stool and blood samples from 30 AD patients and 47 healthy controls in a case-control study. The rs42358/rs4512 (ApoE), rs3851179 (PICALM), rs744373 (BIN1), rs9331888 (CLU), rs670139 (MS4A4E), rs3764650 (ABCA7), rs3865444 (CD33), rs9349407 (CD2AP), rs11771145 (EPHA1), and rs3818361/rs6656401 (CR1) were sequenced, and microbiota composition was characterized using 16S rRNA gene sequencing. The associations of the altered gut bacteria with the risk genetics were analyzed. RESULTS Apolipoprotein ε4 allele and rs744373 were risk loci for the AD among 12 genetic variants. Phylum Proteobacteria; orders Enterobacteriales, Deltaproteobacteria, and Desulfovibrionales; families Enterobacteriaceae and Desulfovibrionaceae; and genera Escherichia-Shigella, Ruminococcaceae_UCG_002, Shuttleworthia, Anaerofustis, Morganelia, Finegoldia, and Anaerotruncus were increased in AD subjects, whereas family Enterococcaceae and genera Megamonas, Enterococcus, and Anaerostipes were more abundant in controls (P < 0.05). Among the altered microbiota, APOE ε4 allele was positively associated with pathogens: Proteobacteria. CONCLUSION The interaction of APOE ε4 gene and the AD-promoting pathogens might be an important factor requiring for the promotion of AD. Targeting to microbiota might be an effective therapeutic strategy for AD susceptible to APOE ε4 allele. This needs further investigation.
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Affiliation(s)
- Min Hou
- School of Public Health, College of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Gaolian Xu
- Nano Biomedical Research Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Maosheng Ran
- Department of Social Work and Social Administration, The University of Hong Kong, Hong Kong, China
| | - Wei Luo
- Xinjin No. 2 People’s Hospital, Chengdu, China
| | - Hui Wang
- School of Public Health, College of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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14
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The relationship between JAK2(V617F) mutation and dermatomyositis-a case report and literature review. Clin Rheumatol 2020; 40:1147-1157. [PMID: 32676918 DOI: 10.1007/s10067-020-05286-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023]
Abstract
The JAK family (JAK1, JAK2, JAK3, and TYK2) have recently emerged as a potential therapeutic management in controlling severe and refractory dermatomyositis. Meanwhile, the progress in the discovery of JAK blockers is significant, with an increasing number of selective JAK inhibitors reported and some are in or prepare for clinical trials. However, the importance of each JAK in dermatomyositis is unclear, which is critical for a comprehensive understanding of dermatomyositis and significant for forming mechanism-based strategy. Here, we presented a case with clinically amyopathic dermatomyositis and essential thrombocytosis with a somatic constitutive active mutation of JAK2(V617F). The coexistence of these two uncommon diseases attracted us to investigate their underlying relationship. To this end, we characterized the clinical course and laboratory findings of this patient. Particularly, we correlated JAK2(V617F) mutation burden in affected peripheral blood subset with clinical activity score of dermatomyositis. Based on our observation, we concluded that these two diseases are independent disorders, and JAK2(V617F) mutation burden is irrelevant to the severity of dermatomyositis. Finally, we reviewed the literature and summarized them with a thorough discussion.
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15
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Limvorapitak W, Parker J, Hughesman C, McNeil K, Foltz L, Karsan A. No Differences in Outcomes Between JAK2 V617F-Positive Patients with Variant Allele Fraction < 2% Versus 2-10%: A 6-Year Province-wide Retrospective Analysis. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2020; 20:e569-e578. [PMID: 32439277 DOI: 10.1016/j.clml.2020.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 02/02/2023]
Abstract
INTRODUCTION JAK2 V617F mutation is one of the major criteria in the diagnosis of myeloproliferative neoplasms (MPN) and its variant allele fraction (VAF) determines the disease phenotype and outcomes. This study aimed to define characteristics and outcomes of patients with JAK2 V617F VAF < 2% compared to patients with VAF 2%-10%. PATIENTS AND METHODS We included 5079 patients with JAK2 V617F tested during 2010-2015 and identified 216 patients (4.3%) with JAK2 V617F VAF < 10%. Twenty-seven patients were excluded because of missing follow-up data. RESULTS A total of 189 patients were included for final analysis (89 patients with VAF < 2% and 100 patients with VAF 2%-10%). Patients with JAK2 V617F 2%-10% VAF had a significantly higher rate of splenomegaly, higher platelet counts, and more MPN diagnoses than the group with VAF < 2%. Ten patients (10.0%) with VAF 2%-10% and 24 patients (27.0%) with VAF < 2% had normal blood count and no thrombosis. There were no differences between the groups in all outcomes, including thrombotic complications (18.0% in both groups), progression to hematologic or solid cancers, and death. Patients without hematologic diagnosis had similar thrombotic incidence (16.7% in VAF < 2% vs. 20.0% in VAF 2%-10%). CONCLUSION Patients with JAK2 V617F mutation VAF < 2% have similar survival and thrombotic incidence as patients with VAF 2%-10%. Patients with low VAF should be monitored in the same manner as patients with higher VAF with the same diagnoses to prevent morbidity and mortality. Patients without hematologic diagnosis may benefit from thrombotic risk reduction strategies such as optimization of cardiovascular risk factors.
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Affiliation(s)
- Wasithep Limvorapitak
- Division of Hematology, Department of Internal Medicine, Faculty of Medicine, Thammasat University, Pathumthani, Thailand; The Leukemia/Bone Marrow Transplant Program of BC, BC Cancer, Vancouver, BC, Canada.
| | - Jeremy Parker
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Curtis Hughesman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kelly McNeil
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Lynda Foltz
- St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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16
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Lee DE, Kim HC, Chong ST, Klein TA, Choi KS, Kim YH, Kim JH, Lee SH. Regional and seasonal detection of resistance mutation frequencies in field populations of Anopheles Hyrcanus Group and Culex pipiens complex in Korea. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 164:33-39. [PMID: 32284134 DOI: 10.1016/j.pestbp.2019.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/19/2019] [Accepted: 12/19/2019] [Indexed: 06/11/2023]
Abstract
Pyrethroid (PYR) and organophosphate (OP) insecticides have been extensively used for mosquito control for several decades in South Korea, and has resulted in the rapid development of resistance in the field. In this study, quantitative sequencing (QS) protocols were developed for the frequency prediction of insecticide resistance alleles [e.g., the L1014F/C mutation on the voltage sensitive sodium channel as a PYR resistance allele and the G119S mutation on the acetylcholinesterase 1 as OP resistance alleles] in four regional populations of Anopheles Hyrcanus Group and Culex pipiens complex. Both of the L1014F/C and G119S mutations were observed in all examined regional populations of An. Hyrcanus Group, suggesting a wide distribution of both PYR and OP resistance. In contrast, populations of the Cx. pipiens complex were determined to possess almost no G119S mutation, but relatively higher frequencies of the L1014F mutation, showing differential resistance patterns between different mosquito groups. The mutation frequencies were also monitored throughout a mosquito season (May-October) at one collection site to determine the seasonal changes of resistance mutation frequency in mosquito populations. Dramatic decreases of both L1014F/C and G119S mutation frequencies were observed in the An. Hyrcanus Group toward the fall, with no mutations observed in the early spring, suggesting a connection between the fitness costs of overwintering and insecticide resistance. However, no apparent trends were detectable in the Cx. pipiens complex populations due to low or zero mutation frequencies.
