Glyphosate-Resistant Junglerice (Echinochloa colona) from Mississippi and Tennessee: Magnitude and Resistance Mechanisms

Weed Science ◽  
2018 ◽  
Vol 66 (5) ◽  
pp. 603-610 ◽  
Author(s):  
Vijay K. Nandula ◽  
Garret B. Montgomery ◽  
Amaranatha R. Vennapusa ◽  
Mithila Jugulam ◽  
Darci A. Giacomini ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Quantitative Polymerase Chain Reaction ◽  
Point Mutations ◽  
Resistance Index ◽  
Glyphosate Resistance ◽  
Resistance Mechanisms ◽  
Site Mutation ◽  
Single Nucleotide ◽  
Treated Leaf ◽  
Polymerase Chain

AbstractRecently, several incidents of glyphosate failure on junglerice [Echinochloa colona(L.) Link] have been reported in the midsouthern United States, specifically in Mississippi and Tennessee. Research was conducted to measure the magnitude of glyphosate resistance and to determine the mechanism(s) of resistance to glyphosate inE. colonapopulations from Mississippi and Tennessee. ED50(dose required to reduce plant growth by 50%) values for a resistant MSGR4 biotype, a resistant TNGR population, and a known susceptible MSGS population were 0.8, 1.62, and 0.23 kg ae ha−1of glyphosate, respectively. The resistance index calculated from the these ED50values indicated that the MSGR4 biotype and TNGR population were 4- and 7-fold, respectively, resistant to glyphosate relative to the MSGS population. The absorption patterns of [14C]glyphosate in the TNGR and MSGS populations were similar. However, the MSGS population translocated 13% more [14C]glyphosate out of the treated leaf compared with the TNGR population at 48 h after treatment.EPSPSgene sequence analyses of TNGRE. colonaindicated no evidence of any point mutations, but several resistant biotypes, including MSGR4, possessed a single-nucleotide substitution of T for C at codon 106 position, resulting in a proline-to-serine substitution (CCA to TCA). Results from quantitative polymerase chain reaction analyses suggested that there was no amplification of theEPSPSgene in the resistant populations and biotypes. Thus, the mechanism of resistance in the MSGR population (and associated biotypes) is, in part, due to a target-site mutation at the 106 loci of theEPSPSgene, while reduced translocation of glyphosate was found to confer glyphosate resistance in the TNGR population.

scholarly journals Cellular microRNA detection with miRacles: microRNA- activated conditional looping of engineered switches

2019 ◽  
Vol 5 (3) ◽  
pp. eaau9443 ◽  
Author(s):  
Arun Richard Chandrasekaran ◽  
Molly MacIsaac ◽  
Paromita Dey ◽  
Oksana Levchenko ◽  
Lifeng Zhou ◽  
...  
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Northern Blotting ◽  
Single Step ◽  
Single Nucleotide ◽  
Disease Biomarkers ◽  
Microrna Detection ◽  
Detection Assay ◽  
Polymerase Chain ◽  
Regulatory Rnas ◽  
Nucleotide Specificity

MicroRNAs are short noncoding regulatory RNAs that are increasingly used as disease biomarkers. Detection of microRNAs can be arduous and expensive and often requires amplification, labeling, or radioactive probes. Here, we report a single-step, nonenzymatic microRNA detection assay using conformationally responsive DNA nanoswitches. Termed miRacles (microRNA-activated conditional looping of engineered switches), our assay has subattomole sensitivity and single-nucleotide specificity using an agarose gel electrophoresis readout. We detect cellular microRNAs from nanogram-scale RNA extracts of differentiating muscle cells and multiplex our detection for several microRNAs from one biological sample. We demonstrate 1-hour detection without expensive equipment or reagents, making this assay a compelling alternative to quantitative polymerase chain reaction and Northern blotting.

scholarly journals The expression and mutation of <i>BMPR1B</i> and its association with litter size in small-tail Han sheep (<i>Ovis aries</i>)

2021 ◽  
Vol 64 (1) ◽  
pp. 211-221
Author(s):  
Yu-Liang Wen ◽  
Xiao-Fei Guo ◽  
Lin Ma ◽  
Xiao-Sheng Zhang ◽  
Jin-Long Zhang ◽  
...  
Keyword(s):  
Litter Size ◽  
Quantitative Polymerase Chain Reaction ◽  
Follicular Development ◽  
Follicular Phase ◽  
Ovis Aries ◽  
Negative Effects ◽  
Single Nucleotide ◽  
Ovarian Granulosa Cell ◽  
Polymerase Chain ◽  
Genotype And Allele Frequencies

