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1. Filtering maxRatio results with machine learning models increases quantitative PCR accuracy over the fit point method

Author:
Marongiu, Luigi; Shain, Eric; Shain, Kevin; Allgayer, Heike
Source:
Journal of microbiological methods 2020 v.169 pp. 105803
ISSN:
0167-7012
Subject:
quantitative polymerase chain reaction,   etc   ; automation; support vector machines;     Show all 3 Subjects
Abstract:
... With qPCR reaching thousands of reactions per run, assay validation needs automation. We applied support vector machine to qPCR analysis and we could identify reactions with 100% accuracy, dispensing them from further validation. We achieved a greatly reduced workload that could improve high-throughput qPCR analysis. ...
DOI:
10.1016/j.mimet.2019.105803

2. Campylobacter in chicken – Critical parameters for international, multicentre evaluation of air sampling and detection methods

Author:
Johannessen, Gro S.; Garofolo, Giuliano; Di Serafino, Gabriella; Koláčková, Ivana; Karpíšková, Renáta; Wieczorek, Kinga; Osek, Jacek; Christensen, Julia; Torp, Mona; Hoorfar, Jeffrey
Source:
Food microbiology 2020 v.90 pp. 103455
ISSN:
0740-0020
Subject:
quantitative polymerase chain reaction,   etc   ; Campylobacter; air filters; air sampling; chickens; farms; flocks; monitoring; Europe;     Show all 9 Subjects
Abstract:
... The present pilot study aimed at evaluating air sampling as a novel method for monitoring Campylobacter in poultry farms. We compared the bacteriological isolation of Campylobacter from boot swabs and air filter samples using ISO 10272–1:2017. A secondary aim was to evaluate the use of molecular methods, i.e. real time PCR, on the same sample set. Samples from 44 flocks from five European countrie ...
DOI:
10.1016/j.fm.2020.103455

3. Novel real-time PCR assay for Lactobacillus casei group species using comparative genomics

Author:
Kim, Eiseul; Yang, Seung-Min; Cho, Eun-Ji; Kim, Hae-Yeong
Source:
Food microbiology 2020 v.90 pp. 103485
ISSN:
0740-0020
Subject:
quantitative polymerase chain reaction,   etc   ; Lactobacillus casei; Lactobacillus paracasei; Lactobacillus rhamnosus; genes; genomics; probiotics; taxonomy;     Show all 8 Subjects
Abstract:
... The Lactobacillus casei group, which includes the closely related species L. casei, L. paracasei, L. rhamnosus, and L. chiayiensis, has been under debate regarding its taxonomy because of the difficulty in distinguishing the species from each other. In the present study, we developed a novel real-time PCR assay for distinguishing the L. casei group species. The pan-genome, as determined by the gen ...
DOI:
10.1016/j.fm.2020.103485

4. Community dynamics of As(V)-reducing and As(III)-oxidizing genes during a wet–dry cycle in paddy soil amended with organic matter, gypsum, or iron oxide

Author:
Yuan, Chaolei; Qiao, Jiangtao; Li, Fangbai; Zhang, Xiaofeng; Du, Yanhong; Hu, Min; Sun, Weimin
Source:
Journal of hazardous materials 2020 v.393 pp. 122485
ISSN:
0304-3894
Subject:
quantitative polymerase chain reaction,   etc   ; arsenic; genes; gypsum; hematite; organic matter; oxidation; paddy soils; soil amendments; submergence;     Show all 10 Subjects
Abstract:
... Microbe-mediated redox transformations regulate arsenic mobility in paddy soil. However, the community dynamics of the related genes, which might be affected by soil ameliorants, have not been systematically investigated during a wet–dry cycle. This study incubated arsenic-contaminated paddy soil amended with organic matter (OM), gypsum, or hematite in microcosms under alternate watering condition ...
DOI:
10.1016/j.jhazmat.2020.122485

