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https://www.readbyqxmd.com/read/28230734/deep%C3%A2-transcriptome%C3%A2-sequencing%C3%A2-of%C3%A2-two%C3%A2-green%C3%A2-algae-chara%C3%A2-vulgaris%C3%A2-and%C3%A2-chlamydomonas%C3%A2-reinhardtii-%C3%A2-provides%C3%A2-no%C3%A2-evidence%C3%A2-of%C3%A2-organellar%C3%A2-rna%C3%A2-editing
#1
A Bruce Cahoon, John A Nauss, Conner D Stanley, Ali Qureshi
Nearly all land plants post-transcriptionally modify specific nucleotides within RNAs, a process known as RNA editing. This adaptation allows the correction of deleterious mutations within the asexually reproducing and presumably non-recombinant chloroplast and mitochondrial genomes. There are no reports of RNA editing in any of the green algae so this phenomenon is presumed to have originated in embryophytes either after the invasion of land or in the now extinct algal ancestor of all land plants. This was challenged when a recent in silico screen for RNA edit sites based on genomic sequence homology predicted edit sites in the green alga Chara vulgaris, a multicellular alga found within the Streptophyta clade and one of the closest extant algal relatives of land plants...
February 20, 2017: Genes
https://www.readbyqxmd.com/read/28224031/first-report-of-tasmanian-sheep-strain-g2-genotype-isolated-from-iranian-goat-using-the-high-resolution-melting-hrm-analysis
#2
Ahmad Hosseini-Safa, Mohammad Ali Mohag Hegh, Nader Pestechian, Maryam Ganji, Rasoul Mohammadi, Reza Mahmoudi Lamouki, Mohammad Rostami-Nejad
AIM: The present study was aimed to evaluate E. granulosus genotypes isolated from goats using HRM analysis in Isfahan province. BACKGROUND: Cystic echincoccosis, so-called hydatidosis, is widespread infection caused by the larval stage of Echinococcus granulosus. This is an important zoonotic disease worldwide, especially in the developing countries such as Iran. To date, molecular studies mainly based on the mitochondrial DNA sequences have identified distinct genotypes termed G1-G10 which can differ in some characteristics such as the growth and infectivity to different intermediate hosts or the survival rate in the definitive hosts that are important for the development of control strategies...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28220743/analysis-of-mutations-causing-familial-hypercholesterolaemia-in-black-south-african-patients-of-different-ancestr
#3
U K Ibe, R Whittall, S E Humphries, G Pilcher, F Raal
BACKGROUND: Familial hypercholesterolaemia (FH) is usually caused by mutations in three genes (LDLR, APOB and PCSK9). OBJECTIVE: To identify the spectrum of FH-causing mutations in black South African (SA) patients. METHODS: DNA samples of 16 unrelated South African FH patients with elevated low-density lipoprotein cholesterol levels, tendon xanthomas and corneal arcus (3 clinically homozygous FH and 13 heterozygous FH) of ethnic African origin were screened for mutations in the LDLR (coding region, promoter and intron/exon boundaries), APOB (part of exon 26) and PCSK9 genes (exon 7), using high-resolution melting...
