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high resolution melt

Dianna Hussmann, Lise Lotte Hansen
Methylation-Sensitive High Resolution Melting (MS-HRM) is an in-tube, PCR-based method to detect methylation levels at specific loci of interest. A unique primer design facilitates a high sensitivity of the assays enabling detection of down to 0.1-1% methylated alleles in an unmethylated background.Primers for MS-HRM assays are designed to be complementary to the methylated allele, and a specific annealing temperature enables these primers to anneal both to the methylated and the unmethylated alleles thereby increasing the sensitivity of the assays...
2018: Methods in Molecular Biology
Maslin Osathanunkul, Srisulak Dheeranupattana, Siriphron Rotarayanont, Siriwoot Sookkhee, Khukrit Osathanunkul, Panagiotis Madesis
DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Kaempferia (Zingiberaceae). Four primer pairs were evaluated (rbcL, rpoC, trnL and ITS1). It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed...
December 7, 2017: Nucleosides, Nucleotides & Nucleic Acids
Mine Erdem, Zülal Kesmen, Esra Özbekar, Bülent Çetin, Hasan Yetim
In the article by Erdem et al. published in Journal of Microbiology 2016; 54, 618-625, the figure 1 should be corrected as below.
December 2017: Journal of Microbiology / the Microbiological Society of Korea
Anushka Naidoo, Veron Ramsuran, Maxwell Chirehwa, Paolo Denti, Helen McIlleron, Kogieleum Naidoo, Nonhlanhla Yende-Zuma, Ravesh Singh, Sinaye Ngcapu, Mamoonah Chaudhry, Michael S Pepper, Nesri Padayatchi
AIM: We assessed the effect of genetic variability in UGT1A and ABCB1 genes on moxifloxacin pharmacokinetics. METHODS: Genotypes for selected UGT1A and ABCB1 SNPs were determined using a TaqMan® Genotyping OpenArray™ and high-resolution melt analysis for rs8175347. A nonlinear mixed-effects model was used to describe moxifloxacin pharmacokinetics. RESULTS: Genotypes of UGT1A SNPs, rs8175347 and rs3755319 (20.6% lower and 11.6% increased clearance, respectively) and ABCB1 SNP rs2032582 (40% reduced bioavailability in one individual) were significantly associated with changes in moxifloxacin pharmacokinetic parameters...
December 6, 2017: Pharmacogenomics
Laurence C Smith, Kang Yang, Lincoln H Pitcher, Brandon T Overstreet, Vena W Chu, Åsa K Rennermalm, Jonathan C Ryan, Matthew G Cooper, Colin J Gleason, Marco Tedesco, Jeyavinoth Jeyaratnam, Dirk van As, Michiel R van den Broeke, Willem Jan van de Berg, Brice Noël, Peter L Langen, Richard I Cullather, Bin Zhao, Michael J Willis, Alun Hubbard, Jason E Box, Brittany A Jenner, Alberto E Behar
Meltwater runoff from the Greenland ice sheet surface influences surface mass balance (SMB), ice dynamics, and global sea level rise, but is estimated with climate models and thus difficult to validate. We present a way to measure ice surface runoff directly, from hourly in situ supraglacial river discharge measurements and simultaneous high-resolution satellite/drone remote sensing of upstream fluvial catchment area. A first 72-h trial for a 63.1-km2 moulin-terminating internally drained catchment (IDC) on Greenland's midelevation (1,207-1,381 m above sea level) ablation zone is compared with melt and runoff simulations from HIRHAM5, MAR3...
December 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
Bin Yang, Junlong Zhang, Lixin Li, Xiaojun Lyu, Wei Wei, Zhuochun Huang, Bei Cai, Lanlan Wang
Ankylosing spondylitis (AS) is a common chronic autoimmune disease characterized by inflammation of axial skeleton and has strong genetic susceptibility. Single nucleotide polymorphisms (SNPs) have been found playing an important role in the development of AS. This study intends to explore whether the susceptibility to AS is associated with rs2171513 C>T, rs1077667 G>A in LIGHT (lymphotoxin, expressed on T lymphocytes) and rs12609318 A>G in B and T lymphocyte attenuator (BTLA) in a Chinese Han population...
October 31, 2017: Oncotarget
Ashley F Cowan, Kelly M Elkins
Psilocybe cubensis, or "magic mushroom," is the most common species of fungus with psychedelic characteristics. Two primer sets were designed to target Psilocybe DNA using web-based software and NBCI gene sequences. DNA was extracted from eighteen samples, including twelve mushroom species, using the Qiagen DNeasy® Plant Mini Kit. The DNA was amplified by the polymerase chain reaction (PCR) using the primers and a master mix containing either a SYBR® Green I, Radiant™ Green, or LCGreen Plus® intercalating dye; amplicon size was determined using agarose gel electrophoresis...
