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Littérature scientifique sur le sujet « High resolution melting analysi »

Auteur : Grafiati
Publié le 10 mars 2023

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Articles de revues sur le sujet "High resolution melting analysi"

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Carillo, Serge, Laurent Henry, Eric Lippert, François Girodon, Isabelle Guiraud, Céline Richard, Frédérique Dubois Galopin et al. « Nested High-Resolution Melting Curve Analysis ». Journal of Molecular Diagnostics 13, no 3 (mai 2011) : 263–70. http://dx.doi.org/10.1016/j.jmoldx.2010.12.002.

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Ro, Na Young, On Sook Hur, Ho Cheol Ko, Sang Gyu Kim, Ju Hee Rhee, Jae-Gyun Gwag, Jin-Kyung Kwon et Byoung-Cheorl Kang. « Evaluation of Resistance in Pepper Germplasm to Cucumber mosaic virus by High Resolution Melting Analysis ». Research in Plant Disease 18, no 4 (30 décembre 2012) : 290–97. http://dx.doi.org/10.5423/rpd.2012.18.4.290.

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Zambounis, Antonios, Eleni Stefanidou, Panagiotis Madesis, Jovana Hrustić, Milica Mihajlović et Brankica Tanović. « Genotypic differentiation of Monilinia spp. populations in Serbia using a high-resolution melting (HRM) analysis ». Plant Protection Science 57, No. 1 (3 décembre 2020) : 38–46. http://dx.doi.org/10.17221/35/2020-pps.

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Monilinia laxa, Monilinia fructicola and Monilinia fructigena are the three main causal agents of brown rot, which is one of the most important diseases of stone fruits in pre- and postharvest conditions. Nowadays, the need for the precise genotyping of these Monilinia species in terms of the genetic diversity of their populations or differences in their pathogenicity and host range is a prerequisite for any efficient disease management. In our study, the genetic structure of Monilinia populations in Serbia from three geographically distinct regions was investigated employing <br /> a high-resolution melting (HRM) analysis which is a sensitive and rapid molecular approach in fungal ge­notyping and diagnostics. Using species-specific primer pairs genotype-specific HRM melting curve profiles were generated allowing to efficiently decipher the genetic diversity of the Monilinia populations. The Monilinia genotypes could be easily distinguished according to their melting curves. The isolates from the northern region were assigned to distinct genotypes and grouped rather independently compared to the isolates of the other two regions among all three tested Monilinia spp. M. fructicola and M. fructigena showed a higher genetic diversity among their populations (44%) compared with the genetic diversity among the M. laxa populations (7%). In contrast, the genetic variance within the pathogen populations was higher in the case of M. laxa (93%). Our data revealed an absence of host specificity in the Monilinia spp. populations.
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Erali, Maria, et Carl T. Wittwer. « High resolution melting analysis for gene scanning ». Methods 50, no 4 (avril 2010) : 250–61. http://dx.doi.org/10.1016/j.ymeth.2010.01.013.

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Tong, S. Y. C., et P. M. Giffard. « Microbiological Applications of High-Resolution Melting Analysis ». Journal of Clinical Microbiology 50, no 11 (8 août 2012) : 3418–21. http://dx.doi.org/10.1128/jcm.01709-12.

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Zumaraga, Mark Pretzel, Marietta Rodriguez, Vanessa Joy Timoteo et Celeste Tanchoco. « Method Validation of a High Resolution Melting Analysis of a Candidate Genetic Marker of Hypertension ». Journal of the ASEAN Federation of Endocrine Societies 30, no 1 (31 mai 2015) : 18–24. http://dx.doi.org/10.15605/jafes.030.01.01.

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Wittwer, Carl T., Gudrun H. Reed, Cameron N. Gundry, Joshua G. Vandersteen et Robert J. Pryor. « High-Resolution Genotyping by Amplicon Melting Analysis Using LCGreen ». Clinical Chemistry 49, no 6 (1 juin 2003) : 853–60. http://dx.doi.org/10.1373/49.6.853.

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Abstract Background: High-resolution amplicon melting analysis was recently introduced as a closed-tube method for genotyping and mutation scanning (Gundry et al. Clin Chem 2003;49:396–406). The technique required a fluorescently labeled primer and was limited to the detection of mutations residing in the melting domain of the labeled primer. Our aim was to develop a closed-tube system for genotyping and mutation scanning that did not require labeled oligonucleotides. Methods: We studied polymorphisms in the hydroxytryptamine receptor 2A (HTR2A) gene (T102C), β-globin (hemoglobins S and C) gene, and cystic fibrosis (F508del, F508C, I507del) gene. PCR was performed in the presence of the double-stranded DNA dye LCGreen, and high-resolution amplicon melting curves were obtained. After fluorescence normalization, temperature adjustment, and/or difference analysis, sequence alterations were distinguished by curve shape and/or position. Heterozygous DNA was identified by the low-temperature melting of heteroduplexes not observed with other dyes commonly used in real-time PCR. Results: The six common β-globin genotypes (AA, AS, AC, SS, CC, and SC) were all distinguished in a 110-bp amplicon. The HTR2A single-nucleotide polymorphism was genotyped in a 544-bp fragment that split into two melting domains. Because melting curve acquisition required only 1–2 min, amplification and analysis were achieved in 10–20 min with rapid cycling conditions. Conclusions: High-resolution melting analysis of PCR products amplified in the presence of LCGreen can identify both heterozygous and homozygous sequence variants. The technique requires only the usual unlabeled primers and a generic double-stranded DNA dye added before PCR for amplicon genotyping, and is a promising method for mutation screening.
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Antonios, Zambounis, Samaras Anastasios, Xanthopoulou Aliki, Osathanunkul Maslin, Schena Leonardo, Tsaftaris Athanasios et Madesis Panagiotis. « Identification of Phytophthora species by a high resolution melting analysis : an innovative tool for rapid differentiation ». Plant Protection Science 52, No. 3 (26 mai 2016) : 176–81. http://dx.doi.org/10.17221/179/2015-pps.