January 30, 2017: South African Medical Journal, Suid-Afrikaanse Tydskrif Vir Geneeskunde
https://www.readbyqxmd.com/read/28216667/a-novel-hrm-assay-for-the-simultaneous-detection-and-differentiation-of-eight-poxviruses-of-medical-and-veterinary-importance
#4
Esayas Gelaye, Lukas Mach, Jolanta Kolodziejek, Reingard Grabherr, Angelika Loitsch, Jenna E Achenbach, Norbert Nowotny, Adama Diallo, Charles Euloge Lamien
Poxviruses belonging to the Orthopoxvirus, Capripoxvirus and Parapoxvirus genera share common host species and create a challenge for diagnosis. Here, we developed a novel multiplex PCR method for the simultaneous detection and differentiation of eight poxviruses, belonging to three genera: cowpox virus (CPXV) and camelpox virus (CMLV) [genus Orthopoxvirus]; goatpox virus (GTPV), sheeppox virus (SPPV) and lumpy skin disease virus (LSDV) [genus Capripoxvirus]; orf virus (ORFV), pseudocowpox virus (PCPV) and bovine papular stomatitis virus (BPSV) [genus Parapoxvirus]...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28215743/a-nlrc3-like-gene-from-blunt-snout-bream-megalobrama-amblycephala-molecular-characterization-expression-and-association-with-resistance-to-aeromonas-hydrophila-infection
#5
Fengjuan Zhou, Qifeng Zhan, Zhujin Ding, Lina Su, Jun Fan, Lei Cui, Nan Chen, Weimin Wang, Hong Liu
NLRC (the nucleotide-oligomerization domain (NOD)-like receptor subfamily C) consists of teleost-specific NLRs (NOD-like receptors) and plays pivotal roles in microbial recognition and regulation of innate immune response. In this study, we cloned and characterized a NLRC3-like gene (MamNLRC3-like) from blunt snout bream (Megalobrama amblycephala) by using the quantitative real-time PCR method, and analyzed the correlation between its polymorphisms and resistance to Aeromonas hydrophila infection. The full length cDNA of MamNLRC3-like was 2863 bp, with a 5'-UTR of 169 bp, ORF of 2301 bp and 3'-UTR of 393 bp, encoding 766 amino acid residues...
February 16, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28212611/impact-of-novel-snps-identified-in-cynara-cardunculus-genes-on-functionality-of-proteins-regulating-phenylpropanoid-pathway-and-their-association-with-biological-activities
#6
Ana Margarida Ferro, Patrícia Ramos, Olinda Guerreiro, Eliana Jerónimo, Inês Pires, Carmen Capel, Juan Capel, Rafael Lozano, Maria F Duarte, M Margarida Oliveira, Sónia Gonçalves
BACKGROUND: Cynara cardunculus L. offers a natural source of phenolic compounds with the predominant molecule being chlorogenic acid. Chlorogenic acid is gaining interest due to its involvement in various biological properties such as, antibacterial, antifungal, antioxidant, hepatoprotective, and anticarcinogenic activities. RESULTS: In this work we screened a Cynara cardunculus collection for new allelic variants in key genes involved in the chlorogenic acid biosynthesis pathway...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28207292/occurrence-of-toxoplasma-gondii-in-carcasses-of-pigs-reared-in-intensive-systems-in-northern-italy
#7
Roberto Papini, Pierluigi di Ciccio, Marianna Marangi, Sergio Ghidini, Emanuela Zanardi, Alberto Vergara, Annunziata Giangaspero, Simona Nardoni, Guido Rocchigiani, Francesca Mancianti, Adriana Ianieri
To evaluate the occurrence of Toxoplasma gondii and to genetically characterize its isolates in carcasses of industrial fattening pigs, blood, diaphragm, and heart samples were collected from 375 carcasses of pigs slaughtered to be processed for Parma ham production. Pigs had been bred on approved farms (n = 75) located in the so-called Food Valley in Italy. Sera were examined for immunoglobulin G antibodies to T. gondii by modified agglutination test (MAT). Both heart and diaphragm samples from seropositive carcasses were processed for the presence of T...
February 16, 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28206954/rassf1a-promoter-methylation-in-high-grade-serous-ovarian-cancer-a-direct-comparison-study-in-primary-tumors-adjacent-morphologically-tumor-cell-free-tissues-and-paired-circulating-tumor-dna
#8
Lydia Giannopoulou, Issam Chebouti, Kitty Pavlakis, Sabine Kasimir-Bauer, Evi S Lianidou
The RASSF1A promoter is frequently methylated in high-grade serous ovarian cancer (HGSC). We examined RASSF1A promoter methylation in primary tumors, adjacent morphologically tumor cell-free tissues and corresponding circulating tumor DNA (ctDNA) samples of patients with HGSC, using a real-time methylation specific PCR (real-time MSP) and a methylation-sensitive high-resolution melting analysis (MS-HRMA) assay for the detection and semi-quantitative estimation of methylation, respectively. Two groups of primary HGSC tumor FFPE samples were recruited (Group A n=67 and Group B n=61), along with matched adjacent morphologically tumor cell-free tissues (n=58) and corresponding plasma samples (n=59) for group B...
