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https://www.readbyqxmd.com/read/28734895/a-sensitive-and-convenient-method-for-clinical-detection-of-non-syndromic-hearing-loss-associated-common-mutations
#1
Er-Feng Yuan, Wei Xia, Jing-Tao Huang, Ling Hu, Xing Liao, Xiang Dai, Song-Mei Liu
BACKGROUND: The majority of non-syndromic hearing loss (NSHL) patients result from causative mutations in GJB2, SLC26A4 and mitochondrial 12S rRNA genes. Accurate detection of these genetic mutations is increasingly recognized for its clinical significance to reduce incidence and guide individual treatment of NSHL. Current methods for clinical practice are labor intensive, expensive or of low sensitivity. METHODS: Genomic DNA from 7 newborns not passing the hearing screening and 94 newborns passing the hearing screening were analyzed for the common mutations using high resolution melting analysis (HRMA) and Sanger sequencing...
July 19, 2017: Gene
https://www.readbyqxmd.com/read/28734843/a-high-resolution-melting-hrm-technology-based-assay-for-cost-efficient-clinical-detection-and-genotyping-of-herpes-simplex-virus-hsv-1-and-hsv-2
#2
M Lieveld, A Carregosa, I Benoy, N Redzic, M Berth, D Vanden Broeck
Genital herpes can be caused by two very similar viruses, herpes simplex virus (HSV)-1 or HSV-2. These two HSV types cannot be distinguished clinically, but genotyping is recommended in the first-episodes of genital herpes to guide counselling and management. Quantitative polymerase chain reaction (qPCR) is the preferred diagnostic method for HSV typing. However, commercial qPCR methods use expensive fluorescent labeled probes for detection. Furthermore, most low-cost methods are not able to differentiate between HSV-1 and -2...
July 19, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28730413/updating-the-elite-rice-variety-kongyu-131-by-improving-the-gn1a-locus
#3
Xiaomin Feng, Chen Wang, Jianzong Nan, Xiaohui Zhang, Rongsheng Wang, Guoqiang Jiang, Qingbo Yuan, Shaoyang Lin
BACKGROUND: Kongyu 131 is an elite japonica rice variety of Heilongjiang Province, China. It has the characteristics of early maturity, superior quality, high yield, cold tolerance and wide adaptability. However, there is potential to improve the yield of Kongyu 131 because of the relatively few grains per panicle compared with other varieties. Hence, we rebuilt the genome of Kongyu 131 by replacing the GRAIN NUMBER1a (Gn1a) locus with a high-yielding allele from a big panicle indica rice variety, GKBR...
December 2017: Rice
https://www.readbyqxmd.com/read/28729554/comparison-of-traditional-and-new-generation-dna-markers-declares-high-genetic-diversity-and-differentiated-population-structure-of-wild-almond-species
#4
Karim Sorkheh, Mehrana Koohi Dehkordi, Sezai Ercisli, Attila Hegedus, Júlia Halász
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28728910/rapid-differentiation-of-bacterial-communities-using-high-resolution-melting-analysis
#5
Steven Everman, Shiao Y Wang
Analysis of microbial communities is of broad interest in biology and high throughput sequencing is now the preferred method. However, some studies may not need the level of detail high throughput sequencing provides and its cost may limit the number of samples that can be sequenced. High resolution melting analysis (HRM) of 16S rRNA gene variable regions has been proposed as an efficient and low cost method to prioritize samples for sequencing but more specific primers are needed and its efficacy needs to be confirmed...
July 17, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28726721/identification-and-validation-of-new-alleles-of-falsiflora-and-compound-inflorescence-genes-controlling-the-number-of-branches-in-tomato-inflorescence
#6
Huan Zheng, Saneyuki Kawabata
The architecture of inflorescences shows extensive diversity in both branching frequency and flower number, which eventually, determines agricultural productivity. In this study, F₂ (second filial) populations derived from a cross between Solanum lycopersicum 10AS111A (highly-branched inflorescence) and the S. pimpinellifolium PI124039 (inflorescence having a single branch) were used to decipher the genetic control of branch number (BN) of inflorescence in plants bearing small-sized tomato fruits. The segregation ratio of single- and moderately-branched types to the highly-branched type was significantly different from 3:1 but not different from 15:1 at p < 0...