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Simko, Ivan. « High-Resolution DNA Melting Analysis in Plant Research ». Trends in Plant Science 21, no 6 (juin 2016) : 528–37. http://dx.doi.org/10.1016/j.tplants.2016.01.004.

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Mader, Eduard, Joana Ruzicka, Corinna Schmiderer et Johannes Novak. « Quantitative high-resolution melting analysis for detecting adulterations ». Analytical Biochemistry 409, no 1 (février 2011) : 153–55. http://dx.doi.org/10.1016/j.ab.2010.10.009.

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Thèses sur le sujet "High resolution melting analysi"

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Dempsey, Nunez Laura. « Spectrum of mutations in MMAA identified by high resolution melting analysis ». Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=110535.

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The gene product of MMAA is required for the intracellular metabolism of cobalamin (Cbl). Mutations in this gene lead to the cblA class of disorders, characterized by isolated methylmalonic aciduria. We have been concerned that somatic cell methods of diagnosis may miss patients with mild cellular phenotypes. A high resolution melting (HRM) analysis assay was developed to rapidly scan the coding exons and flanking intronic regions of the MMAA genes for variants. DNA from 96 unaffected reference individuals, 72 patients with complementation confirmed cblA, and 181 patients with elevated isolated methylmalonic acid, who could not be diagnosed using complementation analysis, were scanned by HRM. Suspected variants were confirmed using Sanger sequencing. In the cblA cohort, HRM correctly identified all previously known mutations as well as an additional 22 variants, 10 of which had not been previously reported. Novel variants included one duplication (C.551dupG, p.C187LfsX3), one deletion (c.387delC, p.Y129YfsX13), one splice site mutation (c.440-2A>G, splice site), 4 missense mutations (c.748G>A, p.E520K; c.820G>A, p.G274S; c.627G>T, p.R209S; c.826A>G, p.K276E), and 3 nonsense mutations (c.960G>A, p.W320X; c.1075C>T, p.E359X; c.1084C>T, p.Q362X). All novel missense variants, listed above, affect highly conserved residues and are predicted to be damaging. Scanning of MMAA in the 181 undiagnosed samples revealed a single novel heterozygous missense change (c.821G>A, p.G274D).
Le produit génique du MMAA est nécessaire pour le métabolisme de la cobalamine intracellulaire (Cbl). Des mutations dans ce gène conduisent à la classe de maladies cblA, caractérisé par l'acidurie méthylmalonique isolée. Nous avons été concernés que les méthodes de diagnostic de cellules somatiques peuvent manquer les patients atteints phénotypes cellulaires moins sévère. Une teste de fusion à haute résolution a été développé pour balayer rapidement les exons codantes et les régions introniques adjacentes du gène MMAA pour des variantes. Nous avons testé l'ADN à partir de 96 personnes de référence qui ne sont pas touchés, 72 patients atteints de cblA confirmé par complémentation et 181 patients présentant une élévation de l'acide méthylmalonique isolée, qui ne pouvaient pas être diagnostiquée à l'aide d'analyse de complémentation. Les variantes suspectes ont été confirmées à l'aide de séquençage Sanger. Dans la cohorte cblA, l'analyse de fusion à haute résolution a correctement identifié toutes les mutations connues antérieurement, ainsi que 22 autres variantes, dont 10 n'avaient pas été signalés précédemment. Nouveaux variantes inclus une duplication (C.551dupG, p.C187LfsX3), une délétion (c.387delC, p.Y129YfsX13), une mutation du site d'épissage (c.440-2A> G, site d'épissage), 4 mutations faux-sens (c. 748G> A, p.E520K; c.820G> A, p.G274S; c.627G> T, p.R209S; c.826A> G, p.K276E), et 3 mutations non-sens (c.960G> A, p.W320X; c.1075C> T, p.E359X; c.1084C> T, p.Q362X). Toutes les variantes faux-sens nouveaux, énumérés ci-dessus, affectent des résidus hautement conservés et sont prévus pour être endommageant. L'analyse de MMAA dans les 181 échantillons non diagnostiqués a révélé un seul changement faux-sens hétérozygote (c.821G> A, p.G274D).
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Illson, Margaret. « Spectrum of mutations in MMAB identified by high resolution melting analysis ». Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=110564.