February 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28194017/in-situ-study-on-atomic-mechanism-of-melting-and-freezing-of-single-bismuth-nanoparticles
#9
Yingxuan Li, Ling Zang, Daniel L Jacobs, Jie Zhao, Xiu Yue, Chuanyi Wang
Experimental study of the atomic mechanism in melting and freezing processes remains a formidable challenge. We report herein on a unique material system that allows for in situ growth of bismuth nanoparticles from the precursor compound SrBi2Ta2O9 under an electron beam within a high-resolution transmission electron microscope (HRTEM). Simultaneously, the melting and freezing processes within the nanoparticles are triggered and imaged in real time by the HRTEM. The images show atomic-scale evidence for point defect induced melting, and a freezing mechanism mediated by crystallization of an intermediate ordered liquid...
February 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28193534/implementation-of-new-tools-in-molecular-epidemiology-studies-of-echinococcus-granulosus-sensu-lato-in-south-america
#10
Héctor G Avila, Guilherme B Santos, Marcela A Cucher, Natalia Macchiaroli, Matías G Pérez, Germán Baldi, Oscar Jensen, Verónica Pérez, Raúl López, Perla Negro, Exequiel Scialfa, Arnaldo Zaha, Henrique B Ferreira, Mara Rosenzvit, Laura Kamenetzky
The aim of this work was to determine Echinococcus granulosus sensu lato species and genotypes in intermediate and definitive hosts and in human isolates from endemic regions of Argentina and Brazil including those where no molecular data is available by a combination of classical and alternative molecular tools. A total of 227 samples were isolated from humans, natural intermediate and definitive hosts. Amplification of cytochrome c oxidase subunit I gene fragment was performed and a combination of AluI digestion assay, High Resolution Melting analysis (HRM) assay and DNA sequencing was implemented for Echinococcus species/genotype determination...
February 11, 2017: Parasitology International
https://www.readbyqxmd.com/read/28178086/identification-of-rare-nonsynonymous-variants-in-syne1-cpg2-in-bipolar-affective-disorder
#11
Sally I Sharp, Jenny Lange, Radhika Kandaswamy, Mazen Daher, Adebayo Anjorin, Nicholas J Bass, Andrew McQuillin
BACKGROUND: Bipolar affective disorder (BPD) is a severe mood disorder with a prevalence of ∼1.5% in the population. The pathogenesis of BPD is poorly understood; however, a strong heritable component has been identified. Previous genome-wide association studies have indicated a region on 6q25, coding for the SYNE1 gene, which increases disease susceptibility. SYNE1 encodes the synaptic nuclear envelope protein-1, nesprin-1. A brain-specific splice variant of SYNE1, CPG2 encoding candidate plasticity gene 2, has been identified...
February 7, 2017: Psychiatric Genetics
https://www.readbyqxmd.com/read/28177832/natural-variation-in-i-circadian-clock-associated-1-i-is-associated-with-flowering-time-in-i-brassica-rapa-i
#12
Hankuil Yi, Xiaonan Li, Seong Ho Lee, Ill-Sup Nou, Yong Pyo Lim, Yoonkang Hur
Flowering time is a very important agronomic trait and the development of molecular markers associated with this trait can facilitate crop breeding. <i>CIRCADIAN CLOCK ASSOCIATED 1</i> (<i>CCA1</i>), a core oscillator component of circadian rhythms that affect metabolic pathways in plants, has been implicated in flowering time control in <i>Brassica</i> species. <i>CCA1</i> gene sequences from three <i>Brassica rapa</i> inbred lines, showing either early flowering or late flowering phenotypes, were analyzed and a high level of ets were designed and tested using various inbred lines of <i>B...