July 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28725235/gateway-compatible-crispr-cas9-vectors-and-a-rapid-detection-by-high-resolution-melting-curve-analysis
#7
Cynthia J Denbow, Samantha Lapins, Nick Dietz, Raelynn Scherer, Zachary L Nimchuk, Sakiko Okumoto
CRISPR-Cas9 system rapidly became an indispensable tool in plant biology to perform targeted mutagenesis. A CRISPR-Cas9-mediated double strand break followed by non-homologous end joining (NHEJ) repair most frequently results in a single base pair deletion or insertions (indels), which is hard to detect using methods based on enzymes that detect heteroduplex DNA. In addition, somatic tissues of the T1 generation inevitably contain a mosaic population, in which the portion of cells carrying the mutation can be too small to be detected by the enzyme-based methods...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28716280/association-of-polymorphisms-and-reduced-expression-levels-of-the-nr4a2-gene-with-parkinson-s-disease-in-a-mexican-population
#8
Elizabeth Ruiz-Sánchez, Petra Yescas, Mayela Rodríguez-Violante, Nancy Martínez-Rodríguez, Jesica N Díaz-López, Adriana Ochoa, Sergio S Valdes-Rojas, Daniel Magos-Rodríguez, Julio C Rojas-Castañeda, Amin Cervantes-Arriaga, Samuel Canizales-Quinteros, Patricia Rojas
INTRODUCTION: The NR4A2 transcription factor is important in the development, survival and phenotype of dopaminergic neurons and it is postulated as a possible biomarker for Parkinson's disease (PD). Therefore, our aim was to analyze in a sample of a Mexican population with idiopathic PD, mutations (in two hotspot mutation regions) and two polymorphisms (rs34884856 in promotor and rs35479735 intronic regions) of the NR4A2 gene. We also evaluate the levels of NR4A2 gene expression in peripheral blood for a Mexican population, and identify whether they are associated with NR4A2 gene polymorphisms...
August 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28716266/sativex%C3%A2-effects-on-promoter-methylation-and-on-cnr1-cnr2-expression-in-peripheral-blood-mononuclear-cells-of-progressive-multiple-sclerosis-patients
#9
Massimo Santoro, Massimiliano Mirabella, Chiara De Fino, Assunta Bianco, Matteo Lucchini, Francesco Losavio, Andrea Sabino, Viviana Nociti
Multiple sclerosis (MS) is a chronic demyelinating central nervous system (CNS) disease that involve oligodendrocyte loss and failure to remyelinate damaged brain areas causing a progressive neurological disability. Studies in MS mouse model suggest that cannabinoids ameliorate symptoms as spasticity, tremor and pain reducing inflammation via cannabinoid-mediated system. The aim of our study is to investigate the changes in cannabinoid type 1 (CNR1) and 2 (CNR2) receptors mRNA expression levels and promoter methylation in peripheral blood mononuclear cells (PBMCs) of MS secondary progressive (MSS-SP) patients treated with Sativex®...
August 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28713835/rapid-detection-of-the-mt3243a%C3%A2-%C3%A2-g-mutation-using-urine-sediment-in-elderly-chinese-type-2-diabetic-patients
#10
Yinan Zhang, Xiujuan Du, Xinqian Geng, Chen Chu, Huijuan Lu, Yixie Shen, Ruihua Chen, Pingyan Fang, Yanmei Feng, Xiaojie Zhang, Yan Chen, Yanping Zhou, Congrong Wang, Weiping Jia
OBJECTIVE: In this study, we aimed to identify mt3243A > G mutation carriers in a group of Chinese elderly type 2 diabetic patients by a rapid and noninvasive diagnostic system. METHODS: DNA was extracted from blood, saliva, and urine sediment samples. The mutation screening and quantitation of heteroplasmy were performed by high-resolution melting (HRM) curve and pyrosequencing, respectively. Patients with mt3243A > G mutation underwent a detailed audiometric, ophthalmologic, neurological, and cardiac examination...
