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https://www.readbyqxmd.com/read/27903892/methylation-sensitive-enrichment-of-minor-dna-alleles-using-a-double-strand-dna-specific-nuclease
#1
Yibin Liu, Chen Song, Ioannis Ladas, Mariana Fitarelli-Kiehl, G Mike Makrigiorgos
Aberrant methylation changes, often present in a minor allelic fraction in clinical samples such as plasma-circulating DNA (cfDNA), are potentially powerful prognostic and predictive biomarkers in human disease including cancer. We report on a novel, highly-multiplexed approach to facilitate analysis of clinically useful methylation changes in minor DNA populations. Methylation Specific Nuclease-assisted Minor-allele Enrichment (MS-NaME) employs a double-strand-specific DNA nuclease (DSN) to remove excess DNA with normal methylation patterns...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27901015/laser-induced-phase-separation-of-silicon-carbide
#2
Insung Choi, Hu Young Jeong, Hyeyoung Shin, Gyeongwon Kang, Myunghwan Byun, Hyungjun Kim, Adrian M Chitu, James S Im, Rodney S Ruoff, Sung-Yool Choi, Keon Jae Lee
Understanding the phase separation mechanism of solid-state binary compounds induced by laser-material interaction is a challenge because of the complexity of the compound materials and short processing times. Here we present xenon chloride excimer laser-induced melt-mediated phase separation and surface reconstruction of single-crystal silicon carbide and study this process by high-resolution transmission electron microscopy and a time-resolved reflectance method. A single-pulse laser irradiation triggers melting of the silicon carbide surface, resulting in a phase separation into a disordered carbon layer with partially graphitic domains (∼2...
November 30, 2016: Nature Communications
https://www.readbyqxmd.com/read/27896842/il-12b-gene-polymorphisms-and-il-12-p70-serum-levels-among-patients-with-rheumatoid-arthritis
#3
A Paradowska-Gorycka, A Sowinska, B Stypińska, E Haladyj, A Pawlik, K Romanowska-Próchnicka, M Olesinska
OBJECTIVES: Rheumatoid arthritis (RA) is one of the autoimmune diseases, where different polymorphisms in cytokine genes play a pathogenic role. IL-12 is now recognized as a critical cytokine in terms of regulating the balance between Th1 and Th2 cells. We investigated the role of single-nucleotide polymorphisms (SNPs) (rs3212227 (A/C) and rs17860508 (CTCTAA/GC)) of the IL-12B gene in the genetic susceptibility to RA and in the severity of the disease. METHODS: Six hundred and thirty four Caucasian RA patients and 341 healthy matched controls were studied using PCR-RFLP method and High-resolution melting analysis...
November 29, 2016: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/27895633/detection-of-sdhb-gene-mutations-in-sdhi-resistant-isolates-of-botrytis-cinerea-using-high-resolution-melting-hrm-analysis
#4
Anastasios Samaras, Panagiotis Madesis, George S Karaoglanidis
Botrytis cinerea, is a high risk pathogen for fungicide resistance development. Pathogen' resistance to SDHIs is associated with several mutations in sdh gene. The diversity of mutations and their differential effect on cross-resistance patterns among SDHIs and the fitness of resistant strains necessitate the availability of a tool for their rapid identification. This study was initiated to develop and validate a high-resolution melting (HRM) analysis for the identification of P225H/F/L//T, N230I, and H272L/R/Y mutations...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27895046/gene-silencing-of-nox4-by-cpg-island-methylation-during-hepatocarcinogenesis-in-rats
#5
Guadalupe S López-Álvarez, Tomasz K Wojdacz, Claudia M García-Cuellar, Hugo C Monroy-Ramírez, Miguel A Rodríguez Segura, Ruth A Pacheco Rivera, Carlos A Valencia-Antúnez, Nancy C Cervantes-Anaya, Ernesto Soto-Reyes, Verónica R Vázquez-Garzón, Yesennia Sánchez-Pérez, Saúl Villa Treviño
The association between the downregulation of genes and DNA methylation in their CpG islands has been extensively studied as a mechanism that favors carcinogenesis. The objective of this study was to analyze the methylation of a set of genes selected based on their microarray expression profiles during the process of hepatocarcinogenesis. Rats were sacrificed at: 24 Hours, 7, 11, 16 and 30 days and 5, 9, 12 and 18 months post-treatment. We evaluated the methylation status in the CpG islands of four deregulated genes (Casp3, Cldn1, Pex11a and Nox4) using methylation-sensitive high-resolution melting technology for the samples obtained from different stages of hepatocarcinogenesis...