December 22, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28176860/massively-parallel-digital-high-resolution-melt-for-rapid-and-absolutely-quantitative-sequence-profiling
#13
Daniel Ortiz Velez, Hannah Mack, Julietta Jupe, Sinead Hawker, Ninad Kulkarni, Behnam Hedayatnia, Yang Zhang, Shelley Lawrence, Stephanie I Fraley
In clinical diagnostics and pathogen detection, profiling of complex samples for low-level genotypes represents a significant challenge. Advances in speed, sensitivity, and extent of multiplexing of molecular pathogen detection assays are needed to improve patient care. We report the development of an integrated platform enabling the identification of bacterial pathogen DNA sequences in complex samples in less than four hours. The system incorporates a microfluidic chip and instrumentation to accomplish universal PCR amplification, High Resolution Melting (HRM), and machine learning within 20,000 picoliter scale reactions, simultaneously...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28165067/microbial-typing-by-machine-learned-dna-melt-signatures
#14
Nadya Andini, Bo Wang, Pornpat Athamanolap, Justin Hardick, Billie J Masek, Simone Thair, Anne Hu, Gideon Avornu, Stephen Peterson, Steven Cogill, Richard E Rothman, Karen C Carroll, Charlotte A Gaydos, Jeff Tza-Huei Wang, Serafim Batzoglou, Samuel Yang
There is still an ongoing demand for a simple broad-spectrum molecular diagnostic assay for pathogenic bacteria. For this purpose, we developed a single-plex High Resolution Melt (HRM) assay that generates complex melt curves for bacterial identification. Using internal transcribed spacer (ITS) region as the phylogenetic marker for HRM, we observed complex melt curve signatures as compared to 16S rDNA amplicons with enhanced interspecies discrimination. We also developed a novel Naïve Bayes curve classification algorithm with statistical interpretation and achieved 95% accuracy in differentiating 89 bacterial species in our library using leave-one-out cross-validation...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28164559/conditions-of-high-resolution-melting-analysis-on-the-cobas-z480-instrument-for-the-genotyping-of-vkorc1-in-the-clinical-routine-laboratory
#15
Christian Paar, Verena Hammerl, Hermann Blessberger, Herbert Stekel, Clemens Steinwender
BACKGROUND: High resolution melting (HRM) of amplicons is a simple method for genotyping of single nucleotide polymorphisms (SNPs). Albeit many applications reported, HRM seems to be rarely used in clinical laboratories. The suitability of HRM-PCR for the clinical laboratory was investigated for genotyping of SNPs of the vitamin K epoxide reductase complex unit 1 gene. METHODS: About 100 DNA samples were analyzed by two different HRM-PCRs on the Cobas z480 instrument and compared with a PCR with fluorescently labeled probes (HybProbe-PCR) on the LightCycler 2...
December 1, 2016: Clinical Laboratory
https://www.readbyqxmd.com/read/28161869/high-resolution-melting-analysis-is-very-useful-to-identify-breast-cancer-type-1-susceptibility-protein-brca1-c-4964_4982del19-rs80359876-founder-calabrian-pathogenic-variant-on-peripheral-blood-and-buccal-swab-dna
#16
Angelo Minucci, Maria De Bonis, Elisa De Paolis, Leonarda Gentile, Concetta Santonocito, Paola Concolino, Flavio Mignone, Ettore Capoluongo
INTRODUCTION: Detection of pathogenic variants in hereditary breast and ovarian cancer-related breast cancer type 1 and type 2 susceptibility proteins (BRCA1/2) genes is an effective strategy in cancer prevention and treatment. Some ethnic and geographical regions show different BRCA1/2 mutation spectrum and prevalence. In Italy, elucidation of founder effect in BRCA1/2 genes can have an impact on the management of hereditary cancer families on a healthcare system level, making genetic testing more affordable and cost effective in certain regions...