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Affiliation(s)
- Do Eun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Heung-Chul Kim
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea, 65th Medical Bridge, Unit 15281, APO AP 96271-5281, USA
| | - Sung-Tae Chong
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea, 65th Medical Bridge, Unit 15281, APO AP 96271-5281, USA
| | - Terry A Klein
- Force Health Protection and Preventive Medicine, Medical Department Activity-Korea, 65th Medical Bridge, Unit 15281, APO AP 96271-5281, USA
| | - Kwang Shik Choi
- School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Young Ho Kim
- Department of Ecological Science, Kyungpook National University, Sangju 37224, Republic of Korea
| | - Ju Hyeon Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Si Hyeock Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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17
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Galliano I, Daprà V, Ciferri F, Montanari P, Calvi C, Alliaudi C, Savino F, Bergallo M. TaqMAMA assay polymerase chain reaction real time for allelic discrimination of Macrophage receptor with collagenous structure rs1318645 polymorphism. MINERVA BIOTECNOL 2020. [DOI: 10.23736/s1120-4826.19.02567-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Orr AR, Quagraine JE, Suwondo P, George S, Harrison LM, Dornas FP, Evans B, Caccone A, Humphries D, Wilson MD, Cappello M. Genetic Markers of Benzimidazole Resistance among Human Hookworms ( Necator americanus) in Kintampo North Municipality, Ghana. Am J Trop Med Hyg 2019; 100:351-356. [PMID: 30734697 DOI: 10.4269/ajtmh.18-0727] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Hookworm infection causes anemia, malnutrition, and growth delay, especially in children living in sub-Saharan Africa. The World Health Organization recommends periodic mass drug administration (MDA) of anthelminthics to school-age children (SAC) as a means of reducing morbidity. Recently, questions have been raised about the effectiveness of MDA as a global control strategy for hookworms and other soil-transmitted helminths (STHs). Genomic DNA was extracted from Necator americanus hookworm eggs isolated from SAC enrolled in a cross-sectional study of STH epidemiology and deworming response in Kintampo North Municipality, Ghana. A polymerase chain reaction (PCR) assay was then used to identify single-nucleotide polymorphisms (SNPs) associated with benzimidazole resistance within the N. americanus β-tubulin gene. Both F167Y and F200Y resistance-associated SNPs were detected in hookworm samples from infected study subjects. Furthermore, the ratios of resistant to wild-type SNP at these two loci were increased in posttreatment samples from subjects who were not cured by albendazole, suggesting that deworming drug exposure may enrich resistance-associated mutations. A previously unreported association between F200Y and a third resistance-associated SNP, E198A, was identified by sequencing of F200Y amplicons. These data confirm that markers of benzimidazole resistance are circulating among hookworms in central Ghana, with unknown potential to impact the effectiveness and sustainability of chemotherapeutic approaches to disease transmission and control.
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Affiliation(s)
- Ambrose R Orr
- Yale Partnerships for Global Health, Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut
| | - Josephine E Quagraine
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana.,Yale Partnerships for Global Health, Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut
| | - Peter Suwondo
- Yale Partnerships for Global Health, Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut
| | - Santosh George
- Yale Partnerships for Global Health, Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut
| | - Lisa M Harrison
- Yale Partnerships for Global Health, Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut
| | - Fabio Pio Dornas
- Yale Partnerships for Global Health, Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut
| | - Benjamin Evans
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Debbie Humphries
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Michael D Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Michael Cappello
- Yale Partnerships for Global Health, Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut
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19
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Quantitative molecular diagnosis of levamisole resistance in populations of Haemonchus contortus. Exp Parasitol 2019; 205:107734. [DOI: 10.1016/j.exppara.2019.107734] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/23/2019] [Accepted: 08/02/2019] [Indexed: 11/20/2022]
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20
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Saadat M, Qasemian-Talgard A, Darvishi FZ, Taghipour N, Saadat I. A new simple method for estimation of allelic frequencies using pooled samples. Gene 2019; 703:13-16. [PMID: 30951855 DOI: 10.1016/j.gene.2019.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/25/2019] [Accepted: 04/01/2019] [Indexed: 11/15/2022]
Abstract
Today several millions polymorphic sites in human genome are well described. Many investigators are studying the association between these polymorphisms and susceptibility to multifactorial traits. These polymorphisms are also used for studying the population's genetic structures. Here, we introduce a new simple one step method for estimating the allelic frequency of polymorphic sites in pooled samples. The method is based on measurement of the intensity of polymorphic bands on agarose gel electrophoresis. This method is very simple, rapid, inexpensive, and is more sensitive compared to the chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry method.
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Affiliation(s)
- Mostafa Saadat
- Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
| | | | | | - Nahid Taghipour
- Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Iraj Saadat
- Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
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21
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Schwarze U, Cundy T, Liu YJ, Hofman PL, Byers PH. Compound heterozygosity for a frameshift mutation and an upstream deletion that reduces expression of SERPINH1 in siblings with a moderate form of osteogenesis imperfecta. Am J Med Genet A 2019; 179:1466-1475. [PMID: 31179625 DOI: 10.1002/ajmg.a.61170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/13/2019] [Accepted: 04/15/2019] [Indexed: 12/12/2022]
Abstract
SERPINH1 encodes the collagen chaperone HSP47 that binds to arginine-rich sequences in the type I procollagen trimers and provides the final steps in the folding and stabilization of the triple helical domain. Loss of both alleles in mice results in very early embryonic lethality. SERPINH1 mutations have been associated with one of the rarest forms of recessively inherited osteogenesis imperfecta (OI) with a moderate to severe phenotype. We identified a family with non-consanguineous unaffected parents who had two children with moderate short stature, low bone density, and fractures. Both children were compound heterozygotes for two mutations: a frameshift in the last exon that deleted the RER retention signal, and a 5,274 bp deletion 2.37 kb upstream from the transcription start site. The maternally-inherited frameshift allele was expressed at normal levels, but the protein was unstable. The mRNA encoded by the second allele represented about 50% of that from the frameshift-containing allele. The upstream deletion was inherited from the father, and the mRNA encoded by that allele in his cultured dermal fibroblasts was also expressed at a low level, which confirmed that this domain had a regulatory function for SERPINH1. Regulatory mutations are uncommon causes of human genetic disorders, and the ability to measure expression levels in appropriate cells is key to their identification.
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Affiliation(s)
- Ulrike Schwarze
- Department of Pathology, University of Washington, Seattle, Washington
| | - Tim Cundy
- Department of Medicine, Faculty of Medical & Health Sciences, University of Auckland, New Zealand
| | - Yajuan J Liu
- Department of Pathology, University of Washington, Seattle, Washington
| | - Paul L Hofman
- Liggins Institute, Faculty of Medical & Health Sciences, University of Auckland, New Zealand
| | - Peter H Byers
- Department of Pathology, University of Washington, Seattle, Washington.,Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington
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22
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Unubol N, Kizilkaya IT, Okullu SO, Koksalan K, Kocagoz T. Simple Identification of Mycobacterial Species by Sequence-Specific Multiple Polymerase Chain Reactions. Curr Microbiol 2019; 76:791-798. [PMID: 31073733 DOI: 10.1007/s00284-019-01661-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/28/2019] [Indexed: 12/29/2022]
Abstract
Several species of mycobacteria cause infections in humans. Species identification of clinical isolates of mycobacteria is very important for the decision of treatment and in choosing the appropriate treatment regimen. We have developed a multiplex PCR method that can identify practically all known species of mycobacteria, by determination of single-nucleotide differences at a total of 13 different polymorphic regions in the genes of rRNA and hsp65, in four PCR mixes. To achieve this goal, single-nucleotide differences in these polymorphic regions were used to divide mycobacterial species into two groups, than four, eight, etc., in an algorithmic manner. It was sufficient to reach single species level by evaluating 13 polymorphic regions. Evaluation of the multiplex PCR patterns by observable real-time electrophoresis (ORTE) simplified species identification. This new method may enable easy, rapid, and cost-effective identification of all species of mycobacteria.
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Affiliation(s)
- Nihan Unubol
- Department of Medical Microbiology, Faculty of Medicine, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | | | - Sinem Oktem Okullu
- Department of Medical Microbiology, Faculty of Medicine, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Kaya Koksalan
- Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Tanil Kocagoz
- Department of Medical Microbiology, Faculty of Medicine, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey.
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey.