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Pathogenic variants in the MMAB gene (OMIM 607958) are responsible for the cblB class of cobalamin-responsive methylmalonic aciduria (MMA) (OMIM 251110). MMAB encodes cobalamin adenosyltransferase, a mitochondrial enzyme responsible for the formation of adenosylcobalamin (AdoCbl). AdoCbl subsequently functions as a cofactor for methylmalonyl-CoA mutase (MCM) during the isomerization of L-methylmalonyl-CoA to succinyl-CoA. Somatic cells studies have been used to evaluate patient samples for cobalamin related disorders. Due to high basal levels of propionate incorporation, some patients with mild MMA biochemical phenotypes cannot be diagnosed by complementation analysis. A high resolution melting analysis (HRMA) assay was developed to rapidly scan the coding exons and flanking intronic regions for variants in the MMAB gene.Three cohorts of samples were scanned by HRMA: an unaffected reference population, 42 samples assigned to the cblB by complementation analysis and 181 patients with unresolved isolated MMA. HRMA correctly identified all of the previously reported mutations in the cblB cohort as well as seven additional variants including a novel nonsense variant (c.12C>A, p.C4X). Scanning of the unresolved MMA cohort identified six samples containing MMAB variants. Two samples, WG3948 and WG4034, contained compound heterozygous variants. They shared a c.572 G>A (p.R191Q) mutation. WG3948, the index case for this study, was found to have c.398 C>T (p.S133F) as the second mutation, and WG4034, the second patient, contained a novel variant c.394 C>T (p.C132R). Samples from four other affected patients contained a single variant. The c.572 G>A (p. R191Q) was found in both WG3546 and WG4090. WG3759 contained a c.521C>T ( p.S174L) substitution, and WG4029 contained a novel c.185 C>T (p.T62M) substitution. The identification of two patients with compound heterozygous variants in the MMAB gene suggests the existence of an infrequent but distinct atypical cblB phenotype. This subclass is characterized by levels of propionate incorporation and of AdoCbl synthesis within reference ranges, preventing diagnosis by somatic cell studies.
Des variantes pathogéniques dans le gène MMAB (OMIM 607958) sont responsables de la classe cblB d'acidurie méthylmalonique (AMM) respondant à la cobalamine (OMIM 251110). MMAB encode cobalamine adénosyltranférase, une enzyme mitochondriale responsable de la formation de l'adénosylcobalamine (AdoCbl). AdoCbl fonctionne par la suite en tant que cofacteur pour méthylmalonyl-CoA mutase (MCM) durant l'isomérisation de L-méthylmalonyl-CoA vers succinyl-CoA. Des analyses sur des cellules somatiques ont été utilisées pour évaluer des échantillons de patients pour des troubles reliés à la cobalamine. En raison de niveaux de base élevés d'incorporation de propionate, certains patients présentant des phénotypes biochimiques bénins d'AMM ne peuvent être diagnostiqués par analyse de complémentation. Une analyse de fusion à haute résolution (AFHR) a été développée pour balayer rapidement les exons codants et les régions introniques avoisinnantes pour des variantes dans le gène MMAB.Trois cohortes d'échantillons ont été balayées par AFHR : une population de référence non-affectée, 42 échantillons assignés au groupe cblB par analyse de complémentation et 181 patients avec une AMM isolée sans diagnostique. L'AFHR a correctement identifié toutes les mutations précédemment rapportées dans la cohorte cblB ainsi que sept variantes additionelles, incluant une nouvelle variante non-sens (c.12C>A, p.C4X). Le balayage de la cohorte avec de l'AMM isolée a identifié six échantillons contenant des variantes dans MMAB. Deux échantillons, WG3948 et WG4034, étaient des porteurs de variantes hétérozygotes composés. Ils partageaient la mutation c.572G>A (p.R191Q). WG3948, le cas index pour cette étude, était porteur du c.398C>T (p.S133F) pour la deuxième mutation et WG4034, le deuxième patient, contenait une nouvel variante c.394C>T (p.C132R). Les échantillons provenant de quatre autres patients atteints contenait une seule variante. Le c.572G>A (p.R191Q) a été trouvé dans WG3546 et WG4090. WG3759 contenait une substitution c.52C>T (p.S174L), et WG4029 contenait une nouvelle substitution c.185C>T (p.T62M).L'identification de deux patients avec des variantes hétérozygotes composées dans le gène MMAB suggère l'existence d'un phénotype rare mais distinct de cblB. Cette sous-classe est charactérisée par des niveaux d'incorporation de propionate et de synthèse d'AdoCbl dans les valeurs normales, empêchant le diagnostique par analyse des cellules somatiques.
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Souza, Roberto Antonio de. « Genotipagem de linhagens de Yersinia spp. por high-resolution melting analysis ». Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/60/60135/tde-27062013-151724/.