December 1, 2017: Journal of Forensic Sciences
Min Li, Martina Jelocnik, Feng Yang, Jianseng Gong, Bernhard Kaltenboeck, Adam Polkinghorne, Zhixin Feng, Yvonne Pannekoek, Nicole Borel, Chunlian Song, Ping Jiang, Jing Li, Jilei Zhang, Yaoyao Wang, Jiawei Wang, Xin Zhou, Chengming Wang
BACKGROUND: Chlamydia suis is an important, globally distributed, highly prevalent and diverse obligate intracellular pathogen infecting pigs. To investigate the prevalence and genetic diversity of C. suis in China, 2,137 nasal, conjunctival, and rectal swabs as well as whole blood and lung samples of pigs were collected in 19 regions from ten provinces of China in this study. RESULTS: We report an overall positivity of 62.4% (1,334/2,137) of C. suis following screening by Chlamydia spp...
December 1, 2017: BMC Veterinary Research
P Kotnik, E Knapič, J Kokošar, J Kovač, R Jerala, T Battelino, S Horvat
BACKGROUND: Recently, we witnessed great progress in the discovery of genetic variants associated with obesity and T2D, especially in adults. Much less is known regarding genetic variants associated with insulin resistance (IR). We hypothesized that novel IR genes could be efficiently detected in a population of obese children and adolescents who may not exhibit comorbidities and other confounding factors. OBJECTIVES: This study aimed to determine if a genome wide association study (GWAS), using a DNA pooling approach, could identify novel genes associated with IR...
November 30, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
Albert Hagelgans, Carsten Jandeck, Markus Friedemann, Anastasia Donchin, Susan Richter, Mario Menschikowski
BACKGROUND/AIM: To date there has been no investigation into the epigenetic regulation of the serine protease inhibitor SERPINA5 in prostate cancer, where lack of this gene was considered to facilitate invasive growth patterns. MATERIALS AND METHODS: Methylation degrees of eight CpG sites of SERPINA5 were analyzed in normal and malignant prostate cells using nucleotide sequencing, methylation-specific high resolution melting and digital droplet PCR techniques. RESULTS: The methylation degree of five CpG sites significantly correlated with lower SERPINA5 expression levels...
December 2017: Anticancer Research
C Kenel, D Grolimund, X Li, E Panepucci, V A Samson, D Ferreira Sanchez, F Marone, C Leinenbach
We present combined in situ X-ray diffraction and high-speed imaging to monitor the phase evolution upon cyclic rapid laser heating and cooling mimicking the direct energy deposition of Ti-6Al-4V in real time. Additive manufacturing of the industrially relevant alloy Ti-6Al-4V is known to create a multitude of phases and microstructures depending on processing technology and parameters. Current setups are limited by an averaged measurement through the solid and liquid parts. In this work the combination of a micro-focused intense X-ray beam, a fast detector and unidirectional cooling provide the spatial and temporal resolution to separate contributions from solid and liquid phases in limited volumes...
November 27, 2017: Scientific Reports
Nikol Reslová, Lucie Škorpíková, Michal Slaný, Edoardo Pozio, Martin Kašný
High resolution melting analysis (HRMA) is a single-tube method, which can be carried out rapidly as an additional step following real-time quantitative PCR (qPCR). The method enables the differentiation of genetic variation (down to single nucleotide polymorphisms) in amplified DNA fragments without sequencing. HRMA has previously been adopted to determine variability in the amplified genes of a number of organisms. However, only one work to date has focused on pathogenic parasites-nematodes from the genus Trichinella...
November 24, 2017: Scientific Reports
Lichen Zhang, Xiaowei Ma, Guoling You, Xiaoqing Zhang, Qihua Fu
Clopidogrel is an antiplatelet medicine used to prevent blood clots in patients who have had a heart attack, stroke, or other symptoms. Variability in the clinical response to clopidogrel treatment has been attributed to genetic factors. In particular, five SNPs of rs4244285, rs4986893, rs12248560, rs662 and rs1045642 have been associated with resistance to clopidogrel therapy in Chinese population. This work involves the development of a multiplex high-resolution melting (HRM) assay to genotype all five of these loci in 2 tubes...
November 22, 2017: Scientific Reports
Scott R Suter, Alexi Ball-Jones, Madeline M Mumbleau, Rachel Valenzuela, Jose Ibarra-Soza, Hassan Owens, Andrew J Fisher, Peter A Beal
SiRNAs can cause unintended gene silencing due to miRNA-like effects because of the similarity in function of an siRNA guide strand and a miRNA. Here we evaluate the effect on miRNA-like off targeting of introducing the adenosine derivative 7-EAA and triazoles prepared from 7-EAA at different positions in an siRNA guide strand. We find that a sterically demanding triazole placed in the RNA duplex major groove at position six of the guide strand dramatically reduces miRNA-like off targeting potency. A high-resolution structure of an RNA duplex bearing a novel, major-groove localized triazole is reported, which suggests that modified triazoles could be disrupting the hAgo2-guide-target RNA ternary complex...
