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high resolution melt

Nikita Zabinyakov, Garrett Bullivant, Feng Cao, Matilde Fernandez Ojeda, Zheng Ping Jia, Xiao-Yan Wen, James J Dowling, Gajja S Salomons, Saadet Mercimek-Andrews
Pyridoxine dependent epilepsy (PDE) is caused by likely pathogenic variants in ALDH7A1 (PDE-ALDH7A1) and inherited autosomal recessively. Neurotoxic alpha-amino adipic semialdehyde (alpha-AASA), piperideine 6-carboxylate and pipecolic acid accumulate in body fluids. Neonatal or infantile onset seizures refractory to anti-epileptic medications are clinical features. Treatment with pyridoxine, arginine and lysine-restricted diet does not normalize neurodevelopmental outcome or accumulation of neurotoxic metabolites...
2017: PloS One
Bin Yang, Yuanwei Xu, Xinle Liu, Zhuochun Huang, Lanlan Wang
The association between the IL-23R and IL-17A polymorphisms and ankylosing spondylitis (AS) in the Southwest Chinese Population is still unclear. The purpose of this study is to detect the association between IL-23R and IL-17A polymorphisms and AS. A case-control study consisting of 486 AS patients and 480 healthy controls was performed. We used the high-resolution melting methods (HRM) to genotype five selected single nucleotide polymorphisms (SNPs), rs6693831, rs7517847, rs1884444, rs10889677 in the IL-23R gene and rs2275913 in the IL-17A gene...
September 19, 2017: Oncotarget
Kennedy Kassaza, Darwin J Operario, Dan Nyehangane, K C Coffey, Mary Namugosa, Lena Turkheimer, Patrick Ojuka, Patrick Orikiriza, Juliet Mwanga-Amumpaire, Frederick Byarugaba, Joel Bazira, Jennifer L Guler, Christopher C Moore, Yap Boum
Background. Microscopic diagnosis of malaria using Giemsa-stained blood smears is the standard of care in resource-limited settings. These smears represent a potential source of DNA for polymerase chain reaction (PCR) testing to confirm Plasmodium infection or for epidemiologic studies of archived samples. Therefore, we assessed the use of DNA extracts from stained blood smears for the detection of Plasmodium species using real-time PCR.Methods. We extracted DNA from archived blood smears and corresponding red blood cell pellets collected from asymptomatic children in Southwestern Uganda in 2010...
October 18, 2017: Journal of Clinical Microbiology
Qingfeng Li, Anne Patricia Alloncle, David Grojo, Philippe Delaporte
When the energy of a short laser pulse is localized in a fluid material, a flow motion is induced that can lead to the generation of free-surface jets. This nozzle-free jetting process is exploited to print conductive materials, typically metal nanoparticle inks, but this approach remains limited to the transfer of low viscosity fluids with a minimum feature size of few micrometers. We introduce a dual-laser method to achieve reproducible high-aspect-ratio jets from thin solid films. A first laser irradiation induces the melting of copper thin films and a second synchronized short pulse irradiation initiates the jetting process...
October 2, 2017: Optics Express
Yue Liu, Li Xiang, Yi Zhang, Xianrong Lai, Chao Xiong, Jingjian Li, Yanyan Su, Wei Sun, Shilin Chen
Sea buckthorn (Hippophae), an ancient crop with modern virtues, is increasingly consumed in source of foods and nutraceuticals. The growing demand leads to the adulteration of commercial sea buckthorn products, which is a common form of food fraud. Herein, a high resolution melting assay, targeting a DNA barcoding region of the internal transcribed spacer 2 (ITS2) (Bar-HRM) was developed to identify the seven native Chinese Hippophae species, and to authenticate commercial sea buckthorn products. Melting data from the HRM assay demonstrated that all Hippophae species could be clearly distinguished...
March 1, 2018: Food Chemistry
Kyumi Jeong, Doil Choi, Jundae Lee
The genomic region cosegregating with the genic male-sterile ms 1 gene of Capsicum annuum L. was delimited to a region of 869.9 kb on chromosome 5 through fine mapping analysis. A strong candidate gene, CA05g06780, a homolog of the Arabidopsis MALE STERILITY 1 gene that controls pollen development, was identified in this region. Genic male sterility caused by the ms 1 gene has been used for the economically efficient production of massive hybrid seeds in paprika (Capsicum annuum L.), a colored bell-type sweet pepper...
October 14, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Mame Cheikh Seck, Julie Thwing, Fatou Ba Fall, Jules Francois Gomis, Awa Deme, Yaye Die Ndiaye, Rachel Daniels, Sarah K Volkman, Medoune Ndiop, Mady Ba, Daouda Ndiaye
BACKGROUND: Malaria transmission in Senegal is highly stratified, from low in the dry north to moderately high in the moist south. In northern Senegal, along the Senegal River Valley and in the Ferlo semi-desert region, annual incidence is less than five cases per 1000 inhabitants. Many nomadic pastoralists have permanent dwellings in the Ferlo Desert and Senegal River Valley, but spend dry season in the south with their herds, returning north when the rains start, leading to a concern that this population could contribute to ongoing transmission in the north...
