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Digital PCR

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https://www.readbyqxmd.com/read/28727825/differentially-expressed-genes-in-the-head-of-the-2nd-instar-pre-molting-larvae-of-the-nm2-mutant-of-the-silkworm-bombyx-mori
#1
Pingyang Wang, Simin Bi, Fan Wu, Pingzhen Xu, Xingjia Shen, Qiaoling Zhao
Molting is an important physiological process in the larval stage of Bombyx mori and is controlled by various hormones and peptides. The silkworm mutant that exhibits the phenotype of non-molting in the 2nd instar (nm2) is incapable of molting in the 2nd instar and dies after seven or more days. The ecdysone titer in the nm2 mutant is lower than that in the wildtype, and the mutant can be rescued by feeding with 20E and cholesterol. The results of positional cloning indicated that structural alteration of BmCPG10 is responsible for the phenotype of the nm2 mutant...
2017: PloS One
https://www.readbyqxmd.com/read/28725028/detection-and-quantitation-of-copy-number-variation-in-the-voltage-gated-sodium-channel-gene-of-the-mosquito-culex-quinquefasciatus
#2
Walter Fabricio Silva Martins, Krishanthi Subramaniam, Keith Steen, Henry Mawejje, Triantafillos Liloglou, Martin James Donnelly, Craig Stephen Wilding
Insecticide resistance is typically associated with alterations to the insecticidal target-site or with gene expression variation at loci involved in insecticide detoxification. In some species copy number variation (CNV) of target site loci (e.g. the Ace-1 target site of carbamate insecticides) or detoxification genes has been implicated in the resistance phenotype. We show that field-collected Ugandan Culex quinquefasciatus display CNV for the voltage-gated sodium channel gene (Vgsc), target-site of pyrethroid and organochlorine insecticides...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28725013/baseline-value-of-intrahepatic-hbv-dna-over-cccdna-predicts-patient-s-response-to-interferon-therapy
#3
Di Mu, Fang-Chao Yuan, Yu Chen, Xiao-Yan Jiang, Liang Yan, Ling-Yu Jiang, Jian-Ping Gong, Da-Zhi Zhang, Hong Ren, Yong Liao
Methodology for accurate quantification of intra-hepatic cccDNA has long been a technical challenge, yet it is highly desired in the clinic. Here, we developed a sensitive method for quantification of intrahepatic cccDNA in liver biopsies from patients, which allowed to predict patient's response to interferon therapy at baseline. Twenty-five patients with HBeAg+ CHB were recruited and liver biopsies were obtained at baseline and 1-year after interferon treatment, respectively. Both intrahepatic cccDNA and HBV DNA were absolutely quantified by a droplet digital PCR amplification system...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724560/accurate-detection-of-methicillin-resistant-staphylococcus-aureus-in-mixtures-utilizing-single-bacterial-duplex-droplet-digital-pcr
#4
Jun Luo, Junhua Li, Hang Yang, Junping Yu, Hongping Wei
Accurate and rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) is needed to screen MRSA carriers and improve treatment. The current widely used duplex PCR methods are not able to differentiate MRSA from the co-existence of methicillin-susceptible S. aureus (MSSA) and other methicillin-resistant Staphylococci In this study, we aimed to develop a direct method for accurate and rapid detection of MRSA in clinical samples from open environments, such as nasal swab. The new molecular assay is based on detecting the co-occurrence of nuc and mecA markers in a single bacterial cell by utilizing droplet digital PCR (ddPCR) with a chimeric lysin ClyH for cell lysis...
July 19, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28723342/molecular-analysis-of-circulating-free-dna-from-lung-cancer-patients-in-routine-laboratory-practice-a-cross-platform-comparison-of-three-different-molecular-methods-for-mutation-detection
#5
Stephan Bartels, Sascha Persing, Britta Hasemeier, Elisa Schipper, Hans Kreipe, Ulrich Lehmann
Cell-free DNA (cfDNA), which is isolated from blood plasma, represents a noninvasive source for the detection of mutations conferring resistance against epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors in non-small-cell lung cancer patients. In advanced disease stages, performing regular biopsies is often not possible because of the general health condition of the patients. Furthermore, a biopsy of a single tumor lesion or metastasis may not reflect the heterogeneous genotype of the tumor and its metastases...