November 22, 2017: Organic & Biomolecular Chemistry
I C Nettore, S Desiderio, E De Nisco, V Cacace, L Albano, N Improda, P Ungaro, M Salerno, A Colao, P E Macchia
BACKGROUND: Congenital hypothyroidism is a frequent disease occurring with an incidence of about 1/1500 newborns/year. In about 75% of the cases, CH is caused by alterations in thyroid morphogenesis, defined "thyroid dysgenesis" (TD). TD is generally a sporadic disease but in about 5% of the cases a genetic origin has been demonstrated. Previous studies indicate that Dnajc17 as a candidate modifier gene for hypothyroidism, since it is expressed in the thyroid bud, interacts with NKX2...
November 20, 2017: Journal of Endocrinological Investigation
Bin Chen, Xuewen Fu, Jau Tang, Mykhaylo Lysevych, Hark Hoe Tan, Chennupati Jagadish, Ahmed H Zewail
Eutectic-related reaction is a special chemical/physical reaction involving multiple phases, solid and liquid. Visualization of a phase reaction of composite nanomaterials with high spatial and temporal resolution provides a key understanding of alloy growth with important industrial applications. However, it has been a rather challenging task. Here, we report the direct imaging and control of the phase reaction dynamics of a single, as-grown free-standing gallium arsenide nanowire encapped with a gold nanoparticle, free from environmental confinement or disturbance, using four-dimensional (4D) electron microscopy...
November 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
Xingbo Song, Huiyu Zhong, Qian Wu, Minjin Wang, Juan Zhou, Yi Zhou, Xiaojun Lu, Binwu Ying
Objective: The present study investigates the influence of genetic variants in miRNA machinery genes (DROSHA, DICER, AGO1, and GEMIN4) on gastric cancer in Chinese Han population, further revealing the genetic mechanisms of gastric cancer occurrence and development. Methods: Genotyping of single nucleotide polymorphisms (SNPs) was performed in 628 patients with GC and 502 frequency-matched (age and gender) controls by the high resolution melting (HRM) method. Results: The SNPs rs3742330 (DICER) and rs7813 (GEMIN4) were associated with susceptibility to gastric cancer (P = 0...
October 17, 2017: Oncotarget
Jun Li, Aixin Liang, Zipeng Li, Chao Du, Guohua Hua, Angela Salzano, Giuseppe Campanile, Bianca Gasparrini, LiGuo Yang
This Research Communication describes the association between genetic variation within the prolactin (PRL) gene and the milk production traits of Italian Mediterranean river buffalo (Bufala mediterranea Italiana). High resolution melting (HRM) techniques were developed for genotyping 465 buffaloes. The association of genetic polymorphism with milk production traits was performed and subsequently the effects of parity and calving season were evaluated. Single nucleotide polymorphisms (SNPs) were identified at exons 2 and 5 and at introns 1 and 2...
November 2017: Journal of Dairy Research
Ali Nikoomanzar, Matthew R Dunn, John C Chaput
Engineered polymerases that can copy genetic information between DNA and xeno-nucleic acids (XNA) hold tremendous value as reagents in future biotechnology applications. However, current XNA polymerases function with inferior activity relative to their natural counterparts, indicating that current polymerase engineering efforts would benefit from new benchmarking assays. Here, we describe a highly parallel, low-cost method for measuring the average rate and substrate specificity of XNA polymerases in a standard qPCR instrument...
November 21, 2017: Analytical Chemistry
Ana Margarida Ferro, Patrícia Ramos, Ângela Guerra, Paula Parreira, Teresa Brás, Olinda Guerreiro, Eliana Jerónimo, Carmen Capel, Juan Capel, Fernando J Yuste-Lisbona, Maria F Duarte, Rafael Lozano, M Margarida Oliveira, Sónia Gonçalves
Cynara cardunculus: L. represents a natural source of terpenic compounds, with the predominant molecule being cynaropicrin. Cynaropicrin is gaining interest since it has been correlated to anti-hyperlipidaemia, antispasmodic and cytotoxicity activity against leukocyte cancer cells. The objective of this work was to screen a collection of C. cardunculus, from different origins, for new allelic variants in germacrene A synthase (GAS) gene involved in the cynaropicrin biosynthesis and correlate them with improved cynaropicrin content and biological activities...
November 16, 2017: Molecular Genetics and Genomics: MGG
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