February 4, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28159677/clinicopathological-and-molecular-features-of-a-large-cohort-of-gastrointestinal-stromal-tumors-gists-and-review-of-the-literature-braf-mutations-in-kit-pdgfra-wildtype-gists-are-rare-events
#17
Sebastian Huss, Hlen Pasternack, Michaela Angelika Ihle, Sabine Merkelbach-Bruse, Birthe Heitkötter, Wolfgang Hartmann, Marcel Trautmann, Heidrun Gevensleben, Reinhard Büttner, Hans-Ulrich Schildhaus, Eva Wardelmann
In KIT/PDGFRA wild-type gastrointestinal stromal tumors (wt-GISTs), BRAF mutations are regarded as alternative pathogenic event driving tumorigenesis. In our study, we aimed at analyzing a large cohort (n=444) of GISTs for BRAF mutations using molecular and immunohistochemical methods. More than 3000 GIST samples from caucasian patients were available in our GIST and Sarcoma Registry NRW. Of these, we selected 172 wt-GISTs to evaluate the frequency of BRAF mutations. Furthermore, 272 GISTs with a representative KIT and PDGFRA mutational status were selected...
January 31, 2017: Human Pathology
https://www.readbyqxmd.com/read/28153952/qmc-pcrx-a-novel-method-for-rapid-mutation-detection
#18
Henry O Ebili, James Hassall, Abutaleb Asiri, Hersh Ham-Karim, Wakkas Fadhil, Ayodeji Johnson Agboola, Mohammad Ilyas
AIMS: We previously described the quick multiplex consensus PCR (QMC-PCR) as a method for rapid mutation screening in low-quality template. QMC-PCR has two-stages: a prediagnostic multiplex (PDM) reaction followed by a single specific diagnostic reaction with high-resolution melting (HRM) analysis. We aimed to develop QMC-PCRx in which second stage was multiplexed to allow testing of multiple targets. METHODS: The PDM reaction was retained without change. For the second stage, in silico design was used to identify targets amenable to a multiplex specific diagnostic reaction and multiplex HRM (mHRM) analysis...
February 2, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28148965/rapid-detection-of-functional-gene-polymorphisms-of-tlrs-and-il-17-using-high-resolution-melting-analysis
#19
Johanna Teräsjärvi, Antti Hakanen, Matti Korppi, Kirsi Nuolivirta, Kirsi Gröndahl-Yli-Hannuksela, Jussi Mertsola, Ville Peltola, Qiushui He
Genetic variations in toll-like receptors (TLRs) and IL-17A have been widely connected to different diseases. Associations between susceptibility and resistance to different infections and single nucleotide polymorphisms (SNPs) in TLR1 to TLR4 and IL17A have been found. In this study, we aimed to develop a rapid and high throughput method to detect functional SNPs of above mentioned proteins. The following most studied and clinically important SNPs: TLR1 (rs5743618), TLR2 (rs5743708), TLR3 (rs3775291), TLR4 (rs4986790) and IL17 (rs2275913) were tested...
February 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28133617/molecular-analysis-of-a-genetic-variants-panel-related-to-nutrients-and-metabolism-association-with-susceptibility-to-gestational-diabetes-and-cardiometabolic-risk-in-affected-women
#20
Marica Franzago, Federica Fraticelli, Antonio Nicolucci, Claudio Celentano, Marco Liberati, Liborio Stuppia, Ester Vitacolonna
Gestational diabetes mellitus (GDM) is the most frequent metabolic disorder in pregnancy. Women with a GDM history are at increased risk of developing diabetes and cardiovascular diseases. Studies have demonstrated a significant correlation between several genes involved in the metabolic pathway of insulin and environmental factors. The aim of this study was to investigate the relationship between clinical parameters in GDM and variants in genes involved with nutrients and metabolism. Several variants PPARG2 rs1801282 (C>G); PPARGC1A rs8192678 (C>T); TCF7L2 rs7903146 (C>T); LDLR rs2228671 (C>T); MTHFR rs1801133 (C>T); APOA5 rs662799 (T>C); GCKR rs1260326 (C>T); FTO rs9939609 (T>A); MC4R rs17782313 (T>C) were genotyped in 168 pregnant Caucasian women with or without GDM by High Resolution Melting (HRM) analysis...
2017: Journal of Diabetes Research
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