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https://www.readbyqxmd.com/read/28810233/an-ultrasensitive-electrochemical-biosensor-for-the-detection-of-meca-gene-in-methicillin-resistant-staphylococcus-aureus
#1
Li Xu, Wen Liang, Yanli Wen, Lele Wang, Xue Yang, Shuzhen Ren, Nengqin Jia, Xiaolei Zuo, Gang Liu
Electrochemical DNA biosensor has unique advantages for on-site pathogenic microorganism detection, yet the detection of long DNA towards genome DNA (gDNA) analysis remains challenge. In this work, we report a novel electrochemical biosensor for the ultrasensitive analysis of mecA DNA on methicillin-resistant Staphylococcus aureus (MRSA) genome, using a multi-signal probes (MSP) system. The MSP consists of 7 biotin-labelled signal probes that will combine to the target DNA in a prehybridization step, and then the complex will be captured by a DNA tetrahedron structure probe (TSP) on the electrode surface...
August 8, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28809862/gnaq-and-gna11-mutations-and-downstream-yap-activation-in-choroidal-nevi
#2
M J C Vader, M C Madigan, M Versluis, H M Suleiman, G Gezgin, N A Gruis, J J Out-Luiting, W Bergman, R M Verdijk, M J Jager, P A van der Velden
BACKGROUND: Mutations in GNAQ/11 genes are considered an early event in the development of uveal melanoma that may derive from a pre-existing nevus. The Hippo pathway, by way of YAP activation, rather than MAP kinase, has a role in the oncogenic capacity of GNAQ/11 mutations. METHODS: We investigated 16 nevi from 13 human eyes for driver GNAQ/11 mutations using droplet digital PCR and determined whether nevi are clonal by quantifying mutant nevus cell fractions...
August 15, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28805606/detection-of-sea-type-%C3%AE-thalassemia-in-embryo-biopsies-by-digital-pcr
#3
Ta-Hsien Lee, Ya-Chiung Hsu, Chia Lin Chang
OBJECTIVE: Accurate and efficient pre-implantation genetic diagnosis (PGD) based on the analysis of single or oligo-cells is needed for timely identification of embryos that are affected by deleterious genetic traits in in vitro fertilization (IVF) clinics. Polymerase chain reaction (PCR) is the backbone of modern genetic diagnoses, and a spectrum of PCR-based techniques have been used to detect various thalassemia mutations in prenatal diagnosis (PND) and PGD. Among thalassemias, SEA-type α-thalassemia is the most common variety found in Asia, and can lead to Bart's hydrops fetalis and serious maternal complications...
August 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28805106/measuring-fetal-brain-and-lung-transcripts-in-amniotic-fluid-supernatant-a-comparison-of-digital-pcr-and-rt-qpcr-methods
#4
Lisa Hui, Sally Beard, Natalie J Hannan
PURPOSE: Amniotic fluid (AF) cell-free RNA is a promising source of information regarding fetal physiology. Digital PCR (dPCR) is a direct approach to nucleic acid detection that reports absolute transcript copy number. The aim of this study was to compare quantification of cell-free fetal brain and lung RNA transcripts in AF by reverse transcription-qPCR and dPCR. MATERIAL AND METHODS: Prospective hospital-based study performed in 2016-2017. Pulmonary genes were quantified in term AF samples collected at elective cesarean birth; neurodevelopmental genes were measured in preterm samples (< 34 weeks) obtained from women undergoing clinically-indicated amniocentesis...
August 14, 2017: Journal of Maternal-fetal & Neonatal Medicine
https://www.readbyqxmd.com/read/28802157/droplet-digital-pcr-for-rapid-enumeration-of-viral-genomes-and-particles-from-cells-and-animals-infected-with-orthopoxviruses
#5
Jeffrey L Americo, Patricia L Earl, Bernard Moss
Droplet digital polymerase chain reaction (ddPCR) was adapted for quantifying the number of orthopoxviral genomes in purified virus samples, infected cell lysates and tissues of infected animals. In contrast to the more commonly used qPCR, the newer ddPCR provides absolute numbers of DNA copies in samples without need for standard curves and has the ability to detect rare mutants in a population. The genome/infectious unit ratio for several sucrose gradient-purified orthopoxviruses varied from 5 to 10, which correlated well with values obtained using the Virocyt, a dedicated fluorescence flow cytometer...