5. A core microbiota of the plant-earthworm interaction conserved across soils

Author:
Jacquiod, Samuel; Puga-Freitas, Ruben; Spor, Aymé; Mounier, Arnaud; Monard, Cécile; Mougel, Christophe; Philippot, Laurent; Blouin, Manuel
Source:
Soil biology & biochemistry 2020 v.144 pp. 107754
ISSN:
0038-0717
Subject:
quantitative polymerase chain reaction,   etc   ; bacteria; clay; earthworms; fungi; hosts; microbial communities; microhabitats; sand; soil types;     Show all 10 Subjects
Abstract:
... The core microbiota defines the fraction of microorganisms common to all individuals from the same host species regardless of the abiotic context, be they located inside (e.g. animal guts) or outside (e.g. plant rhizospheres). While the core microbiota of many host species have been documented, no study attempted to decipher how these core microbiota could be altered when their respective host spe ...
DOI:
10.1016/j.soilbio.2020.107754

6. Validation of a screening method for the detection of colistin-resistant E. coli containing mcr-1 in feral swine feces

Author:
Chandler, Jeffrey C.; Franklin, Alan B.; Bevins, Sarah N.; Bentler, Kevin T.; Bonnedahl, Jonas; Ahlstrom, Christina A.; Bisha, Bledar; Shriner, Susan A.
Source:
Journal of microbiological methods 2020 v.172 pp. 105892
ISSN:
0167-7012
Subject:
quantitative polymerase chain reaction,   etc   ; Escherichia coli; colistin; feces; feral animals; inoculum; screening; swine; vancomycin;     Show all 9 Subjects
Abstract:
... A method was developed and validated for the detection of colistin-resistant Escherichia coli containing mcr-1 in the feces of feral swine. Following optimization of an enrichment method using EC broth supplemented with colistin (1 μg/mL) and vancomycin (8 μg/mL), aliquots derived from 100 feral swine fecal samples were spiked with of one of five different mcr-1 positive E. coli strains (between 1 ...
DOI:
10.1016/j.mimet.2020.105892

7. Chestnut allergen detection in complex food products: Development and validation of a real-time PCR method

Author:
Sanchiz, África; Ballesteros, Isabel; López-García, Adrián; Ramírez, Ana; Rueda, Julia; Cuadrado, Carmen; Linacero, Rosario
Source:
Lebensmittel-Wissenschaft + [i.e. und] Technologie 2020 v.123 pp. 109067
ISSN:
0023-6438
Subject:
quantitative polymerase chain reaction,   etc   ; Castanea; autoclaving; boiling; detection limit; food allergens; genes; heat; processed foods;     Show all 9 Subjects
Abstract:
... Chestnut is gaining importance as food allergen, but a specific detection method has not been performed so far. For the first time, the development of a real-time PCR assay for chestnut allergen detection in processed foods is described. Initially, three sets of novel primers specific for allergen-encoding genes (Cas s 5, Cas s 9 and Cas s TLP) were designed and evaluated for chestnut detection. P ...
DOI:
10.1016/j.lwt.2020.109067

8. Development and comparative study of a pat/bar real‐time PCR assay for integrating the screening strategy of a GMO testing laboratory

Author:
Verginelli, Daniela; Paternò, Annalisa; De Marchis, Maria Laura; Quarchioni, Cinzia; Vinciguerra, Daniela; Bonini, Pamela; Peddis, Stefania; Fusco, Cristiana; Misto, Marisa; Marfoglia, Cristina; Pomilio, Francesco; Marchesi, Ugo
Source:
Journal of the science of food and agriculture 2020 v.100 no.5 pp. 2121-2129
ISSN:
0022-5142
Subject:
quantitative polymerase chain reaction,   etc   ; European Union; comparative study; cost effectiveness; genetically modified organisms; screening;     Show all 6 Subjects
Abstract:
... BACKGROUND: The number and variety of genetically modified organisms (GMOs) used globally for the production of food and feed, and potentially circulating in the European Union (EU), is constantly increasing. This implies an additional effort for the EU enforcement laboratories to optimize available resources, to contain costs and time. A well established approach for streamlining the analytical w ...
DOI:
10.1002/jsfa.10235

