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https://www.readbyqxmd.com/read/28806149/detection-of-nanophyetus-salmincola-in-water-snails-and-fish-tissues-by-quantitative-pcr
#1
Maureen K Purcell, Rachel L Powers, Bonnie L Besijn, Paul K Hershberger
We report the development and validation of two quantitative polymerase chain reaction (qPCR) assays to detect N. salmincola DNA in water samples and fish and snail tissues. Analytical and diagnostic validation demonstrated good sensitivity, specificity and repeatability of both qPCR assays. N. salmincola DNA copy number in kidney tissue was significantly correlated with metacercariae counts based on microscopy. Extraction methods were optimized for the sensitive qPCR detection of N. salmincola DNA in settled water samples...
August 14, 2017: Journal of Aquatic Animal Health
https://www.readbyqxmd.com/read/28805868/a-microfluidic-flow-cytometer-enabling-absolute-quantification-of-single-cell-intracellular-proteins
#2
Xiufeng Li, Beiyuan Fan, Shanshan Cao, Deyong Chen, Xiaoting Zhao, Dong Men, Wentao Yue, Junbo Wang, Jian Chen
Quantification of single-cell proteomics provides key insights into cellular heterogeneity while conventional flow cytometry cannot provide absolute quantification of intracellular proteins of single cells due to the lack of calibration approaches. This paper presents a constriction channel (with a cross sectional area smaller than cells) based microfluidic flow cytometer, capable of collecting copy numbers of specific intracellular proteins. In this platform, single cells stained with fluorescence labelled antibodies were forced to squeeze through the constriction channel with the fluorescence intensities quantified and since cells fully filled the constriction channel during the squeezing process, solutions with fluorescence labelled antibodies were flushed into the constriction channel to obtain calibration curves...
August 14, 2017: Lab on a Chip
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
#3
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/28804721/corrigendum-to-comparative-study-of-exome-copy-number-variation-estimation-tools-using-array-comparative-genomic-hybridization-as-control
#4
Yan Guo, Quanhu Sheng, David C Samuels, Brian Lehmann, Joshua A Bauer, Jennifer Pietenpol, Yu Shyr
[This corrects the article DOI: 10.1155/2013/915636.].
2017: BioMed Research International
https://www.readbyqxmd.com/read/28803992/p-rex1-amplification-promotes-progression-of-cutaneous-melanoma-via-the-pak1-p38-mmp-2-pathway
#5
Jinhua Wang, Hajime Hirose, Guanhua Du, Kelly Chong, Eiji Kiyohara, Isaac P Witz, Dave S B Hoon
P-REX1 (PIP3-dependent Rac exchange factor-1) is a guanine nucleotide exchange factor that activates Rac by catalyzing exchange of GDP for GTP bound to Rac. Aberrant up-regulation of P-REX1 expression has a role in metastasis however, copy number (CN) and function of P-REX1 in cutaneous melanoma are unclear. To explore the role of P-REX1 in melanoma, SNP 6.0 and Exon 1.0 ST microarrays were assessed. There was a higher CN (2.82-fold change) of P-REX1 in melanoma cells than in melanocytes, and P-REX1 expression was significantly correlated with P-REX1 CN...
August 10, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28803790/utility-of-the-cytochrome-c-oxidase-subunit-i-gene-for-the-diagnosis-of-toxoplasmosis-using-pcr
#6
Xue Feng, Kazumi Norose, Kexin Li, Kenji Hikosaka
Toxoplasmosis is caused by the protozoan parasite Toxoplasma gondii, which belongs to the phylum Apicomplexa. Since this parasite causes severe clinical symptoms in immunocompromised patients, early diagnosis of toxoplasmosis is essential. PCR is currently used for early diagnosis, but there is no consensus regarding the most effective method for amplifying Toxoplasma DNA. In this study, we considered the utility of the cytochrome c subunit I (cox1) gene, which is encoded in the mitochondrial DNA of this parasite, as a novel target of PCR for the diagnosis of toxoplasmosis...