July 16, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28722675/using-droplet-digital-pcr-to-analyze-mycn-and-alk-copy-number-in-plasma-from-patients-with-neuroblastoma
#6
Marco Lodrini, Annika Sprüssel, Kathy Astrahantseff, Daniela Tiburtius, Robert Konschak, Holger N Lode, Matthias Fischer, Ulrich Keilholz, Angelika Eggert, Hedwig E Deubzer
The invasive nature of surgical biopsies deters sequential application, and single biopsies often fail to reflect tumor dynamics, intratumor heterogeneity and drug sensitivities likely to change during tumor evolution and treatment. Implementing molecular characterization of cell-free neuroblastoma-derived DNA isolated from blood plasma could improve disease assessment for treatment selection and monitoring of patients with high-risk neuroblastoma. We established droplet digital PCR (ddPCR) protocols for MYCN and ALK copy number status in plasma from neuroblastoma patients...
July 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28720682/reducing-artifactual-egfr-t790m-mutations-in-dna-from-formalin-fixed-paraffin-embedded-tissue-by-use-of-thymine-dna-glycosylase
#7
Hongdo Do, Ramyar Molania, Paul L Mitchell, Rita Vaiskunaite, John D Murdoch, Alexander Dobrovic
BACKGROUND: False-positive EGFR T790M mutations have been reported in formalin-fixed lung tumors, but the cause of the false positives has not been identified. The T790M mutation results from a C>T change at the cytosine of a CpG dinucleotide. The presence or absence of methylation at this cytosine has different consequences following deamination, resulting in a thymine or uracil, respectively, both of which however result in an artifactual change. Uracil-DNA glycosylase (UDG) can be used to eliminate DNA templates with uracil residues but is not active against artifactual thymines...
July 18, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28720421/assessment-of-the-hiv-1-reservoir-in-cd4-regulatory-t-cells-by-a-droplet-digital-pcr-based-approach
#8
Gábor Artúr Dunay, Anastasia Solomatina, Silke Kummer, Anja Hüfner, Julia Katharina Bialek, Johanna Maria Eberhard, Eva Tolosa, Joachim Hauber, Julian Schulze Zur Wiesch
The relative contribution of regulatory T cells (Treg) as reservoir of HIV-1 in patients on chronic antiretroviral therapy is unclear to date. The aim of the current study was to assess the total HIV DNA burden and replication competent viral reservoir in Treg in comparison to central and effector memory cells (Tcm and Tem). Peripheral blood mononuclear cells were obtained from 10 HIV patients treated with antiretroviral therapy and one HIV elite controller. Droplet Digital PCR (ddPCR) was used to quantify total HIV DNA loads in FACS sorted CD4+ Treg (CD25+CD127lo) as compared with Tcm (CD45RO+CCR7+) and Tem (CD45RO+CCR7-)...
July 15, 2017: Virus Research
https://www.readbyqxmd.com/read/28714107/the-braf-and-nras-mutation-prevalence-in-dermoscopic-subtypes-of-acquired-naevi-reveals-constitutive-mapk-pathway-activation
#9
J M Tan, L N Tom, K Jagirdar, D Lambie, H Schaider, R A Sturm, H P Soyer, M S Stark
BACKGROUND: Acquired naevi can have unique dermoscopic patterns that correspond to distinct microanatomical growth patterns. Previous studies on acquired naevi stratified according to dermoscopic pattern, focused on the frequency of somatic BRAF mutations, whereas NRAS mutations remained to be elucidated. OBJECTIVES: To investigate the BRAF and NRAS mutation prevalence and activation of the MAPK pathway in distinct dermoscopic subtypes of acquired naevi. METHODS: Common mutations present in BRAF and NRAS were assessed in 40 globular, reticular, and peripheral rim of globules (PG) subtypes of acquired naevi from 27 participants (19 male, 8 female; mean age 46...
July 17, 2017: British Journal of Dermatology
https://www.readbyqxmd.com/read/28711990/assessment-of-braf-v600e-mutation-in-pulmonary-langerhans-cell-histiocytosis-in-tissue-biopsies-and-bronchoalveolar-lavages-by-droplet-digital-polymerase-chain-reaction
#10
Clémence Pierry, Charline Caumont, Elodie Blanchard, Camille Brochet, Gael Dournes, Audrey Gros, Thomas Bandres, Séverine Verdon, Marion Marty, Hugues Bégueret, Jean-Philippe Merlio
The neoplastic nature of pulmonary Langerhans cell histiocytosis (PLCH) is still debated. As the detection of BRAF (V600E) and MAP2K1 mutations in patients with PCLH is now considered for such assessment, the aim of our study was to evaluate digital droplet polymerase chain reaction (ddPCR) in PCLH diagnosis. We retrospectively analyzed BRAF(V600E) detection in a cohort of 42 PCLH tissues and 18 bronchoalveolar lavages (BALs) by ddPCR, immunohistochemistry, high-resolution melting PCR (HRM), and next-generation sequencing (NGS)...