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23
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Zhao C, Xie S, Wu H, Luan Y, Hu S, Ni J, Lin R, Zhao S, Zhang D, Li X. Quantification of allelic differential expression using a simple Fluorescence primer PCR-RFLP-based method. Sci Rep 2019; 9:6334. [PMID: 31004110 PMCID: PMC6474871 DOI: 10.1038/s41598-019-42815-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 03/29/2019] [Indexed: 12/04/2022] Open
Abstract
Allelic differential expression (ADE) is common in diploid organisms, and is often the key reason for specific phenotype variations. Thus, ADE detection is important for identification of major genes and causal mutations. To date, sensitive and simple methods to detect ADE are still lacking. In this study, we have developed an accurate, simple, and sensitive method, named fluorescence primer PCR-RFLP quantitative method (fPCR-RFLP), for ADE analysis. This method involves two rounds of PCR amplification using a pair of primers, one of which is double-labeled with an overhang 6-FAM. The two alleles are then separated by RFLP and quantified by fluorescence density. fPCR-RFLP could precisely distinguish ADE cross a range of 1- to 32-fold differences. Using this method, we verified PLAG1 and KIT, two candidate genes related to growth rate and immune response traits of pigs, to be ADE both at different developmental stages and in different tissues. Our data demonstrates that fPCR-RFLP is an accurate and sensitive method for detecting ADE on both DNA and RNA level. Therefore, this powerful tool provides a way to analyze mutations that cause ADE.
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Affiliation(s)
- Changzhi Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, P.R. China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Hui Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Yu Luan
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Suqin Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Juan Ni
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Ruiyi Lin
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, P.R. China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Dingxiao Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, P.R. China. .,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, P.R. China.
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, P.R. China. .,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, 430070, P.R. China.
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Kitchen S, Ratnappan R, Han S, Leasure C, Grill E, Iqbal Z, Granger O, O'Halloran DM, Hawdon JM. Isolation and characterization of a naturally occurring multidrug-resistant strain of the canine hookworm, Ancylostoma caninum. Int J Parasitol 2019; 49:397-406. [PMID: 30771359 DOI: 10.1016/j.ijpara.2018.12.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/07/2018] [Accepted: 12/12/2018] [Indexed: 10/27/2022]
Abstract
Soil-transmitted nematodes infect over a billion people and place several billion more at risk of infection. Hookworm disease is the most significant of these soil-transmitted nematodes, with over 500 million people infected. Hookworm infection can result in debilitating and sometimes fatal iron-deficiency anemia, which is particularly devastating in children and pregnant women. Currently, hookworms and other soil-transmitted nematodes are controlled by administration of a single dose of a benzimidazole to targeted populations in endemic areas. While effective, people are quickly re-infected, necessitating frequent treatment. Widespread exposure to anthelmintic drugs can place significant selective pressure on parasitic nematodes to generate resistance, which has severely compromised benzimidazole anthelmintics for control of livestock nematodes in many areas of the world. Here we report, to our knowledge, the first naturally occurring multidrug-resistant strain of the canine hookworm Ancylostoma caninum. We reveal that this isolate is resistant to fenbendazole at the clinical dosage of 50 mg/kg for 3 days. Our data shows that this strain harbors a fixed, single base pair mutation at amino acid 167 of the β-tubulin isotype 1 gene, and by using CRISPR/Cas9 we demonstrate that introduction of this mutation into the corresponding amino acid in the orthologous β-tubulin gene of Caenorhabditis elegans confers a similar level of resistance to thiabendazole. We also show that the isolate is resistant to the macrocyclic lactone anthelmintic ivermectin. Understanding the mechanism of anthelmintic resistance is important for rational design of control strategies to maintain the usefulness of current drugs, and to monitor the emergence of resistance. The isolate we describe represents the first multidrug-resistant strain of A. caninum reported, and our data reveal a resistance marker that can emerge naturally in response to heavy anthelminthic treatment.
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Affiliation(s)
- Shannon Kitchen
- Department of Microbiology, Immunology, and Tropical Medicine, Ross Hall, 2300 I St. NW, The George Washington University, Washington, DC 20052, USA
| | - Ramesh Ratnappan
- Department of Microbiology, Immunology, and Tropical Medicine, Ross Hall, 2300 I St. NW, The George Washington University, Washington, DC 20052, USA
| | - Suhao Han
- Department of Microbiology, Immunology, and Tropical Medicine, Ross Hall, 2300 I St. NW, The George Washington University, Washington, DC 20052, USA
| | - Caitlyn Leasure
- Department of Microbiology, Immunology, and Tropical Medicine, Ross Hall, 2300 I St. NW, The George Washington University, Washington, DC 20052, USA
| | - Emilia Grill
- Department of Microbiology, Immunology, and Tropical Medicine, Ross Hall, 2300 I St. NW, The George Washington University, Washington, DC 20052, USA
| | - Zahra Iqbal
- Department of Microbiology, Immunology, and Tropical Medicine, Ross Hall, 2300 I St. NW, The George Washington University, Washington, DC 20052, USA
| | - Olivia Granger
- Department of Microbiology, Immunology, and Tropical Medicine, Ross Hall, 2300 I St. NW, The George Washington University, Washington, DC 20052, USA
| | - Damien M O'Halloran
- Department of Biological Sciences, The George Washington University, SEH 6000, 800 22nd St NW, Washington, DC 20052, USA
| | - John M Hawdon
- Department of Microbiology, Immunology, and Tropical Medicine, Ross Hall, 2300 I St. NW, The George Washington University, Washington, DC 20052, USA.
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Wang T, Huang D, Chen B, Mao N, Qiao Y, Ji M. Differential expression of photosynthesis-related genes in pentaploid interspecific hybrid and its decaploid of Fragaria spp. Genes Genomics 2018; 40:321-331. [DOI: 10.1007/s13258-018-0647-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/04/2018] [Indexed: 12/26/2022]
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Santos JMLD, Vasconcelos JF, Frota GA, Ribeiro WLC, André WPP, Vieira LDS, Teixeira M, Bevilaqua CML, Monteiro JP. Haemonchus contortus β-tubulin isotype 1 gene F200Y and F167Y SNPs are both selected by ivermectin and oxfendazole treatments with differing impacts on anthelmintic resistance. Vet Parasitol 2017; 248:90-95. [DOI: 10.1016/j.vetpar.2017.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/13/2017] [Accepted: 11/06/2017] [Indexed: 11/15/2022]
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27
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Zhu F, Schlupp I, Tiedemann R. Allele-specific expression at the androgen receptor alpha gene in a hybrid unisexual fish, the Amazon molly (Poecilia formosa). PLoS One 2017; 12:e0186411. [PMID: 29023530 PMCID: PMC5638567 DOI: 10.1371/journal.pone.0186411] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/29/2017] [Indexed: 12/25/2022] Open
Abstract
The all-female Amazon molly (Poecilia formosa) is the result of a hybridization of the Atlantic molly (P. mexicana) and the sailfin molly (P. latipinna) approximately 120,000 years ago. As a gynogenetic species, P. formosa needs to copulate with heterospecific males including males from one of its bisexual ancestral species. However, the sperm only triggers embryogenesis of the diploid eggs. The genetic information of the sperm donor typically will not contribute to the next generation of P. formosa. Hence, P. formosa possesses generally one allele from each of its ancestral species at any genetic locus. This raises the question whether both ancestral alleles are equally expressed in P. formosa. Allele-specific expression (ASE) has been previously assessed in various organisms, e.g., human and fish, and ASE was found to be important in the context of phenotypic variability and disease. In this study, we utilized Real-Time PCR techniques to estimate ASE of the androgen receptor alpha (arα) gene in several distinct tissues of Amazon mollies. We found an allelic bias favoring the maternal ancestor (P. mexicana) allele in ovarian tissue. This allelic bias was not observed in the gill or the brain tissue. Sequencing of the promoter regions of both alleles revealed an association between an Indel in a known CpG island and differential expression. Future studies may reveal whether our observed cis-regulatory divergence is caused by an ovary-specific trans-regulatory element, preferentially activating the allele of the maternal ancestor.
