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1. Effects of different carbon sources on the removal of ciprofloxacin and pollutants by activated sludge: Mechanism and biodegradation

Author:
Cai, Yixiang; Yan, Zhiyong; Ou, Yingjuan; Peng, Boshang; Zhang, Lihua; Shao, Jihai; Lin, Yiqing; Zhang, Jiachao
Source:
Journal of environmental sciences (China) 2022 v.111 pp. 240-248
ISSN:
1001-0742
Subject:
quantitative polymerase chain reaction,   etc   ; Acidobacteria; Microbacterium; Rhodanobacter; activated sludge; biodegradation; carbon; ciprofloxacin; denitrification; glucose; nitrates; nitrification; nitrites; sodium acetate; wastewater; China;     Show all 16 Subjects
Abstract:
... This research investigated the effects of ciprofloxacin (CIP) (0.5, 5, and 20 mg/L) on SBR systems under different carbon source conditions. Microbial community abundance and structure were determined by quantitative PCR and high-throughput sequencing, respectively. The biodegradation production of CIP and possible degradation mechanism were also studied. Results showed that CIP had adverse effect ...
DOI:
10.1016/j.jes.2021.03.037

2. Environmental surveillance of SARS-CoV-2 RNA in wastewater systems and related environments in Wuhan: April to May of 2020

Author:
Zhao, Lu; Atoni, Evans; Nyaruaba, Raphael; Du, Yao; Zhang, Huaiyu; Donde, Oscar; Huang, Doudou; Xiao, Shuqi; Ren, Nanjie; Ma, Teng; Shu, Zhu; Yuan, Zhiming; Tong, Lei; Xia, Han
Source:
Journal of environmental sciences (China) 2022 v.112 pp. 115-120
ISSN:
1001-0742
Subject:
quantitative polymerase chain reaction,   etc   ; COVID-19 infection; RNA; Severe acute respiratory syndrome coronavirus 2; environmental monitoring; epidemiology; feces; gastrointestinal system; groundwater; hospitals; pathogens; reverse transcription; risk; sediments; sludge; soil; surface water; wastewater; wastewater treatment; China;     Show all 20 Subjects
Abstract:
... Wastewater-based epidemiology (WBE) has emerged as an effective environmental surveillance tool in monitoring fecal-oral pathogen infections within a community. Congruently, SARS-CoV-2, the etiologic agent of COVID-19, has been demonstrated to infect the gastrointestinal tissues, and be shed in feces. In the present study, SARS-CoV-2 RNA was concentrated from wastewater, sludge, surface water, gro ...
DOI:
10.1016/j.jes.2021.05.005

3. CtNorm: Real time PCR cycle of threshold (Ct) normalization algorithm

Author:
Ramezani, Amin
Source:
Journal of microbiological methods 2021 v.187 pp. 106267
ISSN:
0167-7012
Subject:
quantitative polymerase chain reaction,   etc   ; algorithms; genes; humans;     Show all 4 Subjects
Abstract:
... In relative quantification with Real Time PCR (qRT-PCR,), accurate analysis requires equal amplification efficiency for both genes (Gene of interest and reference gene) and equal threshold values for all the samples. In this quantification method the expression level in treated samples will be calculated in comparison to the control group. We conducted the present study to design an algorithm for ...
DOI:
10.1016/j.mimet.2021.106267

4. Association of Polymorphic and Haplotype Variants of the MSX1 Gene and the Impacted Teeth Phenomenon

Author:
Trybek, Grzegorz; Jaroń, Aleksandra; Grzywacz, Anna
Source:
Genes 2021 v.12 no.4
ISSN:
2073-4425
Subject:
quantitative polymerase chain reaction,   etc   ; genes; haplotypes; risk;     Show all 4 Subjects
Abstract:
... It is known that genetic factors determine odontogenesis; furthermore, studies have revealed that various genes in humans can regulate the development of different types and generations of teeth. In this study it has been assumed that tooth impaction—at least to some extent—also depends on the presence of specific genetic markers, especially allelic variants of the MSX1 gene. The primary objective ...
DOI:
10.3390/genes12040577