August 9, 2017: Virology
https://www.readbyqxmd.com/read/28801547/early-changes-in-plasma-dna-levels-of-mutant-kras-as-a-sensitive-marker-of-response-to-chemotherapy-in-pancreatic-cancer
#6
Marzia Del Re, Caterina Vivaldi, Eleonora Rofi, Enrico Vasile, Mario Miccoli, Chiara Caparello, Paolo Davide d'Arienzo, Lorenzo Fornaro, Alfredo Falcone, Romano Danesi
Pancreatic cancer (PDAC) is still lacking of reliable markers to monitor tumor response. CA 19-9 is the only biomarker approved, despite it has several limitations in sensitivity and specificity. Since mutations of KRAS occur in more than 90% of tumors, its detection in circulating free tumor DNA (cftDNA) could represent a biomarker to monitor chemotherapy response. Twenty-seven advanced PDAC patients given first-line 5-fluorouracil, irinotecan and oxaliplatin or gemcitabine and nab-paclitaxel were enrolled...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28799053/quality-control-of-digital-pcr-assays-and-platforms
#7
Matthijs Vynck, Jo Vandesompele, Olivier Thas
Digital polymerase chain reaction (digital PCR, dPCR) is a direct nucleic acid quantification method, thus requiring no standard curves unlike quantitative real-time PCR (qPCR). Nevertheless, evaluation of the linear dynamic range, accuracy, and precision of an assay or platform is recommended, as there are several potential causes of important non-linearity, bias, and imprecision. Ignoring these quality issues may lead to erroneous quantification. This necessitates an approach akin to the construction of standard curves...
August 10, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28796824/droplet-digital-polymerase-chain-reaction-ddpcr-assays-integrated-with-an-internal-control-for-quantification-of-bovine-porcine-chicken-and-turkey-species-in-food-and-feed
#8
Hanan R Shehata, Jiping Li, Shu Chen, Helen Redda, Shumei Cheng, Nicole Tabujara, Honghong Li, Keith Warriner, Robert Hanner
Food adulteration and feed contamination are significant issues in the food/feed industry, especially for meat products. Reliable techniques are needed to monitor these issues. Droplet Digital PCR (ddPCR) assays were developed and evaluated for detection and quantification of bovine, porcine, chicken and turkey DNA in food and feed samples. The ddPCR methods were designed based on mitochondrial DNA sequences and integrated with an artificial recombinant plasmid DNA to control variabilities in PCR procedures...
2017: PloS One
https://www.readbyqxmd.com/read/28790159/functional-imaging-and-circulating-biomarkers-of-response-to-regorafenib-in-treatment-refractory-metastatic-colorectal-cancer-patients-in-a-prospective-phase-ii-study
#9
Khurum Khan, Mihaela Rata, David Cunningham, Dow-Mu Koh, Nina Tunariu, Jens C Hahne, George Vlachogiannis, Somaieh Hedayat, Silvia Marchetti, Andrea Lampis, Mahnaz Darvish Damavandi, Hazel Lote, Isma Rana, Anja Williams, Suzanne A Eccles, Elisa Fontana, David Collins, Zakaria Eltahir, Sheela Rao, David Watkins, Naureen Starling, Jan Thomas, Eleftheria Kalaitzaki, Nicos Fotiadis, Ruwaida Begum, Maria Bali, Massimo Rugge, Eleanor Temple, Matteo Fassan, Ian Chau, Chiara Braconi, Nicola Valeri
OBJECTIVE: Regorafenib demonstrated efficacy in patients with metastatic colorectal cancer (mCRC). Lack of predictive biomarkers, potential toxicities and cost-effectiveness concerns highlight the unmet need for better patient selection. DESIGN: Patients with RAS mutant mCRC with biopsiable metastases were enrolled in this phase II trial. Dynamic contrast-enhanced (DCE) MRI was acquired pretreatment and at day 15 post-treatment. Median values of volume transfer constant (K(trans)), enhancing fraction (EF) and their product KEF (summarised median values of K(trans)× EF) were generated...
August 8, 2017: Gut
https://www.readbyqxmd.com/read/28780426/characterization-of-oseltamivir-resistant-influenza-virus-populations-in-immunosuppressed-patients-using-digital-droplet-pcr-comparison-with-qpcr-and-next-generation-sequencing-analysis
#10
Maxime Pichon, Alexandre Gaymard, Laurence Josset, Martine Valette, Gilles Millat, Bruno Lina, Vanessa Escuret
INTRODUCTION: The H275Y substitution in neuraminidase (NA) confers oseltamivir-resistance in A(H1N1) influenza viruses (IV). Droplet digital PCR (ddPCR) is a new technique to explore single nucleotide polymorphisms. The aim of this study was to compare the performances of reverse transcriptase (RT)-ddPCR, RT-qPCR and next generation sequencing (NGS). We also analyzed the proportions of H275Y-NA substitution for two immunosuppressed patients with sustained shedding of A(H1N1)pdm09 IV. METHODS: RT-qPCR was performed using the ABI7500 platform...
