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Journal articles on the topic 'Integrity-PCR'

Author: Grafiati

Published: 9 November 2024

Last updated: 31 July 2025

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1

Perkin, L. C., B. Oppert, S. Duke, and C. P.-C. Suh. "Assessment of DNA Integrity From Trap-Captured Boll Weevil (Coleoptera: Curculionidae) for Use in a New PCR-Based Diagnostic Tool." Journal of Economic Entomology 114, no. 3 (2021): 1321–28. http://dx.doi.org/10.1093/jee/toab073.

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Abstract The boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), is a major pest of commercial cotton (Gossypium hirsutum) in the southern United States and throughout Central and South America. Efforts are underway to develop a PCR-based diagnostic tool that can be used to rapidly and accurately differentiate boll weevils from other weevil species that are commonly captured in pheromone traps. However, the quantity and integrity of weevil DNA must be sufficient for a successful PCR assay. Currently, active eradication programs service traps weekly, but post-eradicatio

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2

Bergerová, E., Z. Godálová, and P. Siekel. "Combined effects of temperature, pressure and low pH on the amplification of DNA of plant derived foods." Czech Journal of Food Sciences 29, No. 4 (2011): 337–45. http://dx.doi.org/10.17221/217/2010-cjfs.

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The effect of food processing on the DNA integrity was studied by means of PCR amplification of soybean, transgenic MON 810 and non-transgenic maize, bean, and pea. The degree of DNA degradation was checked by PCR and visualised by agarose gel electrophoresis. The conditions of technological treatment such as temperature, pH, pressure, and their combination may negatively influence the integrity of DNA in processed foods and hence PCR detection of food components. The DNA over 300 bp was amplifiable when mild processing parameters up to 100&deg;C were performed at approximately neutral or

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Du, Xiongwei, Hongjie An, Bo Jin, Liangyu Meng, and Qingdai Liu. "Carbon Nanotubes Altering Specificity of Repeated PCR and DNA Integrity Properties." Journal of Nanoscience and Nanotechnology 14, no. 7 (2014): 5547–51. http://dx.doi.org/10.1166/jnn.2014.8874.

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Frasquilho, Sonia G., Ignacio Sanchez, Changyoung Yoo, Laurent Antunes, Camille Bellora, and William Mathieson. "Do Tissues Fixed in a Non-crosslinking Fixative Require a Dedicated Formalin-free Processor?" Journal of Histochemistry & Cytochemistry 69, no. 6 (2021): 389–405. http://dx.doi.org/10.1369/00221554211017859.

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We evaluate the consequences of processing alcohol-fixed tissue in a processor previously used for formalin-fixed tissue. Biospecimens fixed in PAXgene Tissue Fixative were cut into three pieces then processed in a flushed tissue processor previously used for formalin-fixed, paraffin-embedded (FFPE) blocks (neutral buffered formalin [NBF]+ve), a formalin-free system (NBF−ve), or left unprocessed. Histomorphology and immunohistochemistry were compared using hematoxylin/eosin staining and antibodies for MLH-1, Ki-67, and CK-7. Nucleic acid was extracted using the PAXgene Tissue RNA/DNA kits and

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Raja, Siva, Jesus Ching, Liqiang Xi, et al. "Technology for Automated, Rapid, and Quantitative PCR or Reverse Transcription-PCR Clinical Testing." Clinical Chemistry 51, no. 5 (2005): 882–90. http://dx.doi.org/10.1373/clinchem.2004.046474.

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Abstract Background: PCR-based assays can improve clinical care, but they remain technically demanding and labor-intensive. We describe a new instrument, the GeneXpert®, that performs automated nucleic acid isolation, reverse transcription, and fluorescence-based quantitative PCR in ∼35 min. Methods: Yield and integrity of RNA isolated on the GeneXpert were compared with Qiagen-based extraction for parallel samples (5-μm frozen tissue sections). The reproducibility of automated RNA isolation, reverse transcription, and quantitative PCR was determined by replicate (n = 10) analysis of 10 tissue

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Fleige, Simone, and Michael W. Pfaffl. "RNA integrity and the effect on the real-time qRT-PCR performance." Molecular Aspects of Medicine 27, no. 2-3 (2006): 126–39. http://dx.doi.org/10.1016/j.mam.2005.12.003.

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Gorzelak-Pabis, Paulina, Emilia Luczak, Katarzyna Wojdan, et al. "Endothelial integrity may be regulated by a specific antigen via an IgE-mediated mechanism." Postępy Higieny i Medycyny Doświadczalnej 71, no. 1 (2017): 0. http://dx.doi.org/10.5604/01.3001.0010.3800.

