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Journal articles on the topic 'PCR-free'

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Author: Grafiati

Published: 10 March 2023

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1

Hou, Chih-Sheng Johnson, Nebojsa Milovic, Michel Godin, Peter R. Russo, Raj Chakrabarti, and Scott R. Manalis. "Label-Free Microelectronic PCR Quantification." Analytical Chemistry 78, no. 8 (April 2006): 2526–31. http://dx.doi.org/10.1021/ac0520689.

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2

Lee, Sang Hun, Jihwan Song, Byungrae Cho, SoonGweon Hong, Ori Hoxha, Taewook Kang, Dongchoul Kim, and Luke P. Lee. "Bubble-free rapid microfluidic PCR." Biosensors and Bioelectronics 126 (February 2019): 725–33. http://dx.doi.org/10.1016/j.bios.2018.10.005.

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3

Erdeniz, Naz, Uffe H. Mortensen, and Rodney Rothstein. "Cloning-Free PCR-Based Allele Replacement Methods." Genome Research 7, no. 12 (December 1, 1997): 1174–83. http://dx.doi.org/10.1101/gr.7.12.1174.

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4

Shao, Zhenyu, Yuexing Liu, Han Xiao, and Genxi Li. "PCR-free electrochemical assay of telomerase activity." Electrochemistry Communications 10, no. 10 (October 2008): 1502–4. http://dx.doi.org/10.1016/j.elecom.2008.07.051.

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5

Chen, Yuchao, and Tae Seok Seo. "PCR-free digital minisatellite tandem repeat genotyping." ELECTROPHORESIS 32, no. 12 (May 30, 2011): 1456–64. http://dx.doi.org/10.1002/elps.201100073.

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6

Jafari, Hamed Mazhab, Karim Abdelhalim, Leyla Soleymani, Edward H. Sargent, Shana O. Kelley, and Roman Genov. "Nanostructured CMOS Wireless Ultra-Wideband Label-Free PCR-Free DNA Analysis SoC." IEEE Journal of Solid-State Circuits 49, no. 5 (May 2014): 1223–41. http://dx.doi.org/10.1109/jssc.2014.2312571.

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7

Brouard, D., O. Ratelle, J. Perreault, D. Boudreau, and M. St-Louis. "PCR-free blood group genotyping using a nanobiosensor." Vox Sanguinis 108, no. 2 (December 3, 2014): 197–204. http://dx.doi.org/10.1111/vox.12207.

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8

Senchyna, Fiona, Rajiv L. Gaur, Saurabh Gombar, Cynthia Y. Truong, Lee F. Schroeder, and Niaz Banaei. "Clostridium difficile PCR Cycle Threshold Predicts Free Toxin." Journal of Clinical Microbiology 55, no. 9 (June 14, 2017): 2651–60. http://dx.doi.org/10.1128/jcm.00563-17.

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ABSTRACTThere is no stand-aloneClostridium difficilediagnostic that can sensitively and rapidly detect fecal free toxins. We investigated the performance of theC. difficilePCR cycle threshold (CT) for predicting free toxin status. Consecutive stool samples (n= 312) positive for toxigenicC. difficileby the GeneXpertC. difficile/EpitcdBPCR assay were tested with the rapid membrane C. Diff Quik Chek Complete immunoassay (RMEIA). RMEIA toxin-negative samples were tested with the cell cytotoxicity neutralization assay (CCNA) and tgcBIOMICS enzyme-linked immunosorbent assay (ELISA). Using RMEIA alone or in combination with CCNA and/or ELISA as the reference method, the accuracy ofCTwas measured at differentCTcutoffs. Using RMEIA as the reference method, aCTcutoff of 26.35 detected toxin-positive samples with a sensitivity, specificity, positive predictive value, and negative predictive value of 96.0% (95% confidence interval [CI], 90.2% to 98.9%), 65.9% (95% CI, 59.0% to 72.2%), 57.4% (95% CI, 52.7% to 62%), and 97.1% (95% CI, 92.8% to 98.9), respectively. Inclusion of CCNA in the reference method improvedCTspecificity to 78.0% (95% CI, 70.7% to 84.2%). Intercartridge lotCTvariability measured as the average coefficient of variation was 2.8% (95% CI, 1.2% to 3.2%). Standardizing the input stool volume did not improveCTtoxin specificity. The medianCTvalues were not significantly different between stool samples with Bristol scores of 5, 6, and 7, between pediatric and adult samples, or between presumptive 027 and non-027 strains. In addition to sensitively detecting toxigenicC. difficilein stool, on-demand PCR may also be used to accurately predict toxin-negative stool samples, thus providing additional results in PCR-positive stool samples to guide therapy.