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O gênero Yersinia pertence à família Enterobacteriaceae e compreende 17 espécies. Y. pestis, Y. pseudotuberculosis e Y. enterocolitica são reconhecidamente patógenos de humanos e animais. Y. pestis cause a peste. Y. pseudotuberculosis e Y. enterocolitica são agentes causadores, sobretudo, de gastroenterites transmitidas por água e alimentos. As demais 14 espécies são, usualmente, consideradas não-patogênicas, com exceção de Y. ruckeri sorogrupo O:1 que causa infecções em peixes. Nas últimas décadas, a tipagem molecular tornou-se uma importante ferramenta nos estudos filogenéticos de numerosos micro-organismos e o desenvolvimento de sistemas de tipagem rápidos e baratos pode facilitar os estudos epidemiológicos de infecções bacterianas. No presente estudo objetivou-se desenvolver um método de genotipagem de Yersinia spp. baseado em high-resolution melting analysis (HRMA) para diferenciar os single-nucleotide polymorphisms (SNPs) presentes nas sequências dos genes 16S rRNA, glnA, gyrB, hsp60 e recA e aplicá-lo na tipagem de 40 linhagens de Y. pseudotuberculosis e 50 linhagens de Y. enterocolitica, bem como separar por HRMA as espécies Y. pseudotuberculosis e Y. enterocolitica. Os SNPs foram determinados nas sequências dos loci acima citados a partir de um conjunto de 119 linhagens de Yersinia spp. depositadas no GenBank/EMBL/DDBJ. Foram encontrados nas sequências dos genes analisados de Y. pseudotuberculosis, Y. enterocolitica, Y. bercovieri, Y. rohdei, Y. intermedia, Y. mollaretii e Y. ruckeri 10, 10, 9, 6, 4, 1 e 1 SNPs, respectivamente. Nenhum SNP foi encontrado nas sequências analisadas de Y. pestis e um grande número de SNPs foi encontrado nas sequências analisadas de Y. frederiksenii, Y. kristensenii e Y. massiliensis, o que impossibilitou a genotipagem dessas espécies por HRMA. As demais espécies não foram analisadas. Foram desenhados pares de primers para flanquear os SNPs encontrados em cada espécie de Yersinia testada. Usando um conjunto de primers espécie-específicos, a diversidade genética de cada espécie de Yersinia foi determinada por HRMA e a análise filogenética foi baseada na sequência concatenada composta pelos nucleotídeos identificados em cada fragmento analisado. O agrupamento foi realizado com o software BioNumerics usando o método UPGMA com 1.000 replicatas de bootstrap. A árvore filogenética ii construída para Y. pseudotuberculosis agrupou as linhagens em clusters bio-sorogrupo específicos. As linhagens do bio-sorogrupo 1/O:1 foram agrupadas em um cluster e as linhagens do bio-sorogrupo 2/O:3 em outro. A árvore filogenética construída para Y. enterocolitica agrupou as linhagens em três grupos. As linhagens altamente patogênicas, do biotipo 1B, foram agrupadas em um cluster, as linhagens de média patogenicidade, dos biotipos 2, 3, 4 e 5, foram agrupadas em um segundo cluster e as linhagens consideradas nãopatogênicas, do biotipo 1A, foram agrupadas em um terceiro cluster. O agrupamento encontrado em Y. pseudotuberculosis e Y. enterocolitica foi consistente com o perfil patogênico característico dessas duas espécies. Nenhuma correlação epidemiológica significativa foi encontrada no agrupamento de Y. bercovieri, Y. rohdei, Y. intermedia, Y. mollaretii e Y. ruckeri de acordo com os resultados de HRMA. Ademais, o método de HRMA aqui desenvolvido foi capaz de separar as espécies Y. pseudotuberculosis e Y. enterocolitica. O método de HRMA desenvolvido nesse estudo pode ser usado como uma alternativa para a genotipagem e para a diferenciação de Y. pseudotuberculosis de Y. enterocolitica. Esse método também pode complementar os métodos baseados em sequências e facilitar os estudos epidemiológicos dessas duas espécies de Yersinia.
The genus Yersinia belongs to the family Enterobacteriaceae and comprises 17 species. Y. pestis, Y. pseudotuberculosis and Y. enterocolitica are well recognized human and animal pathogens. Y. pestis causes plague. Y. pseudotuberculosis and Y. enterocolitica are, usually, causative agents of food-waterborne gastroenteritis. The other 14 Yersinia species are considered to be non-pathogenic, with the exception of Y. ruckeri serogroup O:1 which causes infections in fishes. In the last few decades, molecular typing has become an important tool in phylogenetic studies of several microorganisms and the development of fast and inexpensive typing systems can facilitate epidemiological studies of bacterial infections. The present study aimed to develop a method of Yersinia spp. genotyping based on high-resolution melting analysis (HRMA) in order to differentiate the single-nucleotide polymorphisms (SNPs) present in the 16S rRNA, glnA, gyrB, hsp60 and recA sequences and apply it in the typing of 40 Y. pseudotuberculosis strains and 50 Y. enterocolitica strains, as well as, to separate by HRMA the Y. pseudotuberculosis and Y. enterocolitica species. The SNPs were determined in the sequences of the aforementioned loci using a set of 119 Yersinia strains deposited in the GenBank/EMBL/DDBJ database. It were found in the gene sequences analyzed of Y. pseudotuberculosis, Y. enterocolitica, Y. bercovieri, Y. rohdei, Y. intermedia, Y. mollaretii and Y. ruckeri 10, 10, 9, 6, 4, 1 and 1 SNPs, respectively. No SNPs was found in the analyzed sequences of Y. pestis and a large number of SNPs were found in the analyzed sequences of Y. frederiksenii, Y. kristensenii and Y. massiliensis what prevented their genotyping by HRMA. The remaining Yersinia species were not analyzed. It was designed primer pairs to flank the SNPs found in each Yersinia species tested. Using a specie-specific set of primers, the genetic diversity of each Yersinia species used was determined by HRMA and the phylogenetic analysis was based on the concatenated sequence composed by the nucleotides identified in each fragment analyzed. Clustering was performed with the software package BioNumerics using UPGMA method and 1,000 bootstrap replicates. The phylogenetic tree constructed for Y. pseudotuberculosis grouped the strains into bio-serogroups specific clusters. The strains of 1/O:1 bio-serogroup were grouped into one cluster and the strains of 2/O:3 bio-serogroup into iv other cluster. The phylogenetic tree constructed for Y. enterocolitica grouped the strains in three clusters. The highly pathogenic strains, of biotype 1B, were grouped into one cluster, the moderate pathogenic strains, of biotypes 2, 3, 4 and 5, were grouped into a second cluster and, the non-pathogenic strains, of biotype 1A, were grouped into a third cluster. The clusterization of Y. pseudotuberculosis and Y. enterocolitica were consistent with the pathogenic profile characteristic of these two Yersinia species. No significant epidemiological correlation was found in the grouping of Y. bercovieri, Y. rohdei, Y. intermedia Y. mollaretii and Y. ruckeri according to HRMA results. Moreover, the HRMA-based method develop here was able to separate the Y. pseudotuberculosis and Y. enterocolitica species. The HRMA assay developed in this study can be used as an alternative for the genotyping and the differentiation of Y. pseudotuberculosis and Y. enterocolitica. This method can also complement sequence-based methods and facilitate epidemiological studies of these two Yersinia species.
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Darbandy, Ashna. « Optimization of High Resolution Melting Analysis for Detection of KRAS Gene Mutations ». Thesis, Uppsala University, Department of Medical Biochemistry and Microbiology, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-130751.