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Background: Human vascular endothelial function and integrity may be regulated by many non-specific factors. However, the potential influence of specific antigens via an IgE-mediated mechanism remains unknown. The aim of the study was to determine the expression of the IgE receptors FcεRI and FcεRII in the human vascular endothelium and to assess their relevance in the IgE-mediated regulation of endothelial integrity.Material/Methods: FcεRI and FcεRII expression in human umbilical vein endothelial cells (HUVEC) was genetically assessed by PCR with respective primers and sequencing. HUVEC were

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Oakey, H. Jane. "A Universal Test to Determine the Integrity of RNA, and its Suitability for Reverse Transcription, in Animal Tissue Laboratory Specimens." Journal of Veterinary Diagnostic Investigation 19, no. 5 (2007): 459–64. http://dx.doi.org/10.1177/104063870701900501.

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Degradation of RNA in diagnostic specimens can cause false-negative test results and potential misdiagnosis when tests rely on the detection of specific RNA sequence. Current molecular methods of checking RNA integrity tend to be host species or group specific, necessitating libraries of primers and reaction conditions. The objective here was to develop a universal (multi-species) quality assurance tool for determining the integrity of RNA in animal tissues submitted to a laboratory for analyses. Ribosomal RNA (16S rRNA) transcribed from the mitochondrial 16S rDNA was used as template material

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Cédile, Oriane, Sólja Remisdóttir Veyhe, Marcus Høy Hansen, Kjell Titlestad, and Charlotte Guldborg Nyvold. "Investigation of circulating DNA integrity after blood collection." BioTechniques 71, no. 5 (2021): 550–55. http://dx.doi.org/10.2144/btn-2020-0167.

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Method summary Concentrations of circulating DNA in blood plasma were compared using NanoDrop, Qubit, quantitative PCR and Bioanalyzer, and DNA integrity was evaluated with the Bioanalyzer according to the time of plasma preparation.

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10

Didelot, Audrey, Steve K. Kotsopoulos, Audrey Lupo, et al. "Multiplex Picoliter-Droplet Digital PCR for Quantitative Assessment of DNA Integrity in Clinical Samples." Clinical Chemistry 59, no. 5 (2013): 815–23. http://dx.doi.org/10.1373/clinchem.2012.193409.

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BACKGROUND Assessment of DNA integrity and quantity remains a bottleneck for high-throughput molecular genotyping technologies, including next-generation sequencing. In particular, DNA extracted from paraffin-embedded tissues, a major potential source of tumor DNA, varies widely in quality, leading to unpredictable sequencing data. We describe a picoliter droplet–based digital PCR method that enables simultaneous detection of DNA integrity and the quantity of amplifiable DNA. METHODS Using a multiplex assay, we detected 4 different target lengths (78, 159, 197, and 550 bp). Assays were validat

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Du Cheyne, Charis, Yao Chen, Jurgen De Craene, Olivier Thas, and Ward De Spiegelaere. "Development of a 3’:5’ digital PCR assay to determine horse mRNA integrity." Analytical Biochemistry 626 (August 2021): 114217. http://dx.doi.org/10.1016/j.ab.2021.114217.

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12

Tereshko, Lauren, Xiaohui Zhao, Jake Gagnon, et al. "A novel method for quantitation of AAV genome integrity using duplex digital PCR." PLOS ONE 18, no. 12 (2023): e0293277. http://dx.doi.org/10.1371/journal.pone.0293277.

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Recombinant adeno-associated virus (rAAV) vectors have become a reliable strategy for delivering gene therapies. As rAAV capsid content is known to be heterogeneous, methods for rAAV characterization are critical for assessing the efficacy and safety of drug products. Multiplex digital PCR (dPCR) has emerged as a popular molecular approach for characterizing capsid content due to its high level of throughput, accuracy, and replicability. Despite growing popularity, tools to accurately analyze multiplexed data are scarce. Here, we introduce a novel statistical model to estimate genome integrity

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Prantner, Andrew, and Dianna Maar. "Genome concentration, characterization, and integrity analysis of recombinant adeno-associated viral vectors using droplet digital PCR." PLOS ONE 18, no. 1 (2023): e0280242. http://dx.doi.org/10.1371/journal.pone.0280242.

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Precise, reproducible characterization of AAV is critical for comparing preclinical results between laboratories and determining a safe and effective clinical dose for gene therapy applications. In this study, we systematically evaluated numerous parameters to produce a simple and robust ddPCR protocol for AAV characterization. The protocol uses a low ionic strength buffer containing Pluronic-F68 and polyadenylic acid to dilute the AAV into the ddPCR concentration range and a 10-minute thermal capsid lysis prior to assembling ddPCR reactions containing MspI. A critical finding is that the buff

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Mughal, Kiran, Mohammad Pervez Mughal, Muhammad Umar Farooq, Muhammad Qaiser Saleem, and Rodolfo Haber Guerra. "Helical Milling of CFRP/Ti6Al4V Stacks Using Nano Fluid Based Minimum Quantity Lubrication (NF-MQL): Investigations on Process Performance and Hole Integrity." Materials 16, no. 2 (2023): 566. http://dx.doi.org/10.3390/ma16020566.