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Affiliation(s)
- Fangjun Zhu
- University of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ingo Schlupp
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Ralph Tiedemann
- University of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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A "Ct contrast"-based strain-specific real-time quantitative PCR system for Lactobacilllus paracasei subsp. paracasei NTU 101. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 51:535-544. [PMID: 28693925 DOI: 10.1016/j.jmii.2017.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 06/18/2016] [Accepted: 05/24/2017] [Indexed: 11/23/2022]
Abstract
BACKGROUND/PURPOSES Routine cell number determination for specific Lactobacillus strain by cultivation requires at least 4-7 days. Thus rapid and specific cell number determine methods such as strain-specific quantitative PCR (qPCR) are valuable. However, qPCR method is vulnerable to difficult PCR target such as dimer/secondary structure forming sequence. METHODS In this study, a two-component, "Ct contrast" approach was applied to strain-specific qPCR system following the development of Lactobacillus paracasei subsp. paracasei NTU 101 (NTU 101) strain-specific PCR with random amplification of polymorphic DNA (RAPD)-derived strain-specific sequences. RESULTS The quantitative range of the NTU 101 strain-specific qPCR system was 3.0 × 101 to 3.0 × 105 copies for pure cultures, and 3.0 × 102 to 3.0 × 105 copies for multi-strain or unknown food samples. The results of spike in test and real sample testing suggested that non-specific weak background signals did not compromise test specificity, and demonstrated the potential of the NTU 101 strain-specific qPCR system in food samples. CONCLUSION The two-component, "Ct contrast" approach is useful for qPCR discrimination when no ideal PCR target is available or the variance of the target site is unpredictable. The Ct contrast approach might provide a simple and robust solution for other challenging qPCR targets.
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Bergallo M, Montanari P, Mareschi K, Rassu M, Galliano I, Ravanini P. A novel TaqMAMA assay for allelic discrimination of TLR9 rs352140 polymorphism. J Virol Methods 2017; 243:25-30. [PMID: 28143777 DOI: 10.1016/j.jviromet.2017.01.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/17/2017] [Accepted: 01/17/2017] [Indexed: 12/13/2022]
Abstract
TaqMAMA is an allele-specific PCR-based (ASPCR) method that may be suitable for broad and cost-effective genotyping applications in all types of laboratories. There is evidence that interactions between some toll like receptors (TLRs) with viruses influence both the immune response and outcome of HCMV infection. We developed a TaqMAMA genotyping assay for the detection of rs352140 TLR9 polymorphism in transplant recipients with and without HCMV infections. Performance parameters to ensure a solid pre-validation protocol have been here argued. We analysed a population of 74 kidney transplants recipients subdivided in 58 HCMV PCR positive and 16 HCMV PCR negative in the post-transplant routine control. All 74 samples were tested with 31/74 (41.9%) homozygotes (11 CC and 20 TT) and 43/74 (58.1%) heterozygotes (CT). Our preliminary data suggest that there is no correlation between TLR9 rs352140 polymorphism and frequency of HCMV infection.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136, Turin, Italy.
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136, Turin, Italy
| | - Katia Mareschi
- Pediatric Oncohematology, Stem Cell Transplantation and Cell Therapy Division, A.O.U. Città della Salute e della Scienza-Regina Margherita Children Hospital, Turin, Italy
| | - Marco Rassu
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136, Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136, Turin, Italy
| | - Paolo Ravanini
- Laboratory of Molecular Virology, Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy
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Schulze Heuling E, Knab F, Radke J, Eskilsson E, Martinez-Ledesma E, Koch A, Czabanka M, Dieterich C, Verhaak RG, Harms C, Euskirchen P. Prognostic Relevance of Tumor Purity and Interaction with MGMT Methylation in Glioblastoma. Mol Cancer Res 2017; 15:532-540. [PMID: 28148826 DOI: 10.1158/1541-7786.mcr-16-0322] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/31/2016] [Accepted: 01/24/2017] [Indexed: 11/16/2022]
Abstract
Promoter methylation status of O-6-methylguanine-DNA methyltransferase (MGMT), a DNA repair enzyme, is a critical biomarker in glioblastoma (GBM), as treatment decisions and clinical trial inclusion rely on its accurate assessment. However, interpretation of results is complicated by poor interassay reproducibility as well as a weak correlation between methylation status and expression levels of MGMT. This study systematically investigates the influence of tumor purity on tissue subjected to MGMT analysis. A quantitative, allele-specific real-time PCR (qAS-PCR) assay was developed to determine genotype and mutant allele frequency of telomerase promoter (pTERT) mutations as a direct measure of tumor purity. We studied tumor purity, pTERT mutation by Sanger sequencing, MGMT methylation by pyrosequencing, IDH1 mutation status, and clinical parameters in a cohort of high-grade gliomas (n = 97). The qAS-PCR reliably predicted pTERT genotype and tumor purity compared with independent methods. Tumor purity positively and significantly correlated with the extent of methylation in MGMT methylated GBMs. Extent of MGMT methylation differed significantly with respect to pTERT mutation hotspot (C228T vs. C250T). Interestingly, frontal lobe tumors showed greater tumor purity than those in other locations. Above all, tumor purity was identified as an independent prognostic factor in GBM. In conclusion, we determined mutual associations of tumor purity with MGMT methylation and pTERT mutations and found that the extent of MGMT methylation reflects tumor purity. In turn, tumor purity is prognostic in IDH1 wild-type GBM.Implications: Tumor purity is an independent prognostic marker in glioblastoma and is associated with the extent of MGMT methylation. Mol Cancer Res; 15(5); 532-40. ©2017 AACR.
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Affiliation(s)
- Eva Schulze Heuling
- Department of Experimental Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Knab
- Department of Experimental Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Josefine Radke
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Eskil Eskilsson
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Arend Koch
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Marcus Czabanka
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Dieterich
- Computational RNA Biology and Ageing Group, Max-Planck-Institute for the Biology of Ageing, Cologne, Germany
| | - Roel G Verhaak
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christoph Harms
- Department of Experimental Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany. .,Berlin Institute of Health (BIH), Berlin, Germany.,Center for Stroke Research Berlin, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Philipp Euskirchen
- Department of Experimental Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany. .,Berlin Institute of Health (BIH), Berlin, Germany.,Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
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High levels of benzimidazole resistance and β-tubulin isotype 1 SNP F167Y in Haemonchus contortus populations from Ceará State, Brazil. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2016.11.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Dhas DBB, Ashmi AH, Bhat BV, Parija SC, Banupriya N. Modified low cost SNP genotyping technique using cycle threshold (Ct) & melting temperature (Tm) values in allele specific real-time PCR. Indian J Med Res 2016; 142:555-62. [PMID: 26658590 PMCID: PMC4743342 DOI: 10.4103/0971-5916.171282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background & objectives: Genotyping has now become one of the major diagnostic means for almost all diseases. Among the advanced techniques that are used to study single nucleotide polymorphisms (SNPs), only a few are applicable for routine disease diagnosis. Their applicability mainly depends on three factors: cost, time, and accuracy. The primary objective of this study was to propose allele-specific real-time PCR as a rapid, low cost and simple genotyping method for routine diagnostics. Methods: Two SNPs, rs3014866 and rs2149356 were analysed using allele-specific real-time PCR. The polymerase chain reaction was carried out using RealQ PCR master mix containing SYBR Green DNA I dye followed by melt curve analysis. The results were validated by agarose gel electrophoresis and DNA sequencing. Results: The allelic discrimination and zygosity of the two SNPs were assessed by combined cycle threshold (Ct) and melting temperature (Tm) values. Variations in Ct and Tm values among the two alleles were observed in both rs3014866 (Ct: C allele - 24±1, T allele - 27±1; Tm: C allele - 82.5±0.3, T allele - 86.3±0.2) and rs2149356 (Ct: C allele - 24±1, A allele - 26±1; Tm: C allele - 79.4±0.2, A allele - 80.4±0.3). Based on the variations, homozygous and heterozygous alleles were detected. Agarose gel electrophoresis and DNA sequencing also confirmed the allelic variation and zygosity observed in real-time PCR. Interpretation & conclusions: In diagnostic settings where a large number of samples are analysed daily, allele-specific real-time PCR assay may serve as a simple, low cost and efficient method of genotyping.