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9

Kraytsberg, Yevgenya, and Konstantin Khrapko. "Single-molecule PCR: an artifact-free PCR approach for the analysis of somatic mutations." Expert Review of Molecular Diagnostics 5, no. 5 (September 2005): 809–15. http://dx.doi.org/10.1586/14737159.5.5.809.

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10

Hsieh, Shen-Yuan, Mohammad A. Tariq, Andrea Telatin, Rebecca Ansorge, Evelien M. Adriaenssens, George M. Savva, Catherine Booth, Tom Wileman, Lesley Hoyles, and Simon R. Carding. "Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome." Viruses 13, no. 10 (October 18, 2021): 2093. http://dx.doi.org/10.3390/v13102093.

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The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as “viral dark matter”. However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating “rare” members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.

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11

Temesgen, Berhanu, and Klaus Eschrich. "Simplified Method for Ligase-Free Cloning of PCR Products." BioTechniques 21, no. 5 (November 1996): 828–32. http://dx.doi.org/10.2144/96215bm17.

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12

Piantanida, Luca, and William L. Hughes. "A PCR-free approach to random access in DNA." Nature Materials 20, no. 9 (August 25, 2021): 1173–74. http://dx.doi.org/10.1038/s41563-021-01089-x.

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13

Scior, Annika, Steffen Preissler, Miriam Koch, and Elke Deuerling. "Directed PCR-free engineering of highly repetitive DNA sequences." BMC Biotechnology 11, no. 1 (2011): 87. http://dx.doi.org/10.1186/1472-6750-11-87.

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14

Padua, RA, A. Parrado, J. Larghero, and C. Chomienne. "UV and clean air result in contamination-free PCR." Leukemia 13, no. 11 (November 1999): 1898–99. http://dx.doi.org/10.1038/sj.leu.2401579.

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15

Hastings, Michelle L., Jaime Palma, and Dominik M. Duelli. "Sensitive PCR-based quantitation of cell-free circulating microRNAs." Methods 58, no. 2 (October 2012): 144–50. http://dx.doi.org/10.1016/j.ymeth.2012.07.026.

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16

Yang, Bing, Guohua Zhou, and Lequn Lee Huang. "PCR-free MDR1 polymorphism identification by gold nanoparticle probes." Analytical and Bioanalytical Chemistry 397, no. 5 (May 2, 2010): 1937–45. http://dx.doi.org/10.1007/s00216-010-3750-4.

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17

Mašková, E., I. Paulíčková, J. Rysová, and D. Gabrovská. "Evidence for wheat, rye, and barley presence in gluten free foods by PCR method – comparison with ELISA method." Czech Journal of Food Sciences 29, No. 1 (February 14, 2011): 45–50. http://dx.doi.org/10.17221/171/2010-cjfs.

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A method of the evidence for the presence of wheat, rye, and barley in gluten free foods, based on the polymerase chain reaction (PCR), was validated. DNA was isolated from foods by chaotropic solid phase extraction. The PCR method applied was focused on the intron of the chloroplast gene trnL and utilised primers WBR11 and WBR13. Electrophoresed wheat and rye DNAs were characterised by a 201 bp fragment, barley DNA by a 196 bp fragment. The validated PCR method was applied to the selection of 18 gluten free foods, previously found by ELISA method to contain 1 mg or more of gliadin per 100 g food. The presence of wheat was confirmed by PCR method in all foods analysed. The comparison with the results obtained by ELISA method reliably verified the detection limit of PCR method, i.e., 0.02% wheat.

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18

Woo Kim, Kyung, Yong Shin, Agampodi Promoda Perera, Qing Liu, Jack Sheng Kee, Kyungsup Han, Yong-Jin Yoon, and Mi Kyoung Park. "Label-free, PCR-free chip-based detection of telomerase activity in bladder cancer cells." Biosensors and Bioelectronics 45 (July 2013): 152–57. http://dx.doi.org/10.1016/j.bios.2013.02.001.