July 15, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28711173/presymptomatic-diagnosis-of-spinal-muscular-atrophy-through-newborn-screening
#11
Yin-Hsiu Chien, Shu-Chuan Chiang, Wen-Chin Weng, Ni-Chung Lee, Ching-Jie Lin, Wu-Shiun Hsieh, Wang-Tso Lee, Yuh-Jyh Jong, Tsang-Ming Ko, Wuh-Liang Hwu
OBJECTIVE: To demonstrate the feasibility of presymptomatic diagnosis of spinal muscular atrophy (SMA) through newborn screening (NBS). STUDY DESIGN: We performed a screening trial to assess all newborns who underwent routine newborn metabolic screening at the National Taiwan University Hospital newborn screening center between November 2014 and September 2016. A real-time polymerase chain reaction (RT-PCR) genotyping assay for the SMN1/SMN2 intron 7 c.888+100A/G polymorphism was performed to detect homozygous SMN1 deletion using dried blood spot (DBS) samples...
July 12, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28704793/genome-and-transcriptome-wide-analyses-of-cellulose-synthase-gene-superfamily-in-soybean
#12
Muhammad Amjad Nawaz, Hafiz Mamoon Rehman, Faheem Shehzad Baloch, Babar Ijaz, Muhammad Amjad Ali, Iqrar Ahmad Khan, Jeong Dong Lee, Gyuhwa Chung, Seung Hwan Yang
The plant cellulose synthase gene superfamily belongs to the category of type-2 glycosyltransferases, and is involved in cellulose and hemicellulose biosynthesis. These enzymes are vital for maintaining cell-wall structural integrity throughout plant life. Here, we identified 78 putative cellulose synthases (CS) in the soybean genome. Phylogenetic analysis against 40 reference Arabidopsis CS genes clustered soybean CSs into seven major groups (CESA, CSL A, B, C, D, E and G), located on 19 chromosomes (except chromosome 18)...
April 29, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28704400/genome-wide-analysis-of-the-ccch-zinc-finger-family-identifies-tissue-specific-and-stress-responsive-candidates-in-chickpea-cicer-arietinum-l
#13
Seema Pradhan, Chandra Kant, Subodh Verma, Sabhyata Bhatia
The CCCH zinc finger is a group of proteins characterised by a typical motif consisting of three cysteine residues and one histidine residue. These proteins have been reported to play important roles in regulation of plant growth, developmental processes and environmental responses. In the present study, genome wide analysis of the CCCH zinc finger gene family was carried out in the available chickpea genome. Various bioinformatics tools were employed to predict 58 CCCH zinc finger genes in chickpea (designated CarC3H1-58), which were analysed for their physio-chemical properties...
2017: PloS One
https://www.readbyqxmd.com/read/28702010/comparison-among-the-quantification-of-bacterial-pathogens-by-qpcr-dpcr-and-cultural-methods
#14
Matteo Ricchi, Cristina Bertasio, Maria B Boniotti, Nadia Vicari, Simone Russo, Michela Tilola, Marco A Bellotti, Barbara Bertasi
The demand for rapid methods for the quantification of pathogens is increasing. Among these methods, those based on nucleic acids amplification (quantitative PCRs) are the most widespread worldwide. Together with the qPCR, a new approach named digital PCR (dPCR), has rapidly gained importance. The aim of our study was to compare the results obtained using two different dPCR systems and one qPCR in the quantification of three different bacterial pathogens: Listeria monocytogenes, Francisella tularensis, and Mycobacterium avium subsp...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28699162/spatial-distribution-of-egfr-and-kras-mutation-frequencies-correlates-with-histological-growth-patterns-of-lung-adenocarcinomas
#15
Steffen Dietz, Alexander Harms, Volker Endris, Florian Eichhorn, Mark Kriegsmann, Remi Longuespée, Albrecht Stenzinger, Holger Sültmann, Arne Warth, Daniel Kazdal
Multiregional analysis provided first indications for morphological and molecular heterogeneity in lung adenocarcinomas (ADCs), but comprehensive morpho-molecular comparisons are still lacking. The purpose of this study was to investigate the spatial distribution of EGFR and KRAS alterations systematically throughout whole tumor cross-sections in correlation with the tumor cell content and the histopathological patterns. Central sections of 19 ADCs were subdivided into 467 segments of 5x5 mm. We determined the predominant histological growth pattern and the allele frequencies of driver gene mutations by digital PCR in every segment...