2017: Journal of Diabetes Research
https://www.readbyqxmd.com/read/28713779/ifitm3-rs12252-c-variant-increases-potential-risk-for-severe-influenza-virus-infection-in-chinese-population
#11
Yang Pan, Peng Yang, Tao Dong, Yi Zhang, Weixian Shi, Xiaomin Peng, Shujuan Cui, Daitao Zhang, Guilan Lu, Yimeng Liu, Shuangsheng Wu, Quanyi Wang
Background: Interferon Inducible Transmembrane 3 (IFITM3) is a key factor in interferon pathway and it involves host's immune response against multiple viruses. IFITM3 rs12252-C was associated with severe influenza virus infection in several studies, however whether this association is universal to all types of influenza virus or diverse ethnic populations remain controversial. Method: A case-control genetic association study was performed from September 2013 to April 2014 and September 2014 to April 2015. All samples were tested for influenza using RT-PCR, and genotyped by High Resolution Melting assay...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28711990/assessment-of-braf-v600e-mutation-in-pulmonary-langerhans-cell-histiocytosis-in-tissue-biopsies-and-bronchoalveolar-lavages-by-droplet-digital-polymerase-chain-reaction
#12
Clémence Pierry, Charline Caumont, Elodie Blanchard, Camille Brochet, Gael Dournes, Audrey Gros, Thomas Bandres, Séverine Verdon, Marion Marty, Hugues Bégueret, Jean-Philippe Merlio
The neoplastic nature of pulmonary Langerhans cell histiocytosis (PLCH) is still debated. As the detection of BRAF (V600E) and MAP2K1 mutations in patients with PCLH is now considered for such assessment, the aim of our study was to evaluate digital droplet polymerase chain reaction (ddPCR) in PCLH diagnosis. We retrospectively analyzed BRAF(V600E) detection in a cohort of 42 PCLH tissues and 18 bronchoalveolar lavages (BALs) by ddPCR, immunohistochemistry, high-resolution melting PCR (HRM), and next-generation sequencing (NGS)...
July 15, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28710029/decreased-expression-level-of-ber-genes-in-alzheimer-s-disease-patients-is-not-derivative-of-their-dna-methylation-status
#13
Agnieszka Sliwinska, Przemysław Sitarek, Monika Toma, Piotr Czarny, Ewelina Synowiec, Renata Krupa, Paulina Wigner, Katarzyna Bialek, Dominik Kwiatkowski, Anna Korycinska, Ireneusz Majsterek, Janusz Szemraj, Piotr Galecki, Tomasz Sliwinski
BACKGROUND: Neurodegeneration in Alzheimer's disease can be caused by accumulation of oxidative DNA damage resulting from altered expression of genes involved in the base excision repair system (BER). Promoter methylation can affect the profile of BER genes expression. Decreased expression of BER genes was observed in the brains of AD patients. AIM OF THE STUDY: The aim of our study was to compare the expression and methylation profiles of six genes coding for proteins involved in BER, namely: hOGG1, APE1, MUTYH, NEIL1, PARP1 and XRCC1, in the peripheral blood cells of AD patients and healthy volunteers...
July 11, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28705265/comparison-of-histological-microbiological-and-molecular-methods-in-diagnosis-of-patients-with-tbln-having-different-anti-tb-treatment-background
#14
Nan Ying Che, Shao Jun Huang, Yan Ma, Yi Han, Zi Chen Liu, Chen Zhang, Jing Mu, Dan Zhao, Yang Qu, Hai Qing Zhang, Zhi Dong Liu, Shao Fa Xu
OBJECTIVE: The influence of anti-tuberculosis (TB) treatment history on tuberculous lymphadenitis (TBLN) diagnosis is unclear. Therefore, this study aims to evaluate the diagnostic methods, including histology, microbiology, and molecular tests, used for TBLN. METHODS: In this study, suspected patients with TBLN and having different anti-TB treatment background were enrolled. All the samples were tested simultaneously by histology, Ziehl-Neelsen (ZN) staining, mycobacterial culture (culture), Xpert MTB/RIF (xpert), real-time PCR, and high-resolution melting curve PCR (HRM)...
June 2017: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/28694212/role-of-rs13117307-single-nuclear-polymorphism-in-the-risk-of-uterine-cervical-cancer-from-polish-population-and-its-impact-on-exocyst-complex-component-1-expression
#15
Sebastian Łaźniak, Andrzej Roszak, Adam Balcerek, Żaneta Wareńczak-Florczk, Edyta Prokop, Anna Sowińska, Emianka Sotiri, Alexander Tsibulski, Stefan Sajdak, Pawel P Jagodziński
We evaluated the role of NM_001024924.1:c.1330+1646C>T (rs13117307) single nucleotide polymorphism (SNP), situated in the intronic region of exocyst complex component 1 (EXCO1), in the development and spreading of cervical squamous cell carcinoma (SCC). Utilizing high resolution melting curve analysis, we analyzed this polymorphism in patients with cervical SCC (n=485) and controls (n=509) in the Polish Caucasian population. Logistic regression analysis was used to adjust for age, parity, oral contraceptive use, tobacco smoking, and menopausal status...