August 10, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28803260/microbial-volatile-compounds-alter-the-soil-microbial-community
#7
Jun Yuan, Mengli Zhao, Rong Li, Qiwei Huang, Waseem Raza, Christopher Rensing, Qirong Shen
Volatile organic compounds (VOCs) from soil bacteria are likely to have an important role in the interactions among soil microorganisms. However, their effects on the soil microbial community have not been extensively studied. In this study, the effect of bacterial VOCs generated by growing Bacillus amyloliquefaciens NJN-6 on modified MS medium on soil microbial community was evaluated. B. amyloliquefaciens NJN-6 was able to produce 48 volatile compounds as determined by solid-phase microextraction-GC/MS. MiSeq sequencing data showed that bacterial VOCs could alter the composition of both soil bacterial and soil fungal communities and could decrease the alpha-diversity of the soil microbial community...
August 12, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28802993/microbial-community-structure-and-activity-in-trace-element-contaminated-soils-phytomanaged-by-gentle-remediation-options-gro
#8
M Touceda-González, Á Prieto-Fernández, G Renella, L Giagnoni, A Sessitsch, G Brader, J Kumpiene, I Dimitriou, J Eriksson, W Friesl-Hanl, R Galazka, J Janssen, M Mench, I Müller, S Neu, M Puschenreiter, G Siebielec, J Vangronsveld, P S Kidd
Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe...
August 10, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28802644/rapid-characterization-of-the-cho-platform-cell-line-and-identification-of-pseudo-attp-sites-for-phic31-integrase
#9
Narges Damavandi, Mozhgan Raigani, Atefeh Joudaki, Fatemeh Davami, Sirous Zeinali
The Chinese Hamster Ovary (CHO) cell lines, applicable to post-translational modifications, are preferred systems for biopharmaceutical protein production. In this study, by using the Jump-In™ TI™ technology which employs PhiC31 and R4 bacteriophage recombinases, a platform CHO-K1 cell line containing a R4-attP site was generated. Here, a combination of Quantitative Fluorescent-Polymerase Chain Reaction (QF-PCR) and semi-random, two-step PCR (ST-PCR), was performed to feature the platform cell clones. Our results show that QF-PCR and ST-PCR, can be utilized for efficient and accelerated cell line characterization...
August 9, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28802642/prognostic-value-of-tert-alterations-and-mutational-and-copy-number-alteration-burden-in-urothelial-carcinoma
#10
Sumit Isharwal, François Audenet, Esther Drill, Eugene J Pietzak, Gopa Iyer, Irina Ostrovnaya, Eugene Cha, Timothy Donahue, Maria Arcila, Gowtham Jayakumaran, Michael F Berger, Jonathan E Rosenberg, Dean F Bajorin, Jonathan Coleman, Guido Dalbagni, Victor E Reuter, Bernard H Bochner, David B Solit, Hikmat A Al-Ahmadie
Missense mutations in the TERT gene promoter occur at high frequency in multiple cancers, including urothelial carcinoma (UC). However, the relationship between TERT promoter mutations and UC patient outcomes is unclear due to conflicting reports in the literature. In this study, we examined the association of TERT alterations, tumor mutational burden per megabase (Mb), and copy number alteration (CNA) burden with clinical parameters and their prognostic value in a cohort of 398 urothelial tumors. The majority of TERT mutations were located at two promoter region hotspots (chromosome 5, 1 295 228 C>T and 1 295 250 C>T)...
August 9, 2017: European Urology Focus
https://www.readbyqxmd.com/read/28802254/tdp1-is-critical-for-the-repair-of-dna-breaks-induced-by-sapacitabine-a-nucleoside-also-targeting-atm-and-brca-deficient-tumors
#11
Muthana Al Abo, Hiroyuki Sasanuma, Xiaojun Liu, Vinodh N Rajapakse, Shar-Yin N Huang, Evgeny Kiselev, Shunichi Takeda, William Plunkett, Yves Pommier
2'-C-cyano-2'-deoxy-1-β-D-arabino-pentofuranosylcytosine (CNDAC) is the active metabolite of the anticancer drug, sapacitabine. CNDAC is incorporated into the genome during DNA replication and subsequently undergoes beta-elimination that generates single-strand breaks with abnormal 3'-ends. Because tyrosyl-DNA phosphodiesterase 1 (TDP1) selectively hydrolyzes non-phosphorylated 3'-blocking ends, we tested its role in the repair of CNDAC-induced DNA damage. We show that cells lacking TDP1 (avian TDP1-/- DT40 cells and human TDP1 KO TSCER2 and HCT116 cells) exhibit marked hypersensitivity to CNDAC...