Abstract. Previous studies have shown that BMPR1B promotes follicular development and ovarian granulosa cell proliferation, thereby affecting ovulation in mammals. In this study, the expression and polymorphism of the BMPR1B gene associated with litter size in small-tail Han (STH) sheep were determined. The expression of BMPR1B was detected in 14 tissues of STH sheep during the follicular phase as well as in the hypothalamic–pituitary–gonadal (HPG) axis of monotocous and polytocous STH sheep during the follicular and luteal phases using quantitative polymerase chain reaction (qPCR). Sequenom MassARRAY® single nucleotide polymorphism (SNP) technology was also used to detect the polymorphism of SNPs in seven sheep breeds. Here, BMPR1B was highly expressed in hypothalamus, ovary, uterus, and oviduct tissue during the follicular phase, and BMPR1B was expressed significantly more in the hypothalamus of polytocous ewes than in monotocous ewes during both the follicular and luteal phases (P<0.05). For genotyping, we found that genotype and allele frequencies of three loci of the BMPR1B gene were extremely significantly different (P<0.01) between the monotocous and polytocous groups. Association analysis results showed that the g.29380965A>G locus had significant negative effects on the litter size of STH sheep, and the combination of g.29380965A>G and FecB (Fec – fecundity and B – Booroola; A746G) at the BMPR1B gene showed that the litter size of AG–GG, AA–GG, and GG–GG genotypes was significantly higher compared with other genotypes (P<0.05). This is the first study to find a new molecular marker affecting litter size and to systematically analyze the expression of BMPR1B in different fecundity and physiological periods of STH sheep.

Multiplex SNP genotyping in whole blood using an integrated microfluidic lab-on-a-chip

Lab on a Chip ◽  
2016 ◽  
Vol 16 (20) ◽  
pp. 4012-4019 ◽  
Author(s):  
L. Zhang ◽  
Q. Cai ◽  
R. S. Wiederkehr ◽  
M. Fauvart ◽  
P. Fiorini ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Quantitative Polymerase Chain Reaction ◽  
Cross Flow ◽  
Lab On A Chip ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Blood Lysis ◽  
Polymerase Chain ◽  
Silicon Based

We present a silicon-based integrated microsystem combining a blood lysis chamber, a cross-flow filter, a T-junction mixer, and a microreactor for quantitative polymerase chain reaction. The detection of multiple single nucleotide polymorphisms was demonstrated in the system from human blood.

scholarly journals MRPrimerW2: an enhanced tool for rapid design of valid high-quality primers with multiple search modes for qPCR experiments

2019 ◽  
Vol 47 (W1) ◽  
pp. W614-W622 ◽  
Author(s):  
Hajin Jeon ◽  
Jeongmin Bae ◽  
Sang-Hyun Hwang ◽  
Kyu-Young Whang ◽  
Hyun-Seob Lee ◽  
...  
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Free Access ◽  
Target Sequence ◽  
Single Pair ◽  
High Quality ◽  
Single Nucleotide ◽  
Complete Set ◽  
Polymerase Chain ◽  
Target Sequences ◽  
Search Modes

Abstract For the best results in quantitative polymerase chain reaction (qPCR) experiments, it is essential to design high-quality primers considering a multitude of constraints and the purpose of experiments. The constraints include many filtering constraints, homology test on a huge number of off-target sequences, the same constraints for batch design of primers, exon spanning, and avoiding single nucleotide polymorphism (SNP) sites. The target sequences are either in database or given as FASTA sequences, and the experiment is for amplifying either each target sequence with each corresponding primer pairs designed under the same constraints or all target sequences with a single pair of primers. Many websites have been proposed, but none of them including our previous MRPrimerW fulfilled all the above features. Here, we describe the MRPrimerW2, the update version of MRPrimerW, which fulfils all the features by maintaining the advantages of MRPrimerW in terms of the kinds and sizes of databases for valid primers and the number of search modes. To achieve it, we exploited GPU computation and a disk-based key-value store using PCIe SSD. The complete set of 3 509 244 680 valid primers of MRPrimerW2 covers 99% of nine important organisms in an exhaustive manner. Free access: http://MRPrimerW2.com

scholarly journals Insight into the Significance ofAspergillus fumigatus cyp51APolymorphisms

2018 ◽  
Vol 62 (6) ◽  
Author(s):  
Rocio Garcia-Rubio ◽  
Laura Alcazar-Fuoli ◽  
Maria Candida Monteiro ◽  
Sara Monzon ◽  
Isabel Cuesta ◽  
...  
Keyword(s):  
Galleria Mellonella ◽  
Point Mutations ◽  
Resistance Mechanisms ◽  
Patient Treatment ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Content Type ◽  
Therapeutic Doses ◽  
Insight Into