July 7, 2017: Gene
https://www.readbyqxmd.com/read/28693442/evaluation-of-the-relationship-between-marco-and-cd36-single-nucleotide-polymorphisms-and-susceptibility-to-pulmonary-tuberculosis-in-a-chinese-han-population
#16
Wenting Lao, Hui Kang, Guojiang Jin, Li Chen, Yang Chu, Jiao Sun, Bingqi Sun
BACKGROUND: Gene polymorphisms impact greatly on a person's susceptibility to pulmonary tuberculosis (PTB). Macrophage receptor with collagenous structure (MARCO) and CD36 are two scavenger receptors (SRs) that can recognize Mycobacterium tuberculosis (Mtb) and play a key role in tuberculosis infection. Gene polymorphisms of MARCO and CD36 may contribute to tuberculosis risk. METHODS: To investigate whether genetic polymorphisms of MARCO and CD36 are associated with susceptibility to PTB, genomic DNA samples from patients (n = 202) and healthy controls (n = 216) were collected and analyzed by polymerase chain reaction with high-resolution melting analysis...
July 11, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28693231/impact-of-rassf1a-gene-methylation-on-the-metastatic-axillary-nodal-status-in-breast-cancer-patients
#17
Eva Jezkova, Pavol Zubor, Karol Kajo, Marian Grendar, Karol Dokus, Marian Adamkov, Zora Lasabova, Lukas Plank, Jan Danko
Hypermethylation of CpG islands is a hallmark of cancer and occurs at an early stage in breast tumorigenesis. To gain insight into the epigenetic switches that may promote and/or contribute to the initial neoplastic events during breast carcinogenesis, the present study focused on the DNA methylation profile of invasive breast carcinoma. The aim of the study was to evaluate the prognostic significance of Ras association domain family 1 isoform A (RASSF1A) promoter methylation status in operable breast cancer, and to analyze the utility of this biomarker regarding its association with metastatic and nonmetastatic axillary nodal status...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28684733/detection-of-egfr-mutation-in-plasma-using-multiplex-allele-specific-pcr-mas-pcr-and-surface-enhanced-raman-spectroscopy
#18
Xiaozhou Li, Tianyue Yang, Caesar Siqi Li, Deli Wang, Youtao Song, Lili Jin
In this study, surface enhanced Raman spectroscopy (SERS) in combination with multiplexed polymerase chain reaction (PCR) was utilized to detect mutations of exons 19 and 21 of the epidermal growth factor receptor (EGFR) gene. Through the use of multiplexed PCR, the two mutation types were amplified in a single reaction. SERS was used on the PCR products to detect mutations. DNA mixtures with increasing mutation percentages showed good linear relationship between mutation rates and peak height. Then, this PCR-SERS method was used on the plasma of 48 patients with non-small cell lung cancer (NSCLC) to detect EGFR mutations...
July 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28682466/anomeric-2-deoxycytidines-and-silver-ions-hybrid-base-pairs-with-greatly-enhanced-stability-and-efficient-dna-mismatch-detection-with-%C3%AE-dc
#19
Frank Seela, Xiurong Guo
α-D-Nucleosides are rare in nature but can develop fascinating properties when incorporated in DNA. This work reports on the first silver mediated base pair constructed from two anomeric nucleosides: α-dC and β-dC. The hybrid base pair was integrated in DNA and DNA/RNA double helix. A 12-mer duplex with α-dC and β-dC pair exhibits a greatly higher thermal stability (Tm = 43°C) than that incorporating the β-dC-Ag+-β-dC homo pair (Tm = 34°C). Furthermore: α-dC shows excellent mismatch discrimination for DNA single nucleotide polymorphism (SNP)...
July 6, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28680808/sequence-motifs-capable-of-forming-dna-stem-loop-structures-act-as-a-replication-diode
#20
Andrey Shirak, Uri Seroussi, Elisha Gootwine, Eyal Seroussi
Calculating peak-height ratios between single-nucleotide polymorphisms (SNP) alleles in sequencing chromatograms is a practical method for estimating their copy number proportions (CNPs). However, it is surprising that sequencing DNA from different directions might yield different results. We analyzed three adjacent SNPs within the ovine period circadian-clock 2 (PER2) gene that displayed such behavior. We compared Sanger and DNA-seq sequencing for this locus and applied high-resolution melt and MFOLD analyses to point to the DNA secondary structure that underlined this phenomenon...
July 2017: FEBS Open Bio
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