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https://www.readbyqxmd.com/read/28432840/detection-of-egfr-mutations-in-patients-with-non-small-cell-lung-cancer-by-high-resolution-melting-comparison-with-other-methods
#1
Carlos Martínez-Carretero, Fernando Iguaz Pascual, Antonio Rus, Ivan Bernardo
BACKGROUND: The discovery of mutations in the epidermal growth factor receptor gene (EGFR) related to the clinical response to tyrosine kinase inhibitors, has transformed the management of non-small cell lung cancer (NSCLC). Several methods have been developed for determination of mutations in EGFR, with different sensitivity and potential ability to detect a different number of mutations. METHODS: We developed a screening method by high resolution melting (HRM) to detect EGFR mutations, and compared the results of 123 fixed in formalin and paraffin embedded (FFPE) tumor tissue samples with the detection of mutations by allele-specific PCR...
April 22, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28431361/uncertainty-quantification-and-validation-of-3d-lattice-scaffolds-for-computer-aided-biomedical-applications
#2
Recep M Gorguluarslan, Seung-Kyum Choi, Christopher J Saldana
A methodology is proposed for uncertainty quantification and validation to accurately predict the mechanical response of lattice structures used in the design of scaffolds. Effective structural properties of the scaffolds are characterized using a developed multi-level stochastic upscaling process that propagates the quantified uncertainties at strut level to the lattice structure level. To obtain realistic simulation models for the stochastic upscaling process and minimize the experimental cost, high-resolution finite element models of individual struts were reconstructed from the micro-CT scan images of lattice structures which are fabricated by selective laser melting...
April 12, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28428555/application-of-high-resolution-melting-assay-hrm-to-study-temperature-dependent-intraspecific-competition-in-a-pathogenic-bacterium
#3
Roghaieh Ashrafi, Matthieu Bruneaux, Lotta-Riina Sundberg, Katja Pulkkinen, Tarmo Ketola
Studies on species' responses to climate change have focused largely on the direct effect of abiotic factors and in particular temperature, neglecting the effects of biotic interactions in determining the outcome of climate change projections. Many microbes rely on strong interference competition; hence the fitness of many pathogenic bacteria could be a function of both their growth properties and intraspecific competition. However, due to technical challenges in distinguishing and tracking individual strains, experimental evidence on intraspecific competition has been limited so far...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28425999/three-dimensional-printing-of-transparent-fused-silica-glass
#4
Frederik Kotz, Karl Arnold, Werner Bauer, Dieter Schild, Nico Keller, Kai Sachsenheimer, Tobias M Nargang, Christiane Richter, Dorothea Helmer, Bastian E Rapp
Glass is one of the most important high-performance materials used for scientific research, in industry and in society, mainly owing to its unmatched optical transparency, outstanding mechanical, chemical and thermal resistance as well as its thermal and electrical insulating properties. However, glasses and especially high-purity glasses such as fused silica glass are notoriously difficult to shape, requiring high-temperature melting and casting processes for macroscopic objects or hazardous chemicals for microscopic features...
April 19, 2017: Nature
https://www.readbyqxmd.com/read/28424451/prognostic-impact-of-notch1-myd88-and-sf3b1-mutations-in-polish-population-of-chronic-lymphocytic-leukemia-patients
#5
Maciej Putowski, Marta Podgórniak, Marta Piróg, Joanna Knap, Joanna Zaleska, Joanna Purkot, Jacek Zawiślak, Ewelina Zakrzewska, Agnieszka Karczmarczyk, Paulina Własiuk, Edyta Subocz, Krzysztof Giannopoulos
INTRODUCTION    Currently available prognostic factors determining the course of chronic lymphocytic leukemia (CLL) are not fully efficient especially for newly diagnosed patients. Investigation of molecular changes may help to clarify the reasons of the heterogeneity of the disease. Apart from already confirmed TP53 mutations, novel lesions: NOTCH1, SF3B1 and MYD88 might represent biomarkers of clinical relevance.  OBJECTIVES    The aim was to evaluate mutational status of NOTCH1, MYD88 and SF3B1 and to compare results with confirmed prognostic factors: ZAP-70, CD38 and IGHV mutation...