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Background: Mutations of the KRAS oncogene occur in a variety types of human tumors. By assessing the mutation status of KRAS, clinicians can predict patient response to anti-EGFR therapy such as cetuximab (Erbitux®) or panitumumab (Vectibix®) in patients with metastatic colorectal cancer. The aim of this study was to optimize a real-time PCR method followed by high resolution melting analysis (HRM) in a single step for detection of most common mutations within the KRAS gene. Methods: Seven DNA samples with predefined KRAS mutations and 19 tumor samples from patients with metastatic colorectal cancer were used. KRAS mutation detection was performed by direct sequencing as well as HRM. Optimization was performed using touchdown PCR and co-amplification at lower denaturation-temperature PCR. Results: All DNA samples were successfully analyzed with direct sequencing and HRM. Moreover, the improved amplification efficiency and sensitivity was achieved using optimized PCR run protocol. Conclusion: HRM is a simple, inexpensive and reliable method for mutation detection within KRAS. By applying HRM as prescreening method would help reduce labour, time and costs.

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Burrows, Adria Michelle. « A comparative ancestry analysis of Y-chromosome DNA haplogroups using high resolution melting ». University of the Western Cape, 2018. http://hdl.handle.net/11394/6536.

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>Magister Scientiae - MSc
The objective of this study is to deduce paternal ancestry using ancestry informative single nucleotide polymorphisms (SNPs) by means of High Resolution Melting (HRM). This was completed by producing a multiplex system that was designed in a hierarchical manner according to the YSNP tree. This project mainly focused on African ancestry and was used to infer paternal ancestral lineages on the Johannesburg Coloured population. South Africa has a diverse population that has ancestral history from across the globe. The South African Coloured population is the most admixed population as it is derived from at least five different population groups: these being Khoisan, Bantu, Europeans, Indians and Southeast Asians. There have been studies done on the Western Cape/ Cape Town Coloured populations before but this study focused on the Johannesburg Coloured population.
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Michelle, Burrows Adria. « A comparative ancestry analysis of Y-chromosome DNA haplogroups using high resolution melting ». University of the Western Cape, 2018. http://hdl.handle.net/11394/6489.

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Magister Scientiae - MSc (Biotechnology)
The objective of this study is to deduce paternal ancestry using ancestry informative single nucleotide polymorphisms (SNPs) by means of High Resolution Melting (HRM). This was completed by producing a multiplex system that was designed in a hierarchical manner according to the YSNP tree. This project mainly focused on African ancestry and was used to infer paternal ancestral lineages on the Johannesburg Coloured population. South Africa has a diverse population that has ancestral history from across the globe. The South African Coloured population is the most admixed population as it is derived from at least five different population groups: these being Khoisan, Bantu, Europeans, Indians and Southeast Asians. There have been studies done on the Western Cape/ Cape Town Coloured populations before but this study focused on the Johannesburg Coloured population. The first step was to design the multiplex system. This was done by using inhouse SNPs. A total of seven multiplexes were designed and optimised, each consisting of two, three or four different SNPs respectively. A total of 143 saliva and buccal samples were collected from male Johannesburg Coloureds. DNA was extracted from the saliva samples using an optimised organic method. DNA was extracted from the buccal samples using an optimised salting out method. DNA was successfully extracted from 77 of the male samples. A total of 69 samples were screened using Multiplex 1; of the 69 samples 56 samples were successfully screened to infer the paternal lineage of the samples. The results show that the most frequent haplogroup of the Johannesburg male samples was haplogroup CF (39%). The second most frequent haplogroup was haplogroup DE (38%). Under further analysis of haplogroup DE it was seen that 37% of those samples were derived for the haplogroup E1b1b.
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PIMENTEL, ROMERO CESAR HUGO. « "INNOVATIVE SIGNAL PROCESSING TECHNIQUES IN BIOENGINEERING : COMPRESSED SENSING AND HIGH RESOLUTION DNA MELTING ANALYSIS" ». Doctoral thesis, Università degli studi di Ferrara, 2021. http://hdl.handle.net/11392/2487913.

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The first part starts with an introduction of the Compressed Sensing (CS) theory. After that, an overview of the state-of-the art of some CS adaptations by using additional priors in the different stages is presented in order to explain the new CS adaptation proposed in this work. Some of the CS adaptations reviewed are confronted using synthetic signals, synthetic electrocardiograph (ECG) signals and electroencephalographic (EEG) signals. The second part provides general concepts of biology and current developments in bioinformatics to read and and analyze the DNA. Questions like what a sequencer does?, What kind of data it produces? and How can be analyzed this data? are intended to be answered. Another reliable technique used in the analysis of the DNA without sequencing is the High Resolution Melting (HRM) curves analysis, this technique is used to find differences between two strands of DNA. HRM is also discussed to finally design a HRM analysis software.
La prima parte inizia con un'introduzione alla teoria del Compressed Sensing (CS). Successivamente, viene presentata una panoramica dello stato dell'arte di alcuni adattamenti CS utilizzando nelle diverse fasi, questo per spiegare il nuovo adattamento CS proposto in questo lavoro. Alcuni degli adattamenti CS esaminati vengono confrontati utilizzando segnali sintetici, segnali di elettrocardiografo sintetico (ECG) e segnali elettroencefalografici (EEG). La seconda parte fornisce concetti generali di biologia e sviluppi attuali della bioinformatica per leggere e analizzare il DNA. Domande come Cosa fa un sequencer? Che tipo di dati produce? e Come possono essere analizzati questi dati? sono destinati a ricevere una risposta. Un'altra tecnica affidabile utilizzata nell'analisi del DNA senza sequenziamento è l'analisi High Resolution Melting (HRM) curves, questa tecnica viene utilizzata per trovare differenze tra due filamenti di DNA. Si studia anche le HRM curves per progettare finalmente un software di analisi.
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Tsang, Ho-yin, et 曾皓言. « Detection of clinically silent beta-globin gene mutations in Chinese using high resolution melting analysis ». Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B48334182.