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The structural components in the aeronautical industry require CFRP/Ti6Al4V stacks to be processed together, which results in poor hole integrity due to the thermal properties of the materials and challenges related to processability. These challenges include quality variation of the machined holes because of the limitations in process properties. Therefore, a novel solution through helical milling is investigated in the study using nano fluid based minimum quantity lubrication (NF-MQL). The analysis of variance shows, for Ti6Al4V, eccentricity (PCR = 28.56%), spindle speed (Ti) (PCR = 42.84%)

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Fu, Donglai, and Yanhua Liu. "Remote Attestation on Behavioral Traces for Crowd Quality Control Based on Trusted Platform Module." Security and Communication Networks 2021 (April 26, 2021): 1–12. http://dx.doi.org/10.1155/2021/8859618.

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Behavioral traces of workers have emerged as a new evidence to check the quality of their produced outputs in crowd computing. Whether the evidence is trustworthy or not is a key problem during the process. Challenges will be encountered in addressing this issue, because the evidence comes from unknown or adversarial workers. In this study, we proposed an alternative approach to ensure trustworthy evidence through a hardware-based remote attestation to bridge the gap. The integrity of the evidence was used as the trustworthy criterion. Trusted Platform Module (TPM) was considered the trusted a

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McCanless, Adair, Allison Hultgren, Cesar Escalante, Alyssa Ardt, and Rodrigo A. Valverde. "Effect of two digestive enzymes and pH on the dsRNA of endornaviruses of bell pepper and melon under in vitro conditions." Annals of Microbiology 69, no. 13 (2019): 1583–87. http://dx.doi.org/10.1007/s13213-019-01530-2.

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Abstract Purpose The objective of this investigation was to determine the in vitro effect of two common digestive enzymes, amylase and pepsin, and pH on the integrity of the RI dsRNA of bell pepper endornavirus (BPEV) and Cucumis melo endornavirus (CmEV) evaluated by gel electrophoresis and reverse-transcription PCR (RT-PCR). Methods We conducted experiments on the in vitro effect of two common digestive enzymes, amylase and pepsin, and pH on the structural integrity of the replicative intermediate (RI) dsRNA of bell pepper endornavirus (BPEV) and Cucumis melo endornavirus (CmEV), evaluated by

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Frazer, Zoe, Changyoung Yoo, Manveer Sroya, et al. "Effect of Different Proteinase K Digest Protocols and Deparaffinization Methods on Yield and Integrity of DNA Extracted From Formalin-fixed, Paraffin-embedded Tissue." Journal of Histochemistry & Cytochemistry 68, no. 3 (2020): 171–84. http://dx.doi.org/10.1369/0022155420906234.

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DNA extracted from formalin-fixed, paraffin-embedded tissue sections is often inadequate for sequencing, due to poor yield or degradation. We optimized the proteinase K digest by testing increased volume of enzyme and increased digest length from the manufacturer’s protocol using 54 biospecimens, performing the digest in centrifuge tubes. Doubling the quantity of proteinase K resulted in a median increase in yield of 96%. Applying the optimized proteinase K protocol to sections deparaffinized on microscope slides generated a further increase in yield of 41%, but only at >50,000 epithelial t

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Padhi, Bhaja K., Manjeet Singh, Marianela Rosales, Guillaume Pelletier, and Sabit Cakmak. "A PCR-based quantitative assay for the evaluation of mRNA integrity in rat samples." Biomolecular Detection and Quantification 15 (May 2018): 18–23. http://dx.doi.org/10.1016/j.bdq.2018.02.001.

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Bohan, Amy E., Katelyn N. Purvis, Jason T. Sawyer, Werner G. Bergen, and Terry D. Brandebourg. "Sampling Adipose and Muscle Tissue following Post-Harvest Scalding Does Not Affect RNA Integrity or Real-Time PCR Results in Market Weight Yorkshire Pigs." Foods 11, no. 12 (2022): 1741. http://dx.doi.org/10.3390/foods11121741.

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Improving production efficiency while enhancing pork quality is pivotal for strengthening sustainable pork production. Being able to study both gene expression and indices of pork quality from the same anatomical location of an individual animal would better enable research conducted to study relationships between animal growth and carcass merit. To facilitate gene expression studies, adipose and muscle tissue samples are often collected immediately following exsanguination to maximize RNA integrity, which is a primary determinant of the sensitivity of RNA-based assays, such as real-time PCR.

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Grote, Hans Jürgen, Viola Schmiemann, Mario Sarbia, and Alfred Böcking. "DNA Extraction from Bronchial Aspirates for Molecular Cytology: Which Method to Take?" Analytical Cellular Pathology 25, no. 2 (2003): 83–88. http://dx.doi.org/10.1155/2003/354796.

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Objective: To date, there are only few systematic reports on the quality of DNA extracted from routine diagnostic cytologic specimens. It was the aim of the present study to evaluate the ability of 50% ethanol/2% carbowax (Saccomanno fixative) to preserve bronchial secretions with high quality genomic DNA as well as to compare different DNA extraction methods.Methods: DNA was extracted from 45 bronchial aspirates by four different extraction protocols. Beside DNA yield, DNA quality with regard to purity, integrity, and PCR success rate were investigated.Results: No fragmentation of sample DNA

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Wehmas, Leah C., Charles E. Wood, Brian N. Chorley, Carole L. Yauk, Gail M. Nelson, and Susan D. Hester. "Enhanced Quality Metrics for Assessing RNA Derived From Archival Formalin-Fixed Paraffin-Embedded Tissue Samples." Toxicological Sciences 170, no. 2 (2019): 357–73. http://dx.doi.org/10.1093/toxsci/kfz113.