5. Single-Cell Sequencing Confirms Transcripts and VHDJH Rearrangements of Immunoglobulin Genes in Human Podocytes

Author:
Deng, Zhenling; Yan, Huige; Shi, Zhan; Tian, Xinyu; Cui, Zhuan; Sun, Yingchun; Wang, Song; Zheng, Danxia; Qiu, Xiaoyan; Wang, Yue
Source:
Genes 2021 v.12 no.4
ISSN:
2073-4425
Subject:
polymerase chain reaction,   etc   ; chromium; humans; inflammation; kidneys;     Show all 5 Subjects
Abstract:
... Most glomerular diseases are associated with inflammation caused by deposited pathogenic immunoglobulins (Igs), which are believed to be produced by B cells. However, our previous study indicated that the human podocyte cell line can produce IgG. In this study, we aimed to confirm the transcripts and characterize the repertoires of Igs in primary podocytes at single cell level. First, single-cell ...
DOI:
10.3390/genes12040472

6. Rapid multiplex PCR assay for simultaneous detection of Neisseria gonorrhoeae and Chlamydia trachomatis in genitourinary samples: A 30-minute assay

Author:
Inoue, Takeshi; Chihara, Yoshitomo; Kiba, Keisuke; Hirao, Shuya; Tanaka, Masahiro; Yoneda, Tatsuo; Saka, Toshihisa; Beppu, Ken-ichi; Furubayashi, Keiichi; Takashima, Mizuki; Nagai, Hidenori; Kobayashi, Hiroshi; Fujimoto, Kiyohide
Source:
Journal of microbiological methods 2021 v.180 pp. 106103
ISSN:
0167-7012
Subject:
polymerase chain reaction,   etc   ; ; Chlamydia trachomatis; Neisseria gonorrhoeae;     Show all 4 Subjects
Abstract:
... We developed a rapid multiplex PCR assay available in bedside for the simultaneous detection of Neisseria gonorrhoeae and Chlamydia trachomatis, which enables diagnosis in less than 30 minutes. In this study, we validated the clinical utility of this assay including its sensitivity and specificity for NG and CT detection. ...
DOI:
10.1016/j.mimet.2020.106103

7. Simultaneous detection of four lily-infecting viruses by a multiplex RT-PCR assay

Author:
Lim, Mi Sang; Min, Dong Joo; Hong, Jin Sung; Choi, Sun Hee
Source:
Journal of general plant pathology 2021 v.87 no.4 pp. 219-224
ISSN:
1345-2630
Subject:
reverse transcriptase polymerase chain reaction,   etc   ; cucumbers; mixed infection; plant pathology;     Show all 4 Subjects
Abstract:
... A multiplex reverse-transcription polymerase chain reaction (RT-PCR) system was modified and evaluated for the simultaneous detection of multiple viruses in coinfected lily plants. Four major lily viruses, namely, lily symptomless, cucumber mosaic, lily mottle, and plantago asiatica mosaic viruses, were targeted by simultaneous detection. Analysis of PCR products confirmed the amplification of vir ...
DOI:
10.1007/s10327-021-00992-0

8. The groESL ISR sequence-based species-specific identification of GRAS and non-GRAS Lactiplantibacillus as an alternative to 16S rRNA sequencing

Author:
Lee, Jong Min; Park, So Hee; Jin, Chun-Zhi; Kang, Min-Kyoung; Park, Dong-Jin; Kim, Chang-Jin
Source:
Lebensmittel-Wissenschaft + [i.e. und] Technologie 2021 v.147 pp. 111504
ISSN:
0023-6438
Subject:
polymerase chain reaction,   etc   ; intergenic DNA; phylogeny; probiotics; species identification;     Show all 5 Subjects
Abstract:
... The untranscribed DNA sequences of the intergenic spacer regions (ISR) in the groESL were analyzed to resolve the ambiguity within phylogenetically close GRAS and non-GRAS species. The sequencing results of amplified polymerase chain reaction (PCR) products using groESL-ISR-specific primers accurately distinguished L. plantarum and L. pentosus, which were not distinguished by 16 S rRNA sequences. ...
DOI:
10.1016/j.lwt.2021.111504