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Mutations in the beta-globin (β-globin) gene cause beta-thalassaemia (β-thalassaemia).The screening strategy for β-thalassaemiais based on the value of mean corpuscular volume (MCV) from the complete blood count (CBC) data. Current laboratory practice considers blood samples with MCV higher than 80fL as normal. No further assessment will be done on these samples. However, there are clinically silent β-globin gene mutations with MCV higher than 80fL, for example, heterozygous haemoglobin E (HbE). The importance of finding out this kind of mutations is due to the serious outcome when they occur together with classic β thalassaemia mutations in compound heterozygous states, which may produce a condition mimicking β thalassaemia major. The method used to recognize the presence of clinically silent β-globin gene mutations should be robust and with high sensitivity. High resolution melting (HRM) is a suitable technique to screen gene mutations. It is fast and convenient. The process is completed in a closed system without any post PCR manipulation. The sensitivity is up to a single nucleotide change. Using HRM for mutations screening followed by confirmation with sequencing can reduce time and cost of testing clinically silent β-globin gene mutations on a large scale. This study first shows the ability of HRM in detecting various types of β-globin gene mutations. The technique is then applied to detect clinically silent β-globin gene mutations in a group of high school students with normal CBC data. Mutations with different clinically significance were found. The frequency of mutation found in the samples of the study suggests that screening for β-globin gene mutation may be worthwhile in subjects with MCV higher than 80fL.
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Pathology
Master
Master of Medical Sciences
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Ho, Sophia KW, et 何廣慧. « Detection of clinically silent alpha-globin gene mutations in Chinese using high resolution melting analysis ». Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/206558.

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α-thalassemia is an inherited globin gene disorder commonly found among the Chinese population. It is composed of both non-deletional and deletional α-globin gene mutations. Classical α-thalassemia presents with red cell microcytosis but silent cases with a normal mean corpuscular volume (MCV) are also seen. Routine laboratory testing methods for large-scale detection of silent α-thalassemia mutations are onerous and time-consuming. Furthermore, methods such as denaturing high performance liquid chromatography (HPLC) or denaturing gradient gel electrophoresis (DGGE) for scanning of point mutations are costly and they require post-PCR separation. High resolution melting (HRM) analysis is an economical, sensitive, and fast method for large scale point mutation scanning. Contamination is significantly reduced with HRM because the process is performed in a closed-tube environment and does not require post-PCR manipulation. We used HRM and multiplex gap-PCR analysis to determine the prevalence of silent α-thalassemia carriers in Hong Kong. Of the 223 hematologically normal blood samples scanned by Roche LightCycler 480®, HRM did not show any sample with a non-deletional α-globin gene mutation of clinical significance. α-multiplex gap-PCR analysis revealed 36 samples (16.1%) with single α-globin gene deletions. The detection of single α-globin gene deletions in samples with a MCV greater than 80 fL indicates that the previously reported prevalence of α-thalassemia mutations in our Chinese population based on MCV screening is under-estimated. The data also suggest that non-deletional α-thalassemia mutations presenting with a normal MCV are very rare, and they most likely present with microcytosis. The fact that most silent α-thalassemia mutations are due to large deletions supports the use of traditional molecular techniques such as gap-PCR for their detection. HRM can be used as an adjunct tool for large-scale population screening of non-deletional mutations. This study provides more accurate data on the prevalence of silent α-thalassemia carriers in the Hong Kong Chinese population. The information will facilitate genetic counseling and risk assessment in families carrying α-thalassemia mutations.
published_or_final_version
Pathology
Master
Master of Medical Sciences
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Ozbak, Hani. « The application of High Resolution Melting Analysis (HRMA) for rapid detection of bacteria responsible for bloodstream infections ». Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/the-application-of-high-resolution-melting-analysis-hrma-for-rapid-detection-of-bacteria-responsible-for-bloodstream-infections(b3d5c15b-9541-44c2-873c-f7a32fc60282).html.