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Abstract Formalin-fixed paraffin-embedded (FFPE) tissues provide an important resource for toxicogenomic research. However, variability in the integrity or quality of RNA obtained from archival FFPE specimens can lead to unreliable data and wasted resources, and standard protocols for measuring RNA integrity do not adequately assess the suitability of FFPE RNA. The main goal of this study was to identify improved methods for evaluating FFPE RNA quality for whole-genome sequencing. We examined RNA quality metrics conducted prior to RNA-sequencing in paired frozen and FFPE samples with varying l

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Ren, Sai, Xiaodong Ren, Haiqin Guo, et al. "Concentration and integrity indexes of urine cell-free DNA as promising biomarkers for early lung cancer diagnosis." Personalized Medicine 18, no. 2 (2021): 129–39. http://dx.doi.org/10.2217/pme-2020-0019.

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Aim: To explore the role of urine cell-free DNA (ucfDNA) concentration and integrity indexes as potential biomarkers for lung cancer diagnosis. Materials & methods: Quantitative real-time PCR targeting Arthrobacter luteus ( ALU) repeats at three size fragments ( ALU-60, 115 and 247 bp) was performed in 55 lung cancer patients and 35 healthy individuals. Results: ucfDNA concentration and integrity indexes were significantly higher in lung cancer patients than in healthy controls. The area under the receiver operating characteristic curve for differentiating patients with stage I/II from hea

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Pacheco, Julia Iracema Moura, Ketlen Beatriz Alves dos Anjos, Isabela Vaz Silva, et al. "Comparison of two affordable DNA extraction methods for molecular detection of Salmonella isolates from broiler farm’s boot swabs." Research, Society and Development 12, no. 1 (2023): e28312139618. http://dx.doi.org/10.33448/rsd-v12i1.39618.

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There are many extraction methods available to purify bacterial DNA. PCR efficiency can vary depending on the quantity and quality of the template DNA used. This study evaluated the efficiency, quality, cost and rapidness of two in-house protocols, silica particles and Chelex-100 resin, for the extraction of twenty Salmonella isolates from boot swabs. The aim of this experiment was to compare the extraction methods for Salmonella spp. detection. DNA extraction was performed for each method and subjected to real-time PCR amplification. The amounts and integrity of DNA were determined using spec

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Palmirotta, Raffaele, Maria Laura De Marchis, Giorgia Ludovici, et al. "Impact of Preanalytical Handling and Timing for Peripheral Blood Mononuclear Cells Isolation and RNA Studies: The Experience of the Interinstitutional Multidisciplinary BioBank (BioBIM)." International Journal of Biological Markers 27, no. 2 (2012): 90–98. http://dx.doi.org/10.5301/jbm.2012.9235.

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Multicenter studies and biobanking projects require blood transportation from the participating center to a central collection or diagnostic laboratory. The impact of time delays between venous blood collection and peripheral blood mononuclear cells (PBMC) isolation prior to RNA extraction may affect the quality and quantity of isolated nucleic acids for genomic applications. Thus, standard operating procedure (SOP) optimization for the treatment of biological samples before RNA extraction is crucial in a biological repository. In order to define SOPs for whole blood preservation prior to RNA

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Koentjoro, Maharani Pertiwi, Adyan Donastin, and Endry Nugroho Prasetyo. "A SIMPLE METHOD OF DNA EXTRACTION OF MYCOBACTERIUM TUBERCULOSIS FROM SPUTUM CULTURES FOR SEQUENCING ANALYSIS." African Journal of Infectious Diseases 15, no. 2s (2021): 19–22. http://dx.doi.org/10.21010/ajid.v15i2s.2.

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Background: Concern has been raised about DNA extraction from Mycobacterium tuberculosis due to its complex procedure. This study demonstrates a simple and fast DNA extraction method of mycobacterial genome to subsequent molecular investigation, such as Polymerization Chain Reaction (PCR) amplification, with species-specific primers and sequencing. Materials and Methods: Total DNA was isolated from M. tuberculosis cultured by using boil method. DNA was evaluated via measures of DNA quantity and quality (absorbance at 230, 260 and 280 nm), DNA integrity (electrophoresis). Molecular tests were t

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Phillips, Jamie E., Stephen McCune, Corinne R. Fantz, Julia Engstrom-Melnyk, and John C. Osiecki. "Assay Integrity of a PCR Influenza Point-of-Care Test Remains Following Artificial System Contamination." Journal of Applied Laboratory Medicine 4, no. 3 (2019): 422–26. http://dx.doi.org/10.1373/jalm.2018.028639.