October 13, 2017: Malaria Journal
Pornpat Athamanolap, Kuangwen Hsieh, Liben Chen, Samuel Yang, Tza-Huei Wang
Accurate and timely diagnostics are critical for managing bacterial infections. The current gold standard, culture-based diagnostics can provide clinicians with comprehensive diagnostic information including bacterial identity and antimicrobial susceptibility, but they often require several days of turnaround time, which leads to compromised clinical outcome and promotes the spread of antibiotic resistance. Nucleic acid amplification tests such as PCR have significantly accelerated the detection of specific bacteria, but generally lack the capacities for broad-based bacterial identification or antimicrobial susceptibility testing...
October 13, 2017: Analytical Chemistry
Maslin Osathanunkul, Sarawut Ounjai, Rossarin Osathanunkul, Panagiotis Madesis
It is long believed that some spices may help protect against certain chronic conditions. Spices are usually parts of plants that have been powdered into small pieces. Have you ever wondered what the curry powder in your dish is made of? The aim of this work was to develop an appropriate DNA-based method for assessment of spice identity. Selecting the best marker for species recognition in the Zingiberaceae family. Six DNA regions were investigated in silico, including ITS, matK, rbcL, rpoC, trnH-psbA and trnL...
2017: PloS One
Yong Sun, Guo-Li Yuan, Jun Li, Jianhui Tang, Gen-Hou Wang
Sediment cores from lakes have been used to reconstruct the historic deposition of persistent organic pollutants (POPs), especially in remote alpine areas. To reconstruct the deposition history of organochlorine pesticides (OCPs) in the Tibetan Plateau (TP), two sediment cores from Yamzho Yumco Lake were drilled and dated with high-resolution, from which 23 OCPs were analyzed in greater detail. Regarding several legacy compounds, concentration peaks in the cores were observed in the 1970s, corresponding to the heavy usage of these compounds around the world...
October 4, 2017: Science of the Total Environment
Lulu Li, Yuan Li, Wei Lin, Xiuli Zhao
OBJECTIVE: To identify mutation of GJB2 gene and provide genetic counseling for a family affected with keratitis-ichthyosis-deafness (KID) syndrome. METHODS: Genomic DNA was extracted from peripheral blood samples with a standard phenol-chloroform method. PCR and Sanger sequencing were used to analyze potential mutation in the proband. Suspected mutation was verified with a PCR-high-resolution melting (PCR-HRM) method. T-clone sequencing was applied to determine the parental origin of the mutation...
October 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Mojgan Naghitorabi, Hamid Mir Mohammad Sadeghi, Javad Mohammadi Asl, Mohammad Rabbani, Abbas Jafarian-Dehkordi
Promoter methylation is one of the main epigenetic mechanisms that leads to the inactivation of tumor suppressor genes during carcinogenesis. Due to the reversible nature of DNA methylation, many studies have been performed to correct theses epigenetic defects by inhibiting DNA methyltransferases (DNMTs). In this case novel therapeutics especially siRNA oligonucleotides have been used to specifically knock down the DNMTs at mRNA level. Also many studies have focused on transcriptional gene silencing in mammalian cells via siRNA mediated promoter methylation...
2017: Iranian Journal of Pharmaceutical Research: IJPR
Yupeng Liu, Yibaina Wang, Fulan Hu, Hongru Sun, Zuoming Zhang, Xuan Wang, Xiang Luo, Lin Zhu, Rong Huang, Yan Li, Guangxiao Li, Xia Li, Shangqun Lin, Fan Wang, Yanhong Liu, Jiesheng Rong, Huiping Yuan, Yashuang Zhao
The relationship between gene-specific DNA methylation in peripheral blood leukocytes and colorectal cancer (CRC) susceptibility is unclear. In this case-control study, the methylation status of a panel of 10 CRC-related genes in 428 CRC cases and 428 cancer-free controls were detected with methylation-sensitive high-resolution melting analysis. We calculated a weighted methylation risk score (MRS) that comprehensively combined the methylation status of the panel of 10 genes and found that the MRS_10 was significantly associated with CRC risk...
September 22, 2017: Oncotarget
Alexander D Beaton, Jemma L Wadham, Jon Hawkings, Elizabeth A Bagshaw, Guillaume Lamarche-Gagnon, Matthew C Mowlem, Martyn Tranter
We report the first in situ high-resolution nitrate time series from two proglacial meltwater rivers draining the Greenland Ice Sheet, using a recently developed submersible analyzer based on lab-on-chip (LOC) technology. The low sample volume (320 μL) required by the LOC analyzer meant that low concentration (few micromolar to submicromolar), highly turbid subglacial meltwater could be filtered and colorimetrically analyzed in situ. Nitrate concentrations in rivers draining Leverett Glacier in southwest Greenland and Kiattuut Sermiat in southern Greenland exhibited a clear diurnal signal and a gradual decline at the commencement of the melt season, displaying trends that would not be discernible using traditional daily manual sampling...