August 11, 2017: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/28802157/droplet-digital-pcr-for-rapid-enumeration-of-viral-genomes-and-particles-from-cells-and-animals-infected-with-orthopoxviruses
#12
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/28801929/validation-and-application-of-a-novel-integrated-genetic-screening-method-to-a-cohort-of-1-112-men-with-idiopathic-azoospermia-or-severe-oligozoospermia
#13
Manon S Oud, Liliana Ramos, Moira K O'Bryan, Robert I McLachlan, Özlem Okutman, Stephane Viville, Petra F de Vries, Dominique F C M Smeets, Dorien Lugtenberg, Jayne Y Hehir-Kwa, Christian Gilissen, Maartje van de Vorst, Lisenka E L M Vissers, Alexander Hoischen, Aukje M Meijerink, Kathrin Fleischer, Joris A Veltman, Michiel J Noordam
Microdeletions of the Y chromosome (YCMs), Klinefelter syndrome (47,XXY) and CFTR mutations are known genetic causes of severe male infertility, but the majority of cases remain idiopathic. Here we describe a novel method using single molecule Molecular Inversion Probes (smMIPs), to screen infertile men for mutations and copy number variations (CNVs) affecting known disease genes. We designed a set of 4,525 smMIPs targeting the coding regions of causal (n = 6) and candidate (n = 101) male infertility genes...
August 11, 2017: Human Mutation
https://www.readbyqxmd.com/read/28801450/genomic-analysis-of-hairy-cell-leukemia-identifies-novel-recurrent-genetic-alterations
#14
Benjamin H Durham, Bartlomiej Getta, Sascha Dietrich, Justin Taylor, Helen Won, James M Bogenberger, Sasinya Scott, Eunhee Kim, Young Rock Chung, Stephen S Chung, Jennifer Hüllein, Tatjana Walther, Lu Wang, Sydney X Lu, Christopher C Oakes, Raoul Tibes, Torsten Haferlach, Barry S Taylor, Martin S Tallman, Michael F Berger, Jae H Park, Thorsten Zenz, Omar Abdel-Wahab
Classical hairy cell leukemia (cHCL) is characterized by a near 100% frequency of the BRAFV600E mutation while ~30% of variant HCL (vHCL) have MAP2K1 mutations. However, recurrent genetic alterations cooperating with BRAFV600E or MAP2K1 mutations in HCL, as well as those in MAP2K1- wildtype vHCL, are not well defined. We therefore performed deep targeted mutational and copy number analysis of cHCL (n=53) and vHCL (n=8). The most common genetic alteration in cHCL outside of BRAFV600E was heterozygous loss of chromosome 7q, the minimally deleted region of which targeted wildtype BRAF, subdividing cHCL into those hemizygous versus heterozygous for the BRAFV600E mutation...
August 11, 2017: Blood
https://www.readbyqxmd.com/read/28800945/impact-of-age-at-diagnosis-on-racial-disparities-in-endometrial-cancer-patients
#15
Christopher M Tarney, Chunqiao Tian, Guisong Wang, Elizabeth A Dubil, Nicholas W Bateman, John K Chan, Mohamed A Elshaikh, Michele L Cote, Joellen M Schildkraut, Craig D Shriver, Thomas P Conrads, Chad A Hamilton, G Larry Maxwell, Kathleen M Darcy
INTRODUCTION: Although black patients with endometrial cancer (EC) have worse survival compared with white patients, the interaction between age/race has not been examined. The primary objective was to evaluate the impact of age at diagnosis on racial disparities in disease presentation and outcome in EC. METHODS: We evaluated women diagnosed with EC between 1991 and 2010 from the Surveillance, Epidemiology, and End Results. Mutation status for TP53 or PTEN, or with the aggressive integrative, transcript-based, or somatic copy number alteration-based molecular subtype were acquired from the Cancer Genome Atlas...