9. PCR identification of Salmonella serovars for the E serogroup based on novel specific targets obtained by pan-genome analysis

Author:
Shang, Yuting; Ye, Qinghua; Wu, Qingping; Pang, Rui; Xiang, Xinran; Wang, Chufang; Li, Fan; Zhou, Baoqing; Xue, Liang; Zhang, Yinzhi; Sun, Xiulan; Zhang, Jumei
Source:
Lebensmittel-Wissenschaft + [i.e. und] Technologie 2021 v.145 pp. 110535
ISSN:
0023-6438
Subject:
polymerase chain reaction,   etc   ; Salmonella; humans; monitoring; rapid methods; salmonellosis; serotypes;     Show all 7 Subjects
Abstract:
... Accurate serotyping of Salmonella is essential for epidemiological investigations and surveillance of Salmonella infections. Compared to traditional methods, polymerase chain reaction (PCR) is more sensitive and identifies Salmonella to the serotype level. Few genes have been used as a target for PCR serotyping; thus, research to identify specific targets of common serotypes is needed. The Salmone ...
DOI:
10.1016/j.lwt.2020.110535

10. Timely gene detection assay and reliable screening of genetically engineered plants using an improved direct PCR-based technology

Author:
Ben-Amar, Anis; Mliki, Ahmed
Source:
Transgenic research 2021 v.30 no.3 pp. 263-274
ISSN:
0962-8819
Subject:
polymerase chain reaction,   etc   ; DNA; biotechnology; genetic engineering; genomics; reporter genes;     Show all 6 Subjects
Abstract:
... Engineered plants have been widely produced for fundamental and practical use. Several methods have been developed for genetically modified crop detection and quantification; however; they still laborious and expensive. Efforts are needed to set-up diagnosis-oriented techniques as alternatives to overcome DNA extraction which remains a tedious and time-consuming procedure. Here, we established a s ...
DOI:
10.1007/s11248-021-00250-1

11. Optimum DNA Extraction Methods for Edible Bird’s Nest Identification Using Simple Additive Weighting Technique

Author:
Quek, Meei Chien; Chin, Nyuk Ling; Tan, Sheau Wei
Source:
Foods 2021 v.10 no.5
ISSN:
2304-8158
Subject:
polymerase chain reaction,   etc   ; DNA; commercialization; cost effectiveness; hybrids;     Show all 5 Subjects
Abstract:
... A simple additive weighting (SAW) technique was used to determine and compare the overall performance of five DNA extraction methods from conventional (SDS method) to commercial kits (Qiagen, Wizard, and NucleoSpin) for identifying origins of edible bird’s nest (EBN) using end-point polymerase chain reaction (PCR). A hybrid method (SDS/Qiagen) which has been developed by combining the conventional ...
DOI:
10.3390/foods10051086

12. Association between the FTO A/T Polymorphism and Elite Athlete Status in Caucasian Swimmers

Author:
Zmijewski, Piotr; Leońska-Duniec, Agata
Source:
Genes 2021 v.12 no.5
ISSN:
2073-4425
Subject:
quantitative polymerase chain reaction,   etc   ; alleles; athletic performance; genotyping; homozygosity; sports;     Show all 6 Subjects
Abstract:
... The FTO A/T polymorphism (rs9939609) has been strongly associated with body mass-related traits in nonathletic populations, but rarely with elite athletic performance. The aim of the study was to investigate the association between the A/T polymorphism and athlete status in elite swimmers. Polish swimmers (n = 196) who competed in national and international competition at short- (SDS; 50–200 m; n ...
DOI:
10.3390/genes12050715

13. Development and application of a quadruplex real‐time PCR assay for differential detection of porcine circoviruses (PCV1 to PCV4) in Jiangsu province of China from 2016 to 2020