November 28, 2016: Biology Open
https://www.readbyqxmd.com/read/27888475/assessing-contamination-of-microalgal-astaxanthin-producer-haematococcus-cultures-with-high-resolution-melting-curve-analysis
#6
Adam Dawidziuk, Delfina Popiel, Magda Luboinska, Michal Grzebyk, Maciej Wisniewski, Grzegorz Koczyk
Due to its superior antioxidant capabilities and higher activity than other carotenoids, astaxanthin is used widely in the nutraceutical and medicine industries. The most prolific natural producer of astaxanthin is the unicellular green microalga Haematococcus pluvialis. The correct identification of any contaminants in H. pluvialis cultures is both essential and nontrivial for several reasons. Firstly, while it is possible to distinguish the main microalgal contaminant Coelastrella sp. (in H. pluvialis cultures), in practice, it is frequently a daunting and error-prone task for personnel without extensive experience in the microscopic identification of algal species...
November 26, 2016: Journal of Applied Genetics
https://www.readbyqxmd.com/read/27885689/pathogenesis-and-diagnosis-of-placental-disorders-is-related-to-abnormal-methylation-at-promoters-of-placental-vascularization-mediating-genes
#7
Beenish Rahat, Rauf Ahmad Najar, Abid Hamid, Rashmi Bagga, Jyotdeep Kaur
OBJECTIVES: To investigate the role of methylation levels at promoter regions of placental vascularization genes (VEGF, EGFR and c-jun) in pathogenesis and diagnosis of placental disorders. METHODS: We analyzed DNA and histone methylation at promoters of VEGF, EGFR and c-jun via methylation-sensitive high resolution melting and chromatin immunoprecipitation assay in pregnant women with normal pregnancy in first, second and third trimester (n = 30 in each group) and pregnant women with pregnancy complicated with preeclampsia (n = 30) and hydatidiform mole (n = 15)...
November 24, 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27871826/eroded-tape-the-case-for-an-early-vesicoscopy-rather-than-laser-melting
#8
Philippe Grange, Chryssanthos Kouriefs, Fanourios Georgiades, Stavros Charalambous, Dudley Robinson, Linda Cardozo
OBJECTIVE: To report our experience on vesicoscopic excision of eroded foreign material in the bladder. MATERIALS AND METHODS: The use of xenografts in female urology is becoming more prevalent and so are their complications. Erosion of foreign material into the bladder often goes unrecognized for a long time and patients are troubled by irritative urinary symptoms, recurrent infections and stone formation. The treatment of such erosions is traditionally reported through the transurethral route using LASER or electrocautery to cut the foreign material...
November 18, 2016: Urology
https://www.readbyqxmd.com/read/27864917/genetic-variation-in-the-mir-708-gene-and-its-binding-targets-in-bipolar-disorder
#9
Alessia Fiorentino, Niamh Louise O'Brien, Sally Isabel Sharp, David Curtis, Nicholas James Bass, Andrew McQuillin
OBJECTIVE: rs12576775 was found to be associated with bipolar disorder (BD) in a genome-wide association study (GWAS). The GWAS signal implicates genes for the microRNAs miR-708 and miR-5579 and the first exon of the Odd Oz/ten-m homolog 4 gene (ODZ4). In the present study, miR-708, its surrounding region, and its targets were analyzed for potential BD-associated functional variants. METHODS: The miR-708 gene and surrounding regions were screened for variation using high-resolution melting (HRM) analysis in 1099 cases of BD, followed by genotyping of rare variants in an enlarged sample of 2078 subjects with BD, 1303 subjects with schizophrenia, and 1355 healthy controls...