April 20, 2017: Polish Archives of Internal Medicine
https://www.readbyqxmd.com/read/28422192/polymorphisms-at-1q32-8q24-and-17q22-loci-are-associated-with-nonsyndromic-cleft-lip-with-or-without-cleft-palate-risk-in-the-slovak-population
#6
Jan Salagovic, Lucia Klimcakova, Marianna Zabavnikova, Jana Behunova, Terezia Hudakova, Jozef Fedeles, Agata Molnarova, Ludmila Podracka
BACKGROUND: Nonsyndromic cleft lip with or without cleft palate (nsCL/P) is the most common orofacial birth defect with an aetiology involving both genetic and environmental factors. Genome-wide association studies (GWAS) have identified several genomic susceptibility regions for nsCL/P. In the present study, the three well established single nucleotide polymorphisms (SNPs) identified by GWAS (rs987525 at 8q24, rs7078160 at 10q25, and rs227731 at 17q22 loci) and one SNP identified by candidate gene study (rs642961 in IRF6 gene at 1q32 locus) were analysed for an association with nsCL/P in Slovak population...
March 30, 2017: Biomedical Papers of the Medical Faculty of the University Palacký, Olomouc, Czechoslovakia
https://www.readbyqxmd.com/read/28421327/metal-dna-interactions-improve-signal-in-high-resolution-melting-of-dna-for-species-differentiation-of-plasmodium-parasite
#7
Priyamvada Jain, Babina Chakma, Naveen Singh, Sanjukta Patra, Pranab Goswami
The success of high-resolution melting (HRM) analysis for distinguishing similar DNAs with minor base mismatch differences is limited. Here, metal-mediated structural change in DNA has been exploited to amplify HRM signals leading to differentiation of target DNAs in an orthologous gene corresponding to four Plasmodium species. Conserved 26-mer ssDNAs from ldh gene of the four Plasmodium species were employed as targets. A capture probe (CP) that is fully complementary to the Plasmodium falciparum target (FT) and has two base mismatches each, with the targets of Plasmodium vivax (VT), Plasmodium malariae, (MT), and Plasmodium ovale (OT), was considered...
April 18, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/28420919/association-of-arginine-vasopressin-receptor-1a-gene-polymorphisms-with-hepatorenal-syndrome
#8
Chen Wang, Zhe Yu, Xin Luo, Jianhong Ye, Shourong Liu, Liangbin Miu, Jianfeng Bao, Fei Wang
OBJECTIVE: To assess the association of arginine vasopressin receptor 1a gene single nucleotide polymorphisms with type I hepatorenal syndrome. METHODS: The case-control study was conducted at the Hangzhou City Xixi Hospital, Hangzhou, China, from January 2012 to June 2014, and comprised patients with type I hepatorenal syndrome and individuals with cirrhosis who acted as the control group. Arginine vasopressin receptor 1a gene rs113481894 locus single nucleotide polymorphisms were analysed by high-resolution melting methods...
April 2017: JPMA. the Journal of the Pakistan Medical Association
https://www.readbyqxmd.com/read/28420422/high-resolution-melting-a-useful-field-deployable-method-to-measure-dhfr-and-dhps-drug-resistance-in-both-highly-and-lowly-endemic-plasmodium-populations
#9
Yaye Dié Ndiaye, Cyrille K Diédhiou, Amy K Bei, Baba Dieye, Aminata Mbaye, Nasserdine Papa Mze, Rachel F Daniels, Ibrahima M Ndiaye, Awa B Déme, Amy Gaye, Mouhamad Sy, Tolla Ndiaye, Aida S Badiane, Mouhamadou Ndiaye, Zul Premji, Dyann F Wirth, Souleymane Mboup, Donald Krogstad, Sarah K Volkman, Ambroise D Ahouidi, Daouda Ndiaye
BACKGROUND: Emergence and spread of drug resistance to every anti-malarial used to date, creates an urgent need for development of sensitive, specific and field-deployable molecular tools for detection and surveillance of validated drug resistance markers. Such tools would allow early detection of mutations in resistance loci. The aim of this study was to compare common population signatures and drug resistance marker frequencies between two populations with different levels of malaria endemicity and history of anti-malarial drug use: Tanzania and Sénégal...
April 19, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28416542/high-resolution-melting-analysis-for-the-rapid-detection-of-sequence-type-131-escherichia-coli
#10
Lucas B Harrison, Nancy D Hanson
IntroductionE. coli belonging to sequence type 131 clonal complex (ST131) have been associated with the global distribution of fluoroquinolone and β-lactam resistance. Whole genome sequencing and multi-locus sequence typing identify sequence type but are expensive when evaluating large numbers of samples. This study was designed to develop a cost-effective screening tool using high resolution melting (HRM) analysis to differentiate ST131 from non-ST-131 E. coli in large sample populations in the absence of sequence analysis...