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19

Shuldiner, Alan R., Laurie A. Scott, and Jesse Roth. "PCR-induced (ligase-free) subcloning: a rapid reliable method to subclone polymerase chain reaction (PCR) products." Nucleic Acids Research 18, no. 7 (1990): 1920. http://dx.doi.org/10.1093/nar/18.7.1920.

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20

Goh, Su Kah, Vijayaragavan Muralidharan, Christopher Christophi, Hongdo Do, and Alexander Dobrovic. "Probe-Free Digital PCR Quantitative Methodology to Measure Donor-Specific Cell-Free DNA after Solid-Organ Transplantation." Clinical Chemistry 63, no. 3 (March 1, 2017): 742–50. http://dx.doi.org/10.1373/clinchem.2016.264838.

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Abstract BACKGROUND Donor-specific cell-free DNA (dscfDNA) is increasingly being considered as a noninvasive biomarker to monitor graft health and diagnose graft rejection after solid-organ transplantation. However, current approaches used to measure dscfDNA can be costly and/or laborious. A probe-free droplet digital PCR (ddPCR) methodology using small deletion/insertion polymorphisms (DIPs) was developed to circumvent these limitations without compromising the quantification of dscfDNA. This method was called PHABRE-PCR (Primer to Hybridize across an Allelic BREakpoint-PCR). The strategic placement of one primer to hybridize across an allelic breakpoint ensured highly specific PCR amplification, which then enabled the absolute quantification of donor-specific alleles by probe-free ddPCR. METHODS dscfDNA was serially measured in 3 liver transplant recipients. Donor and recipient genomic DNA was first genotyped against a panel of DIPs to identify donor-specific alleles. Alleles that differentiated donor-specific from recipient-specific DNA were then selected to quantify dscfDNA in the recipient plasma. RESULTS Lack of amplification of nontargeted alleles confirmed that PHABRE-PCR was highly specific. In recipients who underwent transplantation, dscfDNA was increased at day 3, but decreased and plateaued at a low concentration by 2 weeks in the 2 recipients who did not develop any complications. In the third transplant recipient, a marked increase of dscfDNA coincided with an episode of graft rejection. CONCLUSIONS PHABRE-PCR was able to quantify dscfDNA with high analytical specificity and sensitivity. The implementation of a DIP-based approach permits surveillance of dscfDNA as a potential measure of graft health after solid-organ transplantation.

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21

Chen, G. J., N. Qiu, C. Karrer, P. Caspers, and M. G. P. Page. "Restriction Site-Free Insertion of PCR Products Directionally into Vectors." BioTechniques 28, no. 3 (March 2000): 498–505. http://dx.doi.org/10.2144/00283st08.

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22

Nikolaou, Pavlos, Emanuele Luigi Sciuto, Alessandra Zanut, Salvatore Petralia, Giovanni Valenti, Francesco Paolucci, Luca Prodi, and Sabrina Conoci. "Ultrasensitive PCR-Free detection of whole virus genome by electrochemiluminescence." Biosensors and Bioelectronics 209 (August 2022): 114165. http://dx.doi.org/10.1016/j.bios.2022.114165.

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23

Hsiao, Ku-chuan. "Exonuclease III induced ligase-free directional subcloning of PCR products." Nucleic Acids Research 21, no. 23 (1993): 5528–29. http://dx.doi.org/10.1093/nar/21.23.5528.

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24

Le Calvez, Thomas, Marie-Cécile Trouilhé, Philippe Humeau, Marina Moletta-Denat, Jacques Frère, and Yann Héchard. "Detection of free-living amoebae by using multiplex quantitative PCR." Molecular and Cellular Probes 26, no. 3 (June 2012): 116–20. http://dx.doi.org/10.1016/j.mcp.2012.03.003.

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25

Thornton, Brenda, and Chhandak Basu. "Real-time PCR (qPCR) primer design using free online software." Biochemistry and Molecular Biology Education 39, no. 2 (March 2011): 145–54. http://dx.doi.org/10.1002/bmb.20461.

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26

Wood, D. P., and M. Banerjee. "Presence of circulating prostate cells in the bone marrow of patients undergoing radical prostatectomy is predictive of disease-free survival." Journal of Clinical Oncology 15, no. 12 (December 1997): 3451–57. http://dx.doi.org/10.1200/jco.1997.15.12.3451.