9. Longitudinal Characterization of Prevalence and Concentration of Shiga Toxin–Producing Escherichia coli Serogroups in Feces of Individual Feedlot Cattle

Author:
Dixon, Andrea; Cernicchiaro, Natalia; Amachawadi, Raghavendra G.; Shi, Xiaorong; Cull, Charley A.; Renter, David G.
Source:
Foodborne pathogens & disease 2020
ISSN:
1556-7125
Subject:
quantitative polymerase chain reaction,   etc   ; Shiga toxin-producing Escherichia coli; cattle; feces; feedlots; monitoring; pathogens; serotypes;     Show all 8 Subjects
Abstract:
... The objective of this study was to quantify the frequency, distribution, and variability of fecal shedding and super-shedding of Shiga toxin–producing Escherichia coli (STEC) serogroups O26, O45, O103, O111, O121, O145, and O157 in feedlot cattle over time. A total of 750 fecal grab samples were collected over a 5-week period (June–July 2017) from 150 cattle housed in 10 pens at a commercial feedl ...
DOI:
10.1089/fpd.2019.2777

10. Development of a bacterial DNA extraction modular chip using a magnetic particle and portable vibration motor

Author:
Lim, Sun Young; Lee, Tae Jae; Shin, Seol Yi; Bae, Nam Ho; Lee, Seok Jae; Park, Yoo Min
Source:
Analytical methods 2020 v.12 no.9 pp. 1197-1202
ISSN:
1759-9679
Subject:
quantitative polymerase chain reaction,   etc   ; DNA; Escherichia coli O157; gel electrophoresis; magnetism; mixing; pathogens; vibration;     Show all 8 Subjects
Abstract:
... A novel modular chip-based bacterial DNA extraction device was developed to overcome limitations associated with conventional DNA extraction processes that involve lab-scale instrument systems. The DNA extraction modular chip consists of a core chamber, a magnetic jig, and a vibration jig. The vibration jig allows the precise blending of solutions such as a lysis buffer and target bacterial sample ...
DOI:
10.1039/c9ay02690h

11. A TaqMan™-based quantitative PCR screening assay for the probiotic Streptococcus salivarius K12 based on the specific detection of its megaplasmid-associated salivaricin B locus

Author:
Reid, Peter; Heng, Nicholas C.K.; Hale, John D.; Krishnan, Deepti; Crane, Julian; Tagg, John R.; Milne, Trudy J.
Source:
Journal of microbiological methods 2020 v.170 pp. 105837
ISSN:
0167-7012
Subject:
quantitative polymerase chain reaction,   etc   ; Streptococcus salivarius; bacteriocins; genes; loci; probiotics; rapid methods; screening;     Show all 8 Subjects
Abstract:
... In order to assess the colonization efficacy of the oral probiotic Streptococcus salivarius K12, a rapid method for specific detection and enumeration of the strain was developed. Here, we describe a two-step TaqMan™ quantitative PCR assay using primer-probe combinations targeting genes of the locus encoding the lantibiotic bacteriocin salivaricin B. ...
DOI:
10.1016/j.mimet.2020.105837

12. Brucella microti‐like prevalence in French farms producing frogs

Author:
Jaÿ, Maryne; Freddi, Luca; Mick, Virginie; Durand, Benoit; Girault, Guillaume; Perrot, Ludivine; Taunay, Benoit; Vuilmet, Thomas; Azam, Didier; Ponsart, Claire; Zanella, Gina
Source:
Transboundary and emerging diseases 2020 v.67 no.2 pp. 617-625
ISSN:
1865-1674
Subject:
quantitative polymerase chain reaction,   etc   ; Brucella; commercial farms; emerging diseases; farming systems; frogs; humans; pathogenicity; risk; soil;     Show all 10 Subjects
Abstract:
... In the last 10 years, many atypical novel members of Brucella species have been reported, including several Brucella inopinata‐like strains in wild‐caught and “exotic” amphibians from various continents. In 2017, a strain of Brucella was isolated for the first time in animals from a French farm producing frogs—Pelophylax ridibundus—for human consumption and identified as B. microti‐like. Following ...
DOI:
10.1111/tbed.13377