Author:
Chen, Nanhua; Xiao, Yanzhao; Li, Xinshuai; Li, Shubin; Xie, Ningjun; Yan, Xilin; Li, Xiangdong; Zhu, Jianzhong
Source:
Transboundary and emerging diseases 2021 v.68 no.3 pp. 1615-1624
ISSN:
1865-1674
Subject:
quantitative polymerase chain reaction,   etc   ; Circoviridae; mixed infection; phylogeny; swine; China;     Show all 6 Subjects
Abstract:
... To date, four species of porcine circoviruses (PCVs), including PCV1‐4, have been reported to exist in the clinical cases. Fast and effective differential detection is critical to monitor the infection and co‐infection status of PCVs for adopting reliable control strategies. However, currently available methods cannot simultaneously differentiate the four species of PCV strains. In this study, a q ...
DOI:
10.1111/tbed.13833

14. Quantitative PCR for Tenacibaculum dicentrarchi and T. finnmarkense

Author:
Nowlan, Joseph P.; Lumsden, John S.; Russell, Spencer
Source:
Journal of fish diseases 2021 v.44 no.5 pp. 655-659
ISSN:
0140-7775
Subject:
quantitative polymerase chain reaction,   etc   ; aquaculture industry; fish; pathogenesis; sequence homology;     Show all 5 Subjects
Abstract:
... Numerous Tenacibaculum species, including T. dicentrarchi, T. maritimum and T. finnmarkense, are associated with tenacibaculosis in finfish; however, quantitative identification techniques are limited. Quantitative PCR assays were developed to detect T. dicentrarchi and T. finnmarkense. TaqMan assays using 16S rDNA demonstrated low detection limits (0.07–269 bacteria), suitable amplification effic ...
DOI:
10.1111/jfd.13357

15. Improvement in molecular detection of phytoplasma associated with rose by selection of suitable primers and development of a multiplex PCR assay

Author:
Rihne, Tasou; Namita,; Singh, Kanwar Pal; Singh, M. K.; Talukdar, Akshay
Source:
3 Biotech 2021 v.11 no.4 pp. 190
ISSN:
2190-572X
Subject:
polymerase chain reaction,   etc   ; Phytoplasma; cultivars; genes; isopropyl alcohol; polyvinylpyrrolidone; temperature;     Show all 7 Subjects
Abstract:
... Sensitive and effective phytoplasma DNA amplification in symptomatic rose cultivars is a long unresolved problem. In the present study, improvement in standardization for PCR assay for phytoplasma detection was established with rose samples by selection of various combinations of nested primer pairs of 16S ribosomal gene and secA gene. CTAB DNA extraction method was slightly modified by adding 2% ...
DOI:
10.1007/s13205-021-02713-y

16. How to Develop and Prove High-Efficiency Selection of Ligands from Oligonucleotide Libraries: A Universal Framework for Aptamers and DNA-Encoded Small-Molecule Ligands

Author:
Le, An T. H.; Krylova, Svetlana M.; Beloborodov, Stanislav S.; Wang, Tong Y.; Hili, Ryan; Johnson, Philip E.; Li, Feng; Veedu, Rakesh N.; Belyanskaya, Svetlana; Krylov, Sergey N.
Source:
Analytical chemistry 2021 v.93 no.13 pp. 5343-5354
ISSN:
1520-6882
Subject:
polymerase chain reaction,   etc   ; DNA; analytical chemistry; drugs; ligands; oligonucleotides;     Show all 6 Subjects
Abstract:
... Screening molecular libraries for ligands capable of binding proteins is widely used for hit identification in the early drug discovery process. Oligonucleotide libraries provide a very high diversity of compounds, while the combination of the polymerase chain reaction and DNA sequencing allow the identification of ligands in low copy numbers selected from such libraries. Ligand selection from oli ...
DOI:
10.1021/acs.analchem.1c00601