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PURPOSE To determine whether the presence of circulating prostate cells in the bone marrow is associated with disease-free survival in patients undergoing radical prostatectomy. MATERIALS AND METHODS We evaluated the bone marrow of 86 patients with clinically localized prostate cancer treated by radical prostatectomy for the presence of circulating prostate cells using reverse-transcriptase polymerase chain reaction (RT-PCR) amplification of prostate-specific antigen (PSA) mRNA. Follow-up duration ranged from 1 to 43 months (mean, 15.4). RESULTS Two of 47 patients (4%) with negative RT-PCR PSA results and 10 of 39 patients (26%) with positive RT-PCR PSA results have had disease recurrence. Patients whose RT-PCR PSA results were positive had a significantly shorter disease-free survival period than those patients with negative RT-PCR PSA results (P = .004). RT-PCR status correlated significantly with serum PSA level (P = .001) and pathologic stage (P = .003). Based on Cox's proportional hazards models, RT-PCR status was found to be a significant predictor of disease-free survival. However, after controlling for PSA level, RT-PCR status was not significant in predicting disease-free survival. CONCLUSION RT-PCR PSA of bone marrow may be a useful pretreatment prognostic test for patients undergoing radical prostatectomy. Currently, this test should not be used to determine if patients receive definitive local therapy.

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27

Luo, Jian, Wei Ping Zhang, Wu Liu, Feng Cui, Wen Yuan Chen, Xiao Sheng Wu, and Jing Tong Cao. "A Simple and Practicable PCR-Microchip with Bubble-Free Stationary Chamber." Applied Mechanics and Materials 483 (December 2013): 51–55. http://dx.doi.org/10.4028/www.scientific.net/amm.483.51.

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This paper reports on a simple and practicable biochip for polymerase chain reaction (PCR). The micro biochip (12mm×12mm) is a hybrid type which is composed of a polydimethylsiloxane (PDMS) cover with a hexagonal chamber and a glass substrate integrated with platinum (Pt) microheater and microsensor. Bubble formation has been reported as a big problem with PCR chips. In this paper we present a simple and practicable operation schedule to get a bubble free chip, in which a successful PCR process was guaranteed.

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28

Buchan, Blake W., Derek Gerstbrein, Amorina Cruz, Jess Hoff, Emily Sievert, Nathan A. Ledeboer, and Matthew L. Faron. "Evaluation of a High-Definition PCR Assay for the Detection of SARS-CoV-2 in Extracted and Nonextracted Respiratory Specimens Collected in Various Transport Media." American Journal of Clinical Pathology 156, no. 1 (May 3, 2021): 24–33. http://dx.doi.org/10.1093/ajcp/aqab060.

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Abstract Objectives We conducted an analytic and clinical comparison of a novel high-definition polymerase chain reaction PCR (HDPCR) assay to traditional real-time PCR (RT-PCR) for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in upper respiratory specimens. Methods Analytic performance of RT-PCR, HDPCR, and extraction-free HDPCR was established through replicate testing of a serially diluted clinical specimen containing SARS-CoV-2. A clinical comparison of all 3 assays was conducted using 351 prospectively collected upper respiratory swab specimens obtained from symptomatic and asymptomatic individuals collected in various transport media. Results RT-PCR and HDPCR assays using extracted nucleic acid demonstrated similar analytic limits of detection (LoD) and clinical performance, with 100% positive and negative agreement. Extraction-free HDPCR demonstrated a 1.5 to 2.0 log10 increase in LoD based on cycle threshold values. However, clinical performance of extraction-free HDPCR remained high, demonstrating 97.8% positive and 99.6% negative agreement with RT-PCR. An overall increase in “invalid” and “presumptive” results was observed when using the extraction-free method, but this was highly variable based on transport medium used. Conclusions HDPCR performs similar to RT-PCR for the detection of SARS-CoV-2. The use of an extraction-free HDPCR protocol maintained high clinical performance despite reduced analytic LoD, with the benefit of reduced hands-on time and cost of reagents associated with nucleic acid extraction.

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29

Ladetto, Marco, Daniela Drandi, Mara Compagno, Monica Astolfi, Federica Volpato, Claudia Voena, Anna Novarino, et al. "PCR-Detectable Nonneoplastic Bcl-2/IgH Rearrangements Are Common in Normal Subjects and Cancer Patients at Diagnosis but Rare in Subjects Treated With Chemotherapy." Journal of Clinical Oncology 21, no. 7 (April 1, 2003): 1398–403. http://dx.doi.org/10.1200/jco.2003.07.070.