April 17, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28416245/a-simple-and-efficient-method-for-crispr-cas9-induced-mutant-screening
#11
Yufeng Hua, Chun Wang, Jian Huang, Kejian Wang
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system provides a technological breakthrough in mutant generation. Several methods such as the polymerase chain reaction (PCR)/restriction enzyme (RE) assay, T7 endonuclease I (T7EI) assay, Surveyor nuclease assay, PAGE-based genotyping assay, and high-resolution melting (HRM) analysis-based assay have been developed for screening CRISPR/Cas9-induced mutants. However, these methods are time- and labour-intensive and may also be sequence-limited or require very expensive equipment...
April 4, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28411309/calreticulin-mutations-in-bulgarian-mpn-patients
#12
Ivan Pavlov, Evgueniy Hadjiev, Tzvetan Alaikov, Sylva Spassova, Angel Stoimenov, Elissaveta Naumova, Velizar Shivarov, Milena Ivanova
Somatic mutations in JAK2, MPL and CALR are recurrently identified in most of the cases with Philadelphia chromosome negative myeloproliferative neoplasms (MPNs). We applied four molecular genetic methods for identification of CALR exon 9 mutations, including high resolution melt (HRM) analysis, Sanger sequencing, semiconductor target genes sequencing and whole exome sequencing. A total of 78 patients with myeloid malignancies were included in the study. We identified 14 CALR exon 9 mutated cases out of 78 studied patients with myeloid malignancies...
April 14, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28407939/dna-barcoding-coupled-to-hrm-analysis-as-a-new-and-simple-tool-for-the-authentication-of-gadidae-fish-species
#13
Telmo J R Fernandes, Joana Costa, M Beatriz P P Oliveira, Isabel Mafra
This work aimed to exploit the use of DNA mini-barcodes combined with high resolution melting (HRM) for the authentication of gadoid species: Atlantic cod (Gadus morhua), Pacific cod (Gadus macrocephalus), Alaska pollock (Theragra chalcogramma) and saithe (Pollachius virens). Two DNA barcode regions, namely cytochrome c oxidase subunit I (COI) and cytochrome b (cytb), were analysed in silico to identify genetic variability among the four species and used, subsequently, to develop a real-time PCR method coupled with HRM analysis...
September 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28405865/involvement-of-17%C3%AE-hydroxysteroid-dehydrogenase-type-gene-1-937-a-g-polymorphism-in-infertility-in-polish-caucasian-women-with-endometriosis
#14
Maciej Osiński, Adrianna Mostowska, Przemyslaw Wirstlein, Jana Skrzypczak, Paweł Piotr Jagodziński, Malgorzata Szczepańska
PURPOSE: Endometriosis is considered to be an estrogen-related chronic inflammatory disease. The 17β-hydroxysteroid dehydrogenase 1 (HSD17B1) converts estrone to 17β estradiol. The role of HSD17B1 937 A>G (rs605059) single nucleotide polymorphism (SNP) in development of endometriosis is still disputable. This study evaluated the association of the HSD17B1 937 A>G (rs605059) SNP with infertile women affected by endometriosis from Polish Caucasian population. METHODS: The genotyping of cases (n = 290) and fertile women (n = 410) was conducted by high-resolution melting curve analysis...
April 12, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28403857/hypermethylation-of-cdkn2a-exon-2-in-tumor-tumor-adjacent-and-tumor-distant-tissues-from-breast-cancer-patients
#15
Melanie Spitzwieser, Elisabeth Entfellner, Bettina Werner, Walter Pulverer, Georg Pfeiler, Stefan Hacker, Margit Cichna-Markl
BACKGROUND: Breast carcinogenesis is a multistep process involving genetic and epigenetic changes. Tumor tissues are frequently characterized by gene-specific hypermethylation and global DNA hypomethylation. Aberrant DNA methylation levels have, however, not only been found in tumors, but also in tumor-surrounding tissue appearing histologically normal. This phenomenon is called field cancerization. Knowledge of the existence of a cancer field and its spread are of clinical relevance...