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Affiliation(s)
| | | | - B Vishnu Bhat
- Department of Paediatrics, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
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Bugeja MJ, Booth DR, Bennetts BH, Heard RNS, Stewart GJ. An investigation of polymorphisms in the 4q13.3-21.1 CXC chemokine gene cluster for association with multiple sclerosis in Australians. Mult Scler 2016; 12:710-22. [PMID: 17262998 DOI: 10.1177/1352458506070964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Susceptibility to multiple sclerosis (MS) is believed to result from the complex interaction of a number of genes, each with modest effect. Vital to the migration of cells to sites of inflammation, including the central nervous system, are chemokines, many of which are implicated in MS pathogenesis. Most of the CXC chemokine genes are encoded in a cluster on chromosome 4q13.3-21.1, which has been identified in several genome-wide screens as being potentially associated with MS. We conducted a two-stage analysis to investigate the chemokine gene cluster for association with MS. Initially, we sequenced the chemokine genes in several DNA pools to identify common polymorphisms, and then genotyped selected SNPs in 373 Australian MS trio families. We found no evidence that the CXC chemokine gene cluster is genetically associated with MS. However, the existence of common variants conferring small risk factors or rare variants with significant risk cannot be excluded.
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Affiliation(s)
- M J Bugeja
- The Institute for Immunology and Allergy Research, Westmead Millennium Institute, Westmead Campus, University of Sydney, Westmead, NSW 2145, Australia
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Slankard M, Michelis MA, Mansukhani M, McGoey B, Paige A, Andrews H, Lederer D, Canfield S, DiMango E. Impact of the Arg 16 allele of the B2AR gene on the effect of withdrawal of LABA in patients with moderate to severe asthma. J Asthma 2016; 53:783-9. [PMID: 27050801 DOI: 10.3109/02770903.2016.1161049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Long-acting beta agonists (LABAs) are effective for controlling asthma, however questions about their safety have led to concerns over use. Genetic polymorphisms at the 16 amino acid position of the beta-2 adrenergic receptor gene (B2AR) may be associated with increased risk. METHODS A randomized, double blind study was conducted in patients with moderate to severe asthma being treated with combined inhaled corticosteroids/LABA (ICS/LABA), comparing the effect of LABA continuation versus withdrawal on asthma outcomes among patients stratified by B2AR genotype (Arg/Arg vs. Gly/Gly at the 16th amino acid position). RESULTS 67 participants (31 Arg/Arg, 36 Gly/Gly) were randomized to receive fluticasone alone (F) or continue combined fluticasone/salmeterol (F/S) after a run-in period on F/S. Among Gly/Gly subjects, those in the F/S treatment group showed improvement in AM PEFR (+ 8.4 L/s) whereas those receiving F alone experienced a reduction in AM PEFR over the study period (-14.4 L/s), (p = 0.06). There was no significant difference in morning peak expiratory flow rate (AM PEFR) in Arg/Arg participants randomized to receive F/S (-15.7L) vs F alone (-5.6 L/s) (p = 0.61). There was no significant difference in exacerbations in the Arg/Arg subjects treated with F/S compared with those treated with F (p = 0.65). CONCLUSIONS Withdrawal of LABA therapy in asthmatics with the Arg/Arg genotype at the 16th amino acid position of B2AR did not lead to significant improvement in AM PEFR. LABA withdrawal in the Gly/Gly genotype however led to a borderline significant decline in AM PEFR.
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Affiliation(s)
- Marjorie Slankard
- a Department of Medicine , Columbia University , New York , NY , USA
| | - Mary Ann Michelis
- b Department of Medicine and Pediatrics , Hackensack University Medical Center , Hackensack , NJ , USA
| | - Mahesh Mansukhani
- c Department of Pathology , Columbia University , New York , NY , USA
| | - Barbara McGoey
- d Hackensack University Medical Center , Department of Medicine , Hackensack , NJ , USA
| | - Amy Paige
- e Mailman School of Public Health , Columbia University , New York , NY , USA
| | - Howard Andrews
- e Mailman School of Public Health , Columbia University , New York , NY , USA
| | - David Lederer
- a Department of Medicine , Columbia University , New York , NY , USA
| | - Stephen Canfield
- a Department of Medicine , Columbia University , New York , NY , USA
| | - Emily DiMango
- a Department of Medicine , Columbia University , New York , NY , USA
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Abstract
Environmental adaptation is one of the most fundamental features of organisms. Modern genome science has identified some genes associated with adaptive traits of organisms, and has provided insights into environmental adaptation and evolution. However, how genes contribute to adaptive traits and how traits are selected under an environment in the course of evolution remain mostly unclear. To approach these issues, we utilize “Dark-fly”, a Drosophila melanogaster line maintained in constant dark conditions for more than 60 years. Our previous analysis identified 220,000 single nucleotide polymorphisms (SNPs) in the Dark-fly genome, but did not clarify which SNPs of Dark-fly are truly adaptive for living in the dark. We found here that Dark-fly dominated over the wild-type fly in a mixed population under dark conditions, and based on this domination we designed an experiment for genome reselection to identify adaptive genes of Dark-fly. For this experiment, large mixed populations of Dark-fly and the wild-type fly were maintained in light conditions or in dark conditions, and the frequencies of Dark-fly SNPs were compared between these populations across the whole genome. We thereby detected condition-dependent selections toward approximately 6% of the genome. In addition, we observed the time-course trajectory of SNP frequency in the mixed populations through generations 0, 22, and 49, which resulted in notable categorization of the selected SNPs into three types with different combinations of positive and negative selections. Our data provided a list of about 100 strong candidate genes associated with the adaptive traits of Dark-fly.
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Kwon DH, Kang TJ, Kim YH, Lee SH. Phenotypic- and Genotypic-Resistance Detection for Adaptive Resistance Management in Tetranychus urticae Koch. PLoS One 2015; 10:e0139934. [PMID: 26545209 PMCID: PMC4636269 DOI: 10.1371/journal.pone.0139934] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/18/2015] [Indexed: 11/18/2022] Open
Abstract
Rapid resistance detection is necessary for the adaptive management of acaricide-resistant populations of Tetranychus urticae. Detection of phenotypic and genotypic resistance was conducted by employing residual contact vial bioassay (RCV) and quantitative sequencing (QS) methods, respectively. RCV was useful for detecting the acaricide resistance levels of T. urticae, particularly for on-site resistance detection; however, it was only applicable for rapid-acting acaricides (12 out of 19 tested acaricides). QS was effective for determining the frequencies of resistance alleles on a population basis, which corresponded to 12 nonsynonymous point mutations associated with target-site resistance to five types of acaricides [organophosphates (monocrotophos, pirimiphos-methyl, dimethoate and chlorpyrifos), pyrethroids (fenpropathrin and bifenthrin), abamectin, bifenazate and etoxazole]. Most field-collected mites exhibited high levels of multiple resistance, as determined by RCV and QS data, suggesting the seriousness of their current acaricide resistance status in rose cultivation areas in Korea. The correlation analyses revealed moderate to high levels of positive relationships between the resistance allele frequencies and the actual resistance levels in only five of the acaricides evaluated, which limits the general application of allele frequency as a direct indicator for estimating actual resistance levels. Nevertheless, the resistance allele frequency data alone allowed for the evaluation of the genetic resistance potential and background of test mite populations. The combined use of RCV and QS provides basic information on resistance levels, which is essential for choosing appropriate acaricides for the management of resistant T. urticae.