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Purpose: To assess whether nonneoplastic Bcl-2/IgH rearrangements act as a confounding factor in the setting of minimal residual disease analysis by evaluating their incidence in a panel of lymphoma-free subjects, including cancer-free donors and chemotherapy-naive and chemotherapy-treated cancer patients. Patients and Methods: A total of 501 nonlymphoma subjects have been assessed: 258 cancer-free patients and 243 patients with malignancies other than lymphoma, 112 of whom were chemotherapy-naive. Patients were primarily assessed by nested polymerase chain reaction (PCR), followed by real-time quantitative PCR if they scored positive. In addition, six initially PCR-positive cancer-free donors were prospectively reassessed by qualitative and quantitative PCR after 30 and 60 days. Results: The overall incidence of Bcl-2/IgH positivity was 9.6%, with a median number of 11 rearrangements per 1,000,000 diploid genomes (range, 0 to 2,845 rearrangements), as assessed by real-time PCR. The incidence was similar in healthy subjects and cancer patients at diagnosis (12% and 12.5%; P = not significant). In contrast, the incidence of this translocation was only 2.3% in chemotherapy-treated patients (P < .001). In addition, three initially PCR-positive cancer-free donors showed persistence of their rearrangements when assessed after 30 and 60 days. Conclusion: The low incidence of nonneoplastic Bcl-2/IgH rearrangements following chemotherapy provides further evidence of the prognostic role of persistent PCR-positivity in the posttreatment molecular follow-up of follicular lymphoma patients.

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30

Minaei, Mohammad Ebrahim, Mojtaba Saadati, Mostafa Najafi, and Hossein Honari. "Label-free, PCR-free DNA Hybridization Detection of Escherichia coli O157 : H7 Based on Electrochemical Nanobiosensor." Electroanalysis 28, no. 10 (October 2016): 2582–89. http://dx.doi.org/10.1002/elan.201600198.

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31

Zhou, Dianming, Xiaohui Lin, Weichen Gao, Jiafang Piao, Shufei Li, Ning He, Zhiyong Qian, Miao Zhao, and Xiaoqun Gong. "A novel template repairing-PCR (TR-PCR) reaction platform for microRNA detection using translesional synthesis on DNA templates containing abasic sites." Chemical Communications 55, no. 20 (2019): 2932–35. http://dx.doi.org/10.1039/c8cc10226k.

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32

Zhou, Guiju, Meizhen Zhou, Fanwei Zeng, Ningzhi Zhang, Yan Sun, Zhihong Qiao, Xueqin Guo, et al. "Performance characterization of PCR-free whole genome sequencing for clinical diagnosis." Medicine 101, no. 10 (March 11, 2022): e28972. http://dx.doi.org/10.1097/md.0000000000028972.

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33

Nybo, Kristie. "Real-Time qPCR/qRT-PCR Methods: Amplification in Template-Free Controls." BioTechniques 46, no. 2 (February 2009): 91–93. http://dx.doi.org/10.2144/000113063.

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34

Li-Yeh Chuang, Yu-Huei Cheng, and Cheng-Hong Yang. "PCR-CTPP Design for Enzyme-Free SNP Genotyping Using Memetic Algorithm." IEEE Transactions on NanoBioscience 14, no. 1 (January 2015): 13–23. http://dx.doi.org/10.1109/tnb.2015.2392782.

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35

Sato, Shinobu, and Shigeori Takenaka. "PCR-Free Telomerase Assay Using Chronocoulometry Coupled with Hexaammineruthenium(III) Chloride." Analytical Chemistry 84, no. 3 (January 24, 2012): 1772–75. http://dx.doi.org/10.1021/ac202233m.

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36

Yu, Tao, Wei Zhao, Jing-Juan Xu, and Hong-Yuan Chen. "A PCR-free colorimetric strategy for visualized assay of telomerase activity." Talanta 178 (February 2018): 594–99. http://dx.doi.org/10.1016/j.talanta.2017.09.070.