April 12, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28394649/adamtsl4-assessment-in-ectopia-lentis-reveals-a-recurrent-founder-mutation-in-polynesians
#16
Katherine A van Bysterveldt, Rasha Al Taie, Will Ikink, Verity F Oliver, Andrea L Vincent
BACKGROUND: To clinically characterize a cohort of patients with ectopia lentis (EL), or Marfanoid features in whom a definite genetic diagnosis of Marfan syndrome (MFS) had been excluded (atypical MFS), and to evaluate the contribution of mutations in ADAMTSL4 (OMIM * 610113), and P3H2 (LEPREL1; OMIM * 610341) to disease in this population. MATERIALS AND METHODS: Subjects underwent comprehensive ophthalmic examination, including keratometry. Mutational analysis of ADAMTSL4 and P3H2 was undertaken using PCR, high resolution melting analysis, and sequencing...
April 10, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28392841/assessing-alternative-base-substitutions-at-primer-cpg-sites-to-optimise-unbiased-pcr-amplification-of-methylated-sequences
#17
Ida L M Candiloro, Thomas Mikeska, Alexander Dobrovic
BACKGROUND: Determining the role of DNA methylation in various biological processes is dependent on the accurate representation of often highly complex patterns. Accurate representation is dependent on unbiased PCR amplification post bisulfite modification, regardless of methylation status of any given epiallele. This is highly dependent on primer design. Particular difficulties are raised by the analysis of CpG-rich regions, which are the usual regions of interest. Here, it is often difficult or impossible to avoid placing primers in CpG-free regions, particularly if one wants to target a specific part of a CpG-rich region...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28389235/dna-methylated-alleles-of-the-phenylalanine-hydroxylase-promoter-remodeled-at-elevated-phenylalanine-levels-in-newborns-with-hyperphenylalaninemia
#18
Chike Bellarmine Item, Somayeh Farhadi, Andrea Schanzer, Susanne Greber-Platzer
OBJECTIVES: Although high phenylalanine (phe) exposure has been shown to influence the DNA methylation status of leukocytes in hyperphenylalaninemia (HPA), the potential of DNA methylation changes as a biomarker of pretreatment high phe exposure in diet free newborns with HPA has not been explored. We therefore investigated the DNA methylation pattern of the phenylalanine hydroxylase (PAH) gene promoter at different phe levels, and the possibility of DNA methylation pattern changes being a biomarker of high phe exposure in diet free newborns with HPA...
April 4, 2017: Clinical Biochemistry
https://www.readbyqxmd.com/read/28388168/on-the-structure-and-dynamics-of-water-associated-with-single-supported-zwitterionic-and-anionic-membranes
#19
A Miskowiec, Z N Buck, F Y Hansen, H Kaiser, H Taub, M Tyagi, S O Diallo, E Mamontov, K W Herwig
We have used high-resolution quasielastic neutron scattering (QENS) to investigate the dynamics of water molecules (time scale of motion ∼10(-11)-10(-9) s) in proximity to single-supported bilayers of the zwitterioniclipid DMPC (1,2-dimyristoyl-sn-glycero-3-phosphorylcholine) and the anionic lipid DMPG (1,2-dimyristoyl-sn-glycero-3-phosphoglycerol) in the temperature range 160-295 K. For both membranes, the temperature dependence of the intensity of neutronsscattered elastically and incoherently from these samples indicates a series of freezing/melting transitions of the membrane-associated water, which have not been observed in previous studies of multilayer membranes...
March 28, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28384046/cross-validation-of-high-resolution-melting-analysis-based-genotyping-platform
#20
Taimour Langaee, Lynda Stauffer, Cheryl Galloway, Mohamed H Solayman, Larisa Cavallari
AIMS: Developing genetic and pharmacogenetic panels enhances genetic testing in clinical molecular diagnostics and precision medicine. This study was designed to cross-validate the performance of Canon's multiplex high-resolution DNA melting analysis platform with the Applied Biosystems TaqMan(®)-based Quant Studio Real-Time PCR System and Pyrosequencing(®) genotyping platforms for common genetic polymorphisms of the vitamin K epoxide reductase complex 1 (VKORC1) and CYP2C9. MATERIALS AND METHODS: Genomic DNA isolated from 240 blood and saliva samples was used to genotype the VKORC1-1639 G/A (rs9923231), CYP2C9*2 (430C>T, rs28371674), and CYP2C9*3 (1075A>C, rs1057910) single-nucleotide polymorphisms (SNPs) on the three above-mentioned genotyping platforms...
April 2017: Genetic Testing and Molecular Biomarkers
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