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Ekuni, Daisuke, James D. Firth, and Edward E. Putnins. "RNA integrity and in situ RT-PCR in dento-alveolar tissues after microwave accelerated demineralisation." Archives of Oral Biology 51, no. 2 (2006): 164–69. http://dx.doi.org/10.1016/j.archoralbio.2005.06.010.

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Lakpour, Niknam, Azadeh Mirfeizollahi, Shirin Farivar, et al. "The Association of Seminal Plasma Antioxidant Levels and Sperm Chromatin Status with Genetic Variants ofGSTM1andGSTP1(Ile105Val and Ala114Val) in Infertile Men with Oligoasthenoteratozoospermia." Disease Markers 34, no. 3 (2013): 205–10. http://dx.doi.org/10.1155/2013/635091.

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In this study we aimed to examine the effects of genetic variants ofGSTM1andGSTP1(Ile105Val and Ala114Val) on GST activity, seminal oxidative stress and sperm chromatin status in infertile men with oligoasthenoteratozoospermia (OAT). The study population (n= 121) consisted of 95 infertile men with OAT and 26 controls with normozoospermia. Multiplex polymerase chain reaction (PCR) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods were utilized to detect the aforesaid genetic variants. We measured GST activity and total antioxidant capacity (TAC) of semina

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Casadio, Valentina, Daniele Calistri, Samanta Salvi, et al. "Urine Cell-Free DNA Integrity as a Marker for Early Prostate Cancer Diagnosis: A Pilot Study." BioMed Research International 2013 (2013): 1–5. http://dx.doi.org/10.1155/2013/270457.

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Circulating cell-free DNA has been recognized as an accurate marker for the diagnosis of prostate cancer, whereas the role of urine cell-free DNA (UCF DNA) has never been evaluated in this setting. It is known that normal apoptotic cells produce highly fragmented DNA while cancer cells release longer DNA. We thus verified the potential role of UCF DNA integrity for early prostate cancer diagnosis. UCF DNA was isolated from 29 prostate cancer patients and 25 healthy volunteers. Sequences longer than 250 bp (c-Myc,BCAS1, andHER2) were quantified by real-time PCR to verify UCF DNA integrity. Rece

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Gurdal, Necla, Merdan Fayda, Nijat Alishev, et al. "Neoadjuvant volumetric modulated arc therapy in rectal cancer and the correlation of pathological response with diffusion-weighted MRI and apoptotic markers." Tumori Journal 104, no. 4 (2018): 266–72. http://dx.doi.org/10.5301/tj.5000702.

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Purpose: In this prospective observational study, we aimed to report the applicability and tolerability of neoadjuvant volumetric modulated arc therapy with simultaneous integrated boost (SIB-VMAT) and concurrent chemotherapy in patients with locally advanced rectal cancer (LARC), and to evaluate the correlation of pathological response with apparent diffusion coefficient (ADC) measurements on diffusion-weighted magnetic resonance imaging (DW-MRI) and apoptotic markers. Methods: The study enrolled 30 patients with T3 to T4 and/or N+ rectal cancer who preoperatively received SIB-VMAT and concur

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Park, Noh Jin, Yang Li, Tianwei Yu, Brigitta MN Brinkman, and David T. Wong. "Characterization of RNA in Saliva." Clinical Chemistry 52, no. 6 (2006): 988–94. http://dx.doi.org/10.1373/clinchem.2005.063206.

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Abstract Background: We have previously shown that human mRNAs are present in saliva and can be used as biomarkers of oral cancer. In this study, we analyzed the integrity, sources, and stability of salivary RNA. Methods: We measured the integrity of salivary RNA with reverse transcription followed by PCR (RT-PCR) or RT-quantitative PCR (RT-qPCR). To study RNA entry sites into the oral cavity, we used RT-PCR analysis of salivary RNA from the 3 major salivary glands, gingival crevice fluid, and desquamated oral epithelial cells. We measured stability of the salivary β-actin mRNA by RT-qPCR of s

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Zhang, Miaomiao, Xiaopeng Guo, Yue Gao, Dong Lu, and Wenjian Li. "Tumor Cell–Accelerated Senescence Is Associated With DNA-PKcs Status and Telomere Dysfunction Induced by Radiation." Dose-Response 16, no. 2 (2018): 155932581877152. http://dx.doi.org/10.1177/1559325818771527.

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Whether telomere structure integrity is related to radiosensitivity is not well investigated thus far. In this study, we investigated the relation between telomere instability and radiation-induced accelerated senescence. Partial knockdown of DNA-dependent catalytic subunit of protein kinase (DNA-PKcs) in human breast cancer cell line MCF-7 was established by small interfering RNA. Radiosensitivity of control and DNA-PKcs knockdown MCF-7 cells was analyzed by clonogenetic assay. Cell growth was measured by real-time cell electronic sensing. Senescence and apoptosis were evaluated by β-galactos

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El-Shazly, Sherien F., Manal A. Eid, Hesham A. El-Sourogy, Gehan F. Attia, and Sherif A. Ezzat. "Evaluation of Serum Dna Integrity as a Screening and Prognostic Tool in Patients with Hepatitis C Virus-Related Hepatocellular Carcinoma." International Journal of Biological Markers 25, no. 2 (2010): 79–86. http://dx.doi.org/10.1177/172460081002500204.