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37

Li, Hui, Hai-Wei Fu, Ting Zhao, and De-Ming Kong. "Simple, PCR-free telomerase activity detection using G-quadruplex–hemin DNAzyme." RSC Advances 5, no. 9 (2015): 6475–80. http://dx.doi.org/10.1039/c4ra14460k.

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38

Ames-Lastra, G., V. Sánchez, E. Sacristán-Rock, M. Gómez-López, N. Pérez-Vielma, I. A. Castillo-Salazar, A. Hernández-Nava, and C. A. González-Díaz. "Bioimpedance Spectroscopy as a potential technique to detect label-free PCR products." Journal of Physics: Conference Series 2008, no. 1 (August 1, 2021): 012016. http://dx.doi.org/10.1088/1742-6596/2008/1/012016.

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Abstract PCR is a molecular technique that multiplies DNA fragments in a logarithmical way. qPCR uses fluoroscopic dyes or probes to quantify amplicons but it is a complex and expensive technique that should be performed by highly trained personnel. PCR has been used in a wide variety of disciplines such as in food sciences, organ transplant, odontology, oncology and lately, as the standard diagnostic technique for COVID-19. Even when qPCR is a reliable and robust technique, it is hardly accessible for developing countries for its complex labelling procedures and expensive instrumentation, for that, it is of big relevance to search for simpler and cheaper alternative technologies for the detection and analysis of DNA. In this work, we explore the feasibility of using multifrequency bioimpedance measurements to detect label-free PCR products as a proof of principle for the future development of a gene biosensor on the basis of PCR and bioimpedance measurements.

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39

Quistorff, B., L. Johansen, and K. Sahlin. "Absence of phosphocreatine resynthesis in human calf muscle during ischaemic recovery." Biochemical Journal 291, no. 3 (May 1, 1993): 681–86. http://dx.doi.org/10.1042/bj2910681.

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Changes in the metabolites phosphocreatine (PCr), Pi and ATP were quantified by 31P n.m.r. spectroscopy in the human calf muscle during isometric contraction and recovery under ischaemic conditions. Time resolution of the measurements was 10 s. During a 30-60 s ischaemic isometric contraction, PCr decreased linearly at a rate of 1.17%/s (relative to the resting value) at a contraction strength equivalent to 70% of the maximal voluntary contraction (MVC) and at a rate of 2.43%/s at 90% MVC. There was a corresponding increase in Pi but the concentration of ATP did not change. pH decreased linearly during contraction by 4.22 and 8.23 milli-pH units/s at 70 and 90% MVC respectively. During a subsequent 5 min interval of ischaemic recovery, PCr, Pi, ATP, phosphomonoesters and calculated free ADP, free AMP and pH retained the value they had attained by the end of contraction with no significant recovery. Thus it is concluded that anaerobic glycolysis and glycogenolysis is halted momentarily on termination of contraction and that PCr is not resynthesized during ischaemic recovery. This paradoxical arrest of glycolytic flow in spite of the very significantly elevated concentration of potent activators such as Pi and free AMP clearly indicates that parameters other than PCr, ATP, Pi, calculated pH, free ADP and free AMP regulate glycolysis and glycogenolysis of human skeletal muscle very efficiently under ischaemic conditions.

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40

Mazouni, C., F. Peintinger, S. Wan-Kau, F. Andre, A. M. Gonzalez-Angulo, F. Symmans, F. Meric-Bernstam, V. Valero, G. Hortobagyi, and L. Pusztai. "Effect on patient outcome of residual DCIS in patients with complete eradication of invasive breast cancer after neoadjuvant chemotherapy." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 530. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.530.