August 3, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28778025/comparison-of-esr1-mutations-in-tumor-tissue-and-matched-plasma-samples-from-metastatic-breast-cancer-patients
#11
Takashi Takeshita, Yutaka Yamamoto, Mutsuko Yamamoto-Ibusuki, Mai Tomiguchi, Aiko Sueta, Keiichi Murakami, Yoko Omoto, Hirotaka Iwase
BACKGROUND: ESR1 mutation in circulating cell-free DNA (cfDNA) is emerging as a noninvasive biomarker of acquired resistance to endocrine therapy, but there is a paucity of data comparing the status of ESR1 gene in cfDNA with that in its corresponding tumor tissue. The objective of this study is to validate the degree of concordance of ESR1 mutations between plasma and tumor tissue. METHODS: ESR1 ligand-binding domain mutations Y537S, Y537N, Y537C, and D538G were analyzed using droplet digital PCR in 35 patients with metastatic breast cancer (MBC) (35 tumor tissue samples and 67 plasma samples)...
July 31, 2017: Translational Oncology
https://www.readbyqxmd.com/read/28772284/diagnostic-value-of-ca19-9-circulating-tumour-dna-and-circulating-tumour-cells-in-patients-with-solid-pancreatic-tumours
#12
David Sefrioui, France Blanchard, Emmanuel Toure, Paul Basile, Ludivine Beaussire, Claire Dolfus, Anne Perdrix, Marianne Paresy, Michel Antonietti, Isabelle Iwanicki-Caron, Raied Alhameedi, Stephane Lecleire, Alice Gangloff, Lilian Schwarz, Florian Clatot, Jean-Jacques Tuech, Thierry Frébourg, Fabrice Jardin, Jean-Christophe Sabourin, Nasrin Sarafan-Vasseur, Pierre Michel, Frédéric Di Fiore
BACKGROUND: The direct comparison of CA19.9, circulating tumour cells (CTCs) and circulating tumour DNA (ctDNA) using endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) has never been performed for the diagnosis of solid pancreatic tumours (SPTs). METHODS: We included 68 patients with a SPT referred for EUS-FNA. CTCs were analysed using size-based platform and ctDNA using digital PCR. The sensitivity, specificity, negative and positive predictive values were evaluated for each marker and their combination...
August 3, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28771608/detection-and-quantification-of-beef-and-pork-materials-in-meat-products-by-duplex-droplet-digital-pcr
#13
Yicun Cai, Yuping He, Rong Lv, Hongchao Chen, Qiang Wang, Liangwen Pan
Meat products often consist of meat from multiple animal species, and inaccurate food product adulteration and mislabeling can negatively affect consumers. Therefore, a cost-effective and reliable method for identification and quantification of animal species in meat products is required. In this study, we developed a duplex droplet digital PCR (dddPCR) detection and quantification system to simultaneously identify and quantify the source of meat in samples containing a mixture of beef (Bos taurus) and pork (Sus scrofa) in a single digital PCR reaction tube...
2017: PloS One
https://www.readbyqxmd.com/read/28771147/comparison-of-droplet-digital-pcr-and-quantitative-pcr-for-the-detection-of-salmonella-and-its-application-for-river-sediments
#14
Gulshan Singh, Ayanda Sithebe, Abimbola M Enitan, Sheena Kumari, Faizal Bux, Thor Axel Stenström
Despite advances in microbial detection that quantitative polymerase chain reaction (qPCR) has led to, complex environmental samples, such as sediments, remain a challenge due to presence of PCR inhibitors. Aquatic sediments accumulate particle-bound microbial contaminants and thereby reflect a cumulative microbial load over time. The relatively new droplet digital PCR (ddPCR) has emerged as a direct quantitative method, highly tolerant to PCR inhibitors and relinquishing the necessity for calibration/standard curves...
August 2017: Journal of Water and Health
https://www.readbyqxmd.com/read/28764807/akt1-low-quiescent-cancer-cells-persist-after-neoadjuvant-chemotherapy-in-triple-negative-breast-cancer
#15
Sheheryar Kabraji, Xavier Solé, Ying Huang, Clyde Bango, Michaela Bowden, Aditya Bardia, Dennis Sgroi, Massimo Loda, Sridhar Ramaswamy
BACKGROUND: Absence of pathologic complete response (pCR) to neoadjuvant chemotherapy (NACT) correlates with poor long-term survival in patients with triple negative breast cancer (TNBC). These incomplete treatment responses are likely determined by mechanisms that enable cancer cells to resist being killed. However, the detailed characterization of a drug-resistant cancer cell state in residual TNBC tissue after NACT has remained elusive. AKT1(low) quiescent cancer cells (QCCs) are a quiescent, epigenetically plastic, and chemotherapy-resistant subpopulation initially identified in experimental cancer models...
