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1. Droplet digital PCR for quantification of PML-RARα in acute promyelocytic leukemia: a comprehensive comparison with real-time PCR

Author:
Yuan, Dandan; Cui, Ming; Yu, Shuping; Wang, Huimin; Jing, Rongrong
Source:
Analytical and bioanalytical chemistry 2019 v.411 no.4 pp. 895-903
ISSN:
1618-2642
Subject:
quantitative polymerase chain reaction,   etc   ; detection limit; droplets; genes; leukemia; patients;     Show all 6 Subjects
Abstract:
... Real-time quantitative PCR (qPCR) has been widely implemented for molecular testing, but there are still some inherent limitations that hamper its usefulness. Droplet digital PCR (ddPCR), which can provide direct, standards-free quantification, has recently received increasing attention. In our study, a comprehensive comparison of ddPCR with qPCR in relation to the quantification of PML-RARα was p ...
DOI:
10.1007/s00216-018-1508-6

2. Two FAST multiplex real-time PCR reactions to assess the presence of genetically modified organisms in food

Author:
Cottenet, Geoffrey; Blancpain, Carine; Sonnard, Véronique; Chuah, Poh Fong
Source:
Food chemistry 2019 v.274 pp. 760-765
ISSN:
0308-8146
Subject:
quantitative polymerase chain reaction,   etc   ; biotechnology; business enterprises; detection limit; genetically modified organisms; laws and regulations; screening;     Show all 7 Subjects
Abstract:
... Methods to detect the presence of genetically modified organisms (GMOs) are evolving constantly to comply with legislation and include new transgenic traits developed by biotechnology companies. Since traditional screening methods target only a limited number of markers, not all GM-events can be detected easily. To cover a broader range, a new GMO screening method was developed, based on two real- ...
DOI:
10.1016/j.foodchem.2018.09.050

3. Does vacuum centrifugal concentration reduce yield or quality of nucleic acids extracted from FFPE biospecimens?

Author:
Sánchez, Ignacio; Betsou, Fay; Mathieson, William
Source:
Analytical biochemistry 2019 v.566 pp. 16-19
ISSN:
0003-2697
Subject:
quantitative polymerase chain reaction,   etc   ; DNA; RNA; fluorescence emission spectroscopy; reverse transcriptase polymerase chain reaction; temperature;     Show all 6 Subjects
Abstract:
... Vacuum centrifugal (SpeedVac) concentration is commonly applied to nucleic acids extracted from formalin-fixed paraffin-embedded (FFPE) sections, but with an unknown impact. We concentrated DNA and RNA from FFPE biospecimens using different time/temperature SpeedVac combinations of up to 30 min concentration at 45 °C, then used spectrophotometry, spectrofluorometry, RIN, PERM, DV200, qRT-PCR, DIN ...
DOI:
10.1016/j.ab.2018.10.020

4. Development and application of a real-time polymerase chain reaction method for quantification of Escherichia coli in oysters (Crassostrea gigas)

Author:
Miotto, Marília; Fonseca, Antônio A.; Barretta, Clarissa; da Silva, Helen S.; Pellizzaro, Tomás; De Dea Lindner, Juliano; Vieira, Cleide R.W.; Parveen, Salina; Prudencio, Elane S.
Source:
Food microbiology 2019 v.77 pp. 85-92
ISSN:
0740-0020
Subject:
quantitative polymerase chain reaction,   etc   ; Crassostrea gigas; DNA; Escherichia coli; bacteria; genes; mariculture; oysters; pathogens; perishable foods;     Show all 10 Subjects
Abstract:
... Oysters are important mariculture species worldwide. Because of their filter-feeding behaviors, oysters can accumulate microorganisms, including pathogens, from surrounding water and concentrate bacteria in high numbers. Rapid and suitable methods for quantification of Escherichia coli in oysters are necessary considering that oysters are perishable foods often consumed raw and some countries use ...
DOI:
10.1016/j.fm.2018.08.015