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Background Hepatocellular carcinoma (HCC) is a common malignancy in Egypt due to the high frequency of hepatitis C virus (HCV) infection among the general population. Circulating free DNA is a potential molecular marker for the diagnosis and prognosis of malignant tumors. DNA released from apoptotic cells usually consists of short uniform fragments while DNA released from cancer cells is longer. The ratio of long DNA fragments to total DNA (DNA integrity) may be a potential marker for early detection of HCC and its progression in HCV patients. Methods Sera from 25 patients with HCV-related HCC

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Cheng, S., Y. Chen, J. A. Monforte, R. Higuchi, and B. Van Houten. "Template integrity is essential for PCR amplification of 20- to 30-kb sequences from genomic DNA." Genome Research 4, no. 5 (1995): 294–98. http://dx.doi.org/10.1101/gr.4.5.294.

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Wong, Blenda CK, Rossa WK Chiu, Nancy BY Tsui, et al. "Circulating Placental RNA in Maternal Plasma Is Associated with a Preponderance of 5′ mRNA Fragments: Implications for Noninvasive Prenatal Diagnosis and Monitoring." Clinical Chemistry 51, no. 10 (2005): 1786–95. http://dx.doi.org/10.1373/clinchem.2005.052340.

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Abstract Background: The molecular characteristics of placental RNA circulating in maternal plasma are unknown. We investigated the integrity of circulating placental RNA in maternal plasma and tested the relevance of plasma RNA integrity for noninvasive prenatal diagnosis. Methods: Six different placental transcripts and mRNA of the housekeeping gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were quantified for the 5′ and 3′ regions in maternal plasma by 1-step real-time reverse transcription-PCR (RT-PCR) assays. This quantitative strategy was validated by 2-step RT-PCR and serial dilu

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Baert, Leen, Christiane E. Wobus, Els Van Coillie, Larissa B. Thackray, Johan Debevere, and Mieke Uyttendaele. "Detection of Murine Norovirus 1 by Using Plaque Assay, Transfection Assay, and Real-Time Reverse Transcription-PCR before and after Heat Exposure." Applied and Environmental Microbiology 74, no. 2 (2007): 543–46. http://dx.doi.org/10.1128/aem.01039-07.

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ABSTRACT The correlation between the detection of murine norovirus 1 RNA by real-time reverse transcription-PCR and the infectivity by plaque assay before and after heat exposure (80°C) was examined. No correlation was found in the current study. Moreover, heat inactivation had a much stronger detrimental effect on virus infectivity than on the integrity of the viral genome.

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Deng, Yanan, Ziqi Qiao, Changping Zhou, et al. "Endothelial Myosin IIA Is Required for the Maintenance of Blood–Brain Barrier Integrity." Cells 13, no. 19 (2024): 1635. http://dx.doi.org/10.3390/cells13191635.

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Brain endothelial cells (ECs) are essential elements of the blood–brain barrier (BBB), maintaining its integrity through both paracellular junctions and transcellular transport systems. Myosin IIA, a multifunctional protein, plays a significant role in various cellular processes, including cytoskeletal maintenance, cell division, and signal transduction. While Myosin IIA has been implicated in bleeding and ischemic stroke, its role in regulating BBB integrity under physiological conditions remains unclear. In this study, we investigated the impact of Myosin IIA deficiency on BBB integrity usin

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Salvi, Samanta, Giorgia Gurioli, Filippo Martignano, et al. "Urine Cell-Free DNA Integrity Analysis for Early Detection of Prostate Cancer Patients." Disease Markers 2015 (2015): 1–6. http://dx.doi.org/10.1155/2015/574120.

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Introduction. The detection of tumor-specific markers in urine has paved the way for new early noninvasive diagnostic approaches for prostate cancer. We evaluated the DNA integrity in urine supernatant to verify its capacity to discriminate between prostate cancer and benign diseases of the urogenital tract.Patients and Methods. A total of 131 individuals were enrolled: 67 prostate cancer patients and 64 patients with benign diseases of the urogenital tract (control group). Prostate-specific antigen (PSA) levels were determined. Urine cell-free (UCF) DNA was isolated and sequences longer than

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Guerra Naranjo, Cesar David, Tanira Alessandra Silveira Aguirre, and Ana Paula Guedes Frazzon. "DNARS: A safe, environmentally friendly and high-quality DNA extraction method suitable for various biological samples." Polo del Conocimiento 9, no. 10 (2024): 900–918. http://dx.doi.org/10.23857/pc.v9i10.8152.