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Background: The diagnosis of bloodstream infection is a significant challenge for healthcare providers and is often associated with severe illness (sepsis) and poor outcomes. Rapid detection and identification of pathogens followed by characterisation of antibiotic resistance could help direct early treatment and improve patient care. Standard blood culture methods, which usually take 2-5 days to complete, can confirm if there is a bacteraemia or not in suspected patients. However, molecular approaches have been developed and are being increasingly investigated to overcome disadvantages of culture. One of the main potentials of molecular techniques is that they should be able to identify pathogens within a short time which could help clinicians treat patients earlier with rational antimicrobial therapy and limit overuse of antibiotic exposure. Objectives: To present the development and optimisation of a simple, rapid and cost-effective Real Time PCR methods combined with a High Resolution Melting Analysis (HRMA) approach, to detect and identify common bacteria associated with bloodstream infections. Approach: 16S rRNA and Gram classification primers were used on a broad range real-time PCR for molecular Gram typing and HRMA in a single run. Differentiation of bacterial species was achieved using a multi-parameter, decision-tree approach based on Gram typing, grouping according to melting temperature (Tm) and sequential comparisons of melting profiles (Curve shapes) against reference organisms. Findings: A preliminary validation was undertaken by blinded analysis of 53 consecutive bloodstream isolates from a clinical microbiology laboratory. 50 isolates contained organisms present on the panel and 96% of these were identified correctly at genus or species level. A correct Gram classification was reported for all 53 isolates. The strategy of amplification of the bacterial signal to an appropriate level using a short term pre-culture system (STPCS) for up to 12 hours prior to HRMA analysis significantly improved the overall sensitivity of the assay in spiked blood. Conclusion: This study suggests that a PCR-HRMA approach could be used as an alternative cheap approach to other molecular approaches for rapid detection and identification of bacteria responsible for >95% of bloodstream infections especially when combined with a Short Term Pre-Culture System (STPCS). Such development together with the current standard culture-based methods could allow clinicians to establish more effective management and treatment of patients with suspected bloodstream infection at an earlier stage than is possible with only current culture-based approaches.
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Livres sur le sujet "High resolution melting analysi"

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Kaushik, Sanket, et Nagendra Singh, dir. Current Developments in the Detection and Control of Multi Drug Resistance. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/97898150498791220101.

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The rise in the incidence of infections is caused by multi drug resistant (MDR) bacteria, it is essential to elucidate the basic mechanism of antibiotic resistance to discover effective methods for diagnosis and treatment of infections. The use of pathogen-specific probes offers a faster alternative for pathogen detection and could improve the diagnosis of infection. High resolution melting analysis techniques are useful for the detection of multi drug resistant pathogens. Rational Structural Based Drug Design is a common method to identify a lead compound and take it forward for further developments. This book provides information about recent strategies involved in the diagnosis and treatment of infections caused by MDR bacteria. The volume covers the use of molecular probes for the quantification of pathogenic bacteria, along with other techniques mentioned above. Chapters also cover the use of identification of novel drug targets from the Lipid A biosynthesis and also from quorum sensing mediated biofilm formation in MDR bacteria. Chapters also cover herbal alternatives for the treatment of MDR bacteria like the use of Cassia aungustifolia in treatment of various diseases. The reference is suitable for biomedical students, cellular and molecular biologists.
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Chapitres de livres sur le sujet "High resolution melting analysi"

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Tucker, Elise J., et Bao Lam Huynh. « Genotyping by High-Resolution Melting Analysis ». Dans Methods in Molecular Biology, 59–66. New York, NY : Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0446-4_5.

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Bruzzone, Carol M., et Clifford J. Steer. « High-Resolution Melting Analysis of Single Nucleotide Polymorphisms ». Dans Molecular Typing of Blood Cell Antigens, 5–27. New York, NY : Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2690-9_2.

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Vossen, Rolf H. A. M. « Genotyping DNA Variants with High-Resolution Melting Analysis ». Dans Methods in Molecular Biology, 17–28. New York, NY : Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6442-0_2.

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Łukasik, Ewa, Kazimiera Waśniowska, Magdalena Grodecka, Edyta Majorczyk et Marcin Czerwiński. « High-Resolution Melting Analysis for Genotyping Duffy Blood Group Antigens ». Dans Molecular Typing of Blood Cell Antigens, 83–95. New York, NY : Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2690-9_7.

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Grazina, Liliana, Joana Costa, Joana S. Amaral et Isabel Mafra. « High-Resolution Melting Analysis as a Tool for Plant Species Authentication ». Dans Methods in Molecular Biology, 55–73. New York, NY : Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-1201-9_5.

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Day, Robert, et Richard Macknight. « Screening for Imprinted Genes Using High-Resolution Melting Analysis of PCR Amplicons ». Dans Methods in Molecular Biology, 71–83. Totowa, NJ : Humana Press, 2014. http://dx.doi.org/10.1007/978-1-62703-773-0_5.

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Derzelle, Sylviane. « Single-Nucleotide Polymorphism Discrimination Using High-Resolution Melting Analysis for the Genotyping of Bacillus anthracis ». Dans Veterinary Infection Biology : Molecular Diagnostics and High-Throughput Strategies, 361–71. New York, NY : Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-2004-4_26.

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Ozkok, Fatma Ozge, et Mete Celik. « Classification of High Resolution Melting Curves Using Recurrence Quantification Analysis and Data Mining Algorithms ». Dans Engineering Cyber-Physical Systems and Critical Infrastructures, 641–50. Cham : Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-09753-9_49.

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Ferro, Marta, Hada C. Macher, Pilar Noguerol, Pilar Jimenez-Arriscado, Patrocinio Molinero, Juan M. Guerrero et Amalia Rubio. « Non-invasive Prenatal Diagnosis of Feto-Maternal Platelet Incompatibility by Cold High Resolution Melting Analysis ». Dans Advances in Experimental Medicine and Biology, 67–70. Cham : Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-42044-8_13.

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Nhan, B. T., N. T. T. Lan, N. T. N. Thanh, T. V. Thiep et N. T. Hue. « Primary Study of SNP rs2046210 in Vietnamese Breast Cancer Population by High-Resolution Melting Analysis (HRMA) ». Dans 6th International Conference on the Development of Biomedical Engineering in Vietnam (BME6), 229–34. Singapore : Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-4361-1_38.