October 13, 2017: Environmental Science & Technology
Dan Rao, Miaoli Wu, Jing Wang, Wen Yuan, Yujun Zhu, Feng Cong, Fengjiao Xu, Yuexiao Lian, Bihong Huang, Qiwen Wu, Meili Chen, Yu Zhang, Ren Huang, Pengju Guo
Murine parvovirus is one of the most prevalent infectious pathogens in mouse colonies. A specific primer pair targeting the VP2 gene of minute virus of mice (MVM) and mouse parvovirus (MPV) was utilized for high resolution melting (HRM) analysis. The resulting melting curves could distinguish these two virus strains and there was no detectable amplification of the other mouse pathogens which included rat parvovirus (KRV), ectromelia virus (ECT), mouse adenovirus (MAD), mouse cytomegalovirus (MCMV), polyoma virus (Poly), Helicobactor hepaticus (H...
September 23, 2017: Journal of Virological Methods
Yat-Tung Lo, Pang-Chui Shaw
Authentication of food or food supplements with medicinal values is important to avoid adverse toxic effects, provide consumer rights, as well as for certification purpose. Compared to morphological and spectrometric techniques, molecular authentication is found to be accurate, sensitive and reliable. However, DNA degradation and inclusion of inhibitors may lead to failure in PCR amplification. This paper reviews on the existing DNA extraction and PCR protocols, and the use of small size DNA markers with sufficient discriminative power for molecular authentication...
February 1, 2018: Food Chemistry
Christopher A Dunlap, Gabriel M Mascarin, Emiliana M Romagnoli, Mark A Jackson
The current study evaluates the potential of using high resolution DNA melting assays to discriminate species in the genus Isaria. The study utilizes a previously identified 103 base pair PCR amplicon, which was reported to be selective for Isaria fumosorosea. Our study finds the amplicon selective for Isaria javanica and Isaria poprawskii when assayed against all members of the genus. In addition, the high resolution melting profile of this amplicon can be used to discriminate between I. javanica, I. poprawskii and a 1:1 mixture of the two species...
September 20, 2017: Journal of Invertebrate Pathology
Ti-Ying Chen, Chao Jiang, Yuan Yuan, Kang Chen, Jun-Hui Zhou, Yu-Yang Zhao, Lu-Qi Huang
To establish a new high resolution melting analytical method for identification of Lonicera japonica germplasm, the screening of 7 pairs of SSR (simple sequence repeats) primers, determining the suitable diagnostic primers by the differences of peak pattern and Tm was conducted. Then into the DNA template concentration, annealing temperature and the suitable range of cycle number were investigated. Combined with SIMCA-P software for data processing analysis, the results show that three main germplasm honeysuckle could be divided by four sets of primers...
December 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Alicia Rojas, Gilad Segev, Alex Markovics, Itamar Aroch, Gad Baneth
BACKGROUND: Spirocerca lupi, the dog oesophageal nematode, causes a potentially fatal disease in domestic dogs, and is currently clinically diagnosed by coproscopy and oesophagoscopy. To date, a single molecular method, a semi-nested PCR, targeting the cox1 gene, has been developed to aid in the diagnosis of spirocercosis. The present study describes three novel high-resolution melt (HRM) quantitative PCR (qPCR) assays targeting fragments of the ITS1, 18S and cytb loci of S. lupi. The performance of these molecular assays in feces was compared to fecal flotation and to the previously described cox1 gene semi-nested PCR in 18 fecal samples from dogs with clinical oesophageal spirocercosis diagnosed by oesophagoscopy...
September 19, 2017: Parasites & Vectors
Isabelle Joyce de Lima Silva-Fernandes, Emanuele Silva de Oliveira, Juliana Carvalho Santos, Marcelo Lima Ribeiro, Adriana Camargo Ferrasi, Maria Inês de Moura Campos Pardini, Rommel Mário Rodriguez Burbano, Silvia Helena Barem Rabenhorst
Gastric cancer is the fourth most common type of cancer worldwide. Helicobacter pylori is a well-established risk factor and may cause injuries to genomic integrity through an inefficient DNA repair. This study aimed to examine the influence of polymorphisms in DNA repair enzymes using markers for microsatellite instability (MSI). Polymorphisms of DNA repair enzymes were detected by PCR-RFLP and MSI, by high resolution melt (HRM) analysis. Helicobacter pylori detection and genotyping were accomplished by PCR...
July 1, 2017: Mutagenesis
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