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530 Background: To determine whether residual ductal carcinoma in situ (DCIS) after completion of preoperative chemotherapy affects the outcome of patients with hiostologically defined complete eradication of invasive cancer. Methods: Retrospective analysis of a database including 2,302 breast cancer patients treated prospectively with neoadjuvant chemotherapy at the UT MD Anderson Cancer Center between 1980 and 2004 was performed. The overall, disease-free and local recurrence-free survivals were compared for patients with no residual invasive or in situ cancer (pCR) and those with no residual invasive cancer but persistent in situ disease (pCR+DCIS). Results: The mean follow-up was 250 months. Of the 2,302 treated patients 78 (3.4%) had pCR, 199 (8.6%) had pCR+DCIS, and 2025 (88%) had residual invasive cancer. The 5-year (87.1% in both) and 10-year (81.3% vs 81.7%) disease-free survival rates were similar for cases with pCR and pCR+DCIS. The 5-year (91.9% vs. 92.5%) and 10-year (91.8% vs. 92.5%) overall survival rates were also similar and significantly better than the rate of patients with residual invasive cancer (74.4%, p<0.001). The 5-year local-regional recurrence-free survival rates were also not different for patients with pCR (92.8%, 95% CI: 86.1%-96.4%) and those with pCR+DCIS (90.9%, 95% CI: 77.3%- 96.5%), p=0.63. Conclusions: Residual DCIS in patients who experience complete eradication of the invasive cancer in the breast and lymph nodes does not adversely affect survival or local recurrence rate. Inclusion of cases with residual DCIS in the definition of pathologic complete response is justified when this outcome is used as early surrogate for long term-survival. No significant financial relationships to disclose.

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41

Woodford, K., M. N. Weitzmann, and K. Usdin. "The use of K+-free buffers eliminates a common cause of premature chain termination in PCR and PCR sequencing." Nucleic Acids Research 23, no. 3 (1995): 539. http://dx.doi.org/10.1093/nar/23.3.539.

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42

Macori, Guerrino, Siobhán C. McCarthy, Catherine M. Burgess, Séamus Fanning, and Geraldine Duffy. "Investigation of the Causes of Shigatoxigenic Escherichia coli PCR Positive and Culture Negative Samples." Microorganisms 8, no. 4 (April 18, 2020): 587. http://dx.doi.org/10.3390/microorganisms8040587.

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Molecular methods may reveal the presence of pathogens in samples through the detection of specific target gene(s) associated with microorganisms, but often, the subsequent cultural isolation of the pathogen is not possible. This discrepancy may be related to low concentration of the cells, presence of dead cells, competitive microflora, injured cells and cells in a viable but non-culturable state, free DNA and the presence of free bacteriophages which can carry the target gene causing the PCR-positive/culture-negative results. Shiga-toxigenic Escherichia coli (STEC) was used as a model for studying this phenomenon, based on the phage-encoded cytotoxins genes (Stx family) as the detection target in samples through real-time qPCR. Stx phages can be integrated in the STEC chromosome or can be isolated as free particles in the environment. In this study, a combination of PCR with culturing was used for investigating the presence of the stx1 and stx2 genes in 155 ovine recto-anal junction swab samples (method (a)-PCR). Samples which were PCR-positive and culture-negative were subjected to additional analyses including detection of dead STEC cells (method (b)-PCR-PMA dye assay), presence of Stx phages (method (c)-plaque assays) and inducible integrated phages (method (d)-phage induction). Method (a) showed that even though 121 samples gave a PCR-positive result (78%), only 68 samples yielded a culturable isolate (43.9%). Among the 53 (34.2%) PCR-positive/culture-negative samples, 21 (39.6%) samples were shown to have STEC dead cells only, eight (15.1%) had a combination of dead cells and inducible stx phage, while two samples (3.8%) had a combination of dead cells, inducible phage and free stx phage, and a further two samples had Stx1 free phages only (3.8%). It was thus possible to reduce the samples with no explanation to 20 (37.7% of 53 samples), representing a further step towards an improved understanding of the STEC PCR-positive/culture-negative phenomenon.

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Sikora, Aleksandra, Bernhard G. Zimmermann, Corinne Rusterholz, Daniella Birri, Varaprasad Kolla, Olav Lapaire, Irene Hoesli, Vivian Kiefer, Laird Jackson, and Sinuhe Hahn. "Detection of Increased Amounts of Cell-Free Fetal DNA with Short PCR Amplicons." Clinical Chemistry 56, no. 1 (January 1, 2010): 136–38. http://dx.doi.org/10.1373/clinchem.2009.132951.