17. Peripheral Blood MicroRNAs as Potential Biomarkers of Myocardial Damage in Acute Viral Myocarditis

Author:
Marketou, Maria; Kontaraki, Joanna; Patrianakos, Alexandros; Kochiadakis, George; Anastasiou, Ioannis; Fragkiadakis, Konstantinos; Plevritaki, Anthoula; Papadaki, Sofia Thalia; Chlouverakis, Gregory; Parthenakis, Fragiskos
Source:
Genes 2021 v.12 no.3
ISSN:
2073-4425
Subject:
reverse transcriptase polymerase chain reaction,   etc   ; biomarkers; microRNA; myocarditis;     Show all 4 Subjects
Abstract:
... Background: microRNAs (miRs) have emerged as important modulators of cardiovascular development and disease. Our aim was to determine whether cardiac-related miRs such as miR-21-5p and miR-1-3p were differentially expressed in acute viral myocarditis and whether any of them was related with the extent of myocardial damage and left ventricular dysfunction. Methods: We enrolled 40 patients with acut ...
DOI:
10.3390/genes12030420

18. Development of a Luminex microbead-based serotyping assay for Glaesserella parasuis

Author:
Yee, Sarah; Meers, Joanne; Parke, Christopher R.; Barnes, Tamsin S.; Blackall, P.J.; Turni, Conny
Source:
Journal of microbiological methods 2021 v.182 pp. 106159
ISSN:
0167-7012
Subject:
polymerase chain reaction,   etc   ; electrophoresis; gels; hemagglutination; hybridization; microbeads; serotypes; virulence;     Show all 8 Subjects
Abstract:
... Glaesserella parasuis consists of 15 serovars with some of them highly virulent and some of them avirulent. As killed vaccines do not provide crossprotection across serovars, serotyping is of importance. Serotyping, previously done by gel diffusion, is now done by multiplex PCR followed by electrophoresis. Accurately differentiating 15 serovars by electrophoresis is problematic. To overcome this p ...
DOI:
10.1016/j.mimet.2021.106159

19. Mining of novel target genes through pan-genome analysis for multiplex PCR differentiation of the major Listeria monocytogenes serotypes

Author:
Li, Fan; Ye, Qinghua; Chen, Moutong; Zhou, Baoqing; Xiang, Xinran; Wang, Chufang; Shang, Yuting; Zhang, Jumei; Pang, Rui; Wang, Juan; Xue, Liang; Cai, Shuzhen; Ding, Yu; Wu, Qingping
Source:
International journal of food microbiology 2021 v.339 pp. 109026
ISSN:
0168-1605
Subject:
polymerase chain reaction,   etc   ; DNA; Listeria monocytogenes; food microbiology; serotypes;     Show all 5 Subjects
Abstract:
... The abundant information provided by the pan-genome analysis approach reveals the diversity among Listeria monocytogenes serotypes. The objective of this study was to mine novel target genes using pan-genome analysis for multiplex PCR detection and differentiation of the major L. monocytogenes serotypes present in food. Pan-genome analysis and PCR validation revealed a total of 10 specific targets ...
DOI:
10.1016/j.ijfoodmicro.2020.109026

20. Universal LNA Probe-Mediated Multiplex Droplet Digital Polymerase Chain Reaction for Ultrasensitive and Accurate Quantitative Analysis of Genetically Modified Organisms

Author:
Yang, Litao; Chen, Yi; Li, Rong; Xu, Wenting; Cui, Jinjie; Zhang, Dabing; Zhang, Xiujie
Source:
Journal of agricultural and food chemistry 2021 v.69 no.5 pp. 1705-1713
ISSN:
1520-5118
Subject:
polymerase chain reaction,   etc   ; DNA; droplets; food chemistry; quantitative analysis; rice;     Show all 6 Subjects
Abstract:
... Multiplex and high-throughput assays are becoming the main trends in the development of new nucleic acid detection and quantification methods, such as those for genetically modified organism (GMO) analysis. Here, we report a novel universal LNA probe-mediated droplet digital polymerase chain reaction (PCR) method (ULNA-ddPCR) for multiple DNA target quantification in GMOs. In ULNA-ddPCR, only one ...
DOI:
10.1021/acs.jafc.0c06433