ABSTRACTTriazole antifungal compounds are the first treatment choice for invasive aspergillosis. However, in the last decade the rate of azole resistance amongAspergillus fumigatusstrains has increased notoriously. The main resistance mechanisms are well defined and mostly related to point mutations of the azole target, 14-α sterol demethylase (cyp51A), with or without tandem repeat integrations in thecyp51Apromoter. Furthermore, different combinations of five Cyp51A mutations (F46Y, M172V, N248T, D255E, and E427K) have been reported worldwide in about 10% of allA. fumigatusisolates tested. The azole susceptibility profile of these strains shows elevated azole MICs, although on the basis of the azole susceptibility breakpoints, these strains are not considered azole resistant. The purpose of the study was to determine whether thesecyp51Apolymorphisms (single nucleotide polymorphisms [SNPs]) are responsible for the azole susceptibility profile and whether they are reflected in a poorer azole treatment responsein vivothat could compromise patient treatment and outcome. A mutant with acyp51Adeletion was generated and became fully susceptible to all azoles tested. Also, threecyp51Agene constructions with different combinations of SNPs were generated and reintroduced into an azole-susceptible wild-type (WT) strain (the ΔakuBKU80strain). The alternative model hostGalleria mellonellawas used to compare the virulence and voriconazole response ofG. mellonellalarvae infected withA. fumigatusstrains with WTcyp51Aorcyp51Awith SNPs. All strains were pathogenic inG. mellonellalarvae, although they did not respond similarly to voriconazole therapeutic doses. Finally, the full genomes of these strains were sequenced and analyzed in comparison with those ofA. fumigatusWT strains, revealing that they belong to different strain clusters or lineages.

Rigid Ryegrass (Lolium rigidum) Populations Containing a Target Site Mutation in EPSPS and Reduced Glyphosate Translocation Are More Resistant to Glyphosate

Weed Science ◽  
2012 ◽  
Vol 60 (3) ◽  
pp. 474-479 ◽  
Author(s):  
Yazid Bostamam ◽  
Jenna M. Malone ◽  
Fleur C. Dolman ◽  
Peter Boutsalis ◽  
Christopher Preston
Keyword(s):  
Weed Control ◽  
Glyphosate Resistance ◽  
Resistance Mechanisms ◽  
Target Site ◽  
Lolium Rigidum ◽  
Site Mutation ◽  
Susceptible Population ◽  
Intensive Use ◽  
Rigid Ryegrass ◽  
Two Populations

Glyphosate is widely used for weed control in the grape growing industry in southern Australia. The intensive use of glyphosate in this industry has resulted in the evolution of glyphosate resistance in rigid ryegrass. Two populations of rigid ryegrass from vineyards, SLR80 and SLR88, had 6- to 11-fold resistance to glyphosate in dose-response studies. These resistance levels were higher than two previously well-characterized glyphosate-resistant populations of rigid ryegrass (SLR77 and NLR70), containing a modified target site or reduced translocation, respectively. Populations SLR80 and SLR88 accumulated less glyphosate, 12 and 17% of absorbed glyphosate, in the shoot in the resistant populations compared with 26% in the susceptible population. In addition, a mutation within the target enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) where Pro106had been substituted by either serine or threonine was identified. These two populations are more highly resistant to glyphosate as a consequence of expressing two different resistance mechanisms concurrently.

scholarly journals Chromosome 22q11 deletions, velo-cardio-facial syndrome and early-onset psychosis

2003 ◽  
Vol 183 (5) ◽  
pp. 409-413 ◽  
Author(s):  
D. Ivanov ◽  
G. Kirov ◽  
N. Norton ◽  
H. J. Williams ◽  
N. M. Williams ◽  
...  
Keyword(s):  
Early Onset ◽  
Quantitative Polymerase Chain Reaction ◽  
Age At Onset ◽  
Childhood Onset ◽  
Single Nucleotide ◽  
Chromosome 22Q11 ◽  
Childhood Onset Schizophrenia ◽  
Early Onset Psychosis ◽  
Polymerase Chain ◽  
Velo Cardio Facial Syndrome

BackgroundVelo-cardio-facial syndrome (VCFS) is associated with interstitial deletions of chromosome 22q11. About 30% of patients with VCFS have psychosis, and the rate of these deletions in schizophrenia has been reported to be about 1%. Even higher rates of VCFS deletions have been reported for childhood-onset schizophrenia.AimsTo test the hypothesis that there is an increased rate of VCFS among patients with early-onset psychosis (age at onset < 18 years). We screened 192 early-onset patients and 329 patients with adult-onset schizophrenia.MethodWe genotyped the patients and 444 healthy controls for hemizygosity of five microsatellite markers and one single nucleotide polymorphism that map to the 22q11-deleted region.ResultsOne patient had a VCFS deletion, confirmed with semi-quantitative polymerase chain reaction. None of the controls showed a pattern of genotypes consistent with hemizygosity.ConclusionsVCFS may be less frequent among patients with psychosis than previously suggested; this rate is not increased among early-onset patients.