5. Evaluation of mycoplasma removal reagents using qPCR-based quantification

Author:
Lai, Yueyang; Xu, Xuebo; Yan, Ruiying; Hua, Zichun
Source:
Analytical biochemistry 2019 v.564-565 pp. 88-95
ISSN:
0003-2697
Subject:
quantitative polymerase chain reaction,   etc   ; DNA; Mycoplasma; cell membranes; cytoplasm; gel electrophoresis; staining;     Show all 7 Subjects
Abstract:
... In this study, we evaluated the efficacy of various mycoplasma removal reagents using nuclear staining, DNA gel electrophoresis, and qPCR-based quantification. Our results showed Plasmocure and Plasmocin are two effective anti-mycoplasma reagents whose effects can be observed within a week. However, prolonged treatment with Plasmocin led to development of resistance. Withdrawal of anti-mycoplasma ...
DOI:
10.1016/j.ab.2018.10.014

6. Effect of master mixes on the measurement of telomere length by qPCR

Author:
Jiménez, Karen M.; Forero, Diego A.
Source:
Molecular biology reports 2018 v.45 no.4 pp. 633-638
ISSN:
0301-4851
Subject:
quantitative polymerase chain reaction,   etc   ; melting; telomeres;     Show all 3 Subjects
Abstract:
... Alterations in telomere length (TL) have been associated with several diseases and a method based on qPCR, the Monochrome Multiplex Real-Time Quantitative PCR (MMQPCR) technique, has been used extensively for the analysis of TL. Some previous studies have been found that certain methodological conditions can affect the measurement of TL. The aim of the study was to evaluate the performance of eigh ...
DOI:
10.1007/s11033-018-4175-y

7. Response of ammonia-oxidizing archaea to heavy metal contamination in freshwater sediment

Author:
Li, Ningning; Chen, Yao; Zhang, Zhengke; Chang, Sha; Huang, Dawei; Chen, Sili; Guo, Qingwei; Xie, Shuguang; Bing, Yongxin
Source:
Journal of environmental sciences (China) 2019 v.77 pp. 392-399
ISSN:
1001-0742
Subject:
quantitative polymerase chain reaction,   etc   ; Archaea; community structure; ecosystems; freshwater; genes; heavy metals; nitrification; nitrifying bacteria; pollution; sediments; soil;     Show all 12 Subjects
Abstract:
... It has been well-documented that the distribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soils can be affected by heavy metal contamination, whereas information about the impact of heavy metal on these ammonia-oxidizing microorganisms in freshwater sediment is still lacking. The present study explored the change of sediment ammonia-oxidizing microorganisms in a freshwater reservo ...
DOI:
10.1016/j.jes.2018.09.020

8. The biodegradation of cefuroxime, cefotaxime and cefpirome by the synthetic consortium with probiotic Bacillus clausii and investigation of their potential biodegradation pathways

Author:
Kong, Xiu-Xiu; Jiang, Jian-Lan; Qiao, Bin; Liu, Hong; Cheng, Jing-Sheng; Yuan, Ying-Jin
Source:
The Science of the total environment 2019 v.651 pp. 271-280
ISSN:
0048-9697
Subject:
quantitative polymerase chain reaction,   etc   ; Bacillus clausii; antibiotic resistance; beta-lactamase; biodegradation; bioremediation; cefuroxime; coculture; decarboxylation; genes; hydrolysis; pollution; probiotics;     Show all 13 Subjects
Abstract:
... Cephalosporin residues in the environment are a great concern, but bioremediation options do exist. Bacillus clausii T reached a removal rate of 100% within 8 h when challenged with a mixture of cefuroxime (CFX), cefotaxime (CTX), and cefpirome (CPR). The co-culture of B. clausii T and B. clausii O/C displayed a higher removal efficiency for the mixture of CFX, CTX and CPR than a pure culture of B ...
DOI:
10.1016/j.scitotenv.2018.09.187