13. Design of a degenerate primer pair to target a bacterial functional community: The hppd bacterial gene coding for the enzyme targeted by herbicides, a study case

Author:
Thiour-Mauprivez, C.; Devers-Lamrani, M.; Mounier, A.; Beguet, J.; Spor, A.; Calvayrac, C.; Barthelmebs, L.; Martin-Laurent, F.
Source:
Journal of microbiological methods 2020 v.170 pp. 105839
ISSN:
0167-7012
Subject:
quantitative polymerase chain reaction,   etc   ; genes; herbicides; high-throughput nucleotide sequencing; oligodeoxyribonucleotides; soil bacteria; soil sampling;     Show all 7 Subjects
Abstract:
... The present work aimed to design a degenerate primer pair to target a large part of the hppd soil bacterial community, possibly affected by herbicides. We validated these primers by qPCR and high-throughput sequencing analysis of soil samples. ...
DOI:
10.1016/j.mimet.2020.105839

14. Effects of poor sanitation procedures on cross-contamination of animal species in ground meat products

Author:
Chung, Sunjung M.; Hellberg, Rosalee S.
Source:
Food control 2020 v.109 pp. 106927
ISSN:
0956-7135
Subject:
quantitative polymerase chain reaction,   etc   ; cleaning; cross contamination; equipment; grinding; ground beef; meat animals; pork; sanitation;     Show all 9 Subjects
Abstract:
... The presence of <1% of an undeclared species in ground meat is generally thought to be indicative of cross-contamination as opposed to intentional mislabeling; however, this has not been experimentally tested. The objective of this study was to quantify the effects of poor sanitation on the cross-contamination of animal species in ground meat products, with the example of undeclared pork in ground ...
DOI:
10.1016/j.foodcont.2019.106927

15. Establishment and application of a loop-mediated isothermal amplification method with double-stranded displacement probes to quantify the genetically modified rice M12 event

Author:
Deng, Tingting; Huang, Wensheng; Xing, Ranran; Zhang, Jiukai; Ren, Junan; Ge, Yiqiang; Chen, Ying
Source:
European food research & technology 2020 v.246 no.3 pp. 631-641
ISSN:
1438-2377
Subject:
quantitative polymerase chain reaction,   etc   ; crops; genes; loop-mediated isothermal amplification; quantitative analysis; rice; transgenic plants;     Show all 7 Subjects
Abstract:
... For the purpose of supervision and academic research on GMO, it was necessary to establish a simple and effective on-site qualitative and quantitative method for GMO detection. In this paper, double-stranded displacement probes were first designed to monitor the quantitative LAMP amplification, and calcein was used effectively in LAMP reaction for qualitative measurement. High specificity of the m ...
DOI:
10.1007/s00217-020-03430-1

16. Molecular detection of Streptococcus equi subspecies equi in face flies (Musca autumnalis) collected during a strangles outbreak on a Thoroughbred farm

Author:
Pusterla, N.; Bowers, J.; Barnum, S.; Hall, J. A.
Source:
Medical and veterinary entomology 2020 v.34 no.1 pp. 120-122
ISSN:
0269-283X
Subject:
quantitative polymerase chain reaction,   etc   ; Musca autumnalis; Streptococcus equi subsp. equi; Thoroughbred; farms; nucleic acids; strangles;     Show all 7 Subjects
Abstract:
... The objective of this study was to detect Streptococcus equi subspecies equi (S. equi) (Lactobacillales: Streptococcaceae) using quantitative polymerase chain reaction (qPCR) in flies collected from a farm with a documented outbreak of strangles. A total of 1856 face flies [Musca autumnalis (Diptera: Muscidae)] were collected using conventional fly traps. The flies were processed for nucleic acid ...
DOI:
10.1111/mve.12394