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Abstract Aim: A digital PCR approach has recently been suggested to detect greater amounts of cell-free fetal DNA in maternal plasma than conventional real-time quantitative PCR (qPCR). Because the digital qPCR approach uses shorter PCR amplicons than the real-time qPCR assay, we investigated whether a real-time qPCR assay appropriately modified for such short amplicons would improve the detection of cell-free fetal DNA. Method: We developed a novel universal-template (UT) real-time qPCR assay that was specific for the DYS14 sequence on Y chromosome and had a short amplicon size of 50 bp. We examined this “short” assay with 50 maternal plasma samples and compared the results with those for a conventional real-time qPCR assay of the same locus but with a longer amplicon (84 bp). Results: Qualitatively, both assays detected male cell-free fetal DNA with the same specificity and detection capability. Quantitatively, however, the new UT real-time qPCR assay for shorter amplicons detected, on average, almost 1.6-fold more cell-free fetal DNA than the conventional real-time qPCR assay with longer amplicons. Conclusions: The use of short PCR amplicons improves the detection of cell-free fetal DNA. This feature may prove useful in attempts to detect cell-free fetal DNA under conditions in which the amount of template is low, such as in samples obtained early in pregnancy.

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Herlinawati, Sri Wahyu, Hilyatuz Zahroh, Sakura Sakura, Sofa Inayatullah, Hadi Firmansyah, Nunung Ainurohmah, and Rika Yuliwulandari. "PENCEGAHAN PENULARAN COVID-19 MELALUI PENYEDIAAN ALAT PELINDUNG DIRI, TRAINING DIAGNOSTIK COVID-19 DAN PEMERIKSAAN COVID-19 BERBASIS SWAB PCR GRATIS UNTUK TENAGA KESEHATAN DAN MAHASISWA KEPANITERAAN KLINIK FAKULTAS KEDOKTERAN UNIVERSITAS YARSI KERJASAM." Info Abdi Cendekia 4, no. 2 (December 20, 2021): 16. http://dx.doi.org/10.33476/iac.v4i2.29.

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ABSTRACT Currently, Indonesia has the highest number of confirmed Coronavirus Disease 2019 (COVID-19) cases in ASEAN. The large scale detection based on Real-Time Reverse Transcriptase PCR (rRT-PCR) is a key strategy recommended by WHO for controlling COVID-19 spread. Increasing testing capacity is very important for countries with the massive spread of COVID-19. In this community service program, the committee has carried out 3 strategic activities: free COVID-19 diagnosis based on rRT-PCR test, training on SARS-CoV-2 rRT PCR test, and distribution of free personal protective equipment (PPE). The target subjects are clinical clerkship students of medical school of YARSI University, health workers, employees and their family, and academic staff of YARSI University. Keywords : Coronavirus Disease (COVID-19), Swab test rRT-PCR, personal protective equipment (PPE)

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Lin, Wei, Tian Tian, Yongzhong Jiang, Erhu Xiong, Debin Zhu, and Xiaoming Zhou. "A CRISPR/Cas9 eraser strategy for contamination‐free PCR end‐point detection." Biotechnology and Bioengineering 118, no. 5 (March 2021): 2053–66. http://dx.doi.org/10.1002/bit.27718.

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Berrilli, Federica, David Di Cave, Andrea Novelletto, and Margherita Montalbano Di Filippo. "PCR-based identification of thermotolerant free-living amoebae in Italian hot springs." European Journal of Protistology 80 (August 2021): 125812. http://dx.doi.org/10.1016/j.ejop.2021.125812.

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Kim, Yu Kyung, and Soon Hee Chang. "Clinical usefulness of extraction-free PCR assay to detect SARS-CoV-2." Journal of Virological Methods 296 (October 2021): 114217. http://dx.doi.org/10.1016/j.jviromet.2021.114217.

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Murienne, Jérôme, Céline Jeziorski, Hélène Holota, Eric Coissac, Simon Blanchet, and Gaël Grenouillet. "PCR-free shotgun sequencing of the stone loach mitochondrial genome (Barbatula barbatula)." Mitochondrial DNA Part A 27, no. 6 (May 22, 2015): 4211–12. http://dx.doi.org/10.3109/19401736.2015.1022744.

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Nikolaidis, N., and Z. G. Scouras. "A polymerase chain reaction (PCR) application for free-living nematodes (Rhabditida) discrimination." Molecular Ecology Notes 2, no. 3 (September 2002): 248–49. http://dx.doi.org/10.1046/j.1471-8286.2002.00215.x.

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Nikolaidis, N., and Z. G. Scouras. "A polymerase chain reaction (PCR) application for free-living nematodes (Rhabditida) discrimination." Molecular Ecology Notes 2, no. 3 (August 6, 2002): 248–49. http://dx.doi.org/10.1046/j.1471-8286.2002.00215.x-i2.

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