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Affiliation(s)
- Deok Ho Kwon
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151–921, Republic of Korea
- * E-mail: (DHK); (SHL)
| | - Taek-Jun Kang
- Department of Horticultural Crop Research, National Institute of Horticultural and Herbal Science, RDA, Jeonju 565–852, Republic of Korea
| | - Young Ho Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151–921, Republic of Korea
| | - Si Hyeock Lee
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151–921, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151–921, Republic of Korea
- * E-mail: (DHK); (SHL)
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Capper RL, Jin YK, Lundgren PB, Peplow LM, Matz MV, van Oppen MJH. Quantitative high resolution melting: two methods to determine SNP allele frequencies from pooled samples. BMC Genet 2015; 16:62. [PMID: 26070466 PMCID: PMC4465018 DOI: 10.1186/s12863-015-0222-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 05/27/2015] [Indexed: 01/06/2023] Open
Abstract
Background The advent of next-generation sequencing has brought about an explosion of single nucleotide polymorphism (SNP) data in non-model organisms; however, profiling these SNPs across multiple natural populations still requires substantial time and resources. Results Here, we introduce two cost-efficient quantitative High Resolution Melting (qHRM) methods for measuring allele frequencies at known SNP loci in pooled DNA samples: the “peaks” method, which can be applied to large numbers of SNPs, and the “curves” method, which is more labor intensive but also slightly more accurate. Using the reef-building coral Acropora millepora, we show that both qHRM methods can recover the allele proportions from mixtures prepared using two or more individuals of known genotype. We further demonstrate advantages of each method over previously published methods; specifically, the “peaks” method can be rapidly scaled to screen several hundred SNPs at once, whereas the “curves” method is better suited for smaller numbers of SNPs. Conclusions Compared to genotyping individual samples, these methods can save considerable effort and genotyping costs when relatively few candidate SNPs must be profiled across a large number of populations. One of the main applications of this method could be validation of SNPs of interest identified in population genomic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0222-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roxana L Capper
- Department of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Young K Jin
- School of Marine and Tropical Biology, James Cook University, Townsville, Qld, 4811, Australia. .,Australian Institute of Marine Science, PMB3, Townsville MC, Qld, 4810, Australia.
| | - Petra B Lundgren
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Lesa M Peplow
- Australian Institute of Marine Science, PMB3, Townsville MC, Qld, 4810, Australia.
| | - Mikhail V Matz
- Department of Cell and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
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Kwon DH, Clark JM, Lee SH. Toxicodynamic mechanisms and monitoring of acaricide resistance in the two-spotted spider mite. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2015; 121:97-101. [PMID: 26047116 DOI: 10.1016/j.pestbp.2014.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/09/2014] [Accepted: 12/09/2014] [Indexed: 06/04/2023]
Abstract
The two-spotted spider (Tetranychus urticae) is one of the most serious pests world-wide and has developed resistance to many types of acaricides. Various mutations on acaricide target site genes have been determined to be responsible for toxicodynamic resistance, and the genotyping and frequency prediction of these mutations can be employed as an alternative resistance monitoring strategy. A quantitative sequencing (QS) protocol was reported as a population-based genotyping technique, and applied for the determination of resistance allele frequencies in T. urticae field populations. In addition, a modified glass vial bioassay method (residual contact vial bioassay, RCV) was implemented as a rapid on-site resistance monitoring tool. The QS protocol, together with the RCV, would greatly facilitate monitoring of T. urticae resistance. Recent completion of T. urticae genome analysis should facilitate the identification of additional resistance genetic markers that can be employed for molecular resistance monitoring.
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Affiliation(s)
- Deok Ho Kwon
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
| | - J Marshall Clark
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Si Hyeock Lee
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea; Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
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Sensitive detection of point mutation using exponential strand displacement amplification-based surface enhanced Raman spectroscopy. Biosens Bioelectron 2015; 65:191-7. [DOI: 10.1016/j.bios.2014.10.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/29/2014] [Accepted: 10/13/2014] [Indexed: 12/29/2022]
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Klosterman SJ, Anchieta A, McRoberts N, Koike ST, Subbarao KV, Voglmayr H, Choi YJ, Thines M, Martin FN. Coupling Spore Traps and Quantitative PCR Assays for Detection of the Downy Mildew Pathogens of Spinach (Peronospora effusa) and Beet (P. schachtii). PHYTOPATHOLOGY 2014; 104:1349-59. [PMID: 24964150 PMCID: PMC4841388 DOI: 10.1094/phyto-02-14-0054-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Downy mildew of spinach (Spinacia oleracea), caused by Peronospora effusa, is a production constraint on production worldwide, including in California, where the majority of U.S. spinach is grown. The aim of this study was to develop a real-time quantitative polymerase chain reaction (qPCR) assay for detection of airborne inoculum of P. effusa in California. Among oomycete ribosomal DNA (rDNA) sequences examined for assay development, the highest nucleotide sequence identity was observed between rDNA sequences of P. effusa and P. schachtii, the cause of downy mildew on sugar beet and Swiss chard in the leaf beet group (Beta vulgaris subsp. vulgaris). Single-nucleotide polymorphisms were detected between P. effusa and P. schachtii in the 18S rDNA regions for design of P. effusa- and P. schachtii-specific TaqMan probes and reverse primers. An allele-specific probe and primer amplification method was applied to determine the frequency of both P. effusa and P. schachtii rDNA target sequences in pooled DNA samples, enabling quantification of rDNA of P. effusa from impaction spore trap samples collected from spinach production fields. The rDNA copy numbers of P. effusa were, on average, ≈3,300-fold higher from trap samples collected near an infected field compared with those levels recorded at a site without a nearby spinach field. In combination with disease-conducive weather forecasting, application of the assays may be helpful to time fungicide applications for disease management.
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Vlieg AVH, Flinterman LE, Bare LA, Cannegieter SC, Reitsma PH, Arellano AR, Tong CH, Devlin JJ, Rosendaal FR. Genetic Variations Associated With Recurrent Venous Thrombosis. ACTA ACUST UNITED AC 2014; 7:806-13. [DOI: 10.1161/circgenetics.114.000682] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background—
The prediction of recurrent venous thrombosis using individual genetic risk predictors has proven to be challenging. The aim of this study was to assess whether multiple genetic single nucleotide polymorphism (SNP) analysis would predict recurrent venous thrombosis.
Methods and Results—
Patients with a first venous thrombosis were followed for a recurrent venous thrombosis up to 2009 (MEGA follow-up study), which occurred in 608 out of 4100 patients (2.7%/year). Thirty-one common thrombosis-associated single nucleotide polymorphisms (SNPs) were associated with the risk of recurrence. A genetic risk score (GRS) for each individual was calculated by summing the number of risk-increasing alleles for each of the 31 SNPs and for a simplified model consisting of 5 SNPs: rs6025, rs1799963, rs8176719, rs2066865, and rs2036914. The risk of recurrence associated with the GRS was calculated continuously and after stratification in a low and high score. All individual SNPs were at most mildly associated with recurrence risk. Regarding the 31-SNP GRS, recurrence risk was highest in patients with ≥31 and lowest in patients with <21 risk alleles. The discriminative power of the 5-SNP GRS was similar to that of the 31-SNP GRS. The 6-year cumulative incidence of recurrence was high for individuals with ≥5 (20.3%; 95% confidence interval, 16.5–24.1) and low for individuals with ≤1 (9.4%; 95% confidence interval, 6.7–12.1) risk alleles. Predictive power improved after stratification into provoked and unprovoked first events and sex.
Conclusions—
Multiple genetic SNP analysis is useful in the prediction of recurrent thrombosis, even more so when combining this model with clinical risk factors.