9. METase promotes cell autophagy via promoting SNHG5 and suppressing miR-20a in gastric cancer

Author:
Xin, Lin; Zhou, Li-Qiang; Liu, Li; Yuan, Yi-Wu; Zhang, Hou-Ting; Zeng, Fei
Source:
International journal of biological macromolecules 2019 v.122 pp. 1046-1052
ISSN:
0141-8130
Subject:
quantitative polymerase chain reaction,   etc   ; RNA; Western blotting; apoptosis; autophagy; cell lines; humans; luciferase; precipitin tests; stomach neoplasms; tissues;     Show all 11 Subjects
Abstract:
... Gastric cancer (GC) severely threatens human life, and METase seemed to inhibit tumor growth. However, the potential mechanism underlying it is still unclear.Both clinical tissues and cell lines were used in the present study. SNHG5 and miR-20a expressions were determined using real-time PCR. Western blot was performed to determine the expression of autophagy-related proteins. The interaction betw ...
DOI:
10.1016/j.ijbiomac.2018.09.051

10. Child's buccal cell mitochondrial DNA content modifies the association between heart rate variability and recent air pollution exposure at school

Author:
Saenen, Nelly D.; Provost, Eline B.; Cuypers, Ann; Kicinski, Michal; Pieters, Nicky; Plusquin, Michelle; Vrijens, Karen; De Boever, Patrick; Nawrot, Tim S.
Source:
Environment international 2019 v.123 pp. 39-49
ISSN:
0160-4120
Subject:
quantitative polymerase chain reaction,   etc   ; acute exposure; air pollution; children; elementary students; girls; heart rate; mitochondria; mitochondrial DNA; models; particulates;     Show all 11 Subjects
Abstract:
... Studies investigating short-term exposure to ambient air pollution and heart rate variability (HRV) suggest that particulate matter (PM) exposure is associated with reductions in measures of HRV. Mitochondria are sensitive to PM exposure and may represent a biologically relevant underlying mechanism. However, evidence in children is lacking.Here we examine whether PM has an influence on children's ...
DOI:
10.1016/j.envint.2018.11.028

11. Contamination of hospital food with Clostridium difficile in Central Italy

Author:
Primavilla, Sara; Farneti, Silvana; Petruzzelli, Annalisa; Drigo, Ilenia; Scuota, Stefania
Source:
Anaerobe 2019 v.55 pp. 8-10
ISSN:
1075-9964
Subject:
quantitative polymerase chain reaction,   etc   ; Clostridium difficile; cooked foods; food contamination; genes; hospitals; patients; processed foods; risk; Italy;     Show all 10 Subjects
Abstract:
... This study investigates the contamination of foods with Clostridium difficile in 3 hospitals of Central Italy. We used real-time PCR for tpi gene to analyse 350 food samples, including 296 cooked meals and 54 foods to be eaten raw. The molecular screening test was positive for 3 samples, but toxigenic C. difficile was isolated only in two of them. The prevalence in cooked food was 0,3% (1/296), wh ...
DOI:
10.1016/j.anaerobe.2018.10.008

12. Human papillomavirus detection in urine: Effect of a first-void urine collection device and timing of collection

Author:
Pattyn, Jade; Van Keer, Severien; Biesmans, Samantha; Ieven, Margareta; Vanderborght, Charlotte; Beyers, Koen; Vankerckhoven, Vanessa; Bruyndonckx, Robin; Van Damme, Pierre; Vorsters, Alex
Source:
Journal of virological methods 2019 v.264 pp. 23-30
ISSN:
0166-0934
Subject:
quantitative polymerase chain reaction,   etc   ; DNA; Papillomaviridae; ambient temperature; biopsy; cohort studies; genotyping; liquids; statistical models; urine; women;     Show all 11 Subjects
Abstract:
... Great interest has been directed towards the use of first-void (FV) urine as a liquid biopsy for high-risk HPV DNA testing. The aim of this study was to investigate the potential effect of a first generation FV urine collection device on the detection of HPV DNA and to assess if the concentration of HPV DNA varies between FV urine collected in the morning and those collected later during the day. ...
DOI:
10.1016/j.jviromet.2018.11.008