scholarly journals The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants

2022 ◽  
Vol 9 ◽  
Author(s):  
Carlos Barrera-Avalos ◽  
Roberto Luraschi ◽  
Eva Vallejos-Vidal ◽  
Andrea Mella-Torres ◽  
Felipe Hernández ◽  
...  
Keyword(s):  
Detection Efficiency ◽  
Quantitative Polymerase Chain Reaction ◽  
Detection Sensitivity ◽  
Nucleotide Polymorphisms ◽  
False Negatives ◽  
Single Nucleotide ◽  
Rapid Antigen Detection Test ◽  
Current Scenario ◽  
Variant Detection ◽  
Polymerase Chain

Timely detection of severe acute respiratory syndrome due to coronavirus 2 (SARS-CoV-2) by reverse transcription quantitative polymerase chain reaction (RT-qPCR) has been the gold- strategy for identifying positive cases during the current pandemic. However, faster and less expensive methodologies are also applied for the massive diagnosis of COVID-19. In this way, the rapid antigen test (RAT) is widely used. However, it is necessary to evaluate its detection efficiency considering the current pandemic context with the circulation of new viral variants. In this study, we evaluated the sensitivity and specificity of RAT (SD BIOSENSOR, South Korea), widely used for testing and SARS-CoV-2 diagnosis in Santiago of Chile. The RAT showed a 90% (amplification range of 20 ≤ Cq &lt;25) and 10% (amplification range of 25 ≤ Cq &lt;30) of positive SARS-CoV-2 cases identified previously by RT-qPCR. Importantly, a 0% detection was obtained for samples within a Cq value&gt;30. In SARS-CoV-2 variant detection, RAT had a 42.8% detection sensitivity in samples with RT-qPCR amplification range 20 ≤ Cq &lt;25 containing the single nucleotide polymorphisms (SNP) K417N/T, N501Y and E484K, associated with beta or gamma SARS-CoV-2 variants. This study alerts for the special attention that must be paid for the use of RAT at a massive diagnosis level, especially in the current scenario of appearance of several new SARS-CoV-2 variants which could generate false negatives and the compromise of possible viral outbreaks.

scholarly journals Herbicide resistant weeds: the case of resistance to glyphosate

2021 ◽  
Vol 63 (2) ◽  
pp. 74-80
Author(s):  
The Duc Ngo ◽  
Keyword(s):  
Weed Management ◽  
Glyphosate Resistance ◽  
Resistance Mechanisms ◽  
Management Program ◽  
Ambrosia Artemisiifolia ◽  
Target Site ◽  
Integrated Weed Management ◽  
Weed Species ◽  
Site Mutation ◽  
Sites Of Action

Glyphosate has become the most widely used herbicide worldwide since 1974 with a global use of 8.6 billion kg (glyphosate active ingredient) between 1974 and 2014. This study reports on glyphosate resistant (GR) weeds and their resistance mechanisms based on global scientifically reported cases. Forty-nine different weed species have evolved resistance to glyphosate in 29 countries with a total of 318 identified cases worldwide. Fifty percent of these resistance cases were found in glyphosate-resistant cropping systems. There were 255 identified cases (80.2%) of glyphosate resistance in the top five countries (in terms of number of cases and species), namely USA, Australia, Argentina, Brazil, and Canada. The five most popular weed species (in terms of number of cases) found to be resistant to glyphosate were Conyza canadensis, Amaranthus palmeri, Amaranthus tuberculatus, Lolium perenne ssp. Multiflorum,and Ambrosia artemisiifolia with 42, 42, 29, 26, and 21 reported cases, respectively. Out of 49 weed species, 19 GR weed species were found to not only be resistant to glyphosate but also to other herbicide sites of action (multiple herbicide resistance). Glyphosate resistance mechanisms in weeds include (1) target-site alterations: target-site mutation and target-site gene amplification; and (2) non-target-site mechanisms involving different modes of exclusion from the target site: reduced glyphosate uptake, reduced glyphosate translocation, and enhanced glyphosate metabolism. It is essential to have an integrated weed management program that includes not only smart herbicide mixtures and rotations, but also cultural, manual, mechanical, and crop-based weed management methods.

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