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The functional and interactional relationships between nucleic acids and proteins form the foundational framework for molecular biology studies. In this context, obtaining high-quality nucleic acids is a crucial step for successful downstream applications. This study aimed to develop a cost-effective, eco-friendly, and versatile DNA extraction method that yields high-quality DNA from diverse biological samples. We utilized three types of borosilicate-based recycled laboratory glass as a silica source, combined with sodium iodide as a chaotropic agent, creating an efficient system for cell lysi

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Zeng, Mu-Zi, Wei Zhou, Shan-Shan Wen, et al. "Identification and Functional Insights of Knickkopf Genes in the Larval Cuticle of Leptinotarsa decemlineata." Insects 15, no. 8 (2024): 623. http://dx.doi.org/10.3390/insects15080623.

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The Colorado potato beetle (Leptinotarsa decemlineata) is a major pest of potato crops. While Knickkopf (Knk) genes are essential for insect cuticle formation, their roles in pests like L. decemlineata remain unclear. This study aims to identify and characterize Knk genes in L. decemlineata and explore their functions in larval development and cuticle integrity. We used genomic and transcriptomic databases to identify LdKnk-family genes, validated through RT-PCR and RACE. Gene expression was analyzed at various developmental stages and tissues using qRT-PCR. RNA interference (RNAi) and Transmi

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Dieser, Markus, Andreas Nocker, John C. Priscu, and Christine M. Foreman. "Viable microbes in ice: application of molecular assays to McMurdo Dry Valley lake ice communities." Antarctic Science 22, no. 5 (2010): 470–76. http://dx.doi.org/10.1017/s0954102010000404.

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AbstractThe permanent ice covers of the McMurdo Dry Valley lakes, Antarctica, are colonized by a diverse microbial assemblage. We collected ice cores from Lakes Fryxell, Hoare and Bonney. Propidium monoazide (PMA) was used in combination with quantitative PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE) to examine membrane integrity of prokaryotes in these extreme environments. PMA selectively penetrates cells with compromised membranes and modifies their DNA resulting in the suppression of PCR amplification. Our results based on analysis of 16S rRNA genes demonstrate that despite

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Veazey, Janelle, Timothy J. Chapman, Timothy R. Smyth, Sara E. Hillman, Sophia I. Eliseeva, and Steve N. Georas. "Protein Kinase D: A new target in the fight against flu?" Journal of Immunology 204, no. 1_Supplement (2020): 245.13. http://dx.doi.org/10.4049/jimmunol.204.supp.245.13.

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Abstract Summary Antivirals targeting host proteins may slow development of viral resistance and work against multiple viruses. The serine/threonine kinase protein kinase D (PKD) is one promising target as others have shown inhibiting PKD restricts rhinovirus and hepatitis in cell culture. We show inhibiting PKD restricts Influenza A virus (IAV) in cell culture and in mice. Methods The competitive PKD inhibitor, CRT, was given to A549, 16HBE cells and mice, prior to or during stimulation with dsRNA or IAV. Pulmonary barrier integrity was quantified by assaying total protein leak into the lumen

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Park, Seong Kook, Woo Jeong Lee, and Young Il Yang. "Organ Culture at the Air–Liquid Interface Maintains Structural and Functional Integrities of Inflammatory and Fibrovascular Cells of Nasal Polyps." American Journal of Rhinology 21, no. 4 (2007): 402–7. http://dx.doi.org/10.2500/ajr.2007.21.3050.

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Background Both inflammatory and fibrovascular cells play an important role in development of nasal polyps (NPs). In this study, we have developed a culture system to maintain structural and functional integrities of submucosal cells in vitro. Methods NP tissue was cultured on a gelatin sponge at air–liquid (AL) interface or was cultured in submerging. Tissues were analyzed for survival, structural integrity, and vascular endothelial growth factor (VEGF) expression. Results Most cells of NPs cultured in submerging died within 3 days. In culture at the AL interface, epithelium as well as submuc

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Sugiana, Fenny Aulia, Henni Widyowati, Muhammad Ali Warisman, Suryani Suryani, and Desriani Desriani. "Low cost and comprehensive pork detection in processed food products with a different food matrix." Indonesian Journal of Biotechnology 23, no. 1 (2018): 21. http://dx.doi.org/10.22146/ijbiotech.32372.

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The adulteration of processed beef-based meat products with pork is a sensitive issue in Indonesia. In this study, we developed a detection method for the low cost identification of pork in processed meat products. We used the cost-efficient Taq DNA polymerase, DreamTaq Green PCR master mix (2x), and duplex PCR method to recognize pork simultaneously with 18S rRNA detection. A positive control containing a pork gene inserted into pGEM®-T easy was prepared, along with a negative control. The results of the duplex PCR were used to assess its specificity, detection limit, and its ability to recog

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Ragland, Natalie H., Emily L. Miedel, and Robert W. Engelman. "PCR Prevalence of Murine Opportunistic Microbes and their Mitigation by Using Vaporized Hydrogen Peroxide." Journal of the American Association for Laboratory Animal Science 58, no. 2 (2019): 208–15. http://dx.doi.org/10.30802/aalas-jaalas-18-000112.