17. Bacterial inactivation, DNA damage, and faster ATP degradation induced by ultraviolet disinfection

Author:
Yang, Chao; Sun, Wenjun; Ao, Xiuwei
Source:
Frontiers of environmental science & engineering 2020 v.14 no.1 pp. 13
ISSN:
2095-2201
Subject:
quantitative polymerase chain reaction,   etc   ; DNA damage; adenosine triphosphate; bacteria; disinfection; genes; ultraviolet radiation; viability;     Show all 8 Subjects
Abstract:
... The efficacy of ultraviolet (UV) disinfection has been validated in numerous studies by using culture-based methods. However, the discovery of viable but non-culturable bacteria has necessitated the investigation of UV disinfection based on bacterial viability parameters. We used quantitative polymerase chain reaction (qPCR) to investigate DNA damage and evaluated adenosine triphosphate (ATP) to i ...
DOI:
10.1007/s11783-019-1192-6

18. Real‐time PCR based on single‐copy housekeeping genes for quantitative detection of goat meat adulteration with pork

Author:
Wang, Zhicheng; Wang, Zhiying; Li, Tingting; Qiao, Lu; Liu, Rui; Zhao, Yan; Xu, Zhenzhen; Chen, Gang; Yang, Shuming; Chen, Ailiang
Source:
International journal of food science & technology 2020 v.55 no.2 pp. 553-558
ISSN:
0950-5423
Subject:
quantitative polymerase chain reaction,   etc   ; adulterated products; essential genes; false positive results; food law; goat meat; pork;     Show all 7 Subjects
Abstract:
... Adulteration of goat meat with cheaper meat such as pork has been frequently found. Conventional PCR methods to distinguish goat meat from adulteration are qualitative, which easily produce false‐positive results due to contamination but not adulteration. To address this problem, real‐time PCR based on single‐copy housekeeping genes encoding replication protein A1 was developed for goat meat and p ...
DOI:
10.1111/ijfs.14350

19. Two rapid and sensitive methods based on TaqMan qPCR and droplet digital PCR assay for quantitative detection of Bacillus subtilis in rhizosphere

Author:
Xie, Shanshan; Yu, Hengguo; Wang, Qi; Cheng, Yifeng; Ding, Ting
Source:
Journal of applied microbiology 2020 v.128 no.2 pp. 518-527
ISSN:
1364-5072
Subject:
quantitative polymerase chain reaction,   etc   ; Arabidopsis; Bacillus subtilis; droplets; genes; plant growth-promoting rhizobacteria; rhizosphere;     Show all 7 Subjects
Abstract:
... AIMS: Bacillus subtilis, a typical plant growth‐promoting rhizobacteria, can benefit plant through promoting growth and reducing disease. The colonization intensity of B. subtilis in rhizosphere is a key factor for improving their effectiveness of field application. In this study, we developed a rapid and sensitive method for detecting B. subtilis in rhizosphere via TaqMan qPCR and droplet digital ...
DOI:
10.1111/jam.14481

20. Quantification and Single-Base Resolution Analysis of N1-Methyladenosine in mRNA by Ligation-Assisted Differentiation

Author:
Ding, Jiang-Hui; Ma, Cheng-Jie; Chen, Meng-Yuan; Chen, Bei; Yuan, Bi-Feng; Feng, Yu-Qi
Source:
Analytical chemistry 2020 v.92 no.3 pp. 2612-2619
ISSN:
1520-6882
Subject:
quantitative polymerase chain reaction,   etc   ; DNA; adenosine; carcinogenesis; ligases; lung neoplasms; messenger RNA; moieties; proteins; tissues; uridine;     Show all 11 Subjects
Abstract:
... RNA modification, such as N1-methyladenosine (m¹A), affects the secondary structure of RNA and its ability to recognize specific reader proteins. Methods for detecting site-specific m¹A are in demand. We report here a ligation-assisted differentiation approach for quantitative detection of m¹A in mRNA with single-base resolution. The methyl group in m¹A disrupts the Watson–Crick base pairing with ...
DOI:
10.1021/acs.analchem.9b04454