July 12, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28698171/natural-compounds-for-the-treatment-of-psoriatic-arthritis-a-proposal-based-on-multi-targeted-osteoclastic-regulation-and-on-a-preclinical-study
#16
Shiqiang Deng, Jianwen Cheng, Jinmin Zhao, Felix Yao, Jiake Xu
BACKGROUND: Psoriatic arthritis (PsA) is a chronic inflammatory arthritis affecting approximately 2% to 3% of the population globally, and is characterized by both peripheral articular manifestations and axial skeletal involvement. Conventional therapies for PsA have not been fully satisfactory, though natural products (NPs) have been shown to be highly effective and represent important treatment options for psoriasis. PsA is a multigenic autoimmune disease with both environmental and genetic factors contributing to its pathogenesis...
July 11, 2017: JMIR Research Protocols
https://www.readbyqxmd.com/read/28694163/mice-maintain-predominantly-maternal-g%C3%AE-s-expression-throughout-life-in-brown-fat-tissue-bat-but-not-other-tissues
#17
Olta Tafaj, Steven Hann, Ugur Ayturk, Matthew L Warman, Harald Jüppner
The murine Gnas (human GNAS) locus gives rise to Gαs and different splice variants thereof. The Gαs promoter is not methylated thus allowing biallelic expression in most tissues. In contrast, the alternative first Gnas/GNAS exons and their promoters undergo parent specific methylation, which limits transcription to the non-methylated allele. Pseudohypoparathyroidism type Ia (PHP1A) or type Ib (PHP1B) are caused by heterozygous maternal GNAS mutations suggesting that little or no Gαs is derived in some tissues from the non-mutated paternal GNAS thereby causing hormonal resistance...
July 8, 2017: Bone
https://www.readbyqxmd.com/read/28694015/predicting-treatment-resistance-and-relapse-through-circulating-dna
#18
Emma Beddowes, Stephen J Sammut, Meiling Gao, Carlos Caldas
The use of circulating DNA(ctDNA) to provide a non-invasive, personalised genomic snapshot of a patients' tumour has huge potential. Over the past five years this area of research has gained huge momentum. A number of studies in metastatic breast cancer have shown the potential of ctDNA to predict prognosis and treatment response using ctDNA. Further developments have included deeper sequencing using whole exome and shallow whole genome approaches which has the potential to identify new mutations and chromosomal copy number changes which appear upon resistance to treatment...
July 7, 2017: Breast: Official Journal of the European Society of Mastology
https://www.readbyqxmd.com/read/28692535/effect-of-cmv-and-ebv-replication-on-intestinal-mucosal-gene-expression-and-microbiome-composition-of-hiv-infected-and-uninfected-individuals
#19
Sara Gianella, Antoine Chaillon, Ece A Mutlu, Phillip A Engen, Robin M Voigt, Ali Keshavarzian, John Losurdo, Prachi Chakradeo, Steven M Lada, Masato Nakazawa, Alan L Landay
BACKGROUND: HIV-infection is associated with dramatic changes in the intestinal mucosa. The impact of other viral pathogens is unclear. METHODS: Eighty biopsies from left and right colon (n=63) and terminal ileum (n = 17) were collected from 19 HIV-infected and 22 HIV-uninfected subjects. Levels of cytomegalovirus (CMV) and Epstein Barr Virus (EBV) DNA were measured by droplet-digital (dd)PCR. Mucosal gene expression was measured via multiplex-assay. Microbiome analysis was performed using bacterial 16S-rDNA-pyrosequencing...
July 7, 2017: AIDS
https://www.readbyqxmd.com/read/28683077/dna-isolation-protocol-effects-on-nuclear-dna-analysis-by-microarrays-droplet-digital-pcr-and-whole-genome-sequencing-and-on-mitochondrial-dna-copy-number-estimation
#20
Elizabeth Nacheva, Katya Mokretar, Aynur Soenmez, Alan M Pittman, Colin Grace, Roberto Valli, Ayesha Ejaz, Selina Vattathil, Emanuela Maserati, Henry Houlden, Jan-Willem Taanman, Anthony H Schapira, Christos Proukakis
Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol...
2017: PloS One
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