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Exposing immunodeficient mice to opportunistic microbes introduces risks of data variability, morbidity, mortality, and the invalidation of studies involving unique human reagents, including the loss of primary human hematopoietic cells, patient-derived xenografts, and experimental therapeutics. The prevalence of 15 opportunistic microbes in a murine research facility was determined by yearlong PCR-based murine and IVC equipment surveillance comprising 1738 specimens. Of the 8 microbes detected, 3 organisms— Staphylococcus xylosus, Proteus mirabilis, and Pasteurella pneumotropica biotype Heyl—

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Duanmu, Luyang, Youji Shen, Ping Gong, Hao Zhang, Xiangkai Meng, and Yuanhua Yu. "Constant Pressure-Regulated Microdroplet Polymerase Chain Reaction in Microfluid Chips: A Methodological Study." Micromachines 15, no. 1 (2023): 8. http://dx.doi.org/10.3390/mi15010008.

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Digital polymerase chain reaction (PCR) technology in microfluidic systems often results in bubble formation post-amplification, leading to microdroplet fragmentation and compromised detection accuracy. To solve this issue, this study introduces a method based on the constant pressure regulation of microdroplets during PCR within microfluidic chips. An ideal pressure reference value for continuous pressure control was produced by examining air solubility in water at various pressures and temperatures as well as modeling air saturation solubility against pressure for various temperature scenari

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Randhawa, Gurinder Jit, and Monika Singh. "Multiplex, Construct-Specific, and Real-Time PCR-Based Analytical Methods for Bt Rice with cry1Ac Gene." Journal of AOAC INTERNATIONAL 95, no. 1 (2012): 186–94. http://dx.doi.org/10.5740/jaoacint.10-429.

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Abstract Qualitative and quantitative analytical methods based on PCR for Bacillus thuringiensis (Bt) rice hybrid, namely, MRP 5401 Bt expressing a modified version of the Bt cry1Ac gene, are reported here. Multiplex PCR assays were developed to target the cry1Ac transgene, Cauliflower mosaic virus (CaMV) 35S promoter, Agrobacterium tumefaciens nopaline synthase (nos) terminator, the neomycin phosphotransferase II (nptII) marker gene, and an endogenous α-tubulin (TubA) gene in Bt rice. The 3.178 kb region of inserted gene construct comprising the region of the CaMV 35S promoter and cry1Ac gene

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Mostofinejad, Zahra, Md Akheruzzaman, Md Abu Bakkar Siddik, Presheet Patkar, Nikhil V. Dhurandhar, and Vijay Hegde. "Antidiabetic E4orf1 protein prevents hepatic steatosis and reduces markers of aging-related cellular damage in high fat fed older mice." BMJ Open Diabetes Research & Care 9, no. 1 (2021): e002096. http://dx.doi.org/10.1136/bmjdrc-2020-002096.

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IntroductionOlder age is associated with greater prevalence of hyperinsulinemia, type 2 diabetes, and fatty liver disease. These metabolic conditions and aging are bidirectionally linked to mitochondrial dysfunction and telomere attrition. Although effectively addressing these conditions is important for influencing the health and the lifespan, it is particularly challenging in older age. We reported that E4orf1, a protein derived from human adenovirus Ad36, reduces hyperinsulinemia, improves glucose clearance, and protects against hepatic steatosis in younger mice exposed to high fat diet (HF

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Relova, Damarys, Lester J. Pérez, Liliam Ríos, et al. "Short communication: Stability and integrity of classical swine fever virus RNA stored at room temperature." Spanish Journal of Agricultural Research 15, no. 3 (2017): e05SC03. http://dx.doi.org/10.5424/sjar/2017153-10776.

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Worldwide cooperation between laboratories working with classical swine fever virus (CSFV) requires exchange of virus isolates. For this purpose, shipment of CSFV RNA is a safe alternative to the exchange of infectious material. New techniques using desiccation have been developed to store RNA at room temperature and are reported as effective means of preserving RNA integrity. In this study, we evaluated the stability and integrity of dried CSFV RNA stored at room temperature. First, we determined the stability of CSFV RNA covering CSFV genome regions used typically for the detection of viral

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Stellino, Chiara, Gaël Hamot, Camille Bellora, Johanna Trouet, and Fay Betsou. "Preanalytical robustness of blood collection tubes with RNA stabilizers." Clinical Chemistry and Laboratory Medicine (CCLM) 57, no. 10 (2019): 1522–29. http://dx.doi.org/10.1515/cclm-2019-0170.

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Abstract Background Efficient blood stabilization is essential to obtaining reliable and comparable RNA analysis data in preclinical operations. PAXgene (Qiagen, Becton Dickinson) and Tempus (Applied Biosystems, Life Technologies) blood collection tubes with RNA stabilizers both avoid preanalytical degradation of mRNA by endogenous nucleases and modifications in specific mRNA concentrations by unintentional up- or down-regulation of gene expression. Methods Sixteen different preanalytical conditions were tested in PAXgene and Tempus blood samples from seven donors: different mixing after colle

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