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Affiliation(s)
- Astrid van Hylckama Vlieg
- From the Department of Clinical Epidemiology (A.v.H.V., L.E.F., S.C.C., F.R.R.), Department of Thrombosis and Haemostasis (P.H.R., F.R.R.), and Einthoven Laboratory for Experimental Vascular Medicine (A.v.H.V., S.C.C., P.H.R., F.R.R.), Leiden University Medical Center, Leiden, the Netherlands; and Celera, Alameda, CA (L.A.B., A.R.A., C.H.T., J.J.D.)
| | - Linda E. Flinterman
- From the Department of Clinical Epidemiology (A.v.H.V., L.E.F., S.C.C., F.R.R.), Department of Thrombosis and Haemostasis (P.H.R., F.R.R.), and Einthoven Laboratory for Experimental Vascular Medicine (A.v.H.V., S.C.C., P.H.R., F.R.R.), Leiden University Medical Center, Leiden, the Netherlands; and Celera, Alameda, CA (L.A.B., A.R.A., C.H.T., J.J.D.)
| | - Lance A. Bare
- From the Department of Clinical Epidemiology (A.v.H.V., L.E.F., S.C.C., F.R.R.), Department of Thrombosis and Haemostasis (P.H.R., F.R.R.), and Einthoven Laboratory for Experimental Vascular Medicine (A.v.H.V., S.C.C., P.H.R., F.R.R.), Leiden University Medical Center, Leiden, the Netherlands; and Celera, Alameda, CA (L.A.B., A.R.A., C.H.T., J.J.D.)
| | - Suzanne C. Cannegieter
- From the Department of Clinical Epidemiology (A.v.H.V., L.E.F., S.C.C., F.R.R.), Department of Thrombosis and Haemostasis (P.H.R., F.R.R.), and Einthoven Laboratory for Experimental Vascular Medicine (A.v.H.V., S.C.C., P.H.R., F.R.R.), Leiden University Medical Center, Leiden, the Netherlands; and Celera, Alameda, CA (L.A.B., A.R.A., C.H.T., J.J.D.)
| | - Pieter H. Reitsma
- From the Department of Clinical Epidemiology (A.v.H.V., L.E.F., S.C.C., F.R.R.), Department of Thrombosis and Haemostasis (P.H.R., F.R.R.), and Einthoven Laboratory for Experimental Vascular Medicine (A.v.H.V., S.C.C., P.H.R., F.R.R.), Leiden University Medical Center, Leiden, the Netherlands; and Celera, Alameda, CA (L.A.B., A.R.A., C.H.T., J.J.D.)
| | - Andre R. Arellano
- From the Department of Clinical Epidemiology (A.v.H.V., L.E.F., S.C.C., F.R.R.), Department of Thrombosis and Haemostasis (P.H.R., F.R.R.), and Einthoven Laboratory for Experimental Vascular Medicine (A.v.H.V., S.C.C., P.H.R., F.R.R.), Leiden University Medical Center, Leiden, the Netherlands; and Celera, Alameda, CA (L.A.B., A.R.A., C.H.T., J.J.D.)
| | - Carmen H. Tong
- From the Department of Clinical Epidemiology (A.v.H.V., L.E.F., S.C.C., F.R.R.), Department of Thrombosis and Haemostasis (P.H.R., F.R.R.), and Einthoven Laboratory for Experimental Vascular Medicine (A.v.H.V., S.C.C., P.H.R., F.R.R.), Leiden University Medical Center, Leiden, the Netherlands; and Celera, Alameda, CA (L.A.B., A.R.A., C.H.T., J.J.D.)
| | - James J. Devlin
- From the Department of Clinical Epidemiology (A.v.H.V., L.E.F., S.C.C., F.R.R.), Department of Thrombosis and Haemostasis (P.H.R., F.R.R.), and Einthoven Laboratory for Experimental Vascular Medicine (A.v.H.V., S.C.C., P.H.R., F.R.R.), Leiden University Medical Center, Leiden, the Netherlands; and Celera, Alameda, CA (L.A.B., A.R.A., C.H.T., J.J.D.)
| | - Frits R. Rosendaal
- From the Department of Clinical Epidemiology (A.v.H.V., L.E.F., S.C.C., F.R.R.), Department of Thrombosis and Haemostasis (P.H.R., F.R.R.), and Einthoven Laboratory for Experimental Vascular Medicine (A.v.H.V., S.C.C., P.H.R., F.R.R.), Leiden University Medical Center, Leiden, the Netherlands; and Celera, Alameda, CA (L.A.B., A.R.A., C.H.T., J.J.D.)
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Kimura A, Kanayama N, Ogawa A, Shibata H, Nakashita H, Takarada T, Maeda M. Thermodynamics-based rational design of DNA block copolymers for quantitative detection of single-nucleotide polymorphisms by affinity capillary electrophoresis. Anal Chem 2014; 86:11425-33. [PMID: 25358129 DOI: 10.1021/ac503522f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diblock copolymers composed of allele-specific oligodeoxyribonucleotide (ODN) and poly(ethylene glycol) (PEG) are used as an affinity probe of free-solution capillary electrophoresis to quantitatively detect single-base substitutions in genetic samples. During electrophoresis, the probe binds strongly to a wild-type single-stranded DNA analyte (WT) through hybridization, while it binds weakly to its single-base-mutated DNA analyte (MT) due to a mismatch. Complex formation with the probe augments the hydrodynamic friction of either analyte, thereby retarding its migration. The difference in affinity strength leads to separation of the WT, MT, and contaminants, including the PCR primers used for sample preparation. The optimal sequence of the probe's ODN segment is rationally determined in such a way that the binding constant between the ODN segment and MT at the capillary temperature is on the order of 10(6) M(-1). The validity of this guideline is verified using various chemically synthesized DNA analytes, as well as those derived from a bacterial genome. The peak area ratio of MT agrees well with its feed ratio, suggesting the prospective use of the present method in SNP allele frequency estimation.
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Affiliation(s)
- Ayumi Kimura
- Bioengineering Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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43
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Whole-genome sequencing of Burkholderia pseudomallei isolates from an unusual melioidosis case identifies a polyclonal infection with the same multilocus sequence type. J Clin Microbiol 2014; 53:282-6. [PMID: 25339397 DOI: 10.1128/jcm.02560-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Twelve Burkholderia pseudomallei isolates collected over a 32-month period from a patient with chronic melioidosis demonstrated identical multilocus sequence types (STs). However, whole-genome sequencing suggests a polyclonal infection. This study is the first to report a mixed infection with the same ST.
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44
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Knapp S, Meghjee N, Cassidy S, Jamil K, Thursz M. Detection of allele specific differences in IFNL3 (IL28B) mRNA expression. BMC MEDICAL GENETICS 2014; 15:104. [PMID: 25287681 PMCID: PMC4411934 DOI: 10.1186/s12881-014-0104-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 09/05/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND Variants of the interferon-lambda3 (IFNL3) gene have been associated with both spontaneous and treatment induced clearance of HCV infection. Attempts to link polymorphisms of the IFNL3 gene with variation in the level of IFNL3 expression have been inconclusive. This is partially due to the difficulty to design assays distinguishing IFNL3 from IFNL2. METHODS In this study an allele specific real-time PCR (RT-PCR) assay was developed which allows the relative quantification of the two IFNL3 transcripts in cells heterozygous for SNP IFNL3.rs4803217 in the 3'UTR of the IFNL3 gene. This SNP is in strong linkage disequilibrium (LD) with the predictive marker rs12979860. RESULTS Raji cells showed two-fold increased levels of IFNL3.rs4803217 C-allele expression. In peripheral blood mononuclear cells (PBMCs) of eight uninfected donors, two donors showed increased IFNL3.rs4803217 C-allele expression. CONCLUSION This indicates that allele specific differences in IFNL3 expression vary between individuals and might contribute to the variety of outcomes in HCV infected patients.
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Affiliation(s)
- Susanne Knapp
- Imperial College, St Mary's Hospital, 10th floor QEQM Wing, Liver Unit, South Wharf Road, London, W2 1NY, UK.
| | - Naeem Meghjee
- Imperial College, St Mary's Hospital, 10th floor QEQM Wing, Liver Unit, South Wharf Road, London, W2 1NY, UK.
| | - Sorcha Cassidy
- Imperial College, St Mary's Hospital, 10th floor QEQM Wing, Liver Unit, South Wharf Road, London, W2 1NY, UK.
| | - Khaleel Jamil
- Imperial College, St Mary's Hospital, 10th floor QEQM Wing, Liver Unit, South Wharf Road, London, W2 1NY, UK.
| | - Mark Thursz
- Imperial College, St Mary's Hospital, 10th floor QEQM Wing, Liver Unit, South Wharf Road, London, W2 1NY, UK.