13. Response of freshwater sediment archaeal community to metal spill

Author:
Guo, Qingwei; Li, Ningning; Chen, Sili; Chen, Yao; Xie, Shuguang
Source:
Chemosphere 2019 v.217 pp. 584-590
ISSN:
0045-6535
Subject:
quantitative polymerase chain reaction,   etc   ; Euryarchaeota; biogeochemical cycles; freshwater; genes; heavy metals; pollutants; pollution; ribosomal RNA; sediments; temporal variation; wastewater;     Show all 12 Subjects
Abstract:
... Archaea play an important role in the biogeochemical cycling of elements in the environment. Heavy metals are ubiquitous pollutants in the environment. Previous studies have revealed a considerable influence of metal pollution on the archaeal community, but the short-term response of the archaeal community to metal pollution remains unclear. Hence, the present study investigated the short versus l ...
DOI:
10.1016/j.chemosphere.2018.11.054

14. Ultra-fast, sensitive and quantitative on-chip detection of group B streptococci in clinical samples

Author:
Cai, Qing; Fauvart, Maarten; Wiederkehr, Rodrigo Sergio; Jones, Benjamin; Cools, Piet; Goos, Peter; Vaneechoutte, Mario; Stakenborg, Tim
Source:
Talanta 2019 v.192 pp. 220-225
ISSN:
0039-9140
Subject:
quantitative polymerase chain reaction,   etc   ; Streptococcus agalactiae; infectious diseases; manufacturing; melting; point-of-care testing; protocols; semiconductors; silicon;     Show all 9 Subjects
Abstract:
... PCR enables sensitive and specific detection of infectious disease agents, but application in point-of-care diagnostic testing remains scarce. A compact tool that runs PCR assays in less than a few minutes and that relies on mass-producible, disposable reactors could revolutionize while-you-wait molecular testing. We here exploit well-established semiconductor manufacturing processes to produce si ...
DOI:
10.1016/j.talanta.2018.09.041

15. High-throughput blood sample preparation for single nucleotide polymorphism genotyping in less than 25 min

Author:
Wang, Jidong; Zheng, Jiaying; Zhang, Shaohua; Du, Jihui; Chen, Yongxin; Liu, Xiaolei; Zhang, Huisheng; Jiang, Xingyu; Chen, Wenwen
Source:
Talanta 2019 v.191 pp. 119-125
ISSN:
0039-9140
Subject:
quantitative polymerase chain reaction,   etc   ; DNA; blood sampling; blood serum; genotyping; leukocyte count; protocols; single nucleotide polymorphism; triacylglycerols; uric acid;     Show all 10 Subjects
Abstract:
... Straightforward, rapid and high-throughput pretreatment for single nucleotide polymorphisms (SNP) genotyping is critically needed in clinical practice. However, all existing SNP genotyping methods require DNA purification step, which is labor-intensive and time-consuming. We develop a protocol for SNP genotyping by combining whole blood lysis (WBL) with qPCR and justify the practicality of our met ...
DOI:
10.1016/j.talanta.2018.08.051

16. A real-time PCR assay for detection and absolute quantitation of Citrus exocortis viroid in two sensitive and tolerant rootstocks

Author:
Ghobakhloo, Marzie; Dizadji, Akbar; Yamchi, Ahad
Source:
Crop protection 2019 v.115 pp. 27-30
ISSN:
0261-2194
Subject:
quantitative polymerase chain reaction,   etc   ; Citroncirus webberi; Citrus aurantium; Citrus exocortis viroid; Citrus sinensis; Poncirus trifoliata; bark; host plants; rootstocks; seedlings;     Show all 10 Subjects
Abstract:
... Citrus exocortis viroid (CEVd) is the causal agent of exocortis disease, the economically important viroid disease of citrus. In this research, CEVd copy number was quantified in sour orange (Citrus aurantium L.) and citrange (Poncirus trifoliata L. Raf. × Citrus sinensis L.) seedlings by absolute real-time PCR. A full-length in vitro transcript of a single-sequence CEVd-S1 variant was synthesized ...
DOI:
10.1016/j.cropro.2018.09.006