August 1, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28755030/the-human-vascular-endothelial-cell-line-huv-ec-c-harbors-the-integrated-hhv-6b-genome-which-remains-stable-in-long-term-culture
#16
Setsuko Shioda, Fumio Kasai, Midori Ozawa, Noriko Hirayama, Motonobu Satoh, Yousuke Kameoka, Ken Watanabe, Norio Shimizu, Huamin Tang, Yasuko Mori, Arihiro Kohara
Human herpes virus 6 (HHV-6) is a common human pathogen that is most often detected in hematopoietic cells. Although human cells harboring chromosomally integrated HHV-6 can be generated in vitro, the availability of such cell lines originating from in vivo tissues is limited. In this study, chromosomally integrated HHV-6B has been identified in a human vascular endothelial cell line, HUV-EC-C (IFO50271), derived from normal umbilical cord tissue. Sequence analysis revealed that the viral genome was similar to the HHV-6B HST strain...
July 28, 2017: Cytotechnology
https://www.readbyqxmd.com/read/28754904/robust-and-accurate-digital-measurement-for-her2-amplification-in-her2-equivocal-breast-cancer-diagnosis
#17
Yuefeng Wang, Julia Y S Tsang, Yongmei Cui, Ji Cui, Ying Lin, Songli Zhao, Patrick T W Law, Sai Yin Cheung, Enders K O Ng, Gary M K Tse, Zunfu Ke
Currently, there are no recommended alternative assays for HER2 cases deemed equivocal by immunohistochemistry and fluorescent in situ hybridization. Digital PCR (ddPCR), a highly accurate method to determine DNA copy number, could be a robust alternative for clinical HER2 diagnostics. HER2 and CEP17 copy numbers were quantified using two ddPCR platforms (QX200 and RainDrop) in 102 samples of invasive breast cancers. Compared to routine assays, ddPCR gave a sensitivity and specificity of 82.8% and 97.3% respectively, with a kappa value of 0...
July 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28749991/nanofluidic-digital-pcr-for-the-quantification-of-norovirus-for-water-quality-assessment
#18
Silvia Monteiro, Ricardo Santos
Sensitive detection of water- and foodborne enteric viruses is extremely relevant, especially due to the low concentrations in which they are found. Accurate and sensitive detection of Norovirus, the primary responsible for water- and foodborne outbreaks, is of particular importance. Quantification of Norovirus is commonly performed by quantitative RT-PCR (RT-qPCR). In recent years a new platform was developed, digital PCR, that quantifies without the need for a standard curve thus decreasing the errors associated with its utilization...
2017: PloS One
https://www.readbyqxmd.com/read/28748500/digital-droplet-pcr-ddpcr-for-the-detection-and-quantification-of-hpv-16-18-33-and-45%C3%A2-a-short-report
#19
Gabriella Lillsunde Larsson, Gisela Helenius
PURPOSE: Human papilloma virus (HPV) infection is associated with several anogenital malignancies. Here, we set out to evaluate digital droplet PCR (ddPCR) as a tool for HPV 16, 18, 33 and 45 viral load quantification and, in addition, to compare the efficacy of the ddPCR assay for HPV 16 detection with that of quantitative real-time PCR (qPCR). METHODS: Clinical samples, positive for HPV genotypes 16, 18, 33 and 45 were analyzed for viral load using ddPCR. Sample DNA was cleaved before droplet generation and PCR...
July 26, 2017: Cellular Oncology (Dordrecht)
https://www.readbyqxmd.com/read/28743297/identification-of-reference-mirnas-in-plasma-useful-for-the-study-of-oestrogen-responsive-mirnas-associated-with-acquired-protein-s-deficiency-in-pregnancy
#20
J W Tay, I James, Q W Hughes, J Y Tiao, R I Baker
BACKGROUND: Accumulating evidence indicate that circulating microRNAs (miRNAs) are useful independent non-invasive biomarkers, with unique miRNA signatures defined for various pathophysiological conditions. However, there are no established universal housekeeping miRNAs for the normalisation of miRNAs in body fluids. We have previously identified an oestrogen-responsive miRNA, miR-494, in regulating the anticoagulant, Protein S, in HuH-7 liver cells. Moreover, increased thrombotic risk associated with elevated circulating oestrogen levels is frequently observed in pregnant women and oral contraceptive users...
July 25, 2017: BMC Research Notes
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