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45
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Drum M, Kranaster R, Ewald C, Blasczyk R, Marx A. Variants of a Thermus aquaticus DNA polymerase with increased selectivity for applications in allele- and methylation-specific amplification. PLoS One 2014; 9:e96640. [PMID: 24800860 PMCID: PMC4011760 DOI: 10.1371/journal.pone.0096640] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/09/2014] [Indexed: 01/25/2023] Open
Abstract
The selectivity of DNA polymerases is crucial for many applications. For example, high discrimination between the extension of matched versus mismatched primer termini is desired for the detection of a single nucleotide variation at a particular locus within the genome. Here we describe the generation of thermostable mutants of the large fragment of Thermus aquaticus DNA polymerase (KlenTaq) with increased mismatch extension selectivity. In contrast to previously reported much less active KlenTaq mutants with mismatch discrimination abilities, many of the herein discovered mutants show conserved wild-type-like high activities. We demonstrate for one mutant containing the single amino acid exchange R660V the suitability for application in allele-specific amplifications directly from whole blood without prior sample purification. Also the suitability of the mutant for methylation specific amplification in the diagnostics of 5-methyl cytosines is demonstrated. Furthermore, the identified mutant supersedes other commercially available enzymes in human leukocyte antigen (HLA) analysis by sequence-specific primed polymerase chain reactions (PCRs).
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Affiliation(s)
- Matthias Drum
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Ramon Kranaster
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
- myPOLS Biotec, University of Konstanz, Konstanz, Germany
| | - Christina Ewald
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Rainer Blasczyk
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
- * E-mail:
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46
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Chen Y, Bogema DR, Barchia IM, Herron GA. Quantification of the pirimicarb resistance allele frequency in pooled cotton aphid (Aphis gossypii Glover) samples by TaqMan SNP genotyping assay. PLoS One 2014; 9:e91104. [PMID: 24614533 PMCID: PMC3948748 DOI: 10.1371/journal.pone.0091104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 02/07/2014] [Indexed: 11/25/2022] Open
Abstract
Background Pesticide resistance monitoring is a crucial part to achieving sustainable integrated pest management (IPM) in agricultural production systems. Monitoring of resistance in arthropod populations is initially performed by bioassay, a method that detects a phenotypic response to pesticides. Molecular diagnostic assays, offering speed and cost improvements, can be developed when the causative mutation for resistance has been identified. However, improvements to throughput are limited as genotyping methods cannot be accurately applied to pooled DNA. Quantifying an allele frequency from pooled DNA would allow faster and cheaper monitoring of pesticide resistance. Methodology/Principal Findings We demonstrate a new method to quantify a resistance allele frequency (RAF) from pooled insects via TaqMan assay by using raw fluorescence data to calculate the transformed fluorescence ratio k’ at the inflexion point based on a four parameter sigmoid curve. Our results show that k’ is reproducible and highly correlated with RAF (r >0.99). We also demonstrate that k’ has a non-linear relationship with RAF and that five standard points are sufficient to build a prediction model. Additionally, we identified a non-linear relationship between runs for k’, allowing the combination of samples across multiple runs in a single analysis. Conclusions/Significance The transformed fluorescence ratio (k') method can be used to monitor pesticide resistance in IPM and to accurately quantify allele frequency from pooled samples. We have determined that five standards (0.0, 0.2, 0.5, 0.8, and 1.0) are sufficient for accurate prediction and are statistically-equivalent to the 13 standard points used experimentally
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Affiliation(s)
- Yizhou Chen
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Daniel R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Idris M Barchia
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Grant A Herron
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
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Bidzhieva B, Laassri M, Chumakov K. Allele-specific PCR for quantitative analysis of mutants in live viral vaccines. J Virol Methods 2014; 201:86-92. [PMID: 24607431 DOI: 10.1016/j.jviromet.2014.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 11/29/2022]
Abstract
Monitoring consistency of genetic composition of oral polio vaccine (OPV) is a part of its quality control. It is performed by mutant analysis by PCR and restriction enzyme cleavage (MAPREC) used to quantify neurovirulent revertants in the viral genome. Here an alternative method based on quantitative PCR is proposed. Allele-specific quantitative polymerase chain reaction (asqPCR) uses a "tethered" oligonucleotide primer consisting of two specific parts connected by a polyinosine stretch. Homogeneous DNA from plasmids containing wild Leon/37 and attenuated Sabin 3 sequences with 100% 472(C) and 100% 472(T) could only be amplified using homologous primers. Real-time implementation of the allele-specific PCR resulted in sensitive detection of 472(C) revertants with the limit of quantitation of less than 0.05%. Monovalent vaccine batches and international viral references for MAPREC test were used to validate the method. asqPCR performed with the WHO references and monovalent batches of vaccine showed that the new method could measure accurately and reproducibly the content of revertants producing values comparable to MAPREC results. This suggests that asqPCR could be used as an alternative to MAPREC for lot release of OPV. The method could also be used for the quantitation of other mutants in populations of microorganisms.
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Affiliation(s)
- Bella Bidzhieva
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 1401 Rockville Pike, HFM 470, Rockville, MD 20852, USA
| | - Majid Laassri
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 1401 Rockville Pike, HFM 470, Rockville, MD 20852, USA
| | - Konstantin Chumakov
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 1401 Rockville Pike, HFM 470, Rockville, MD 20852, USA.
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48
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Identification and quantification of benzimidazole resistance polymorphisms in Haemonchus contortus isolated in Northeastern Brazil. Vet Parasitol 2014; 199:160-4. [DOI: 10.1016/j.vetpar.2013.11.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 11/01/2013] [Accepted: 11/09/2013] [Indexed: 11/20/2022]
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49
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Satterfield BC. Cooperative primers: 2.5 million-fold improvement in the reduction of nonspecific amplification. J Mol Diagn 2013; 16:163-73. [PMID: 24370857 DOI: 10.1016/j.jmoldx.2013.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 10/26/2013] [Accepted: 10/30/2013] [Indexed: 10/25/2022] Open
Abstract
The increasing need to multiplex nucleic acid reactions presses test designers to the limits of amplification specificity in PCR. Although more than a dozen hot starts have been developed for PCR to reduce primer-dimer formation, none can stop the propagation of primer-dimers once formed. Even a small number of primer-dimers can result in false-negatives and/or false-positives. Herein, we demonstrate a new class of primer technology that greatly reduces primer-dimer propagation, showing successful amplification of 60 template copies with no signal dampening in a background of 150,000,000 primer-dimers. In contrast, normal primers, with or without a hot start, experienced signal dampening with as few as 60 primer-dimers and false-negatives with only 600 primer-dimers. This represents more than a 2.5 million-fold improvement in reduction of nonspecific amplification. We also show how a probe can be incorporated into the cooperative primer, with 2.5 times more signal than conventional fluorescent probes.
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50
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Cheng Y, Zhao J, Jia H, Yuan Z, Li Z. Ligase chain reaction coupled with rolling circle amplification for high sensitivity detection of single nucleotide polymorphisms. Analyst 2013; 138:2958-63. [PMID: 23535938 DOI: 10.1039/c3an36920j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a highly sensitive and homogeneous assay for the detection of single nucleotide polymorphisms (SNPs) by ligase chain reaction (LCR) coupled with rolling circle amplification (RCA). The LCR probes include one pair of probes and a padlock probe (PLP). In the LCR, one pair of probes composed of X and Y, perfectly hybridize with the upper strand of the target DNA after thermal denaturation. They are then ligated by the thermostable ligase to form the ligation product of XY. At the same time, the PLP hybridizes with the lower strand of the target DNA and are ligated to form the circular PLP (cPLP). After repeated cycles of denaturation, annealing, and ligation, the target DNA is amplified exponentially to generate a large number of XY and cPLPs. Subsequently, RCA is triggered by the cPLP as a template and XY as a primer, producing large numbers of long strand DNA products, which are detected by binding with the fluorescent dye, SYBR Green I, in a homogeneous manner. This method is simple, and avoids the need for detection of the LCR products with labeled probes and complex separation steps. The assay is sensitive and specific enough to detect a 1 fM target DNA molecule. It is possible to accurately determine the allele frequency as low as 1.0%. The LCR coupled with RCA assay extends the application of the LCR and RCA, and provides a new strategy for detecting SNPs as well as nucleic acid analysis, immunoassay, and molecular diagnosis.
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Affiliation(s)
- Yongqiang Cheng
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding, 071002, P. R. China.
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