17. Detection of Listeria monocytogenes using Dynabeads® anti-Listeria combined with real-time PCR in soybean sprouts

Author:
Wei, Shuai; Park, Byung-Jae; Kim, Se-Hun; Seo, Kun-Ho; Jin, Yong-Guo; Oh, Deog-Hwan
Source:
Lebensmittel-Wissenschaft + [i.e. und] Technologie 2019 v.99 pp. 533-539
ISSN:
0023-6438
Subject:
quantitative polymerase chain reaction,   etc   ; DNA; Listeria monocytogenes; bacteria; bean sprouts; detection limit; genes; immunomagnetic separation; protocols; rapid methods; soybeans;     Show all 11 Subjects
Abstract:
... A rapid detection protocol for Listeria monocytogenes in soybean sprout samples was developed and evaluated using immunomagnetic separation (IMS) combined with real-time PCR. Dynabeads® anti-Listeria was mixed with food samples, separated with a particle concentrator, followed by DNA extraction for real-time PCR targeting the hly gene. The amount of Dynabeads® anti-Listeria used to determine conju ...
DOI:
10.1016/j.lwt.2018.10.023

18. Ferrihydrite treatment to mitigate inhibition of RT-qPCR virus detection from large-volume environmental water samples

Author:
Canh, Vu Duc; Osawa, Hideki; Inoue, Kentaro; Kasuga, Ikuro; Takizawa, Satoshi; Furumai, Hiroaki; Katayama, Hiroyuki
Source:
Journal of virological methods 2019 v.263 pp. 60-67
ISSN:
0166-0934
Subject:
quantitative polymerase chain reaction,   etc   ; Aichivirus A; Pepper mild mottle virus; bacteriophages; ferrihydrite; humic acids; reverse transcriptase polymerase chain reaction; seawater;     Show all 8 Subjects
Abstract:
... Molecular assays are currently the most widely used method to quantify pathogenic viruses in water; however, their performance is often disrupted by matrices present in environmental samples. The present study used ferrihydrite (Fh) treatment to mitigate inhibition of RT-qPCR virus detection from environmental water concentrates. Fh treatment was performed to improve the detection of spiked Aichi ...
DOI:
10.1016/j.jviromet.2018.10.018

19. Progress toward full scale application of the anaerobic side-stream reactor (ASSR) process

Author:
Ferrentino, R.; Langone, M.; Andreottola, G.
Source:
Bioresource technology 2019 v.272 pp. 267-274
ISSN:
0960-8524
Subject:
quantitative polymerase chain reaction,   etc   ; activated sludge; ammonium nitrogen; carbon; chemical oxygen demand; denitrifying bacteria; microbial communities; nitrogen; phosphates;     Show all 9 Subjects
Abstract:
... In order to reduce the investment costs of the anaerobic side-stream reactor (ASSR) process coupled with an activated sludge system and promote the full scale application, the impact of 1 d anaerobic solid retention time (SRTASSR) and 100% interchange ratio (IR) has been investigated on sludge reduction, carbon and nutrient removal efficiency and microbial community, in a sequencing batch reactor ...
DOI:
10.1016/j.biortech.2018.10.028

20. Updating a 2-class attributes sampling plan to account for changes in laboratory methods

Author:
Williams, Michael S.; Ebel, Eric D.; Golden, Neal J.
Source:
International journal of food microbiology 2018 v.282 pp. 24-27
ISSN:
0168-1605
Subject:
quantitative polymerase chain reaction,   etc   ; food analysis; microbiological criteria;     Show all 3 Subjects
Abstract:
... Advances in microbiological testing methods have led to faster and less expensive assays. Given these advances, it is logical to employ these assays for use in the sampling plan of an existing microbiological criterion. A change in the performance characteristics of the assay can affect the intended effect of the microbiological criterion. This study describes a method for updating a 2-class attri ...
DOI:
10.1016/j.ijfoodmicro.2018.05.028