August 8, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/28800828/culture-dependent-and-culture-independent-assessment-of-spoilage-community-growth-on-vp-lamb-meat-from-packaging-to-past-end-of-shelf-life
#16
Mandeep Kaur, Hongshan Shang, Mark Tamplin, Tom Ross, John P Bowman
Packaging and storage temperature are important factors that influence the shelf-life of vacuum packed (VP) meat. In this study the shelf-life of VP bone-in lamb hind shanks stored at 8 °C and -1.2 °C was determined in parallel to analyses of starting and eventual spoilage bacterial communities via Illumina MiSeq based 16S rRNA amplicon sequencing. The mean total viable counts (TVC) and lactic acid bacterial viable counts (LAB) were observed to increase to log 7.5 CFU/cm(2) and 7 CFU/cm(2) after 6 and 42 days at 8 °C and -1...
December 2017: Food Microbiology
https://www.readbyqxmd.com/read/28800016/fish-analysis-of-top2a-and-her-2-aberrations-in-female-breast-carcinoma-on-archived-material-egyptian-nci-experience
#17
Omnia M Badawy, Iman Loay
BACKGROUND: HER-2 and TOP2A genes are considered of great importance in breast cancer. Their copy number variability has been proposed to be a marker for the degree of chromosomal instability. Owing to the close proximity of TOP2A gene to HER-2 gene chromosome 17, TOP2A status is believed to affect therapeutic plan. The percentage of TOP2A aberrations is greatly variable among different studies. AIM OF WORK: Is to investigate the relation between TOP2A and HER-2 gene amplification using fluorescence in situ hybridization technique...
August 9, 2017: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/28799737/method-to-assemble-genomic-dna-fragments-or-genes-on-human-artificial-chromosome-with-regulated-kinetochore-using-a-multi-integrase-system
#18
Nicholas C O Lee, Jung-Hyun Kim, Nikolai Petrov, Hee-Sheung Lee, Hiroshi Masumoto, William C Earnshaw, Vladimir Larionov, Natalay Kouprina
The production of cells capable of carrying multiple transgenes to Mb-size genomic loci has multiple applications in biomedicine and biotechnology. In order to achieve this goal, three key steps are required: i) Cloning of large genomic segments; ii) Insertion of multiple DNA blocks at a precise location and iii) The capability to eliminate the assembled region from cells. In this study, we designed the Iterative Integration System (IIS) that utilizes recombinases Cre, ΦC31 and ΦBT1, and combined it with Human Artificial Chromosome (HAC) possessing a regulated kinetochore (alphoid(tetO)-HAC)...
August 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28799406/a-polymorphic-ggc-repeat-in-the-npas2-gene-and-its-association-with-melanoma
#19
Alessandra Franzoni, Elitza Markova-Car, Sanja Dević-Pavlić, Davor Jurišić, Cinzia Puppin, Catia Mio, Marila De Luca, Giulia Petruz, Giuseppe Damante, Sandra Kraljević Pavelić
Circadian clock regulation in mammals is controlled by feedback loops of a set of circadian genes. One of these circadian genes, NPAS2, encodes for a member of the bHLH-PAS class of transcription factors and is expressed in the forebrain and in some peripheral organs such as liver and skin. Other biological processes are also regulated by circadian genes. For example, NPAS2 is involved in cell proliferation, DNA damage repair and malignant transformation. Aberrant expression of clock genes has been previously observed in melanoma which led to our effort to sequence the NPAS2 promoter region in this cancer type...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28798405/progress-in-genome-wide-association-studies-of-schizophrenia-in-han-chinese-populations
#20
REVIEW
Weihua Yue, Xin Yu, Dai Zhang
Since 2006, genome-wide association studies of schizophrenia have led to the identification of numerous novel risk loci for this disease. However, there remains a geographical imbalance in genome-wide association studies, which to date have primarily focused on Western populations. During the last 6 years, genome-wide association studies in Han Chinese populations have identified both the sharing of susceptible loci across ethnicities and genes unique to Han Chinese populations. Here, we review recent progress in genome-wide association studies of schizophrenia in Han Chinese populations...
August 10, 2017: NPJ Schizophrenia
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