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Actes de conférences sur le sujet "High resolution melting analysi"

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Bel’kovich, Y. I., E. V. Snitkov et B. A. Tonkonogov. « ALGORITHMS FOR RESULTS’ CLUSTERING OF MELTING CURVES’ ANALYSIS WITH HIGH RESOLUTION ». Dans SAKHAROV READINGS 2022 : ENVIRONMENTAL PROBLEMS OF THE XXI CENTURY. International Sakharov Environmental Institute of Belarusian State University, 2022. http://dx.doi.org/10.46646/sakh-2022-2-416-419.

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Basic principles of data clustering are considered, stages of its implementation and methods to determine object similarity and result interpretation are described and characteristics of various conduct methods for DNA melting are given.
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Boulton, J., E. Masiero et T. Sgamma. « Barcode High Resolution Melting (Bar-HRM) analysis for authentication of Echinacea products ». Dans GA – 69th Annual Meeting 2021, Virtual conference. Georg Thieme Verlag, 2021. http://dx.doi.org/10.1055/s-0041-1736809.

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Daugaard, Iben L., Lasse S. Kristensen, Tina Kjeldsen, Stephen Hamilton Dutoit, Henrik Hager et Lise Lotte Hansen. « Abstract 2115 : Increased sensitivity ofKRASmutation detection by High-Resolution Melting analysis of COLD-PCR products ». Dans Proceedings : AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010 ; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-2115.

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Hussein, Rusul Muzher, Alaa Shawqi Abdulbari et Mohammed A. B. Al-Ayash. « Detection of hepatitis B virus for genotype B and C by using high resolution melting analysis ». Dans PROCEEDING OF THE 1ST INTERNATIONAL CONFERENCE ON ADVANCED RESEARCH IN PURE AND APPLIED SCIENCE (ICARPAS2021) : Third Annual Conference of Al-Muthanna University/College of Science. AIP Publishing, 2022. http://dx.doi.org/10.1063/5.0093406.

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Deschoolmeester, Vanessa, Christophe Deben, Marc Baay, An Wouters, Marc Peeters, Filip Lardon et Patrick Pauwels. « Abstract 2103 : High resolution melting analysis : a sensitive screening method for the detection of MDM2 promotor SNP309 ». Dans Proceedings : AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012 ; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-2103.

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Deschoolmeester, Vanessa, Carolien Boeckx, Wim Wuyts, Eric Van Marck, Peter Vermeulen, Patrick Pauwels, Marc Peeters, Filip Lardon, Jan B. Vermorken et Marc Baay. « Abstract 2122:KRASmutation detection using high resolution melting analysis and its prognostic value in archival colorectal cancer tissues ». Dans Proceedings : AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010 ; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-2122.

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Sharma, Kusum, Aman Sharma et Mandeep Dhillon. « SAT0471 HIGH-RESOLUTION MELTING CURVE ANALYSIS : A RAPID AND PRAGMATIC APPROACH FOR SCREENING OF MULTIDRUG RESISTANT OSTEOARTICULAR TUBERCULOSIS (OATB) ». Dans Annual European Congress of Rheumatology, EULAR 2019, Madrid, 12–15 June 2019. BMJ Publishing Group Ltd and European League Against Rheumatism, 2019. http://dx.doi.org/10.1136/annrheumdis-2019-eular.6941.

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Schiza, Christina, Sofia Farkona, Maria Chimonidou, Panos Vorkas, Nikos Malamos, Vasilis Georgoulias et Evi S. Lianidou. « Abstract 2088 : Detection ofPIK3CAsomatic mutations in cell-free DNA of breast cancer patients by high-resolution melting curve analysis ». Dans Proceedings : AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012 ; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-2088.

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Hashida, Shinsuke, Junichi Soh, Shinichi Toyooka, Ryuhei Tada, Kazuhiko Shien, Masashi Furukawa, Hiromasa Yamamoto, Hiroaki Asano, Kazunori Tsukuda et Shinichiro Miyoshi. « Abstract 4219 : A novel high-sensitive assay for detection of EGFR T790M mutation using high resolution melting analysis with mutant-enriched COLD PCR. » Dans Proceedings : AACR 104th Annual Meeting 2013 ; Apr 6-10, 2013 ; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-4219.

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Villinger, Jandouwe. « Unraveling host-vector-arbovirus interactions by two-gene high resolution melting mosquito bloodmeal analysis in a Kenyan wildlife-livestock interface ». Dans 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.114306.

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Rapports d'organisations sur le sujet "High resolution melting analysi"

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Lever, James, Susan Taylor, Arnold Song, Zoe Courville, Ross Lieblappen et Jason Weale. The mechanics of snow friction as revealed by micro-scale interface observations. Engineer Research and Development Center (U.S.), décembre 2021. http://dx.doi.org/10.21079/11681/42761.

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The mechanics of snow friction are central to competitive skiing, safe winter driving and efficient polar sleds. For nearly 80 years, prevailing theory has postulated that self-lubrication accounts for low kinetic friction on snow: dry-contact sliding warms snow grains to the melting point, and further sliding produces meltwater layers that lubricate the interface. We sought to verify that self-lubrication occurs at the grain scale and to quantify the evolution of real contact area to aid modeling. We used high-resolution (15 μm) infrared thermography to observe the warming of stationary snow under a rotating polyethylene slider. Surprisingly, we did not observe melting at contacting snow grains despite low friction values. In some cases, slider shear failed inter-granular bonds and produced widespread snow movement with no persistent contacts to melt (μ < 0.03). When the snow grains did not move and persistent contacts evolved, the slider abraded rather than melted the grains at low resistance (μ < 0.05). Optical microscopy revealed that the abraded particles deposited in air pockets between grains and thereby carried heat away from the interface, a process not included in current models. Overall, our results challenge whether self-lubrication is indeed the dominant mechanism underlying low snow kinetic friction.
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