November 16, 2016: Bipolar Disorders
https://www.readbyqxmd.com/read/27856299/als-and-ftd-linked-ggggcc-repeat-containing-dna-oligonucleotide-folds-into-two-distinct-g-quadruplexes
#10
Jasna Brčić, Janez Plavec
BACKGROUND: The most common genetic cause of neurological disorders ALS and FTD is a largely increased number of GGGGCC repeats in C9orf72 gene. Non-canonical structures including G-quadruplexes adopted by expanded repeats are hypothesized to be crucial in pathogenesis. Recently, we have shown that structural polymorphism of oligonucleotide d(G4C2)3G4 is reduced by dG to 8Br-dG substitution. High-resolution structure of one of the two major G-quadruplexes adopts antiparallel topology comprising of four G-quartets...
November 14, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27855276/detection-of-calr-and-mpl-mutations-in-low-allelic-burden-jak2-v617f-essential-thrombocythemia
#11
Fabrice Usseglio, Nathalie Beaufils, Anne Calleja, Sophie Raynaud, Jean Gabert
Myeloproliferative neoplasms are clonal hematopoietic stem cell disorders characterized by aberrant proliferation and an increased tendency toward leukemic transformation. The genes JAK2, MPL, and CALR are frequently altered in these syndromes, and their mutations are often a strong argument for diagnosis. We analyzed the mutational profiles of these three genes in a cohort of 164 suspected myeloproliferative neoplasms. JAK2 V617F mutation was detected by real-time PCR, whereas high-resolution melting analysis followed by Sanger sequencing were used for searching for mutations in JAK2 exon 12, CALR, and MPL...
November 14, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27846723/-novel-approaches-in-dna-methylation-studies-ms-hrm-analysis-and-electrochemistry
#12
M Bartošík, E Ondroušková
Cytosine methylation in DNA is an epigenetic mechanism regulating gene expression and plays a vital role in cell differentiation or proliferation. Tumor cells often exhibit aberrant DNA methylation, e.g. hypermethylation of tumor suppressor gene promoters. New methods, capable of determining methylation status of specific DNA sequences, are thus being developed. Among them, MS-HRM (methylation-specific high resolution melting) and electrochemistry offer relatively inexpensive instrumentation, fast assay times and possibility of screening multiple samples/DNA regions simultaneously...
2016: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/27837117/high-resolution-melting-hrm-analysis-as-a-new-tool-for-rapid-identification-of-salmonella-enterica-serovar-gallinarum-biovars-pullorum-and-gallinarum
#13
Xingxing Ren, Ying Fu, Chenggang Xu, Zhou Feng, Miao Li, Lina Zhang, Jianmin Zhang, Ming Liao
Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum represent the most common causative agents of chicken salmonellosis, which result in high mortality and morbidity throughout the world. It is difficult and laborious to discriminate these diseases based on biochemical or phenotypic methods. Herein, we report the development of a single nucleotide polymorphism (SNP) PCR-high resolution melt (PCR-HRM) assay for the detection and discrimination of both S Pullorum and S Gallinarun. The gene rfbS, which encodes a factor involved in the biosynthesis of ADP paratose in serogroup D of Salmonella, has been identified as a robust genetic marker for the identification of S Pullorum and S Gallinarun based on polymorphisms at positions 237 and 598...
November 11, 2016: Poultry Science
https://www.readbyqxmd.com/read/27834463/gene-expression-profile-of-renal-cell-carcinomas-after-neoadjuvant-treatment-with-sunitinib-new-pathways-revealed
#14
Carlos Dzik, Sabrina T Reis, Nayara I Viana, Glauber Brito, Isis Paloppi, Willian Nahas, Miguel Srougi, Katia R M Leite
BACKGROUND: In renal cell carcinoma (RCC) of the clear cell type, inactivity of the VHL gene induces overexpression of HIF1 α and its targets, the tyrosine kinase receptors, promoting RCC development and progression. The discovery of tyrosine kinase inhibitors (TKIs) changed the treatment of these tumors. Other molecular pathways involved in the TKI mechanisms of action have not been described in the literature. The aim of our study was to elucidate alternative mechanisms of action of sunitinib in tumor tissue after neoadjuvant treatment of RCC...
November 1, 2016: International Journal of Biological Markers
https://www.readbyqxmd.com/read/27833775/assessment-for-melting-temperature-measurement-of-nucleic-acid-by-hrm
#15
Jing Wang, Xiaoming Pan, Xingguo Liang
High resolution melting (HRM), with a high sensitivity to distinguish the nucleic acid species with small variations, has been widely applied in the mutation scanning, methylation analysis, and genotyping. For the aim of extending HRM for the evaluation of thermal stability of nucleic acid secondary structures on sequence dependence, we investigated effects of the dye of EvaGreen, metal ions, and impurities (such as dNTPs) on melting temperature (Tm ) measurement by HRM. The accuracy of HRM was assessed as compared with UV melting method, and little difference between the two methods was found when the DNA Tm was higher than 40°C...
2016: Journal of Analytical Methods in Chemistry
https://www.readbyqxmd.com/read/27822854/genotyping-dna-variants-with-high-resolution-melting-analysis
#16
Rolf H A M Vossen
High-resolution melting analysis (HRMA) is a simple, quick, and effective method to scan and screen PCR amplicons for sequence variants. HRMA is a nondestructive closed tube assay; after PCR, DNA melting can directly be performed on the amplified samples without any purification or separation steps. For single SNP genotyping, HRMA is an attractive alternative to Sanger sequencing, restriction enzyme analysis, and hydrolysis probes.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27820652/development-of-coding-single-nucleotide-polymorphic-markers-in-the-pearl-oyster-pinctada-fucata-based-on-next-generation-sequencing-and-high-resolution-melting-analysis
#17
S G Fan, J F Wei, Y H Guo, G J Huang, D H Yu
The pearl oyster Pinctada fucata is an important commercial marine shellfish that is cultured for producing saltwater pearls. In this study, 468 single nucleotide polymorphisms (SNPs) were screened from P. fucata transcriptome data, and 119 polymorphic SNPs were successfully isolated by a two-step small-amplicon high-resolution melting assay. Of these, 88 were annotated with BLAST in the Nr database and 90 were in the open reading frame, including 16 non-synonymous SNPs and 74 synonymous SNPs; 12 SNPs were in the 3'-untranslated region (UTR) and 1 was in the 5'-UTR...
November 3, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27817772/-an-epidemiological-study-on-human-rhinovirus-c-in-hospitalized-children-with-respiratory-tract-infections
#18
Li Li, Wei Ji, Xue-Jun Shao, Jun Xu, Wu-Jun Jiang, Zheng-Rong Chen, Yong-Dong Yan
OBJECTIVE: To investigate the detection rates, epidemical characteristics, and clinical features of human rhinovirus C (HRV-C) in hospitalized children with respiratory tract infections (RTIs) in Suzhou, China. METHODS: A total of 1 702 hospitalized children with RTIs from January to December, 2014 were enrolled, and 1 702 nasopharyngeal aspirate samples were collected from all children. RT-PCR was used to measure HRV mRNA, and quantitative real-time PCR combined with high-resolution melting curve was used to measure HRV-C...
November 2016: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/27808161/structural-basis-of-the-high-thermal-stability-of-the-histone-like-hu-protein-from-the-mollicute-spiroplasma-melliferum-kc3
#19
Konstantin M Boyko, Tatiana V Rakitina, Dmitry A Korzhenevskiy, Anna V Vlaskina, Yuliya K Agapova, Dmitry E Kamashev, Sergey Y Kleymenov, Vladimir O Popov
The three-dimensional structure of the histone-like HU protein from the mycoplasma Spiroplasma melliferum KC3 (HUSpm) was determined at 1.4 Å resolution, and the thermal stability of the protein was evaluated by differential scanning calorimetry. A detailed analysis revealed that the three-dimensional structure of the HUSpm dimer is similar to that of its bacterial homologues but is characterized by stronger hydrophobic interactions at the dimer interface. This HUSpm dimer interface lacks salt bridges but is stabilized by a larger number of hydrogen bonds...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27802263/seismic-evidence-for-a-cold-serpentinized-mantle-wedge-beneath-mount-st-helens
#20
S M Hansen, B Schmandt, A Levander, E Kiser, J E Vidale, G A Abers, K C Creager
Mount St Helens is the most active volcano within the Cascade arc; however, its location is unusual because it lies 50 km west of the main axis of arc volcanism. Subduction zone thermal models indicate that the down-going slab is decoupled from the overriding mantle wedge beneath the forearc, resulting in a cold mantle wedge that is unlikely to generate melt. Consequently, the forearc location of Mount St Helens raises questions regarding the extent of the cold mantle wedge and the source region of melts that are responsible for volcanism...
November 1, 2016: Nature Communications
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